Starting phenix.real_space_refine on Sat Mar 23 21:54:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lv0_23528/03_2024/7lv0_23528_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lv0_23528/03_2024/7lv0_23528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lv0_23528/03_2024/7lv0_23528.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lv0_23528/03_2024/7lv0_23528.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lv0_23528/03_2024/7lv0_23528_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lv0_23528/03_2024/7lv0_23528_updated.pdb" } resolution = 3.2 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= 0.007 sd= 1.205 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 4729 5.49 5 S 155 5.16 5 C 73945 2.51 5 N 27454 2.21 5 O 41047 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b GLU 81": "OE1" <-> "OE2" Residue "b ASP 83": "OD1" <-> "OD2" Residue "b TYR 95": "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 GLU 99": "OE1" <-> "OE2" Residue "c PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 169": "NH1" <-> "NH2" Residue "c ARG 184": "NH1" <-> "NH2" 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 ASP 91": "OD1" <-> "OD2" 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 "d ASP 176": "OD1" <-> "OD2" Residue "e GLU 41": "OE1" <-> "OE2" 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 PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 114": "NH1" <-> "NH2" Residue "e ARG 132": "NH1" <-> "NH2" Residue "e PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "f GLU 41": "OE1" <-> "OE2" Residue "f ARG 152": "NH1" <-> "NH2" Residue "f ARG 162": "NH1" <-> "NH2" Residue "f ARG 169": "NH1" <-> "NH2" Residue "h ASP 7": "OD1" <-> "OD2" Residue "h ASP 36": "OD1" <-> "OD2" Residue "h GLU 70": "OE1" <-> "OE2" Residue "i GLU 122": "OE1" <-> "OE2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j GLU 31": "OE1" <-> "OE2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "k TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 45": "OE1" <-> "OE2" Residue "k GLU 92": "OE1" <-> "OE2" Residue "k GLU 110": "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 ARG 78": "NH1" <-> "NH2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 18": "NH1" <-> "NH2" 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 TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 84": "OE1" <-> "OE2" Residue "o ARG 94": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "o GLU 112": "OE1" <-> "OE2" Residue "p GLU 10": "OE1" <-> "OE2" Residue "p PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 20": "NH1" <-> "NH2" Residue "p ARG 38": "NH1" <-> "NH2" Residue "p PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 61": "NH1" <-> "NH2" Residue "p ARG 88": "NH1" <-> "NH2" Residue "p TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 100": "NH1" <-> "NH2" 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 TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 32": "NH1" <-> "NH2" Residue "q ARG 47": "NH1" <-> "NH2" Residue "q ARG 69": "NH1" <-> "NH2" Residue "q ASP 90": "OD1" <-> "OD2" Residue "q ASP 96": "OD1" <-> "OD2" Residue "q ASP 101": "OD1" <-> "OD2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r ASP 26": "OD1" <-> "OD2" Residue "r GLU 31": "OE1" <-> "OE2" 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 77": "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 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 GLU 7": "OE1" <-> "OE2" Residue "v TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ASP 60": "OD1" <-> "OD2" Residue "w PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 75": "OE1" <-> "OE2" Residue "y GLU 24": "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 "z GLU 57": "OE1" <-> "OE2" 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 PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 107": "NH1" <-> "NH2" Residue "G GLU 139": "OE1" <-> "OE2" Residue "G PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 191": "OD1" <-> "OD2" Residue "G ASP 193": "OD1" <-> "OD2" Residue "G ASP 203": "OD1" <-> "OD2" Residue "G TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "H PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "H GLU 169": "OE1" <-> "OE2" Residue "H TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 77": "OE1" <-> "OE2" Residue "I GLU 94": "OE1" <-> "OE2" Residue "I GLU 159": "OE1" <-> "OE2" Residue "J ASP 141": "OD1" <-> "OD2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "J GLU 161": "OE1" <-> "OE2" Residue "K TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 16": "OE1" <-> "OE2" Residue "K GLU 40": "OE1" <-> "OE2" Residue "K TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 89": "OE1" <-> "OE2" Residue "L GLU 122": "OE1" <-> "OE2" Residue "L GLU 138": "OE1" <-> "OE2" Residue "L GLU 145": "OE1" <-> "OE2" Residue "M ASP 8": "OD1" <-> "OD2" Residue "M GLU 123": "OE1" <-> "OE2" Residue "N TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 55": "OD1" <-> "OD2" Residue "N GLU 96": "OE1" <-> "OE2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "N PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 40": "OE1" <-> "OE2" Residue "R PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 81": "OD1" <-> "OD2" Residue "S GLU 38": "OE1" <-> "OE2" Residue "S ASP 39": "OD1" <-> "OD2" Residue "T GLU 25": "OE1" <-> "OE2" Residue "T GLU 82": "OE1" <-> "OE2" Residue "U PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "V GLU 25": "OE1" <-> "OE2" Residue "V PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "W GLU 15": "OE1" <-> "OE2" Residue "W GLU 19": "OE1" <-> "OE2" Residue "W TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 71": "OD1" <-> "OD2" Residue "X PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 14": "OE1" <-> "OE2" Residue "Z PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 35": "OE1" <-> "OE2" Residue "Z TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 66": "NH1" <-> "NH2" Residue "a ARG 7": "NH1" <-> "NH2" Residue "a ARG 12": "NH1" <-> "NH2" Residue "a GLU 25": "OE1" <-> "OE2" Residue "a ARG 162": "NH1" <-> "NH2" Residue "a TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 181": "OD1" <-> "OD2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 147330 Number of models: 1 Model: "" Number of chains: 60 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: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 440 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "h" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 593 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "i" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 511 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 67} 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: "A" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 364 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} 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: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1705 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 210} 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: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 818 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, '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': 99, 'rna2p_pyr': 63, 'rna3p_pur': 775, 'rna3p_pyr': 602} Link IDs: {'rna2p': 162, 'rna3p': 1376} 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': 221, 'rna2p_pyr': 113, 'rna3p_pur': 1453, 'rna3p_pyr': 1116} Link IDs: {'rna2p': 334, 'rna3p': 2568} 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': 6, 'rna2p_pyr': 3, 'rna3p_pur': 59, 'rna3p_pyr': 52} Link IDs: {'rna2p': 9, 'rna3p': 110} Chain: "5" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1647 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 7, 'rna3p_pur': 31, 'rna3p_pyr': 30} Link IDs: {'rna2p': 16, 'rna3p': 60} Chain: "6" 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': 5, 'rna2p_pyr': 5, 'rna3p_pur': 34, 'rna3p_pyr': 33} Link IDs: {'rna2p': 10, 'rna3p': 66} Chain: "4" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 388 Classifications: {'RNA': 18} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 12, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "1" 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 Chain: "5" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Time building chain proxies: 59.05, per 1000 atoms: 0.40 Number of scatterers: 147330 At special positions: 0 Unit cell: (271.41, 250.66, 243.19, 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 155 16.00 P 4729 15.00 O 41047 8.00 N 27454 7.00 C 73945 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 11 " - pdb=" SG CYS F 14 " distance=2.95 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: 71.93 Conformation dependent library (CDL) restraints added in 7.7 seconds 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10750 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: 179 helices and 69 sheets defined 38.5% alpha, 17.4% beta 1475 base pairs and 2248 stacking pairs defined. Time for finding SS restraints: 82.71 Creating SS restraints... Processing helix chain 'b' and resid 11 through 16 removed outlier: 4.189A pdb=" N VAL b 15 " --> pdb=" O GLY b 11 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N VAL b 16 " --> pdb=" O ARG b 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 11 through 16' 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: 3.950A pdb=" N ALA b 210 " --> pdb=" O LYS b 206 " (cutoff:3.500A) Processing helix chain 'b' and resid 220 through 225 removed outlier: 4.340A pdb=" N MET b 224 " --> pdb=" O ARG b 220 " (cutoff:3.500A) removed outlier: 5.486A 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 267 removed outlier: 6.086A pdb=" N ASP b 263 " --> pdb=" O ASN b 259 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LYS b 264 " --> pdb=" O LYS b 260 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N PHE b 265 " --> pdb=" O ARG b 261 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE b 266 " --> pdb=" O THR b 262 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N VAL b 267 " --> pdb=" O ASP b 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 259 through 267' Processing helix chain 'b' and resid 196 through 201 removed outlier: 3.695A pdb=" N MET b 200 " --> pdb=" O ALA b 197 " (cutoff:3.500A) Processing helix chain 'c' and resid 61 through 72 removed outlier: 4.027A pdb=" N ALA c 71 " --> pdb=" O HIS c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 120 through 125 Processing helix chain 'c' and resid 97 through 103 removed outlier: 3.990A pdb=" N LEU c 100 " --> pdb=" O SER c 97 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP c 103 " --> pdb=" O LEU c 100 " (cutoff:3.500A) Processing helix chain 'd' and resid 24 through 41 removed outlier: 3.728A pdb=" N ALA d 39 " --> pdb=" O TYR d 35 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG d 40 " --> pdb=" O ALA d 36 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N GLN d 41 " --> pdb=" O ALA d 37 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 116 removed outlier: 4.067A pdb=" N LYS d 106 " --> pdb=" O ARG d 102 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER d 107 " --> pdb=" O GLY d 103 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 142 removed outlier: 4.404A pdb=" N LEU d 134 " --> pdb=" O LYS d 130 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 165 removed outlier: 4.461A pdb=" N ALA d 160 " --> pdb=" O ASN d 156 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ARG d 162 " --> pdb=" O PHE d 158 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASN d 163 " --> pdb=" O LEU d 159 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU d 164 " --> pdb=" O ALA d 160 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N HIS d 165 " --> pdb=" O ALA d 161 " (cutoff:3.500A) Processing helix chain 'd' and resid 176 through 184 removed outlier: 6.803A pdb=" N ASP d 184 " --> pdb=" O LEU d 180 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 201 removed outlier: 3.513A pdb=" N LYS d 194 " --> pdb=" O ALA d 190 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA d 201 " --> pdb=" O GLU d 197 " (cutoff:3.500A) Processing helix chain 'd' and resid 15 through 21 removed outlier: 3.618A pdb=" N GLY d 20 " --> pdb=" O SER d 15 " (cutoff:3.500A) Processing helix chain 'e' and resid 1 through 10 removed outlier: 4.235A pdb=" N ASP e 5 " --> pdb=" O ALA e 1 " (cutoff:3.500A) Processing helix chain 'e' and resid 11 through 20 removed outlier: 3.786A pdb=" N THR e 17 " --> pdb=" O LYS e 13 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLU e 18 " --> pdb=" O LYS e 14 " (cutoff:3.500A) Processing helix chain 'e' and resid 46 through 61 removed outlier: 3.527A pdb=" N ILE e 59 " --> pdb=" O ASP e 55 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY e 61 " --> pdb=" O ALA e 57 " (cutoff:3.500A) Processing helix chain 'e' and resid 92 through 110 removed outlier: 3.744A pdb=" N TRP e 96 " --> pdb=" O GLY e 92 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU e 97 " --> pdb=" O GLU e 93 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE e 98 " --> pdb=" O ARG e 94 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL e 107 " --> pdb=" O ILE e 103 " (cutoff:3.500A) Proline residue: e 108 - end of helix Processing helix chain 'e' and resid 141 through 146 removed outlier: 6.213A pdb=" N VAL e 145 " --> pdb=" O ASP e 141 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ASP e 146 " --> pdb=" O TYR e 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 141 through 146' Processing helix chain 'e' and resid 161 through 173 removed outlier: 4.462A pdb=" N PHE e 172 " --> pdb=" O LEU e 168 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP e 173 " --> pdb=" O LEU e 169 " (cutoff:3.500A) Processing helix chain 'f' and resid 1 through 6 removed outlier: 4.037A pdb=" N ALA f 6 " --> pdb=" O ARG f 2 " (cutoff:3.500A) Processing helix chain 'f' and resid 60 through 80 removed outlier: 3.626A pdb=" N VAL f 78 " --> pdb=" O MET f 74 " (cutoff:3.500A) Processing helix chain 'f' and resid 136 through 152 removed outlier: 3.543A pdb=" N TYR f 150 " --> pdb=" O ASP f 146 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ARG f 151 " --> pdb=" O LEU f 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 33 removed outlier: 4.938A pdb=" N VAL g 31 " --> pdb=" O ARG g 27 " (cutoff:3.500A) Proline residue: g 32 - end of helix Processing helix chain 'g' and resid 40 through 50 removed outlier: 4.171A pdb=" N ARG g 50 " --> pdb=" O PHE g 46 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 19 removed outlier: 3.694A pdb=" N VAL h 18 " --> pdb=" O GLU h 14 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA h 19 " --> pdb=" O VAL h 15 " (cutoff:3.500A) Processing helix chain 'h' and resid 33 through 48 removed outlier: 3.980A pdb=" N LYS h 37 " --> pdb=" O VAL h 33 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET h 38 " --> pdb=" O THR h 34 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR h 39 " --> pdb=" O VAL h 35 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG h 46 " --> pdb=" O ARG h 42 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU h 47 " --> pdb=" O LYS h 43 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA h 48 " --> pdb=" O ALA h 44 " (cutoff:3.500A) Processing helix chain 'h' and resid 62 through 68 removed outlier: 3.711A pdb=" N GLY h 66 " --> pdb=" O ARG h 62 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR h 67 " --> pdb=" O ALA h 63 " (cutoff:3.500A) Proline residue: h 68 - end of helix No H-bonds generated for 'chain 'h' and resid 62 through 68' Processing helix chain 'h' and resid 71 through 78 removed outlier: 4.734A pdb=" N ALA h 75 " --> pdb=" O CYS h 71 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL h 77 " --> pdb=" O LYS h 73 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLY h 78 " --> pdb=" O ASP h 74 " (cutoff:3.500A) Processing helix chain 'i' and resid 74 through 83 removed outlier: 3.850A pdb=" N ALA i 82 " --> pdb=" O LEU i 78 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA i 83 " --> pdb=" O LEU i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 91 through 96 removed outlier: 4.519A pdb=" N LYS i 96 " --> pdb=" O PRO i 92 " (cutoff:3.500A) Processing helix chain 'i' and resid 101 through 110 removed outlier: 3.692A pdb=" N ILE i 108 " --> pdb=" O GLN i 104 " (cutoff:3.500A) Processing helix chain 'i' and resid 111 through 116 Processing helix chain 'i' and resid 120 through 136 removed outlier: 3.846A pdb=" N ILE i 128 " --> pdb=" O MET i 124 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU i 129 " --> pdb=" O THR i 125 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 38 Processing helix chain 'j' and resid 67 through 72 Processing helix chain 'j' and resid 88 through 96 Processing helix chain 'j' and resid 97 through 110 removed outlier: 4.338A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (cutoff:3.500A) removed outlier: 4.613A 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: 4.475A pdb=" N LYS j 121 " --> pdb=" O ALA j 117 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU j 122 " --> pdb=" O MET j 118 " (cutoff:3.500A) Processing helix chain 'j' and resid 130 through 135 removed outlier: 4.185A pdb=" N ALA j 133 " --> pdb=" O HIS j 130 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA j 134 " --> pdb=" O ASN j 131 " (cutoff:3.500A) Processing helix chain 'k' and resid 112 through 120 Proline residue: k 120 - end of helix Processing helix chain 'k' and resid 104 through 109 removed outlier: 5.299A pdb=" N SER k 109 " --> pdb=" O GLU k 106 " (cutoff:3.500A) Processing helix chain 'l' and resid 37 through 42 removed outlier: 4.332A pdb=" N ARG l 41 " --> pdb=" O GLY l 37 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N SER l 42 " --> pdb=" O GLN l 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 37 through 42' Processing helix chain 'l' and resid 56 through 62 removed outlier: 3.793A pdb=" N LEU l 61 " --> pdb=" O LEU l 57 " (cutoff:3.500A) Proline residue: l 62 - end of helix Processing helix chain 'l' and resid 68 through 75 removed outlier: 4.057A pdb=" N ALA l 72 " --> pdb=" O SER l 68 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE l 73 " --> pdb=" O ARG l 69 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR l 74 " --> pdb=" O LYS l 70 " (cutoff:3.500A) removed outlier: 6.332A 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 80 through 85 removed outlier: 4.435A pdb=" N LYS l 84 " --> pdb=" O SER l 80 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL l 85 " --> pdb=" O ASP l 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 80 through 85' Processing helix chain 'l' and resid 91 through 99 removed outlier: 4.012A pdb=" N LEU l 95 " --> pdb=" O ASP l 91 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS l 96 " --> pdb=" O LEU l 92 " (cutoff:3.500A) removed outlier: 5.410A 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: 3.513A pdb=" N ILE m 46 " --> pdb=" O THR m 42 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG m 55 " --> pdb=" O ARG m 51 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA m 56 " --> pdb=" O ALA m 52 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 125 removed outlier: 3.617A 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 removed outlier: 3.746A pdb=" N GLN n 18 " --> pdb=" O SER n 14 " (cutoff:3.500A) Processing helix chain 'n' and resid 38 through 58 removed outlier: 4.418A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) Proline residue: n 50 - end of helix removed outlier: 4.409A pdb=" N THR n 57 " --> pdb=" O THR n 53 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ASP n 58 " --> pdb=" O LEU n 54 " (cutoff:3.500A) Processing helix chain 'n' and resid 59 through 71 removed outlier: 3.593A pdb=" N ARG n 69 " --> pdb=" O LEU n 65 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N THR n 70 " --> pdb=" O ALA n 66 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG n 71 " --> pdb=" O PHE n 67 " (cutoff:3.500A) Processing helix chain 'n' and resid 72 through 88 removed outlier: 4.182A pdb=" N PHE n 80 " --> pdb=" O VAL n 76 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN n 81 " --> pdb=" O ALA n 77 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LEU n 83 " --> pdb=" O LEU n 79 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N GLY n 84 " --> pdb=" O PHE n 80 " (cutoff:3.500A) Proline residue: n 85 - end of helix Processing helix chain 'o' and resid 2 through 22 removed outlier: 3.508A pdb=" N ILE o 8 " --> pdb=" O LYS o 4 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG o 9 " --> pdb=" O SER o 5 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 63 removed outlier: 6.189A pdb=" N GLN o 61 " --> pdb=" O ALA o 57 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU o 62 " --> pdb=" O ILE o 58 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LYS o 63 " --> pdb=" O ALA o 59 " (cutoff:3.500A) Processing helix chain 'o' and resid 67 through 86 Processing helix chain 'o' and resid 101 through 113 removed outlier: 3.589A pdb=" N ALA o 109 " --> pdb=" O ALA o 105 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 12 Processing helix chain 'p' and resid 96 through 103 removed outlier: 4.858A pdb=" N ARG p 100 " --> pdb=" O LEU p 96 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU p 101 " --> pdb=" O TYR p 97 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ARG p 102 " --> pdb=" O TYR p 98 " (cutoff:3.500A) removed outlier: 5.392A 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 6 through 21 removed outlier: 4.005A pdb=" N GLN q 19 " --> pdb=" O LYS q 15 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS q 21 " --> pdb=" O LEU q 17 " (cutoff:3.500A) Processing helix chain 'q' and resid 25 through 30 removed outlier: 3.749A pdb=" N ARG q 29 " --> pdb=" O GLY q 25 " (cutoff:3.500A) Processing helix chain 'q' and resid 38 through 72 removed outlier: 4.090A pdb=" N ARG q 50 " --> pdb=" O TYR q 46 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LYS q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) Processing helix chain 'q' and resid 74 through 86 removed outlier: 3.574A pdb=" N SER q 86 " --> pdb=" O LEU q 82 " (cutoff:3.500A) Processing helix chain 'q' and resid 90 through 101 removed outlier: 3.501A pdb=" N ASP q 96 " --> pdb=" O LYS q 92 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP q 101 " --> pdb=" O ILE q 97 " (cutoff:3.500A) Processing helix chain 'q' and resid 102 through 117 Processing helix chain 's' and resid 13 through 25 removed outlier: 4.401A pdb=" N LEU s 23 " --> pdb=" O LEU s 19 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ILE s 24 " --> pdb=" O VAL s 20 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ARG s 25 " --> pdb=" O ALA s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 40 removed outlier: 5.335A pdb=" N TYR s 38 " --> pdb=" O ASP s 34 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ASN s 40 " --> pdb=" O LEU s 36 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 61 Processing helix chain 't' and resid 2 through 11 removed outlier: 3.625A pdb=" N ARG t 6 " --> pdb=" O ILE t 2 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS t 9 " --> pdb=" O GLU t 5 " (cutoff:3.500A) removed outlier: 4.077A 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 51 Processing helix chain 'u' and resid 65 through 70 removed outlier: 4.698A pdb=" N VAL u 69 " --> pdb=" O GLN u 65 " (cutoff:3.500A) removed outlier: 5.571A 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: 3.510A pdb=" N ALA v 22 " --> pdb=" O ARG v 18 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN v 24 " --> pdb=" O LEU v 20 " (cutoff:3.500A) Processing helix chain 'v' and resid 43 through 53 removed outlier: 4.265A pdb=" N VAL v 47 " --> pdb=" O ASP v 43 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA v 52 " --> pdb=" O MET v 48 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS v 53 " --> pdb=" O ASN v 49 " (cutoff:3.500A) Processing helix chain 'v' and resid 54 through 59 removed outlier: 4.880A pdb=" N SER v 58 " --> pdb=" O ALA v 54 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU v 59 " --> pdb=" O GLU v 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 54 through 59' Processing helix chain 'x' and resid 51 through 61 Processing helix chain 'x' and resid 62 through 74 removed outlier: 3.812A pdb=" N LEU x 67 " --> pdb=" O ILE x 63 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA x 68 " --> pdb=" O ASP x 64 " (cutoff:3.500A) Processing helix chain 'y' and resid 2 through 7 removed outlier: 3.963A pdb=" N LEU y 6 " --> pdb=" O LYS y 2 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG y 7 " --> pdb=" O ALA y 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 2 through 7' Processing helix chain 'y' and resid 9 through 35 removed outlier: 3.506A pdb=" N LEU y 19 " --> pdb=" O ASN y 15 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU y 24 " --> pdb=" O ASN y 20 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN y 25 " --> pdb=" O LEU y 21 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N PHE y 26 " --> pdb=" O LEU y 22 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASN y 27 " --> pdb=" O ARG y 23 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET y 30 " --> pdb=" O PHE y 26 " (cutoff:3.500A) Processing helix chain 'y' and resid 39 through 62 removed outlier: 4.265A pdb=" N LEU y 43 " --> pdb=" O GLN y 39 " (cutoff:3.500A) removed outlier: 4.290A 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 20 removed outlier: 4.884A pdb=" N HIS B 18 " --> pdb=" O MET B 14 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASP B 19 " --> pdb=" O ARG B 15 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA B 20 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 16 removed outlier: 3.584A pdb=" N HIS D 16 " --> pdb=" O ARG D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 24 removed outlier: 4.455A pdb=" N THR D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 38 Processing helix chain 'E' and resid 6 through 14 removed outlier: 4.089A pdb=" N ARG E 12 " --> pdb=" O GLY E 8 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LYS E 14 " --> pdb=" O ALA E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 4.175A pdb=" N LYS E 35 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ALA E 36 " --> pdb=" O LEU E 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 31 through 36' Processing helix chain 'E' and resid 37 through 45 removed outlier: 3.519A pdb=" N LEU E 43 " --> pdb=" O ARG E 39 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG E 44 " --> pdb=" O LYS E 40 " (cutoff:3.500A) Proline residue: E 45 - end of helix Processing helix chain 'E' and resid 53 through 62 removed outlier: 3.572A pdb=" N VAL E 57 " --> pdb=" O ASP E 53 " (cutoff:3.500A) Proline residue: E 62 - end of helix Processing helix chain 'E' and resid 25 through 30 removed outlier: 4.650A pdb=" N LEU E 28 " --> pdb=" O HIS E 25 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ARG E 29 " --> pdb=" O ALA E 26 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N HIS E 30 " --> pdb=" O ASN E 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 25 through 30' Processing helix chain 'G' and resid 41 through 61 removed outlier: 3.610A pdb=" N THR G 45 " --> pdb=" O ASN G 41 " (cutoff:3.500A) Proline residue: G 47 - end of helix removed outlier: 3.511A pdb=" N GLU G 51 " --> pdb=" O PRO G 47 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE G 59 " --> pdb=" O GLU G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 87 removed outlier: 5.691A pdb=" N SER G 76 " --> pdb=" O LYS G 72 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLU G 77 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ALA G 78 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER G 85 " --> pdb=" O ASP G 81 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N CYS G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 122 removed outlier: 3.799A pdb=" N GLN G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS G 111 " --> pdb=" O ARG G 107 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG G 112 " --> pdb=" O GLN G 108 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLN G 121 " --> pdb=" O GLU G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 147 removed outlier: 3.585A pdb=" N ARG G 136 " --> pdb=" O GLU G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 169 removed outlier: 4.993A pdb=" N GLU G 168 " --> pdb=" O ASP G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 179 removed outlier: 4.244A pdb=" N ASN G 177 " --> pdb=" O LYS G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 224 removed outlier: 4.701A pdb=" N VAL G 209 " --> pdb=" O ALA G 205 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR G 219 " --> pdb=" O ALA G 215 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG G 224 " --> pdb=" O VAL G 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 11 removed outlier: 4.462A pdb=" N ARG H 10 " --> pdb=" O PRO H 6 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU H 11 " --> pdb=" O ASN H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 46 Processing helix chain 'H' and resid 71 through 77 Processing helix chain 'H' and resid 80 through 95 removed outlier: 3.602A pdb=" N GLU H 84 " --> pdb=" O GLY H 80 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE H 93 " --> pdb=" O VAL H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 126 removed outlier: 4.194A pdb=" N ARG H 126 " --> pdb=" O GLN H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 144 removed outlier: 3.675A pdb=" N ARG H 135 " --> pdb=" O ARG H 131 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA H 140 " --> pdb=" O ALA H 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 15 removed outlier: 4.053A pdb=" N LEU I 10 " --> pdb=" O PRO I 6 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER I 11 " --> pdb=" O LYS I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 65 Processing helix chain 'I' and resid 68 through 82 removed outlier: 4.983A pdb=" N LYS I 82 " --> pdb=" O ALA I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 96 removed outlier: 3.838A pdb=" N LEU I 90 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY I 95 " --> pdb=" O ALA I 91 " (cutoff:3.500A) removed outlier: 4.357A 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: 3.882A pdb=" N LYS I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 165 removed outlier: 6.230A pdb=" N LYS I 155 " --> pdb=" O GLN I 151 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU I 159 " --> pdb=" O LYS I 155 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU I 160 " --> pdb=" O ALA I 156 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA I 161 " --> pdb=" O ALA I 157 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU I 162 " --> pdb=" O LEU I 158 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLU I 165 " --> pdb=" O ALA I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 191 removed outlier: 4.375A pdb=" N SER I 191 " --> pdb=" O ARG I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 205 removed outlier: 6.027A pdb=" N ILE I 199 " --> pdb=" O ASN I 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 70 removed outlier: 3.804A pdb=" N GLN J 60 " --> pdb=" O PRO J 56 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU J 64 " --> pdb=" O GLN J 60 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LYS J 65 " --> pdb=" O LYS J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 118 removed outlier: 6.047A pdb=" N ALA J 112 " --> pdb=" O GLY J 108 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL J 113 " --> pdb=" O ALA J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 147 removed outlier: 6.183A pdb=" N ASN J 147 " --> pdb=" O LEU J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 156 removed outlier: 4.779A pdb=" N LYS J 155 " --> pdb=" O MET J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 165 removed outlier: 3.664A pdb=" N ILE J 163 " --> pdb=" O SER J 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 33 Proline residue: K 19 - end of helix removed outlier: 3.507A pdb=" N ILE K 29 " --> pdb=" O TYR K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 81 removed outlier: 3.783A pdb=" N ASP K 72 " --> pdb=" O GLN K 68 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE K 78 " --> pdb=" O LEU K 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 31 removed outlier: 3.690A pdb=" N ASN L 27 " --> pdb=" O ALA L 23 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU L 29 " --> pdb=" O PHE L 25 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N VAL L 31 " --> pdb=" O ASN L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 53 removed outlier: 3.618A pdb=" N SER L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 70 removed outlier: 7.083A pdb=" N ALA L 60 " --> pdb=" O SER L 56 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE L 61 " --> pdb=" O GLU L 57 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASN L 67 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL L 68 " --> pdb=" O ALA L 64 " (cutoff:3.500A) Proline residue: L 70 - end of helix Processing helix chain 'L' and resid 91 through 111 removed outlier: 4.347A pdb=" N ASN L 96 " --> pdb=" O PRO L 92 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS L 109 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ARG L 110 " --> pdb=" O ALA L 106 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLY L 111 " --> pdb=" O ALA L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 115 through 129 removed outlier: 3.928A pdb=" N ALA L 120 " --> pdb=" O ALA L 116 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 148 removed outlier: 3.969A pdb=" N GLU L 145 " --> pdb=" O HIS L 141 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA L 146 " --> pdb=" O ARG L 142 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN L 147 " --> pdb=" O MET L 143 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS L 148 " --> pdb=" O ALA L 144 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 20 removed outlier: 3.665A pdb=" N ILE M 13 " --> pdb=" O MET M 9 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 43 Processing helix chain 'M' and resid 111 through 119 removed outlier: 4.155A pdb=" N GLN M 117 " --> pdb=" O ARG M 113 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY M 119 " --> pdb=" O ALA M 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 33 through 38 removed outlier: 3.794A pdb=" N PHE N 38 " --> pdb=" O LEU N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 53 removed outlier: 4.713A pdb=" N VAL N 47 " --> pdb=" O ALA N 43 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ARG N 48 " --> pdb=" O ARG N 44 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 70 through 86 Processing helix chain 'N' and resid 90 through 101 removed outlier: 5.548A pdb=" N GLU N 96 " --> pdb=" O SER N 92 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS N 99 " --> pdb=" O SER N 95 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 33 removed outlier: 3.615A pdb=" N ASP O 19 " --> pdb=" O HIS O 15 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU O 24 " --> pdb=" O GLN O 20 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N THR O 32 " --> pdb=" O THR O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 90 removed outlier: 3.794A pdb=" N VAL O 84 " --> pdb=" O THR O 80 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ASP O 85 " --> pdb=" O GLU O 81 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG O 89 " --> pdb=" O ASP O 85 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU O 90 " --> pdb=" O ALA O 86 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 50 removed outlier: 4.484A pdb=" N GLY P 50 " --> pdb=" O ALA P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 58 removed outlier: 3.623A pdb=" N SER P 57 " --> pdb=" O GLY P 53 " (cutoff:3.500A) removed outlier: 4.293A 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 74 removed outlier: 3.724A pdb=" N ALA P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL P 73 " --> pdb=" O CYS P 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 89 through 103 removed outlier: 5.177A pdb=" N GLU P 93 " --> pdb=" O GLY P 89 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER P 94 " --> pdb=" O PRO P 90 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR P 95 " --> pdb=" O GLY P 91 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE P 96 " --> pdb=" O ARG P 92 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG P 97 " --> pdb=" O GLU P 93 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA P 101 " --> pdb=" O ARG P 97 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA P 102 " --> pdb=" O ALA P 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 10 removed outlier: 3.660A pdb=" N ARG Q 8 " --> pdb=" O ASN Q 4 " (cutoff:3.500A) Proline residue: Q 10 - end of helix Processing helix chain 'Q' and resid 21 through 26 removed outlier: 5.738A pdb=" N ALA Q 25 " --> pdb=" O PRO Q 21 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N CYS Q 26 " --> pdb=" O ALA Q 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 21 through 26' Processing helix chain 'Q' and resid 112 through 117 removed outlier: 5.354A pdb=" N TYR Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) removed outlier: 3.980A 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: 3.698A pdb=" N SER R 20 " --> pdb=" O ILE R 16 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE R 21 " --> pdb=" O ALA R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 37 removed outlier: 3.658A pdb=" N ALA R 36 " --> pdb=" O ILE R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 48 removed outlier: 4.943A pdb=" N SER R 48 " --> pdb=" O ILE R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 63 removed outlier: 5.596A pdb=" N THR R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS R 61 " --> pdb=" O ASP R 57 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE R 62 " --> pdb=" O GLU R 58 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N VAL R 63 " --> pdb=" O VAL R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 83 removed outlier: 3.614A pdb=" N ARG R 70 " --> pdb=" O GLY R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 93 Processing helix chain 'R' and resid 105 through 110 removed outlier: 4.359A 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 23 removed outlier: 3.501A pdb=" N ARG S 12 " --> pdb=" O ARG S 8 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR S 19 " --> pdb=" O LEU S 15 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE S 20 " --> pdb=" O ALA S 16 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ALA S 21 " --> pdb=" O ASP S 17 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N LYS S 22 " --> pdb=" O LYS S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 29 Processing helix chain 'S' and resid 37 through 51 removed outlier: 3.796A pdb=" N TRP S 41 " --> pdb=" O ASP S 37 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA S 43 " --> pdb=" O ASP S 39 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN S 48 " --> pdb=" O VAL S 44 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR S 49 " --> pdb=" O LEU S 45 " (cutoff:3.500A) Proline residue: S 51 - end of helix Processing helix chain 'S' and resid 55 through 60 removed outlier: 4.121A pdb=" N GLN S 59 " --> pdb=" O SER S 55 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ARG S 60 " --> pdb=" O PRO S 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 55 through 60' Processing helix chain 'S' and resid 79 through 90 Processing helix chain 'T' and resid 3 through 15 removed outlier: 3.803A pdb=" N ILE T 10 " --> pdb=" O ALA T 6 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 43 removed outlier: 3.903A pdb=" N GLY T 40 " --> pdb=" O ASN T 36 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS T 41 " --> pdb=" O HIS T 37 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 73 removed outlier: 3.565A pdb=" N GLY T 54 " --> pdb=" O HIS T 50 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 85 removed outlier: 3.642A pdb=" N GLU T 82 " --> pdb=" O THR T 78 " (cutoff:3.500A) 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 Processing helix chain 'W' and resid 24 through 33 removed outlier: 3.947A pdb=" N LEU W 28 " --> pdb=" O ASP W 24 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN W 30 " --> pdb=" O ALA W 26 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR W 31 " --> pdb=" O THR W 27 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N THR W 33 " --> pdb=" O LYS W 29 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 45 removed outlier: 3.532A pdb=" N THR W 44 " --> pdb=" O PRO W 40 " (cutoff:3.500A) 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: 4.431A pdb=" N PHE X 73 " --> pdb=" O LYS X 69 " (cutoff:3.500A) removed outlier: 5.065A 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 'X' and resid 63 through 68 removed outlier: 3.925A pdb=" N VAL X 66 " --> pdb=" O ASP X 63 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS X 68 " --> pdb=" O MET X 65 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 41 removed outlier: 3.524A pdb=" N MET Y 26 " --> pdb=" O SER Y 22 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 62 Proline residue: Y 55 - end of helix Processing helix chain 'Y' and resid 67 through 86 removed outlier: 5.857A pdb=" N ALA Y 71 " --> pdb=" O HIS Y 67 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 23 removed outlier: 4.983A pdb=" N ARG Z 20 " --> pdb=" O ARG Z 16 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS Z 22 " --> pdb=" O PHE Z 18 " (cutoff:3.500A) Processing helix chain 'Z' and resid 26 through 33 removed outlier: 4.510A pdb=" N GLU Z 30 " --> pdb=" O GLY Z 26 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ARG Z 33 " --> pdb=" O ALA Z 29 " (cutoff:3.500A) Processing helix chain 'Z' and resid 38 through 61 removed outlier: 3.704A pdb=" N ALA Z 60 " --> pdb=" O ALA Z 56 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 14 removed outlier: 3.508A pdb=" N LYS a 14 " --> pdb=" O VAL a 10 " (cutoff:3.500A) Processing helix chain 'a' and resid 22 through 35 removed outlier: 5.139A pdb=" N LYS a 31 " --> pdb=" O ILE a 27 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N GLU a 32 " --> pdb=" O ALA a 28 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR a 35 " --> pdb=" O LYS a 31 " (cutoff:3.500A) Processing helix chain 'a' and resid 181 through 200 removed outlier: 3.610A pdb=" N LYS a 198 " --> pdb=" O VAL a 194 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'b' and resid 32 through 35 No H-bonds generated for sheet with id= 1 Processing sheet with id= 2, first strand: chain 'b' and resid 79 through 82 removed outlier: 6.797A pdb=" N LEU b 92 " --> pdb=" O GLU b 78 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ILE b 73 " --> pdb=" O SER b 117 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N SER b 117 " --> pdb=" O ILE b 73 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASP b 113 " --> pdb=" O VAL b 77 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N GLY b 126 " --> pdb=" O GLN b 114 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLN b 116 " --> pdb=" O GLY b 126 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'b' and resid 161 through 164 removed outlier: 6.220A pdb=" N THR b 172 " --> pdb=" O VAL b 164 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLU b 179 " --> pdb=" O LEU b 175 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'b' and resid 90 through 95 removed outlier: 3.684A pdb=" N GLU b 99 " --> pdb=" O TYR b 95 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'c' and resid 3 through 9 removed outlier: 3.513A pdb=" N LYS c 8 " --> pdb=" O SER c 199 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N SER c 199 " --> pdb=" O LYS c 8 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ASP c 200 " --> pdb=" O THR c 112 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N THR c 112 " --> pdb=" O ASP c 200 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'c' and resid 11 through 16 removed outlier: 3.855A pdb=" N VAL c 20 " --> pdb=" O THR c 16 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'c' and resid 32 through 35 removed outlier: 6.747A pdb=" N GLN c 49 " --> pdb=" O THR c 35 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'c' and resid 46 through 51 removed outlier: 5.911A pdb=" N ARG c 46 " --> pdb=" O LEU c 84 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'c' and resid 105 through 108 removed outlier: 6.002A pdb=" N LYS c 105 " --> pdb=" O VAL c 177 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'd' and resid 117 through 120 removed outlier: 3.632A 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: 3.741A pdb=" N GLY e 85 " --> pdb=" O THR e 67 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET e 37 " --> pdb=" O CYS e 86 " (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: 6.458A pdb=" N THR f 128 " --> pdb=" O LEU f 88 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'f' and resid 101 through 105 Processing sheet with id= 16, first strand: chain 'g' and resid 2 through 5 removed outlier: 6.227A pdb=" N GLN g 2 " --> pdb=" O ALA g 39 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'j' and resid 50 through 54 Processing sheet with id= 18, first strand: chain 'j' and resid 74 through 78 removed outlier: 7.416A pdb=" N GLY j 83 " --> pdb=" O THR j 78 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'k' and resid 17 through 21 removed outlier: 6.550A pdb=" N ARG k 17 " --> pdb=" O VAL k 10 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL k 10 " --> pdb=" O ARG k 17 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N THR k 6 " --> pdb=" O CYS k 21 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ASN k 82 " --> pdb=" O MET k 7 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'k' and resid 39 through 42 Processing sheet with id= 21, first strand: chain 'm' and resid 62 through 66 removed outlier: 6.731A pdb=" N LEU m 102 " --> pdb=" O ARG m 66 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N SER m 30 " --> pdb=" O LYS m 133 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'n' and resid 33 through 37 removed outlier: 5.800A pdb=" N ALA n 108 " --> pdb=" O PHE n 102 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE n 102 " --> pdb=" O ALA n 108 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N MET n 110 " --> pdb=" O CYS n 100 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS n 100 " --> pdb=" O MET n 110 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'o' and resid 49 through 53 removed outlier: 3.630A pdb=" N VAL o 49 " --> pdb=" O VAL o 39 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE o 35 " --> pdb=" O THR o 53 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL o 28 " --> pdb=" O ASP o 93 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'p' and resid 37 through 44 removed outlier: 6.540A pdb=" N THR p 24 " --> pdb=" O LYS p 86 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER p 82 " --> pdb=" O LYS p 28 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'p' and resid 48 through 51 removed outlier: 3.622A pdb=" N ALA p 48 " --> pdb=" O THR p 59 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N SER p 56 " --> pdb=" O THR p 75 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG p 71 " --> pdb=" O VAL p 60 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'r' and resid 11 through 15 removed outlier: 3.667A pdb=" N TYR r 2 " --> pdb=" O ALA r 42 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET r 40 " --> pdb=" O VAL r 4 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASN r 43 " --> pdb=" O GLU r 45 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'r' and resid 18 through 23 removed outlier: 4.406A pdb=" N GLN r 18 " --> pdb=" O ILE r 98 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU r 31 " --> pdb=" O VAL r 63 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'r' and resid 65 through 76 removed outlier: 5.671A pdb=" N GLN r 91 " --> pdb=" O GLY r 69 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS r 71 " --> pdb=" O HIS r 89 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N HIS r 89 " --> pdb=" O LYS r 71 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LYS r 73 " --> pdb=" O GLN r 87 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLN r 87 " --> pdb=" O LYS r 73 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL r 75 " --> pdb=" O LYS r 85 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS r 85 " --> pdb=" O VAL r 75 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 's' and resid 2 through 8 removed outlier: 4.841A pdb=" N THR s 3 " --> pdb=" O VAL s 107 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL s 107 " --> pdb=" O THR s 3 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL s 106 " --> pdb=" O THR s 72 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 's' and resid 73 through 78 Processing sheet with id= 31, first strand: chain 's' and resid 79 through 88 removed outlier: 3.721A pdb=" N THR s 100 " --> pdb=" O PRO s 80 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG s 92 " --> pdb=" O ARG s 88 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 't' and resid 12 through 15 removed outlier: 5.337A pdb=" N VAL t 31 " --> pdb=" O HIS t 15 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LYS t 66 " --> pdb=" O ARG t 77 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ASP t 79 " --> pdb=" O LYS t 64 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LYS t 64 " --> pdb=" O ASP t 79 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LYS t 81 " --> pdb=" O VAL t 62 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL t 62 " --> pdb=" O LYS t 81 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA t 83 " --> pdb=" O THR t 60 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR t 60 " --> pdb=" O ALA t 83 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL t 85 " --> pdb=" O VAL t 58 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL t 58 " --> pdb=" O VAL t 85 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'u' and resid 8 through 12 removed outlier: 5.208A pdb=" N ASP u 8 " --> pdb=" O VAL u 24 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL u 10 " --> pdb=" O GLY u 22 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS u 20 " --> pdb=" O VAL u 12 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'u' and resid 39 through 47 removed outlier: 4.948A pdb=" N ASN u 39 " --> pdb=" O ALA u 62 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY u 56 " --> pdb=" O GLN u 45 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'u' and resid 82 through 86 Processing sheet with id= 36, first strand: chain 'v' and resid 2 through 5 Processing sheet with id= 37, first strand: chain 'v' and resid 37 through 42 removed outlier: 3.784A pdb=" N ILE v 89 " --> pdb=" O PRO v 27 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'w' and resid 41 through 44 removed outlier: 7.149A pdb=" N ILE w 78 " --> pdb=" O GLY w 44 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'w' and resid 47 through 50 removed outlier: 3.916A pdb=" N THR w 54 " --> pdb=" O GLY w 50 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'x' and resid 11 through 18 removed outlier: 3.983A pdb=" N THR x 24 " --> pdb=" O ASN x 16 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASN x 22 " --> pdb=" O SER x 18 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'z' and resid 33 through 38 removed outlier: 4.876A pdb=" N HIS z 33 " --> pdb=" O GLN z 8 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS z 5 " --> pdb=" O GLU z 57 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET z 53 " --> pdb=" O THR z 9 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'A' and resid 11 through 16 removed outlier: 3.533A pdb=" N ASN A 20 " --> pdb=" O CYS A 16 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'C' and resid 6 through 11 Processing sheet with id= 44, first strand: chain 'C' and resid 33 through 37 removed outlier: 6.440A pdb=" N LEU C 33 " --> pdb=" O GLU C 50 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'E' and resid 21 through 24 removed outlier: 5.562A pdb=" N PHE E 21 " --> pdb=" O VAL E 49 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'F' and resid 14 through 19 Processing sheet with id= 47, first strand: chain 'G' and resid 30 through 33 removed outlier: 3.864A pdb=" N VAL G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'G' and resid 88 through 91 removed outlier: 3.897A pdb=" N PHE G 183 " --> pdb=" O LEU G 160 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE G 185 " --> pdb=" O VAL G 162 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE G 197 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA G 184 " --> pdb=" O PHE G 197 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'H' and resid 53 through 58 Processing sheet with id= 50, first strand: chain 'H' and resid 164 through 168 removed outlier: 3.620A pdb=" N GLY H 147 " --> pdb=" O PHE H 202 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY H 196 " --> pdb=" O SER H 153 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY H 193 " --> pdb=" O THR H 190 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL H 197 " --> pdb=" O SER H 186 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER H 186 " --> pdb=" O VAL H 197 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN H 184 " --> pdb=" O VAL H 199 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'I' and resid 139 through 143 removed outlier: 8.620A pdb=" N TRP I 169 " --> pdb=" O LYS I 182 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'J' and resid 15 through 24 removed outlier: 3.644A pdb=" N ALA J 16 " --> pdb=" O LEU J 35 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ILE J 29 " --> pdb=" O LYS J 22 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY J 27 " --> pdb=" O VAL J 24 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY J 50 " --> pdb=" O ALA J 34 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG J 44 " --> pdb=" O ASP J 40 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'J' and resid 82 through 85 removed outlier: 7.487A pdb=" N HIS J 82 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N TYR J 127 " --> pdb=" O ARG J 92 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'K' and resid 38 through 41 removed outlier: 4.808A pdb=" N ASN K 63 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU K 40 " --> pdb=" O LEU K 61 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE K 8 " --> pdb=" O VAL K 60 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE K 6 " --> pdb=" O MET K 62 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N HIS K 3 " --> pdb=" O THR K 92 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N GLU K 5 " --> pdb=" O MET K 90 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N MET K 90 " --> pdb=" O GLU K 5 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET K 9 " --> pdb=" O ARG K 86 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ARG K 86 " --> pdb=" O MET K 9 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'K' and resid 44 through 47 removed outlier: 5.987A pdb=" N LEU K 47 " --> pdb=" O HIS K 55 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N HIS K 55 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'L' and resid 72 through 78 Processing sheet with id= 57, first strand: chain 'M' and resid 22 through 26 removed outlier: 7.682A pdb=" N ALA M 22 " --> pdb=" O LEU M 62 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU M 51 " --> pdb=" O GLU M 57 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS M 49 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASP M 47 " --> pdb=" O THR M 61 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'M' and resid 101 through 105 removed outlier: 6.529A 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: 4.210A pdb=" N GLY N 9 " --> pdb=" O ALA N 16 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'O' and resid 44 through 52 removed outlier: 3.705A pdb=" N GLU O 47 " --> pdb=" O ILE O 67 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ILE O 8 " --> pdb=" O VAL O 74 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG O 9 " --> pdb=" O GLN O 99 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'P' and resid 41 through 44 removed outlier: 3.510A pdb=" N GLY P 42 " --> pdb=" O ILE P 33 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N VAL P 83 " --> pdb=" O THR P 107 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'Q' and resid 28 through 32 removed outlier: 4.942A pdb=" N LEU Q 80 " --> pdb=" O VAL Q 97 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'Q' and resid 34 through 40 removed outlier: 4.701A pdb=" N ARG Q 35 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG Q 53 " --> pdb=" O ARG Q 35 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'U' and resid 4 through 10 removed outlier: 3.785A pdb=" N ALA U 7 " --> pdb=" O GLN U 18 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'V' and resid 6 through 10 removed outlier: 6.873A pdb=" N GLU V 59 " --> pdb=" O VAL V 75 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'V' and resid 18 through 30 removed outlier: 6.789A pdb=" N LYS V 18 " --> pdb=" O ASP V 47 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LYS V 35 " --> pdb=" O HIS V 30 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'X' and resid 45 through 50 removed outlier: 4.586A pdb=" N LEU X 46 " --> pdb=" O VAL X 61 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'a' and resid 61 through 64 Processing sheet with id= 69, first strand: chain 'a' and resid 169 through 174 removed outlier: 4.891A pdb=" N GLY a 169 " --> pdb=" O LEU a 48 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE a 171 " --> pdb=" O VAL a 46 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL a 46 " --> pdb=" O ILE a 171 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR a 173 " --> pdb=" O VAL a 44 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER a 215 " --> pdb=" O ASP a 43 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA a 45 " --> pdb=" O SER a 213 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER a 213 " --> pdb=" O ALA a 45 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE a 214 " --> pdb=" O VAL a 222 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA a 220 " --> pdb=" O THR a 216 " (cutoff:3.500A) 1723 hydrogen bonds defined for protein. 5076 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3698 hydrogen bonds 5980 hydrogen bond angles 0 basepair planarities 1475 basepair parallelities 2248 stacking parallelities Total time for adding SS restraints: 247.78 Time building geometry restraints manager: 77.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.28: 11586 1.28 - 1.44: 67968 1.44 - 1.59: 71197 1.59 - 1.75: 9090 1.75 - 1.90: 277 Bond restraints: 160118 Sorted by residual: bond pdb=" C VAL e 73 " pdb=" O VAL e 73 " ideal model delta sigma weight residual 1.234 1.460 -0.226 1.15e-02 7.56e+03 3.85e+02 bond pdb=" C ASP K 13 " pdb=" O ASP K 13 " ideal model delta sigma weight residual 1.236 1.447 -0.210 1.15e-02 7.56e+03 3.34e+02 bond pdb=" C ALA h 44 " pdb=" O ALA h 44 " ideal model delta sigma weight residual 1.236 1.436 -0.200 1.31e-02 5.83e+03 2.34e+02 bond pdb=" C THR d 150 " pdb=" O THR d 150 " ideal model delta sigma weight residual 1.236 1.380 -0.144 9.60e-03 1.09e+04 2.25e+02 bond pdb=" C ILE o 58 " pdb=" O ILE o 58 " ideal model delta sigma weight residual 1.242 1.414 -0.172 1.17e-02 7.31e+03 2.16e+02 ... (remaining 160113 not shown) Histogram of bond angle deviations from ideal: 98.61 - 105.71: 25095 105.71 - 112.81: 89130 112.81 - 119.91: 63921 119.91 - 127.02: 49335 127.02 - 134.12: 12141 Bond angle restraints: 239622 Sorted by residual: angle pdb=" N ILE d 73 " pdb=" CA ILE d 73 " pdb=" C ILE d 73 " ideal model delta sigma weight residual 113.71 101.97 11.74 9.50e-01 1.11e+00 1.53e+02 angle pdb=" C PHE k 112 " pdb=" N MET k 113 " pdb=" CA MET k 113 " ideal model delta sigma weight residual 120.38 103.22 17.16 1.46e+00 4.69e-01 1.38e+02 angle pdb=" N ARG P 126 " pdb=" CA ARG P 126 " pdb=" C ARG P 126 " ideal model delta sigma weight residual 110.91 123.90 -12.99 1.17e+00 7.31e-01 1.23e+02 angle pdb=" CA ASP K 13 " pdb=" C ASP K 13 " pdb=" O ASP K 13 " ideal model delta sigma weight residual 120.82 132.34 -11.52 1.05e+00 9.07e-01 1.20e+02 angle pdb=" C ARG L 95 " pdb=" N ASN L 96 " pdb=" CA ASN L 96 " ideal model delta sigma weight residual 120.31 104.85 15.46 1.52e+00 4.33e-01 1.03e+02 ... (remaining 239617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 90693 35.91 - 71.83: 10828 71.83 - 107.74: 1112 107.74 - 143.66: 22 143.66 - 179.57: 19 Dihedral angle restraints: 102674 sinusoidal: 86015 harmonic: 16659 Sorted by residual: dihedral pdb=" C4' C 1 490 " pdb=" C3' C 1 490 " pdb=" C2' C 1 490 " pdb=" C1' C 1 490 " ideal model delta sinusoidal sigma weight residual -35.00 35.89 -70.89 1 8.00e+00 1.56e-02 1.01e+02 dihedral pdb=" C5' C 1 490 " pdb=" C4' C 1 490 " pdb=" C3' C 1 490 " pdb=" O3' C 1 490 " ideal model delta sinusoidal sigma weight residual 147.00 76.71 70.29 1 8.00e+00 1.56e-02 9.94e+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 33.36 -68.36 1 8.00e+00 1.56e-02 9.47e+01 ... (remaining 102671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 26276 0.134 - 0.269: 3956 0.269 - 0.403: 373 0.403 - 0.538: 31 0.538 - 0.672: 5 Chirality restraints: 30641 Sorted by residual: chirality pdb=" C3' A 31201 " pdb=" C4' A 31201 " pdb=" O3' A 31201 " pdb=" C2' A 31201 " both_signs ideal model delta sigma weight residual False -2.74 -2.07 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" CA ILE R 6 " pdb=" N ILE R 6 " pdb=" C ILE R 6 " pdb=" CB ILE R 6 " both_signs ideal model delta sigma weight residual False 2.43 3.09 -0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA PRO b 7 " pdb=" N PRO b 7 " pdb=" C PRO b 7 " pdb=" CB PRO b 7 " both_signs ideal model delta sigma weight residual False 2.72 2.10 0.62 2.00e-01 2.50e+01 9.54e+00 ... (remaining 30638 not shown) Planarity restraints: 12773 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C 11909 " -0.280 2.00e-02 2.50e+03 1.45e-01 4.76e+02 pdb=" N1 C 11909 " 0.014 2.00e-02 2.50e+03 pdb=" C2 C 11909 " 0.034 2.00e-02 2.50e+03 pdb=" O2 C 11909 " 0.159 2.00e-02 2.50e+03 pdb=" N3 C 11909 " -0.035 2.00e-02 2.50e+03 pdb=" C4 C 11909 " -0.016 2.00e-02 2.50e+03 pdb=" N4 C 11909 " -0.187 2.00e-02 2.50e+03 pdb=" C5 C 11909 " 0.150 2.00e-02 2.50e+03 pdb=" C6 C 11909 " 0.161 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 11328 " 0.269 2.00e-02 2.50e+03 1.16e-01 3.71e+02 pdb=" N9 A 11328 " -0.016 2.00e-02 2.50e+03 pdb=" C8 A 11328 " -0.105 2.00e-02 2.50e+03 pdb=" N7 A 11328 " -0.090 2.00e-02 2.50e+03 pdb=" C5 A 11328 " -0.049 2.00e-02 2.50e+03 pdb=" C6 A 11328 " 0.040 2.00e-02 2.50e+03 pdb=" N6 A 11328 " 0.177 2.00e-02 2.50e+03 pdb=" N1 A 11328 " 0.018 2.00e-02 2.50e+03 pdb=" C2 A 11328 " -0.054 2.00e-02 2.50e+03 pdb=" N3 A 11328 " -0.102 2.00e-02 2.50e+03 pdb=" C4 A 11328 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 12262 " 0.226 2.00e-02 2.50e+03 1.25e-01 3.52e+02 pdb=" N1 U 12262 " -0.009 2.00e-02 2.50e+03 pdb=" C2 U 12262 " -0.047 2.00e-02 2.50e+03 pdb=" O2 U 12262 " -0.079 2.00e-02 2.50e+03 pdb=" N3 U 12262 " -0.047 2.00e-02 2.50e+03 pdb=" C4 U 12262 " -0.043 2.00e-02 2.50e+03 pdb=" O4 U 12262 " 0.226 2.00e-02 2.50e+03 pdb=" C5 U 12262 " -0.120 2.00e-02 2.50e+03 pdb=" C6 U 12262 " -0.107 2.00e-02 2.50e+03 ... (remaining 12770 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.11: 3 2.11 - 2.81: 33795 2.81 - 3.51: 214982 3.51 - 4.20: 476419 4.20 - 4.90: 617351 Nonbonded interactions: 1342550 Sorted by model distance: nonbonded pdb=" O3' A 5 76 " pdb=" C PRO 5 101 " model vdw 1.414 3.270 nonbonded pdb=" O3' A 5 76 " pdb=" CA PRO 5 101 " model vdw 2.032 3.470 nonbonded pdb=" O GLN l 38 " pdb=" N SER l 40 " model vdw 2.067 2.520 nonbonded pdb=" OG SER Q 114 " pdb=" O3' C 3 501 " model vdw 2.178 2.440 nonbonded pdb=" O ALA H 49 " pdb=" OG1 THR H 69 " model vdw 2.189 2.440 ... (remaining 1342545 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: 8.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.150 Extract box with map and model: 32.850 Check model and map are aligned: 1.700 Set scattering table: 1.090 Process input model: 575.170 Find NCS groups from input model: 3.010 Set up NCS constraints: 0.390 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:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 625.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 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 : 0.012 0.226 160118 Z= 0.768 Angle : 1.254 19.479 239622 Z= 0.819 Chirality : 0.098 0.672 30641 Planarity : 0.017 0.145 12773 Dihedral : 23.311 179.571 91921 Min Nonbonded Distance : 1.414 Molprobity Statistics. All-atom Clashscore : 29.31 Ramachandran Plot: Outliers : 1.95 % Allowed : 19.01 % Favored : 79.04 % Rotamer: Outliers : 3.83 % Allowed : 10.43 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.79 (0.09), residues: 5743 helix: -3.01 (0.10), residues: 1577 sheet: -2.89 (0.15), residues: 987 loop : -3.46 (0.09), residues: 3179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.009 TRP b 212 HIS 0.004 0.001 HIS b 52 PHE 0.050 0.007 PHE V 27 TYR 0.094 0.012 TYR k 32 ARG 0.014 0.001 ARG x 26 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1492 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1309 time to evaluate : 6.724 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: b 2 VAL cc_start: 0.8063 (OUTLIER) cc_final: 0.7832 (p) REVERT: c 49 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7633 (tm-30) REVERT: c 88 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.5943 (pm20) REVERT: c 173 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.6957 (pp30) REVERT: c 187 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7469 (mm) REVERT: d 124 PHE cc_start: 0.8560 (t80) cc_final: 0.7892 (t80) REVERT: d 171 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7574 (p0) REVERT: d 191 ASP cc_start: 0.8435 (m-30) cc_final: 0.8223 (t70) REVERT: e 25 MET cc_start: 0.9054 (ppp) cc_final: 0.8625 (ppp) REVERT: e 46 LYS cc_start: 0.7020 (mmtm) cc_final: 0.6784 (pttt) REVERT: e 97 GLU cc_start: 0.8555 (mp0) cc_final: 0.8214 (mp0) REVERT: f 68 ARG cc_start: 0.8829 (tmt170) cc_final: 0.8404 (tmt-80) REVERT: g 18 GLN cc_start: 0.7838 (mm110) cc_final: 0.7083 (tm-30) REVERT: i 116 MET cc_start: -0.1032 (ttm) cc_final: -0.1405 (ttp) REVERT: j 136 GLN cc_start: 0.8500 (mt0) cc_final: 0.8259 (mt0) REVERT: k 40 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8339 (tptt) REVERT: k 92 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7147 (mp0) REVERT: l 76 GLU cc_start: 0.7809 (pt0) cc_final: 0.7443 (pt0) REVERT: l 91 ASP cc_start: 0.8106 (t70) cc_final: 0.7370 (m-30) REVERT: m 90 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7246 (pm20) REVERT: m 132 THR cc_start: 0.8312 (m) cc_final: 0.8081 (t) REVERT: n 5 LYS cc_start: 0.9011 (mtpt) cc_final: 0.8772 (mtpt) REVERT: n 20 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.7899 (tpp) REVERT: n 114 GLU cc_start: 0.8166 (pp20) cc_final: 0.7799 (pp20) REVERT: o 92 PHE cc_start: 0.8856 (t80) cc_final: 0.8527 (t80) REVERT: o 116 GLN cc_start: 0.8510 (tm-30) cc_final: 0.8298 (tm-30) REVERT: q 60 TRP cc_start: 0.8626 (m-10) cc_final: 0.8337 (m-10) REVERT: r 60 LYS cc_start: 0.7481 (tppt) cc_final: 0.7062 (tptt) REVERT: s 1 MET cc_start: 0.7370 (ppp) cc_final: 0.7057 (ppp) REVERT: s 75 PHE cc_start: 0.9239 (OUTLIER) cc_final: 0.8737 (p90) REVERT: s 100 THR cc_start: 0.8170 (p) cc_final: 0.7903 (t) REVERT: t 42 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7619 (mt-10) REVERT: t 80 TRP cc_start: 0.8594 (p-90) cc_final: 0.7914 (p-90) REVERT: t 86 THR cc_start: 0.8781 (p) cc_final: 0.8546 (p) REVERT: u 17 ASP cc_start: 0.7975 (m-30) cc_final: 0.7775 (m-30) REVERT: u 36 GLU cc_start: 0.8229 (pm20) cc_final: 0.7643 (pm20) REVERT: v 35 GLU cc_start: 0.7289 (pm20) cc_final: 0.6999 (pm20) REVERT: F 12 ARG cc_start: 0.7825 (mmm-85) cc_final: 0.7606 (mmm-85) REVERT: G 41 ASN cc_start: 0.8054 (t0) cc_final: 0.7505 (t0) REVERT: G 48 MET cc_start: 0.8560 (mtt) cc_final: 0.8167 (mmm) REVERT: G 93 HIS cc_start: 0.7394 (m-70) cc_final: 0.7145 (m-70) REVERT: G 135 MET cc_start: 0.7859 (tpp) cc_final: 0.7639 (tpp) REVERT: G 138 ARG cc_start: 0.7589 (ttm170) cc_final: 0.7034 (mmm160) REVERT: H 24 ASN cc_start: 0.8412 (m-40) cc_final: 0.8147 (m-40) REVERT: H 31 ASN cc_start: 0.7971 (m-40) cc_final: 0.7694 (m110) REVERT: H 35 ASP cc_start: 0.8733 (m-30) cc_final: 0.8370 (m-30) REVERT: H 129 PHE cc_start: 0.7802 (p90) cc_final: 0.7576 (p90) REVERT: H 189 HIS cc_start: 0.6827 (p-80) cc_final: 0.6344 (p-80) REVERT: I 49 ASP cc_start: 0.8313 (t70) cc_final: 0.8033 (t0) REVERT: I 73 ASN cc_start: 0.8814 (OUTLIER) cc_final: 0.8589 (m-40) REVERT: I 74 TYR cc_start: 0.8399 (m-80) cc_final: 0.8133 (m-80) REVERT: I 131 ILE cc_start: 0.7902 (mm) cc_final: 0.7449 (pt) REVERT: I 133 SER cc_start: 0.7909 (p) cc_final: 0.7668 (m) REVERT: I 135 GLN cc_start: 0.8853 (mm-40) cc_final: 0.8471 (mm110) REVERT: J 146 MET cc_start: 0.8192 (tmm) cc_final: 0.7509 (tmm) REVERT: K 5 GLU cc_start: 0.8359 (pt0) cc_final: 0.7834 (pt0) REVERT: K 90 MET cc_start: 0.7668 (mtp) cc_final: 0.7445 (mtp) REVERT: N 21 LYS cc_start: 0.8167 (tttt) cc_final: 0.7752 (tptt) REVERT: N 42 THR cc_start: 0.6126 (m) cc_final: 0.5891 (t) REVERT: N 109 GLN cc_start: 0.8699 (pp30) cc_final: 0.8477 (pp30) REVERT: N 111 GLU cc_start: 0.8591 (pt0) cc_final: 0.8310 (pt0) REVERT: O 19 ASP cc_start: 0.9345 (t70) cc_final: 0.9035 (t70) REVERT: O 27 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8020 (tt0) REVERT: P 14 GLN cc_start: 0.7665 (tp40) cc_final: 0.7437 (mm-40) REVERT: P 28 ASN cc_start: 0.7411 (OUTLIER) cc_final: 0.7210 (t0) REVERT: Q 19 ASN cc_start: 0.8073 (p0) cc_final: 0.7571 (p0) REVERT: Q 66 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8722 (pt) REVERT: R 43 LYS cc_start: 0.8605 (mttt) cc_final: 0.8136 (mmtt) REVERT: S 9 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.7808 (mm-30) REVERT: S 22 LYS cc_start: 0.8125 (ptpp) cc_final: 0.7454 (ptmt) REVERT: S 41 TRP cc_start: 0.7531 (m100) cc_final: 0.7297 (m100) REVERT: T 34 GLN cc_start: 0.8771 (tp-100) cc_final: 0.8320 (mm-40) REVERT: U 28 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7258 (ptm-80) REVERT: U 34 GLU cc_start: 0.8399 (pp20) cc_final: 0.8158 (pp20) REVERT: U 76 LYS cc_start: 0.8248 (mmtm) cc_final: 0.7774 (tptp) REVERT: X 10 ILE cc_start: 0.8440 (pt) cc_final: 0.7709 (pt) REVERT: X 40 PHE cc_start: 0.7273 (m-10) cc_final: 0.7056 (m-80) REVERT: X 64 GLU cc_start: 0.7300 (tp30) cc_final: 0.6950 (tp30) REVERT: Y 28 ARG cc_start: 0.8975 (mmt90) cc_final: 0.8614 (mtp85) REVERT: a 16 ASP cc_start: 0.7523 (t70) cc_final: 0.7305 (t0) outliers start: 183 outliers final: 103 residues processed: 1432 average time/residue: 1.3133 time to fit residues: 3281.2004 Evaluate side-chains 1104 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 985 time to evaluate : 6.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 140 VAL Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 196 ASN Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 237 ARG Chi-restraints excluded: chain b residue 241 LYS Chi-restraints excluded: chain b residue 251 THR Chi-restraints excluded: chain c residue 49 GLN Chi-restraints excluded: chain c residue 88 GLU Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 156 PHE Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 173 GLN Chi-restraints excluded: chain c residue 178 VAL Chi-restraints excluded: chain c residue 187 LEU Chi-restraints excluded: chain d residue 132 LYS Chi-restraints excluded: chain d residue 171 ASP Chi-restraints excluded: chain e residue 129 MET Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 70 THR Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain k residue 32 TYR Chi-restraints excluded: chain k residue 40 LYS Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 92 GLU Chi-restraints excluded: chain l residue 19 LEU Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain m residue 18 ARG Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 90 GLU Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 110 GLU Chi-restraints excluded: chain m residue 125 PRO Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain n residue 20 MET Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain p residue 19 PHE Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 75 PHE Chi-restraints excluded: chain s residue 103 ILE Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 39 ASN Chi-restraints excluded: chain u residue 61 GLU Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 51 ARG Chi-restraints excluded: chain x residue 40 GLU Chi-restraints excluded: chain z residue 3 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 40 HIS Chi-restraints excluded: chain I residue 68 GLU Chi-restraints excluded: chain I residue 73 ASN Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 28 ASN Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 116 TYR Chi-restraints excluded: chain S residue 8 ARG Chi-restraints excluded: chain S residue 9 GLU Chi-restraints excluded: chain S residue 56 PRO Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 62 ARG Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 28 ARG Chi-restraints excluded: chain U residue 70 ARG Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain X residue 5 LYS Chi-restraints excluded: chain X residue 14 LEU Chi-restraints excluded: chain X residue 29 PRO Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain a residue 7 ARG Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 217 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1031 random chunks: chunk 870 optimal weight: 10.0000 chunk 781 optimal weight: 0.9990 chunk 433 optimal weight: 10.0000 chunk 266 optimal weight: 6.9990 chunk 527 optimal weight: 6.9990 chunk 417 optimal weight: 6.9990 chunk 808 optimal weight: 8.9990 chunk 312 optimal weight: 5.9990 chunk 491 optimal weight: 5.9990 chunk 601 optimal weight: 10.0000 chunk 936 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 44 ASN ** b 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 238 ASN b 259 ASN c 49 GLN ** c 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 26 GLN j 40 HIS j 138 GLN k 5 GLN ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 14 GLN q 13 HIS q 70 GLN ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 92 ASN u 73 ASN x 16 ASN ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 20 ASN y 25 GLN ** y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 58 ASN z 19 HIS D 13 ASN G 57 ASN ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN I 135 GLN ** I 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 GLN N 4 GLN N 36 GLN N 109 GLN ** O 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 58 ASN O 64 GLN P 37 GLN Q 4 ASN R 11 HIS R 104 ASN ** S 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 70 HIS W 18 GLN W 30 ASN X 42 ASN ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 68 HIS ** Y 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 54 GLN a 57 GLN ** a 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 160 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 160118 Z= 0.249 Angle : 0.764 11.959 239622 Z= 0.392 Chirality : 0.042 0.359 30641 Planarity : 0.006 0.070 12773 Dihedral : 23.701 177.940 80621 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.47 % Favored : 87.31 % Rotamer: Outliers : 5.25 % Allowed : 16.06 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.10), residues: 5743 helix: -1.56 (0.11), residues: 1774 sheet: -2.20 (0.16), residues: 932 loop : -3.04 (0.10), residues: 3037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 103 HIS 0.009 0.001 HIS m 13 PHE 0.043 0.002 PHE k 79 TYR 0.037 0.002 TYR I 75 ARG 0.009 0.001 ARG n 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1427 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 1176 time to evaluate : 6.644 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: c 88 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.6325 (pm20) REVERT: c 173 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.6786 (pp30) REVERT: f 25 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7669 (tt) REVERT: i 116 MET cc_start: -0.1194 (ttm) cc_final: -0.1491 (ttp) REVERT: j 136 GLN cc_start: 0.8409 (mt0) cc_final: 0.8145 (mt0) REVERT: k 2 ILE cc_start: 0.8414 (mm) cc_final: 0.7982 (mt) REVERT: k 40 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8201 (tptt) REVERT: l 10 GLU cc_start: 0.8316 (pp20) cc_final: 0.7507 (pm20) REVERT: l 76 GLU cc_start: 0.7522 (pt0) cc_final: 0.7163 (pt0) REVERT: l 91 ASP cc_start: 0.8108 (t70) cc_final: 0.7415 (m-30) REVERT: n 5 LYS cc_start: 0.8918 (mtpt) cc_final: 0.8629 (mtpt) REVERT: n 114 GLU cc_start: 0.7906 (pp20) cc_final: 0.7475 (pp20) REVERT: p 54 LEU cc_start: 0.8197 (tp) cc_final: 0.7915 (tp) REVERT: p 109 ILE cc_start: 0.8353 (mp) cc_final: 0.8107 (mt) REVERT: r 60 LYS cc_start: 0.7378 (tppt) cc_final: 0.7022 (tptt) REVERT: s 1 MET cc_start: 0.7317 (ppp) cc_final: 0.6981 (ppp) REVERT: s 8 ARG cc_start: 0.8189 (ttm110) cc_final: 0.7603 (ttm110) REVERT: t 27 SER cc_start: 0.7729 (m) cc_final: 0.7455 (t) REVERT: t 32 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8689 (pp) REVERT: t 39 THR cc_start: 0.8580 (p) cc_final: 0.8210 (t) REVERT: t 42 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7250 (mt-10) REVERT: t 80 TRP cc_start: 0.8473 (p-90) cc_final: 0.7893 (p-90) REVERT: u 36 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7599 (pm20) REVERT: u 61 GLU cc_start: 0.7917 (pp20) cc_final: 0.7684 (pp20) REVERT: v 34 LYS cc_start: 0.8284 (mmmt) cc_final: 0.8077 (mtmt) REVERT: v 35 GLU cc_start: 0.7310 (pm20) cc_final: 0.7002 (pm20) REVERT: x 75 GLU cc_start: 0.6296 (pt0) cc_final: 0.6083 (pt0) REVERT: F 12 ARG cc_start: 0.7790 (mmm-85) cc_final: 0.7472 (mmm-85) REVERT: G 127 LYS cc_start: 0.2451 (mppt) cc_final: 0.1736 (mmtm) REVERT: G 135 MET cc_start: 0.7309 (tpp) cc_final: 0.6926 (tpp) REVERT: G 138 ARG cc_start: 0.7230 (ttm170) cc_final: 0.6825 (mmm160) REVERT: H 24 ASN cc_start: 0.8312 (m-40) cc_final: 0.8033 (m-40) REVERT: H 129 PHE cc_start: 0.7804 (p90) cc_final: 0.7527 (p90) REVERT: I 73 ASN cc_start: 0.8784 (OUTLIER) cc_final: 0.8528 (m110) REVERT: I 118 SER cc_start: 0.8576 (OUTLIER) cc_final: 0.8117 (p) REVERT: I 134 TYR cc_start: 0.7516 (t80) cc_final: 0.6929 (t80) REVERT: K 97 THR cc_start: 0.6255 (t) cc_final: 0.5675 (m) REVERT: L 17 PHE cc_start: 0.7575 (p90) cc_final: 0.7323 (p90) REVERT: M 46 GLU cc_start: 0.8245 (tp30) cc_final: 0.7974 (mm-30) REVERT: M 72 GLU cc_start: 0.7505 (pt0) cc_final: 0.7155 (pt0) REVERT: N 21 LYS cc_start: 0.8015 (tttt) cc_final: 0.7589 (ttmm) REVERT: N 49 GLN cc_start: 0.8334 (mm-40) cc_final: 0.8066 (mt0) REVERT: N 109 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8394 (pp30) REVERT: O 19 ASP cc_start: 0.9068 (t70) cc_final: 0.8821 (t70) REVERT: P 14 GLN cc_start: 0.7380 (tp40) cc_final: 0.7149 (mm-40) REVERT: U 31 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7697 (tmm-80) REVERT: X 64 GLU cc_start: 0.7092 (tp30) cc_final: 0.6752 (tp30) REVERT: X 72 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7187 (mm-30) REVERT: Y 28 ARG cc_start: 0.8861 (mmt90) cc_final: 0.8605 (mtp85) REVERT: Y 57 VAL cc_start: 0.9249 (OUTLIER) cc_final: 0.9038 (t) REVERT: Y 74 HIS cc_start: 0.8237 (m170) cc_final: 0.7858 (m90) REVERT: Y 77 ASN cc_start: 0.8620 (OUTLIER) cc_final: 0.8333 (t0) REVERT: Z 52 VAL cc_start: 0.8500 (p) cc_final: 0.8196 (m) REVERT: Z 62 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6344 (pp20) outliers start: 251 outliers final: 151 residues processed: 1314 average time/residue: 1.2618 time to fit residues: 2923.8692 Evaluate side-chains 1171 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1007 time to evaluate : 6.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 145 MET Chi-restraints excluded: chain b residue 156 SER Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 196 ASN Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 251 THR Chi-restraints excluded: chain c residue 49 GLN Chi-restraints excluded: chain c residue 88 GLU Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain c residue 133 THR Chi-restraints excluded: chain c residue 156 PHE Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 173 GLN Chi-restraints excluded: chain c residue 178 VAL Chi-restraints excluded: chain c residue 187 LEU Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 146 ASP Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 25 ILE Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 70 THR Chi-restraints excluded: chain j residue 78 THR Chi-restraints excluded: chain k residue 13 ASN Chi-restraints excluded: chain k residue 40 LYS Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 19 LEU Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 102 LEU Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 90 VAL Chi-restraints excluded: chain o residue 106 LEU Chi-restraints excluded: chain p residue 19 PHE Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 103 VAL Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 43 ILE Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain u residue 21 ARG Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain v residue 58 SER Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain z residue 9 THR Chi-restraints excluded: chain z residue 23 LEU Chi-restraints excluded: chain z residue 24 LEU Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 202 ASN Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 40 HIS Chi-restraints excluded: chain I residue 68 GLU Chi-restraints excluded: chain I residue 73 ASN Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain N residue 36 GLN Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 109 GLN Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 28 ASN Chi-restraints excluded: chain P residue 37 GLN Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 116 TYR Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 81 ILE Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 31 ARG Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain X residue 5 LYS Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 73 PHE Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 8 LYS Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 77 ASN Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Z residue 62 GLU Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 27 ILE Chi-restraints excluded: chain a residue 56 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1031 random chunks: chunk 520 optimal weight: 20.0000 chunk 290 optimal weight: 5.9990 chunk 779 optimal weight: 20.0000 chunk 637 optimal weight: 10.0000 chunk 258 optimal weight: 30.0000 chunk 937 optimal weight: 10.0000 chunk 1013 optimal weight: 20.0000 chunk 835 optimal weight: 20.0000 chunk 930 optimal weight: 50.0000 chunk 319 optimal weight: 20.0000 chunk 752 optimal weight: 10.0000 overall best weight: 11.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 199 HIS b 225 ASN ** b 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 185 ASN d 115 GLN ** h 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN ** o 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 16 ASN y 20 ASN y 25 GLN ** y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 ASN ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 ASN ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 GLN I 73 ASN I 99 ASN ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 GLN N 30 ASN N 31 GLN N 36 GLN O 58 ASN O 64 GLN P 21 HIS P 117 HIS R 11 HIS S 42 ASN S 59 GLN T 61 GLN U 18 GLN ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.139 160118 Z= 0.421 Angle : 0.844 12.976 239622 Z= 0.430 Chirality : 0.046 0.384 30641 Planarity : 0.006 0.086 12773 Dihedral : 23.898 179.959 80492 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.74 % Favored : 84.07 % Rotamer: Outliers : 8.11 % Allowed : 19.03 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.10), residues: 5743 helix: -1.29 (0.11), residues: 1782 sheet: -2.02 (0.16), residues: 995 loop : -3.11 (0.10), residues: 2966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP G 103 HIS 0.009 0.002 HIS I 119 PHE 0.042 0.003 PHE k 79 TYR 0.041 0.003 TYR I 75 ARG 0.010 0.001 ARG m 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1415 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 388 poor density : 1027 time to evaluate : 6.583 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: c 173 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.6854 (pp30) REVERT: e 25 MET cc_start: 0.8914 (ppp) cc_final: 0.8692 (ppp) REVERT: f 87 GLN cc_start: 0.7651 (tm-30) cc_final: 0.7418 (tm-30) REVERT: f 168 VAL cc_start: 0.8009 (OUTLIER) cc_final: 0.7353 (t) REVERT: i 129 GLU cc_start: 0.5807 (OUTLIER) cc_final: 0.5543 (tm-30) REVERT: j 136 GLN cc_start: 0.8456 (mt0) cc_final: 0.8178 (mt0) REVERT: k 40 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8196 (tptt) REVERT: l 10 GLU cc_start: 0.8353 (pp20) cc_final: 0.7597 (pm20) REVERT: l 47 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7039 (ttp-110) REVERT: l 76 GLU cc_start: 0.7590 (pt0) cc_final: 0.7172 (pt0) REVERT: l 91 ASP cc_start: 0.8138 (t70) cc_final: 0.7375 (m-30) REVERT: m 75 GLU cc_start: 0.7464 (pm20) cc_final: 0.6884 (pm20) REVERT: m 90 GLU cc_start: 0.7393 (pm20) cc_final: 0.6975 (pm20) REVERT: n 114 GLU cc_start: 0.7994 (pp20) cc_final: 0.7743 (pp20) REVERT: p 109 ILE cc_start: 0.8380 (mp) cc_final: 0.8152 (mt) REVERT: q 23 TYR cc_start: 0.8211 (m-80) cc_final: 0.8008 (m-80) REVERT: q 43 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8249 (mm110) REVERT: r 60 LYS cc_start: 0.7592 (tppt) cc_final: 0.7159 (tptt) REVERT: s 1 MET cc_start: 0.6924 (ppp) cc_final: 0.6370 (ppp) REVERT: s 8 ARG cc_start: 0.8401 (ttm110) cc_final: 0.7554 (ttm110) REVERT: t 32 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8728 (pp) REVERT: t 80 TRP cc_start: 0.8534 (p-90) cc_final: 0.7883 (p-90) REVERT: u 36 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7329 (pm20) REVERT: u 61 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7696 (pp20) REVERT: v 35 GLU cc_start: 0.7094 (pm20) cc_final: 0.6821 (pm20) REVERT: v 44 HIS cc_start: 0.7066 (t-90) cc_final: 0.6655 (t-90) REVERT: v 51 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7120 (pp30) REVERT: B 51 ARG cc_start: 0.7235 (mpt180) cc_final: 0.6885 (mpt180) REVERT: G 96 LEU cc_start: 0.7928 (mt) cc_final: 0.7648 (tt) REVERT: G 103 TRP cc_start: 0.8482 (t-100) cc_final: 0.8183 (t-100) REVERT: G 138 ARG cc_start: 0.7187 (ttm170) cc_final: 0.6767 (mmm160) REVERT: G 153 MET cc_start: 0.7938 (tmm) cc_final: 0.7709 (tmm) REVERT: H 24 ASN cc_start: 0.8285 (m-40) cc_final: 0.7607 (p0) REVERT: H 129 PHE cc_start: 0.7827 (p90) cc_final: 0.7550 (p90) REVERT: I 74 TYR cc_start: 0.8403 (m-80) cc_final: 0.7861 (m-80) REVERT: I 118 SER cc_start: 0.8797 (OUTLIER) cc_final: 0.8229 (p) REVERT: I 134 TYR cc_start: 0.7608 (t80) cc_final: 0.7073 (t80) REVERT: I 170 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.6572 (pp) REVERT: J 60 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8150 (pm20) REVERT: K 13 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.7189 (p0) REVERT: K 40 GLU cc_start: 0.6894 (tm-30) cc_final: 0.5454 (tm-30) REVERT: K 42 TRP cc_start: 0.8273 (m-90) cc_final: 0.8072 (m-90) REVERT: L 142 ARG cc_start: 0.6449 (ptm160) cc_final: 0.6081 (ppt170) REVERT: M 9 MET cc_start: 0.6948 (OUTLIER) cc_final: 0.6537 (tmm) REVERT: M 42 GLU cc_start: 0.7836 (tp30) cc_final: 0.7591 (tp30) REVERT: M 46 GLU cc_start: 0.8230 (tp30) cc_final: 0.7995 (mm-30) REVERT: M 72 GLU cc_start: 0.7457 (pt0) cc_final: 0.7118 (pt0) REVERT: N 21 LYS cc_start: 0.7968 (tttt) cc_final: 0.7535 (ttmm) REVERT: N 42 THR cc_start: 0.6280 (OUTLIER) cc_final: 0.5969 (t) REVERT: O 19 ASP cc_start: 0.9092 (t70) cc_final: 0.8805 (t70) REVERT: P 14 GLN cc_start: 0.7351 (tp40) cc_final: 0.7145 (mm-40) REVERT: R 43 LYS cc_start: 0.8404 (mttt) cc_final: 0.8052 (mmtt) REVERT: V 78 VAL cc_start: 0.6459 (OUTLIER) cc_final: 0.5926 (t) REVERT: W 47 ARG cc_start: 0.6828 (mpt180) cc_final: 0.6376 (mpt180) REVERT: X 13 HIS cc_start: 0.5955 (OUTLIER) cc_final: 0.5475 (t-90) REVERT: X 55 GLN cc_start: 0.7864 (mp10) cc_final: 0.7427 (pt0) REVERT: X 72 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7224 (mm-30) REVERT: Y 12 GLN cc_start: 0.8388 (tm-30) cc_final: 0.8150 (tm-30) REVERT: Y 28 ARG cc_start: 0.8853 (mmt90) cc_final: 0.8641 (mtp85) REVERT: Y 53 MET cc_start: 0.9447 (tmm) cc_final: 0.9097 (ppp) REVERT: Z 37 TYR cc_start: 0.6461 (OUTLIER) cc_final: 0.6070 (m-80) REVERT: Z 52 VAL cc_start: 0.8543 (p) cc_final: 0.8254 (m) REVERT: Z 62 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6282 (pp20) outliers start: 388 outliers final: 263 residues processed: 1265 average time/residue: 1.2062 time to fit residues: 2696.3214 Evaluate side-chains 1228 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 945 time to evaluate : 6.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 87 SER Chi-restraints excluded: chain b residue 97 ASP Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 140 VAL Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 145 MET Chi-restraints excluded: chain b residue 156 SER Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 196 ASN Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 251 THR Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 91 THR Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 133 THR Chi-restraints excluded: chain c residue 156 PHE Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 173 GLN Chi-restraints excluded: chain c residue 178 VAL Chi-restraints excluded: chain c residue 187 LEU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 167 VAL Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 117 SER Chi-restraints excluded: chain e residue 129 MET Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 146 ASP Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 25 ILE Chi-restraints excluded: chain f residue 29 ASN Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain f residue 168 VAL Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain i residue 129 GLU Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 70 THR Chi-restraints excluded: chain j residue 78 THR Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 13 ASN Chi-restraints excluded: chain k residue 25 LEU Chi-restraints excluded: chain k residue 40 LYS Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 19 LEU Chi-restraints excluded: chain l residue 47 ARG Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 102 LEU Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 90 VAL Chi-restraints excluded: chain o residue 106 LEU Chi-restraints excluded: chain p residue 12 MET Chi-restraints excluded: chain p residue 19 PHE Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 43 GLN Chi-restraints excluded: chain q residue 79 ILE Chi-restraints excluded: chain q residue 86 SER Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 83 TYR Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 13 SER Chi-restraints excluded: chain s residue 37 THR Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 55 ILE Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 43 ILE Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain t residue 85 VAL Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 21 ARG Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 39 ASN Chi-restraints excluded: chain u residue 61 GLU Chi-restraints excluded: chain u residue 88 ASP Chi-restraints excluded: chain v residue 41 GLU Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 51 GLN Chi-restraints excluded: chain v residue 58 SER Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 63 ILE Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 3 THR Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 9 THR Chi-restraints excluded: chain z residue 23 LEU Chi-restraints excluded: chain z residue 24 LEU Chi-restraints excluded: chain z residue 28 LEU Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 37 CYS Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 202 ASN Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 40 HIS Chi-restraints excluded: chain I residue 68 GLU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 60 GLN Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 5 GLU Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 9 MET Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 56 HIS Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 67 GLU Chi-restraints excluded: chain P residue 80 ASN Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 116 TYR Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 54 THR Chi-restraints excluded: chain R residue 57 ASP Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 81 ILE Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 31 ARG Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 11 VAL Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain W residue 21 ASP Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain X residue 5 LYS Chi-restraints excluded: chain X residue 13 HIS Chi-restraints excluded: chain X residue 23 GLU Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 8 LYS Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Z residue 37 TYR Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 62 GLU Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 212 VAL Chi-restraints excluded: chain a residue 222 VAL Chi-restraints excluded: chain a residue 224 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1031 random chunks: chunk 926 optimal weight: 40.0000 chunk 705 optimal weight: 30.0000 chunk 486 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 447 optimal weight: 20.0000 chunk 629 optimal weight: 10.0000 chunk 941 optimal weight: 10.0000 chunk 996 optimal weight: 10.0000 chunk 491 optimal weight: 5.9990 chunk 892 optimal weight: 10.0000 chunk 268 optimal weight: 10.0000 overall best weight: 8.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 32 ASN ** i 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 86 GLN ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 97 GLN o 38 GLN ** o 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 25 GLN A 20 ASN ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN O 56 HIS O 64 GLN ** P 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 HIS S 59 GLN ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 160118 Z= 0.336 Angle : 0.754 11.209 239622 Z= 0.386 Chirality : 0.042 0.386 30641 Planarity : 0.006 0.079 12773 Dihedral : 23.871 179.667 80482 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.67 % Favored : 86.16 % Rotamer: Outliers : 7.90 % Allowed : 20.82 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.10), residues: 5743 helix: -1.01 (0.11), residues: 1801 sheet: -1.82 (0.16), residues: 962 loop : -2.95 (0.10), residues: 2980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP I 169 HIS 0.009 0.001 HIS I 119 PHE 0.038 0.002 PHE k 79 TYR 0.035 0.002 TYR I 75 ARG 0.008 0.001 ARG f 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1409 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 378 poor density : 1031 time to evaluate : 6.835 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: b 170 TYR cc_start: 0.7510 (m-10) cc_final: 0.7282 (m-10) REVERT: c 173 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.6865 (pp30) REVERT: e 139 GLU cc_start: 0.8380 (tm-30) cc_final: 0.7993 (tm-30) REVERT: f 25 ILE cc_start: 0.7851 (mt) cc_final: 0.7498 (tt) REVERT: f 76 ILE cc_start: 0.8647 (mm) cc_final: 0.8297 (mt) REVERT: g 41 LYS cc_start: 0.7091 (ptpt) cc_final: 0.6861 (tppt) REVERT: h 35 VAL cc_start: -0.1857 (OUTLIER) cc_final: -0.2065 (p) REVERT: i 116 MET cc_start: -0.1233 (ttt) cc_final: -0.1483 (ttp) REVERT: i 129 GLU cc_start: 0.5742 (OUTLIER) cc_final: 0.5488 (tm-30) REVERT: j 136 GLN cc_start: 0.8396 (mt0) cc_final: 0.8124 (mt0) REVERT: l 10 GLU cc_start: 0.8295 (pp20) cc_final: 0.7570 (pm20) REVERT: l 47 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7336 (ttp-110) REVERT: l 76 GLU cc_start: 0.7605 (pt0) cc_final: 0.7205 (pt0) REVERT: l 91 ASP cc_start: 0.8057 (t70) cc_final: 0.7333 (m-30) REVERT: m 55 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7341 (mmp80) REVERT: m 75 GLU cc_start: 0.7531 (pm20) cc_final: 0.6525 (pm20) REVERT: m 90 GLU cc_start: 0.7432 (pm20) cc_final: 0.6502 (pm20) REVERT: p 109 ILE cc_start: 0.8404 (mp) cc_final: 0.8203 (mt) REVERT: q 23 TYR cc_start: 0.8186 (m-80) cc_final: 0.7956 (m-80) REVERT: q 43 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8242 (mm110) REVERT: r 60 LYS cc_start: 0.7574 (tppt) cc_final: 0.7110 (tptt) REVERT: r 70 GLU cc_start: 0.8368 (mp0) cc_final: 0.8163 (mp0) REVERT: s 1 MET cc_start: 0.7012 (ppp) cc_final: 0.6620 (ppp) REVERT: s 8 ARG cc_start: 0.8392 (ttm110) cc_final: 0.7767 (ttm110) REVERT: s 62 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7354 (p0) REVERT: t 32 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8806 (pp) REVERT: t 80 TRP cc_start: 0.8570 (p-90) cc_final: 0.8075 (p-90) REVERT: u 36 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7436 (pm20) REVERT: u 61 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7683 (pp20) REVERT: v 1 MET cc_start: 0.6961 (ppp) cc_final: 0.6360 (ppp) REVERT: v 12 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7577 (tt0) REVERT: v 35 GLU cc_start: 0.7060 (pm20) cc_final: 0.6850 (pm20) REVERT: v 44 HIS cc_start: 0.6873 (t-90) cc_final: 0.6462 (t-90) REVERT: v 51 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7314 (pp30) REVERT: x 19 HIS cc_start: 0.8356 (OUTLIER) cc_final: 0.8057 (t70) REVERT: A 25 ARG cc_start: 0.8076 (mmp80) cc_final: 0.7765 (mmp80) REVERT: G 94 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.7087 (ttp80) REVERT: G 153 MET cc_start: 0.7671 (tmm) cc_final: 0.7333 (tmm) REVERT: H 24 ASN cc_start: 0.8303 (m-40) cc_final: 0.7572 (p0) REVERT: H 129 PHE cc_start: 0.7833 (p90) cc_final: 0.7538 (p90) REVERT: I 74 TYR cc_start: 0.8442 (m-80) cc_final: 0.8013 (m-80) REVERT: I 118 SER cc_start: 0.8725 (OUTLIER) cc_final: 0.8211 (p) REVERT: I 123 MET cc_start: 0.7941 (tpp) cc_final: 0.7725 (tpp) REVERT: I 134 TYR cc_start: 0.7652 (t80) cc_final: 0.7185 (t80) REVERT: I 170 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6537 (pp) REVERT: I 181 PHE cc_start: 0.8019 (t80) cc_final: 0.7813 (t80) REVERT: J 59 ILE cc_start: 0.9465 (OUTLIER) cc_final: 0.9230 (mp) REVERT: J 60 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8202 (pm20) REVERT: K 13 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7203 (p0) REVERT: K 40 GLU cc_start: 0.6762 (tm-30) cc_final: 0.5310 (tm-30) REVERT: K 97 THR cc_start: 0.6448 (t) cc_final: 0.5894 (m) REVERT: L 142 ARG cc_start: 0.6648 (ptm160) cc_final: 0.6256 (ppt170) REVERT: M 9 MET cc_start: 0.6949 (OUTLIER) cc_final: 0.6462 (tmm) REVERT: M 46 GLU cc_start: 0.8185 (tp30) cc_final: 0.7956 (mm-30) REVERT: M 72 GLU cc_start: 0.7473 (pt0) cc_final: 0.7141 (pt0) REVERT: N 21 LYS cc_start: 0.7893 (tttt) cc_final: 0.7450 (ttmm) REVERT: N 42 THR cc_start: 0.6159 (m) cc_final: 0.5842 (t) REVERT: O 19 ASP cc_start: 0.9076 (t0) cc_final: 0.8784 (t70) REVERT: O 71 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7908 (pp) REVERT: P 13 LYS cc_start: 0.7684 (mmmm) cc_final: 0.6978 (tppp) REVERT: P 14 GLN cc_start: 0.7234 (tp40) cc_final: 0.7024 (mm-40) REVERT: V 78 VAL cc_start: 0.6283 (OUTLIER) cc_final: 0.5667 (t) REVERT: W 47 ARG cc_start: 0.6849 (mpt180) cc_final: 0.6251 (mpt180) REVERT: X 11 ASP cc_start: 0.6632 (OUTLIER) cc_final: 0.6015 (t70) REVERT: X 13 HIS cc_start: 0.5815 (OUTLIER) cc_final: 0.4920 (t-90) REVERT: X 55 GLN cc_start: 0.7834 (mp10) cc_final: 0.7489 (mp-120) REVERT: X 72 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7234 (mm-30) REVERT: Y 12 GLN cc_start: 0.8371 (tm-30) cc_final: 0.8126 (tm-30) REVERT: Y 23 ARG cc_start: 0.8216 (mtp85) cc_final: 0.7952 (mtp85) REVERT: Y 28 ARG cc_start: 0.8798 (mmt90) cc_final: 0.8566 (mtp85) REVERT: Y 53 MET cc_start: 0.9387 (tmm) cc_final: 0.9160 (ppp) REVERT: Z 37 TYR cc_start: 0.6406 (OUTLIER) cc_final: 0.6059 (m-80) REVERT: Z 41 THR cc_start: 0.8317 (OUTLIER) cc_final: 0.8105 (p) REVERT: Z 52 VAL cc_start: 0.8542 (OUTLIER) cc_final: 0.8307 (m) REVERT: Z 62 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.6120 (pp20) outliers start: 378 outliers final: 269 residues processed: 1267 average time/residue: 1.2301 time to fit residues: 2765.4100 Evaluate side-chains 1243 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 297 poor density : 946 time to evaluate : 6.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 87 SER Chi-restraints excluded: chain b residue 97 ASP Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 156 SER Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 196 ASN Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 251 THR Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 91 THR Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain c residue 133 THR Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 173 GLN Chi-restraints excluded: chain c residue 178 VAL Chi-restraints excluded: chain c residue 187 LEU Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 75 SER Chi-restraints excluded: chain d residue 146 VAL Chi-restraints excluded: chain d residue 167 VAL Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 65 LEU Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 117 SER Chi-restraints excluded: chain e residue 129 MET Chi-restraints excluded: chain e residue 142 TYR Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 146 ASP Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain h residue 35 VAL Chi-restraints excluded: chain i residue 85 ILE Chi-restraints excluded: chain i residue 129 GLU Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 70 THR Chi-restraints excluded: chain j residue 78 THR Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 13 ASN Chi-restraints excluded: chain k residue 25 LEU Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 73 ASP Chi-restraints excluded: chain k residue 79 PHE Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain l residue 47 ARG Chi-restraints excluded: chain l residue 100 ILE Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 55 ARG Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 102 LEU Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain n residue 117 ASP Chi-restraints excluded: chain n residue 119 SER Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 58 ILE Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 90 VAL Chi-restraints excluded: chain o residue 106 LEU Chi-restraints excluded: chain p residue 19 PHE Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 43 GLN Chi-restraints excluded: chain q residue 79 ILE Chi-restraints excluded: chain q residue 86 SER Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 83 TYR Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 13 SER Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 62 ASP Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 43 ILE Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain u residue 21 ARG Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 39 ASN Chi-restraints excluded: chain u residue 61 GLU Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain u residue 88 ASP Chi-restraints excluded: chain u residue 100 GLU Chi-restraints excluded: chain v residue 12 GLN Chi-restraints excluded: chain v residue 41 GLU Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 51 GLN Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain x residue 19 HIS Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 50 VAL Chi-restraints excluded: chain z residue 3 THR Chi-restraints excluded: chain z residue 23 LEU Chi-restraints excluded: chain z residue 28 LEU Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 94 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 202 ASN Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 40 HIS Chi-restraints excluded: chain I residue 68 GLU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 59 ILE Chi-restraints excluded: chain J residue 60 GLN Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 5 GLU Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 14 ASP Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 9 MET Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 80 ASN Chi-restraints excluded: chain P residue 111 ASP Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain Q residue 14 LYS Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 116 TYR Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 57 ASP Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain S residue 59 GLN Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain T residue 17 ASP Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 81 ILE Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain U residue 18 GLN Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 31 ARG Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 46 HIS Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain X residue 5 LYS Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 13 HIS Chi-restraints excluded: chain X residue 14 LEU Chi-restraints excluded: chain X residue 23 GLU Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 73 PHE Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 8 LYS Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain Z residue 37 TYR Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain Z residue 62 GLU Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 47 ASN Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 212 VAL Chi-restraints excluded: chain a residue 214 ILE Chi-restraints excluded: chain a residue 218 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1031 random chunks: chunk 829 optimal weight: 20.0000 chunk 565 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 742 optimal weight: 30.0000 chunk 411 optimal weight: 6.9990 chunk 850 optimal weight: 10.0000 chunk 688 optimal weight: 30.0000 chunk 1 optimal weight: 0.1980 chunk 508 optimal weight: 6.9990 chunk 894 optimal weight: 10.0000 chunk 251 optimal weight: 10.0000 overall best weight: 6.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 136 GLN j 86 GLN ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN ** o 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 55 GLN ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 25 GLN y 36 GLN ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 119 HIS ** I 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN N 36 GLN O 64 GLN ** O 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 HIS U 9 HIS W 18 GLN ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 160118 Z= 0.277 Angle : 0.702 12.308 239622 Z= 0.361 Chirality : 0.040 0.374 30641 Planarity : 0.005 0.076 12773 Dihedral : 23.823 179.831 80470 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.76 % Favored : 86.09 % Rotamer: Outliers : 8.36 % Allowed : 21.68 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.91 (0.10), residues: 5743 helix: -0.78 (0.12), residues: 1813 sheet: -1.65 (0.16), residues: 963 loop : -2.85 (0.10), residues: 2967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP K 42 HIS 0.009 0.001 HIS I 119 PHE 0.036 0.002 PHE k 79 TYR 0.033 0.002 TYR I 75 ARG 0.009 0.001 ARG a 7 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1413 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 400 poor density : 1013 time to evaluate : 6.276 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: c 173 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.6881 (pp30) REVERT: f 25 ILE cc_start: 0.7873 (mt) cc_final: 0.7488 (tt) REVERT: f 76 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8309 (mt) REVERT: g 41 LYS cc_start: 0.7115 (ptpt) cc_final: 0.6910 (tppt) REVERT: i 116 MET cc_start: -0.0949 (ttt) cc_final: -0.1557 (ttp) REVERT: i 129 GLU cc_start: 0.5675 (OUTLIER) cc_final: 0.5434 (tm-30) REVERT: j 136 GLN cc_start: 0.8348 (mt0) cc_final: 0.8067 (mt0) REVERT: l 10 GLU cc_start: 0.8268 (pp20) cc_final: 0.7565 (pm20) REVERT: l 47 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7319 (ttp-110) REVERT: l 76 GLU cc_start: 0.7581 (pt0) cc_final: 0.7161 (pt0) REVERT: l 91 ASP cc_start: 0.7990 (t70) cc_final: 0.7390 (m-30) REVERT: m 75 GLU cc_start: 0.7534 (pm20) cc_final: 0.6508 (pm20) REVERT: m 90 GLU cc_start: 0.7364 (pm20) cc_final: 0.6389 (pm20) REVERT: o 85 LYS cc_start: 0.8130 (mmpt) cc_final: 0.7863 (mmmm) REVERT: q 17 LEU cc_start: 0.8895 (mm) cc_final: 0.8516 (tp) REVERT: q 43 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8203 (mm110) REVERT: q 60 TRP cc_start: 0.8501 (m-10) cc_final: 0.8290 (m-10) REVERT: r 60 LYS cc_start: 0.7530 (tppt) cc_final: 0.7093 (tptt) REVERT: s 1 MET cc_start: 0.7020 (ppp) cc_final: 0.6629 (ppp) REVERT: s 62 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7330 (p0) REVERT: t 32 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8828 (pp) REVERT: t 80 TRP cc_start: 0.8544 (p-90) cc_final: 0.8125 (p-90) REVERT: u 36 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7387 (pm20) REVERT: v 1 MET cc_start: 0.6867 (ppp) cc_final: 0.6367 (ppp) REVERT: v 12 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7589 (tt0) REVERT: v 35 GLU cc_start: 0.7024 (pm20) cc_final: 0.6785 (pm20) REVERT: v 44 HIS cc_start: 0.6796 (t-90) cc_final: 0.6352 (t-90) REVERT: v 51 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.6971 (pp30) REVERT: x 19 HIS cc_start: 0.8316 (OUTLIER) cc_final: 0.8050 (t70) REVERT: A 44 PHE cc_start: 0.6408 (p90) cc_final: 0.6066 (p90) REVERT: C 34 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7297 (mt-10) REVERT: G 15 PHE cc_start: 0.6861 (p90) cc_final: 0.6620 (p90) REVERT: G 51 GLU cc_start: 0.8579 (pm20) cc_final: 0.8153 (pm20) REVERT: H 24 ASN cc_start: 0.8282 (m-40) cc_final: 0.8018 (m-40) REVERT: H 129 PHE cc_start: 0.7841 (p90) cc_final: 0.7527 (p90) REVERT: I 74 TYR cc_start: 0.8436 (m-10) cc_final: 0.8059 (m-80) REVERT: I 123 MET cc_start: 0.7916 (tpp) cc_final: 0.7693 (tpp) REVERT: I 134 TYR cc_start: 0.7658 (t80) cc_final: 0.7252 (t80) REVERT: I 170 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.6534 (pp) REVERT: I 176 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8260 (mmtt) REVERT: I 190 LEU cc_start: 0.8259 (pt) cc_final: 0.7915 (pt) REVERT: J 59 ILE cc_start: 0.9466 (OUTLIER) cc_final: 0.9264 (mp) REVERT: J 60 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8127 (pm20) REVERT: K 13 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.7155 (p0) REVERT: K 17 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7265 (pp30) REVERT: L 141 HIS cc_start: 0.8287 (OUTLIER) cc_final: 0.7940 (m170) REVERT: L 142 ARG cc_start: 0.6647 (ptm160) cc_final: 0.6298 (ppt170) REVERT: M 72 GLU cc_start: 0.7488 (pt0) cc_final: 0.7170 (pt0) REVERT: N 21 LYS cc_start: 0.7841 (tttt) cc_final: 0.7410 (ttmm) REVERT: N 42 THR cc_start: 0.6201 (OUTLIER) cc_final: 0.5878 (t) REVERT: O 19 ASP cc_start: 0.9028 (t0) cc_final: 0.8738 (t70) REVERT: O 42 LEU cc_start: 0.8673 (mt) cc_final: 0.8446 (mt) REVERT: O 47 GLU cc_start: 0.6662 (mp0) cc_final: 0.6407 (mp0) REVERT: O 71 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8066 (pt) REVERT: W 47 ARG cc_start: 0.6771 (mpt180) cc_final: 0.6286 (mpt180) REVERT: X 13 HIS cc_start: 0.5844 (OUTLIER) cc_final: 0.4819 (t-90) REVERT: X 72 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7240 (mm-30) REVERT: Y 12 GLN cc_start: 0.8326 (tm-30) cc_final: 0.8100 (tm-30) REVERT: Y 28 ARG cc_start: 0.8771 (mmt90) cc_final: 0.8529 (mtp85) REVERT: Z 37 TYR cc_start: 0.6328 (OUTLIER) cc_final: 0.5999 (m-80) REVERT: Z 52 VAL cc_start: 0.8527 (OUTLIER) cc_final: 0.8320 (m) REVERT: Z 62 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.6048 (pp20) outliers start: 400 outliers final: 291 residues processed: 1267 average time/residue: 1.2879 time to fit residues: 2916.8320 Evaluate side-chains 1267 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 316 poor density : 951 time to evaluate : 5.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 59 GLN Chi-restraints excluded: chain b residue 87 SER Chi-restraints excluded: chain b residue 97 ASP Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 145 MET Chi-restraints excluded: chain b residue 156 SER Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 196 ASN Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 204 LEU Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 251 THR Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 91 THR Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 133 THR Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 173 GLN Chi-restraints excluded: chain c residue 178 VAL Chi-restraints excluded: chain c residue 187 LEU Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 75 SER Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 100 MET Chi-restraints excluded: chain d residue 146 VAL Chi-restraints excluded: chain d residue 167 VAL Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 117 SER Chi-restraints excluded: chain e residue 129 MET Chi-restraints excluded: chain e residue 142 TYR Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 146 ASP Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 29 ASN Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 76 ILE Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain i residue 85 ILE Chi-restraints excluded: chain i residue 121 ILE Chi-restraints excluded: chain i residue 129 GLU Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 70 THR Chi-restraints excluded: chain j residue 78 THR Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 13 ASN Chi-restraints excluded: chain k residue 25 LEU Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 79 PHE Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 47 ARG Chi-restraints excluded: chain l residue 100 ILE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 102 LEU Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain n residue 117 ASP Chi-restraints excluded: chain n residue 119 SER Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 58 ILE Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 90 VAL Chi-restraints excluded: chain o residue 106 LEU Chi-restraints excluded: chain p residue 19 PHE Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 64 SER Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 43 GLN Chi-restraints excluded: chain q residue 79 ILE Chi-restraints excluded: chain q residue 86 SER Chi-restraints excluded: chain q residue 93 ILE Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 83 TYR Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 13 SER Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 62 ASP Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 43 ILE Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain t residue 70 HIS Chi-restraints excluded: chain t residue 85 VAL Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 21 ARG Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 39 ASN Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain u residue 88 ASP Chi-restraints excluded: chain u residue 100 GLU Chi-restraints excluded: chain v residue 12 GLN Chi-restraints excluded: chain v residue 41 GLU Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 51 GLN Chi-restraints excluded: chain v residue 58 SER Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain x residue 19 HIS Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain z residue 3 THR Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 23 LEU Chi-restraints excluded: chain z residue 24 LEU Chi-restraints excluded: chain z residue 28 LEU Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 202 ASN Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 40 HIS Chi-restraints excluded: chain I residue 68 GLU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 176 LYS Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 59 ILE Chi-restraints excluded: chain J residue 60 GLN Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 14 ASP Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 141 HIS Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 80 ASN Chi-restraints excluded: chain P residue 111 ASP Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 14 LYS Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 69 GLU Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 116 TYR Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 54 THR Chi-restraints excluded: chain R residue 57 ASP Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain T residue 17 ASP Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 81 ILE Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain U residue 18 GLN Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 31 ARG Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 63 CYS Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain X residue 5 LYS Chi-restraints excluded: chain X residue 13 HIS Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 73 PHE Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 8 LYS Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Z residue 34 ARG Chi-restraints excluded: chain Z residue 37 TYR Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain Z residue 62 GLU Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 47 ASN Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 212 VAL Chi-restraints excluded: chain a residue 214 ILE Chi-restraints excluded: chain a residue 218 MET Chi-restraints excluded: chain a residue 224 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1031 random chunks: chunk 335 optimal weight: 3.9990 chunk 897 optimal weight: 10.0000 chunk 196 optimal weight: 9.9990 chunk 585 optimal weight: 20.0000 chunk 246 optimal weight: 20.0000 chunk 997 optimal weight: 20.0000 chunk 828 optimal weight: 20.0000 chunk 461 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 329 optimal weight: 6.9990 chunk 523 optimal weight: 1.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN ** o 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 55 GLN ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 25 GLN ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN K 46 GLN M 66 GLN ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 64 GLN R 11 HIS ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 160118 Z= 0.247 Angle : 0.672 11.805 239622 Z= 0.346 Chirality : 0.038 0.370 30641 Planarity : 0.005 0.073 12773 Dihedral : 23.782 179.391 80465 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.83 % Favored : 87.05 % Rotamer: Outliers : 8.13 % Allowed : 22.60 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.11), residues: 5743 helix: -0.60 (0.12), residues: 1813 sheet: -1.62 (0.16), residues: 973 loop : -2.71 (0.11), residues: 2957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP G 103 HIS 0.009 0.001 HIS O 70 PHE 0.035 0.002 PHE k 79 TYR 0.034 0.002 TYR M 127 ARG 0.008 0.001 ARG X 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1416 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 389 poor density : 1027 time to evaluate : 6.653 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: c 173 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.6856 (pp30) REVERT: f 25 ILE cc_start: 0.7857 (mt) cc_final: 0.7488 (tt) REVERT: f 76 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8293 (mt) REVERT: f 87 GLN cc_start: 0.7511 (tm-30) cc_final: 0.7094 (tm-30) REVERT: g 41 LYS cc_start: 0.7171 (ptpt) cc_final: 0.6969 (tppt) REVERT: j 136 GLN cc_start: 0.8332 (mt0) cc_final: 0.8051 (mt0) REVERT: l 10 GLU cc_start: 0.8243 (pp20) cc_final: 0.7659 (pm20) REVERT: l 47 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7387 (ttp-110) REVERT: l 76 GLU cc_start: 0.7557 (pt0) cc_final: 0.7162 (pt0) REVERT: l 91 ASP cc_start: 0.7900 (t70) cc_final: 0.7348 (m-30) REVERT: m 75 GLU cc_start: 0.7421 (pm20) cc_final: 0.6463 (pm20) REVERT: m 90 GLU cc_start: 0.7349 (pm20) cc_final: 0.6282 (pm20) REVERT: n 106 ASP cc_start: 0.7324 (p0) cc_final: 0.7115 (p0) REVERT: o 85 LYS cc_start: 0.8151 (mmpt) cc_final: 0.7911 (mmmm) REVERT: q 18 LYS cc_start: 0.8299 (mmmm) cc_final: 0.8082 (tptp) REVERT: q 48 ASP cc_start: 0.7786 (t0) cc_final: 0.7550 (t0) REVERT: r 60 LYS cc_start: 0.7522 (tppt) cc_final: 0.7068 (tptt) REVERT: s 1 MET cc_start: 0.7014 (ppp) cc_final: 0.6617 (ppp) REVERT: s 62 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7291 (p0) REVERT: t 32 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8795 (pp) REVERT: t 80 TRP cc_start: 0.8554 (p-90) cc_final: 0.8179 (p-90) REVERT: u 36 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7370 (pm20) REVERT: v 1 MET cc_start: 0.6998 (ppp) cc_final: 0.6424 (ppp) REVERT: v 12 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7519 (tt0) REVERT: v 35 GLU cc_start: 0.7022 (pm20) cc_final: 0.6785 (pm20) REVERT: v 44 HIS cc_start: 0.6618 (t-90) cc_final: 0.6248 (t-90) REVERT: v 51 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.6975 (pp30) REVERT: A 25 ARG cc_start: 0.7860 (mmp80) cc_final: 0.7640 (mmp80) REVERT: A 44 PHE cc_start: 0.6428 (p90) cc_final: 0.6085 (p90) REVERT: B 26 SER cc_start: 0.8448 (m) cc_final: 0.7948 (t) REVERT: C 34 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7252 (mt-10) REVERT: F 12 ARG cc_start: 0.7679 (mmm-85) cc_final: 0.7453 (mmm-85) REVERT: G 15 PHE cc_start: 0.6716 (p90) cc_final: 0.6437 (p90) REVERT: G 51 GLU cc_start: 0.8482 (pm20) cc_final: 0.8116 (pm20) REVERT: G 127 LYS cc_start: 0.2562 (mppt) cc_final: 0.1837 (mmtm) REVERT: H 24 ASN cc_start: 0.8277 (m-40) cc_final: 0.8020 (m-40) REVERT: H 58 ARG cc_start: 0.6496 (mmt90) cc_final: 0.5128 (mmt90) REVERT: H 79 LYS cc_start: 0.6141 (mptt) cc_final: 0.5320 (mmmt) REVERT: H 129 PHE cc_start: 0.7823 (p90) cc_final: 0.7500 (p90) REVERT: I 4 LEU cc_start: 0.6351 (OUTLIER) cc_final: 0.5852 (mt) REVERT: I 74 TYR cc_start: 0.8423 (m-10) cc_final: 0.8138 (m-80) REVERT: I 123 MET cc_start: 0.7884 (tpp) cc_final: 0.7658 (tpp) REVERT: I 134 TYR cc_start: 0.7666 (t80) cc_final: 0.7278 (t80) REVERT: I 170 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6502 (pp) REVERT: J 59 ILE cc_start: 0.9457 (OUTLIER) cc_final: 0.9252 (mp) REVERT: J 60 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8086 (pm20) REVERT: L 47 GLU cc_start: 0.6037 (OUTLIER) cc_final: 0.5580 (mp0) REVERT: L 141 HIS cc_start: 0.8291 (OUTLIER) cc_final: 0.7944 (m170) REVERT: L 142 ARG cc_start: 0.6684 (ptm160) cc_final: 0.6381 (ppt170) REVERT: M 72 GLU cc_start: 0.7372 (pt0) cc_final: 0.7098 (pt0) REVERT: N 21 LYS cc_start: 0.7768 (tttt) cc_final: 0.7342 (ttmm) REVERT: N 42 THR cc_start: 0.6064 (OUTLIER) cc_final: 0.5736 (t) REVERT: O 14 ASP cc_start: 0.8199 (t70) cc_final: 0.7967 (t70) REVERT: O 19 ASP cc_start: 0.8997 (t0) cc_final: 0.8697 (t70) REVERT: O 42 LEU cc_start: 0.8626 (mt) cc_final: 0.8388 (mt) REVERT: O 71 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8134 (pt) REVERT: S 19 TYR cc_start: 0.7356 (m-80) cc_final: 0.7142 (m-10) REVERT: S 62 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6814 (ptp-170) REVERT: W 47 ARG cc_start: 0.6633 (mpt180) cc_final: 0.6273 (mpt180) REVERT: X 13 HIS cc_start: 0.5868 (OUTLIER) cc_final: 0.4787 (t-90) REVERT: X 55 GLN cc_start: 0.7811 (mp10) cc_final: 0.7437 (pm20) REVERT: X 72 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7259 (mm-30) REVERT: Y 12 GLN cc_start: 0.8318 (tm-30) cc_final: 0.8095 (tm-30) REVERT: Y 81 GLN cc_start: 0.8576 (mm-40) cc_final: 0.8204 (mm-40) REVERT: Z 37 TYR cc_start: 0.6196 (OUTLIER) cc_final: 0.5839 (m-80) REVERT: Z 52 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.8321 (m) REVERT: Z 62 GLU cc_start: 0.6518 (OUTLIER) cc_final: 0.6010 (pp20) outliers start: 389 outliers final: 297 residues processed: 1275 average time/residue: 1.2051 time to fit residues: 2725.0258 Evaluate side-chains 1283 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 319 poor density : 964 time to evaluate : 6.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 59 GLN Chi-restraints excluded: chain b residue 87 SER Chi-restraints excluded: chain b residue 97 ASP Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 145 MET Chi-restraints excluded: chain b residue 156 SER Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 204 LEU Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 251 THR Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 21 SER Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 91 THR Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 133 THR Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 173 GLN Chi-restraints excluded: chain c residue 178 VAL Chi-restraints excluded: chain c residue 187 LEU Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 100 MET Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 167 VAL Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 65 LEU Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 117 SER Chi-restraints excluded: chain e residue 129 MET Chi-restraints excluded: chain e residue 142 TYR Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 146 ASP Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 76 ILE Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain i residue 85 ILE Chi-restraints excluded: chain i residue 121 ILE Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 70 THR Chi-restraints excluded: chain j residue 78 THR Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 13 ASN Chi-restraints excluded: chain k residue 25 LEU Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 73 ASP Chi-restraints excluded: chain k residue 79 PHE Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 47 ARG Chi-restraints excluded: chain l residue 100 ILE Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 102 LEU Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 74 GLU Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain n residue 117 ASP Chi-restraints excluded: chain n residue 119 SER Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 58 ILE Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 90 VAL Chi-restraints excluded: chain o residue 106 LEU Chi-restraints excluded: chain p residue 19 PHE Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 64 SER Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 79 ILE Chi-restraints excluded: chain q residue 86 SER Chi-restraints excluded: chain q residue 93 ILE Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 83 TYR Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 13 SER Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 62 ASP Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain t residue 70 HIS Chi-restraints excluded: chain t residue 85 VAL Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 21 ARG Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 39 ASN Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain u residue 88 ASP Chi-restraints excluded: chain u residue 100 GLU Chi-restraints excluded: chain v residue 12 GLN Chi-restraints excluded: chain v residue 41 GLU Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 51 GLN Chi-restraints excluded: chain v residue 58 SER Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 32 ILE Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 3 THR Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 23 LEU Chi-restraints excluded: chain z residue 24 LEU Chi-restraints excluded: chain z residue 28 LEU Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 202 ASN Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 40 HIS Chi-restraints excluded: chain I residue 68 GLU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 59 ILE Chi-restraints excluded: chain J residue 60 GLN Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 14 ASP Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 47 GLU Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 141 HIS Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 80 ASN Chi-restraints excluded: chain P residue 111 ASP Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 14 LYS Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 69 GLU Chi-restraints excluded: chain Q residue 74 GLN Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 116 TYR Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain S residue 62 ARG Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain T residue 17 ASP Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 51 SER Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain U residue 18 GLN Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 46 HIS Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 63 CYS Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 5 LYS Chi-restraints excluded: chain X residue 13 HIS Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 73 PHE Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 8 LYS Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain Z residue 34 ARG Chi-restraints excluded: chain Z residue 37 TYR Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain Z residue 62 GLU Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 47 ASN Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 212 VAL Chi-restraints excluded: chain a residue 214 ILE Chi-restraints excluded: chain a residue 224 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1031 random chunks: chunk 961 optimal weight: 20.0000 chunk 112 optimal weight: 3.9990 chunk 568 optimal weight: 30.0000 chunk 728 optimal weight: 20.0000 chunk 564 optimal weight: 20.0000 chunk 839 optimal weight: 10.0000 chunk 557 optimal weight: 10.0000 chunk 993 optimal weight: 40.0000 chunk 621 optimal weight: 20.0000 chunk 605 optimal weight: 20.0000 chunk 458 optimal weight: 20.0000 overall best weight: 12.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 40 GLN ** q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 55 GLN ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 38 GLN B 4 GLN ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 135 GLN ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 64 GLN ** O 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 HIS ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 ASN ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 160118 Z= 0.471 Angle : 0.866 12.293 239622 Z= 0.435 Chirality : 0.047 0.422 30641 Planarity : 0.006 0.081 12773 Dihedral : 24.004 178.148 80460 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 21.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 15.85 % Favored : 84.02 % Rotamer: Outliers : 8.86 % Allowed : 23.00 % Favored : 68.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.10), residues: 5743 helix: -0.95 (0.11), residues: 1811 sheet: -1.72 (0.16), residues: 995 loop : -2.88 (0.10), residues: 2937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP G 103 HIS 0.008 0.002 HIS b 14 PHE 0.041 0.003 PHE k 79 TYR 0.034 0.003 TYR I 75 ARG 0.012 0.001 ARG N 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1377 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 424 poor density : 953 time to evaluate : 6.755 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: c 83 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.6777 (ttt90) REVERT: c 173 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.6815 (pp30) REVERT: f 76 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8353 (mt) REVERT: f 87 GLN cc_start: 0.7427 (tm-30) cc_final: 0.6945 (tm-30) REVERT: j 136 GLN cc_start: 0.8458 (mt0) cc_final: 0.8132 (mt0) REVERT: l 10 GLU cc_start: 0.8329 (pp20) cc_final: 0.7623 (pm20) REVERT: l 47 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7034 (ttp-110) REVERT: l 76 GLU cc_start: 0.7618 (pt0) cc_final: 0.7223 (pt0) REVERT: m 75 GLU cc_start: 0.7637 (pm20) cc_final: 0.6792 (pm20) REVERT: m 90 GLU cc_start: 0.7430 (pm20) cc_final: 0.6837 (pm20) REVERT: r 60 LYS cc_start: 0.7583 (tppt) cc_final: 0.7144 (tptt) REVERT: s 1 MET cc_start: 0.7013 (ppp) cc_final: 0.6589 (ppp) REVERT: s 62 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7447 (p0) REVERT: t 32 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8667 (pp) REVERT: u 36 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7409 (pm20) REVERT: v 1 MET cc_start: 0.7130 (ppp) cc_final: 0.6611 (ppp) REVERT: v 35 GLU cc_start: 0.7132 (pm20) cc_final: 0.6910 (pm20) REVERT: v 44 HIS cc_start: 0.7161 (t-90) cc_final: 0.6728 (t-90) REVERT: v 51 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7026 (pp30) REVERT: x 19 HIS cc_start: 0.8448 (OUTLIER) cc_final: 0.8178 (t70) REVERT: A 44 PHE cc_start: 0.6405 (p90) cc_final: 0.6021 (p90) REVERT: C 34 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7370 (mt-10) REVERT: G 51 GLU cc_start: 0.8559 (pm20) cc_final: 0.8167 (pm20) REVERT: G 224 ARG cc_start: 0.5083 (OUTLIER) cc_final: 0.4544 (pmt-80) REVERT: H 24 ASN cc_start: 0.8349 (m-40) cc_final: 0.8027 (m-40) REVERT: H 79 LYS cc_start: 0.6070 (mptt) cc_final: 0.5276 (mmmt) REVERT: H 129 PHE cc_start: 0.7859 (p90) cc_final: 0.7504 (p90) REVERT: I 4 LEU cc_start: 0.6343 (OUTLIER) cc_final: 0.5917 (mt) REVERT: I 134 TYR cc_start: 0.7705 (t80) cc_final: 0.7469 (t80) REVERT: I 135 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8392 (mm110) REVERT: I 170 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.6644 (pp) REVERT: J 59 ILE cc_start: 0.9492 (OUTLIER) cc_final: 0.9273 (mp) REVERT: J 60 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8210 (pm20) REVERT: K 17 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7143 (pp30) REVERT: L 141 HIS cc_start: 0.8310 (OUTLIER) cc_final: 0.8051 (m170) REVERT: M 9 MET cc_start: 0.6991 (OUTLIER) cc_final: 0.6489 (tmm) REVERT: M 72 GLU cc_start: 0.7453 (pt0) cc_final: 0.7219 (pt0) REVERT: N 21 LYS cc_start: 0.7890 (tttt) cc_final: 0.7455 (ttmm) REVERT: O 19 ASP cc_start: 0.9134 (t0) cc_final: 0.8784 (t70) REVERT: O 47 GLU cc_start: 0.6741 (mp0) cc_final: 0.6438 (mp0) REVERT: O 71 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7956 (pp) REVERT: S 62 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.6913 (ptp-170) REVERT: W 47 ARG cc_start: 0.6925 (mpt180) cc_final: 0.6096 (mpt180) REVERT: X 13 HIS cc_start: 0.5876 (OUTLIER) cc_final: 0.4819 (t-90) REVERT: X 72 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7258 (mm-30) REVERT: Y 12 GLN cc_start: 0.8410 (tm-30) cc_final: 0.8203 (tm-30) REVERT: Y 35 TYR cc_start: 0.7718 (OUTLIER) cc_final: 0.4735 (t80) REVERT: Y 81 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8225 (mm-40) REVERT: Z 52 VAL cc_start: 0.8482 (OUTLIER) cc_final: 0.8262 (m) REVERT: Z 62 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6248 (pp20) outliers start: 424 outliers final: 329 residues processed: 1224 average time/residue: 1.3796 time to fit residues: 3052.3704 Evaluate side-chains 1284 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 353 poor density : 931 time to evaluate : 5.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 87 SER Chi-restraints excluded: chain b residue 97 ASP Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 156 SER Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 204 LEU Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 251 THR Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 21 SER Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 83 ARG Chi-restraints excluded: chain c residue 91 THR Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 133 THR Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 173 GLN Chi-restraints excluded: chain c residue 178 VAL Chi-restraints excluded: chain c residue 187 LEU Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 75 SER Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 65 LEU Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 117 SER Chi-restraints excluded: chain e residue 129 MET Chi-restraints excluded: chain e residue 142 TYR Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 146 ASP Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 76 ILE Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain i residue 85 ILE Chi-restraints excluded: chain i residue 121 ILE Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 70 THR Chi-restraints excluded: chain j residue 78 THR Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain j residue 98 GLU Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 13 ASN Chi-restraints excluded: chain k residue 25 LEU Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 73 ASP Chi-restraints excluded: chain k residue 79 PHE Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 47 ARG Chi-restraints excluded: chain l residue 100 ILE Chi-restraints excluded: chain l residue 103 ILE Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain n residue 117 ASP Chi-restraints excluded: chain n residue 119 SER Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 58 ILE Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 90 VAL Chi-restraints excluded: chain o residue 106 LEU Chi-restraints excluded: chain p residue 12 MET Chi-restraints excluded: chain p residue 19 PHE Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 64 SER Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 79 ILE Chi-restraints excluded: chain q residue 86 SER Chi-restraints excluded: chain q residue 93 ILE Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 83 TYR Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 13 SER Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 62 ASP Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain t residue 70 HIS Chi-restraints excluded: chain t residue 85 VAL Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 21 ARG Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 39 ASN Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain u residue 88 ASP Chi-restraints excluded: chain v residue 41 GLU Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 51 GLN Chi-restraints excluded: chain v residue 58 SER Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 19 HIS Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 4 LYS Chi-restraints excluded: chain y residue 50 VAL Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 3 THR Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 9 THR Chi-restraints excluded: chain z residue 23 LEU Chi-restraints excluded: chain z residue 24 LEU Chi-restraints excluded: chain z residue 28 LEU Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 37 CYS Chi-restraints excluded: chain B residue 4 GLN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 202 ASN Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 31 CYS Chi-restraints excluded: chain I residue 40 HIS Chi-restraints excluded: chain I residue 68 GLU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 59 ILE Chi-restraints excluded: chain J residue 60 GLN Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 14 ASP Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 141 HIS Chi-restraints excluded: chain M residue 9 MET Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain P residue 80 ASN Chi-restraints excluded: chain P residue 111 ASP Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 14 LYS Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 116 TYR Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain S residue 62 ARG Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain T residue 17 ASP Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 51 SER Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 81 ILE Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain U residue 18 GLN Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 46 HIS Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 63 CYS Chi-restraints excluded: chain W residue 21 ASP Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 5 LYS Chi-restraints excluded: chain X residue 13 HIS Chi-restraints excluded: chain X residue 14 LEU Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 73 PHE Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 8 LYS Chi-restraints excluded: chain Y residue 35 TYR Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain Z residue 62 GLU Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 22 ASP Chi-restraints excluded: chain a residue 47 ASN Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 212 VAL Chi-restraints excluded: chain a residue 214 ILE Chi-restraints excluded: chain a residue 215 SER Chi-restraints excluded: chain a residue 224 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1031 random chunks: chunk 614 optimal weight: 20.0000 chunk 396 optimal weight: 5.9990 chunk 593 optimal weight: 10.0000 chunk 299 optimal weight: 20.0000 chunk 195 optimal weight: 5.9990 chunk 192 optimal weight: 8.9990 chunk 631 optimal weight: 10.0000 chunk 677 optimal weight: 20.0000 chunk 491 optimal weight: 9.9990 chunk 92 optimal weight: 20.0000 chunk 781 optimal weight: 10.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 196 ASN ** b 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN ** o 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 70 HIS ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 HIS ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 ASN ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 160118 Z= 0.318 Angle : 0.734 12.404 239622 Z= 0.375 Chirality : 0.041 0.390 30641 Planarity : 0.005 0.078 12773 Dihedral : 23.914 179.452 80460 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.27 % Favored : 86.59 % Rotamer: Outliers : 8.01 % Allowed : 24.61 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.86 (0.10), residues: 5743 helix: -0.79 (0.12), residues: 1816 sheet: -1.66 (0.16), residues: 971 loop : -2.77 (0.10), residues: 2956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP G 103 HIS 0.006 0.001 HIS v 44 PHE 0.037 0.002 PHE k 79 TYR 0.037 0.002 TYR I 75 ARG 0.008 0.001 ARG X 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1373 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 383 poor density : 990 time to evaluate : 6.669 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: c 1 MET cc_start: 0.6054 (OUTLIER) cc_final: 0.5375 (ptp) REVERT: c 173 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.6790 (pp30) REVERT: d 132 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8168 (mtmm) REVERT: f 76 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8357 (mt) REVERT: f 148 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7710 (ttp80) REVERT: f 169 ARG cc_start: 0.7551 (mmm160) cc_final: 0.7330 (mmm160) REVERT: j 136 GLN cc_start: 0.8435 (mt0) cc_final: 0.8081 (mt0) REVERT: l 10 GLU cc_start: 0.8289 (pp20) cc_final: 0.7696 (pm20) REVERT: l 47 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7385 (ttp-110) REVERT: l 76 GLU cc_start: 0.7613 (pt0) cc_final: 0.7196 (pt0) REVERT: m 75 GLU cc_start: 0.7547 (pm20) cc_final: 0.6648 (pm20) REVERT: m 90 GLU cc_start: 0.7357 (pm20) cc_final: 0.6637 (pm20) REVERT: o 4 LYS cc_start: 0.8299 (ptmm) cc_final: 0.7728 (ptmm) REVERT: o 85 LYS cc_start: 0.8121 (mmpt) cc_final: 0.7833 (mmmm) REVERT: q 18 LYS cc_start: 0.8267 (mmmm) cc_final: 0.8051 (tptp) REVERT: r 60 LYS cc_start: 0.7576 (tppt) cc_final: 0.7125 (tptt) REVERT: s 1 MET cc_start: 0.6959 (ppp) cc_final: 0.6485 (ppp) REVERT: t 32 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8787 (pp) REVERT: u 36 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7457 (pm20) REVERT: v 1 MET cc_start: 0.7059 (ppp) cc_final: 0.6538 (ppp) REVERT: v 12 GLN cc_start: 0.7749 (tt0) cc_final: 0.7268 (tt0) REVERT: v 35 GLU cc_start: 0.6995 (pm20) cc_final: 0.6761 (pm20) REVERT: v 44 HIS cc_start: 0.6994 (t-90) cc_final: 0.6543 (t-90) REVERT: v 51 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.6773 (pp30) REVERT: w 66 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6769 (mm-30) REVERT: A 44 PHE cc_start: 0.6447 (p90) cc_final: 0.6094 (p90) REVERT: C 34 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7350 (mt-10) REVERT: G 15 PHE cc_start: 0.6863 (p90) cc_final: 0.6620 (p90) REVERT: G 224 ARG cc_start: 0.5118 (OUTLIER) cc_final: 0.4577 (pmt-80) REVERT: H 19 SER cc_start: 0.8192 (m) cc_final: 0.7624 (p) REVERT: H 24 ASN cc_start: 0.8363 (m-40) cc_final: 0.8113 (m-40) REVERT: H 79 LYS cc_start: 0.6107 (mptt) cc_final: 0.5265 (mmmt) REVERT: H 129 PHE cc_start: 0.7842 (p90) cc_final: 0.7478 (p90) REVERT: I 4 LEU cc_start: 0.6327 (OUTLIER) cc_final: 0.5896 (mt) REVERT: I 134 TYR cc_start: 0.7702 (t80) cc_final: 0.7398 (t80) REVERT: I 170 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.6579 (pp) REVERT: J 59 ILE cc_start: 0.9473 (OUTLIER) cc_final: 0.9247 (mp) REVERT: J 60 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8150 (pm20) REVERT: L 47 GLU cc_start: 0.5767 (OUTLIER) cc_final: 0.5419 (mp0) REVERT: L 141 HIS cc_start: 0.8266 (OUTLIER) cc_final: 0.8001 (m170) REVERT: L 142 ARG cc_start: 0.6685 (ptm160) cc_final: 0.6392 (ppt170) REVERT: M 72 GLU cc_start: 0.7503 (pt0) cc_final: 0.7290 (pt0) REVERT: N 21 LYS cc_start: 0.7819 (tttt) cc_final: 0.7384 (ttmm) REVERT: N 129 ARG cc_start: 0.6887 (mtm-85) cc_final: 0.6589 (mtm-85) REVERT: O 19 ASP cc_start: 0.9032 (t0) cc_final: 0.8701 (t70) REVERT: O 47 GLU cc_start: 0.6683 (mp0) cc_final: 0.6414 (mp0) REVERT: O 71 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8170 (pt) REVERT: S 62 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6830 (ptp-170) REVERT: W 47 ARG cc_start: 0.6755 (mpt180) cc_final: 0.6178 (mpt180) REVERT: X 13 HIS cc_start: 0.5897 (OUTLIER) cc_final: 0.5489 (t70) REVERT: X 36 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7325 (ptm160) REVERT: X 55 GLN cc_start: 0.7902 (mp10) cc_final: 0.7459 (pm20) REVERT: X 72 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7487 (mm-30) REVERT: Y 12 GLN cc_start: 0.8431 (tm-30) cc_final: 0.8217 (tm-30) REVERT: Y 35 TYR cc_start: 0.7714 (OUTLIER) cc_final: 0.4724 (t80) REVERT: Y 81 GLN cc_start: 0.8581 (mm-40) cc_final: 0.8169 (mm-40) REVERT: Z 62 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.6163 (pp20) outliers start: 383 outliers final: 322 residues processed: 1230 average time/residue: 1.3510 time to fit residues: 2987.9850 Evaluate side-chains 1304 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 346 poor density : 958 time to evaluate : 6.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 59 GLN Chi-restraints excluded: chain b residue 87 SER Chi-restraints excluded: chain b residue 97 ASP Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 156 SER Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 196 ASN Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 204 LEU Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 251 THR Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 21 SER Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 91 THR Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 133 THR Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 173 GLN Chi-restraints excluded: chain c residue 178 VAL Chi-restraints excluded: chain c residue 187 LEU Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 75 SER Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 132 LYS Chi-restraints excluded: chain d residue 167 VAL Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 65 LEU Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 117 SER Chi-restraints excluded: chain e residue 129 MET Chi-restraints excluded: chain e residue 142 TYR Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 146 ASP Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 76 ILE Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 148 ARG Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain i residue 85 ILE Chi-restraints excluded: chain i residue 121 ILE Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 70 THR Chi-restraints excluded: chain j residue 76 HIS Chi-restraints excluded: chain j residue 78 THR Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 13 ASN Chi-restraints excluded: chain k residue 25 LEU Chi-restraints excluded: chain k residue 38 ILE Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 73 ASP Chi-restraints excluded: chain k residue 79 PHE Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 47 ARG Chi-restraints excluded: chain l residue 100 ILE Chi-restraints excluded: chain l residue 103 ILE Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 102 LEU Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain n residue 117 ASP Chi-restraints excluded: chain n residue 119 SER Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 58 ILE Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 90 VAL Chi-restraints excluded: chain o residue 106 LEU Chi-restraints excluded: chain p residue 19 PHE Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 64 SER Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 79 ILE Chi-restraints excluded: chain q residue 86 SER Chi-restraints excluded: chain q residue 93 ILE Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 83 TYR Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 13 SER Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 55 ILE Chi-restraints excluded: chain s residue 62 ASP Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain t residue 70 HIS Chi-restraints excluded: chain t residue 85 VAL Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 21 ARG Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 39 ASN Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain u residue 88 ASP Chi-restraints excluded: chain u residue 95 PHE Chi-restraints excluded: chain u residue 100 GLU Chi-restraints excluded: chain v residue 41 GLU Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 51 GLN Chi-restraints excluded: chain v residue 58 SER Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 32 ILE Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 66 GLU Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 69 GLU Chi-restraints excluded: chain x residue 75 GLU Chi-restraints excluded: chain y residue 50 VAL Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 3 THR Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 23 LEU Chi-restraints excluded: chain z residue 24 LEU Chi-restraints excluded: chain z residue 28 LEU Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 202 ASN Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 31 CYS Chi-restraints excluded: chain I residue 40 HIS Chi-restraints excluded: chain I residue 68 GLU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 59 ILE Chi-restraints excluded: chain J residue 60 GLN Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 14 ASP Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 47 GLU Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 141 HIS Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 80 ASN Chi-restraints excluded: chain P residue 111 ASP Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 14 LYS Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 69 GLU Chi-restraints excluded: chain Q residue 74 GLN Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 116 TYR Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain S residue 62 ARG Chi-restraints excluded: chain T residue 17 ASP Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 51 SER Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain U residue 18 GLN Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 46 HIS Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 63 CYS Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 5 LYS Chi-restraints excluded: chain X residue 13 HIS Chi-restraints excluded: chain X residue 36 ARG Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 73 PHE Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 8 LYS Chi-restraints excluded: chain Y residue 35 TYR Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Z residue 62 GLU Chi-restraints excluded: chain a residue 22 ASP Chi-restraints excluded: chain a residue 47 ASN Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 212 VAL Chi-restraints excluded: chain a residue 214 ILE Chi-restraints excluded: chain a residue 224 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1031 random chunks: chunk 903 optimal weight: 10.0000 chunk 952 optimal weight: 10.0000 chunk 868 optimal weight: 20.0000 chunk 926 optimal weight: 40.0000 chunk 951 optimal weight: 20.0000 chunk 557 optimal weight: 6.9990 chunk 403 optimal weight: 7.9990 chunk 727 optimal weight: 20.0000 chunk 284 optimal weight: 20.0000 chunk 836 optimal weight: 20.0000 chunk 875 optimal weight: 20.0000 overall best weight: 10.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 196 ASN ** b 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 58 GLN s 15 GLN ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 HIS S 34 ASN ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 ASN W 18 GLN ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 160118 Z= 0.408 Angle : 0.806 12.078 239622 Z= 0.408 Chirality : 0.044 0.402 30641 Planarity : 0.006 0.083 12773 Dihedral : 23.970 179.625 80458 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 15.41 % Favored : 84.45 % Rotamer: Outliers : 8.09 % Allowed : 24.94 % Favored : 66.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.10), residues: 5743 helix: -0.90 (0.12), residues: 1817 sheet: -1.67 (0.16), residues: 983 loop : -2.83 (0.10), residues: 2943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP G 103 HIS 0.007 0.002 HIS a 172 PHE 0.038 0.002 PHE k 79 TYR 0.043 0.003 TYR I 75 ARG 0.013 0.001 ARG f 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1343 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 387 poor density : 956 time to evaluate : 6.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 83 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.6787 (ttt90) REVERT: d 132 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8214 (mtmm) REVERT: f 76 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8368 (mt) REVERT: f 148 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7731 (ttp80) REVERT: j 136 GLN cc_start: 0.8488 (mt0) cc_final: 0.8131 (mt0) REVERT: l 10 GLU cc_start: 0.8305 (pp20) cc_final: 0.7697 (pm20) REVERT: l 47 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.6996 (ttp-110) REVERT: l 76 GLU cc_start: 0.7616 (pt0) cc_final: 0.7213 (pt0) REVERT: m 75 GLU cc_start: 0.7592 (pm20) cc_final: 0.6700 (pm20) REVERT: m 90 GLU cc_start: 0.7414 (pm20) cc_final: 0.6741 (pm20) REVERT: o 4 LYS cc_start: 0.8304 (ptmm) cc_final: 0.7727 (ptmm) REVERT: r 60 LYS cc_start: 0.7595 (tppt) cc_final: 0.7131 (tptt) REVERT: s 1 MET cc_start: 0.6981 (ppp) cc_final: 0.6537 (ppp) REVERT: s 62 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7388 (p0) REVERT: t 32 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8721 (pp) REVERT: u 36 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7432 (pm20) REVERT: v 1 MET cc_start: 0.7117 (ppp) cc_final: 0.6618 (ppp) REVERT: v 12 GLN cc_start: 0.7857 (tt0) cc_final: 0.7442 (tt0) REVERT: v 35 GLU cc_start: 0.7110 (pm20) cc_final: 0.6872 (pm20) REVERT: v 44 HIS cc_start: 0.7083 (t-90) cc_final: 0.6646 (t-90) REVERT: v 51 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.6969 (pp30) REVERT: w 66 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6819 (mm-30) REVERT: y 4 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7260 (mttt) REVERT: A 44 PHE cc_start: 0.6495 (p90) cc_final: 0.6138 (p90) REVERT: C 34 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7364 (mt-10) REVERT: C 43 ARG cc_start: 0.7760 (mtp180) cc_final: 0.7423 (mtp180) REVERT: G 15 PHE cc_start: 0.6901 (p90) cc_final: 0.6642 (p90) REVERT: G 224 ARG cc_start: 0.5037 (OUTLIER) cc_final: 0.4468 (pmt-80) REVERT: H 19 SER cc_start: 0.8217 (m) cc_final: 0.7550 (p) REVERT: H 24 ASN cc_start: 0.8306 (m-40) cc_final: 0.8038 (m-40) REVERT: H 79 LYS cc_start: 0.6002 (mptt) cc_final: 0.5204 (mmmt) REVERT: H 129 PHE cc_start: 0.7855 (p90) cc_final: 0.7483 (p90) REVERT: H 151 GLU cc_start: 0.7593 (pm20) cc_final: 0.7212 (pm20) REVERT: I 4 LEU cc_start: 0.6304 (OUTLIER) cc_final: 0.5874 (mt) REVERT: I 134 TYR cc_start: 0.7667 (t80) cc_final: 0.7396 (t80) REVERT: I 170 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.6729 (pp) REVERT: J 59 ILE cc_start: 0.9482 (OUTLIER) cc_final: 0.9263 (mp) REVERT: J 60 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8169 (pm20) REVERT: L 53 SER cc_start: 0.6797 (t) cc_final: 0.6347 (m) REVERT: L 142 ARG cc_start: 0.6586 (ptm160) cc_final: 0.6329 (ppt170) REVERT: M 72 GLU cc_start: 0.7497 (pt0) cc_final: 0.7262 (pt0) REVERT: N 21 LYS cc_start: 0.7864 (tttt) cc_final: 0.7437 (ttmm) REVERT: N 129 ARG cc_start: 0.6880 (mtm-85) cc_final: 0.6581 (mtm-85) REVERT: O 19 ASP cc_start: 0.9076 (t0) cc_final: 0.8737 (t70) REVERT: O 47 GLU cc_start: 0.6733 (mp0) cc_final: 0.6477 (mp0) REVERT: O 71 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8175 (pt) REVERT: R 30 LYS cc_start: 0.7857 (tppt) cc_final: 0.6456 (ptpp) REVERT: S 22 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.6878 (pttp) REVERT: S 62 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6907 (ptp-170) REVERT: W 47 ARG cc_start: 0.6826 (mpt180) cc_final: 0.6223 (mpt180) REVERT: X 13 HIS cc_start: 0.5919 (OUTLIER) cc_final: 0.4863 (t-90) REVERT: X 36 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7367 (ptm160) REVERT: X 55 GLN cc_start: 0.7913 (mp10) cc_final: 0.7505 (pm20) REVERT: X 72 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7303 (mm-30) REVERT: Y 12 GLN cc_start: 0.8399 (tm-30) cc_final: 0.8192 (tm-30) REVERT: Y 35 TYR cc_start: 0.7721 (OUTLIER) cc_final: 0.4848 (t80) REVERT: Y 60 GLN cc_start: 0.8654 (mm110) cc_final: 0.8293 (mm110) REVERT: Y 81 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8244 (mm-40) REVERT: Z 62 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6229 (pp20) outliers start: 387 outliers final: 336 residues processed: 1201 average time/residue: 1.1877 time to fit residues: 2534.1970 Evaluate side-chains 1303 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 360 poor density : 943 time to evaluate : 6.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 59 GLN Chi-restraints excluded: chain b residue 87 SER Chi-restraints excluded: chain b residue 97 ASP Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 156 SER Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 196 ASN Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 204 LEU Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 251 THR Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 21 SER Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 83 ARG Chi-restraints excluded: chain c residue 91 THR Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 133 THR Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 173 GLN Chi-restraints excluded: chain c residue 178 VAL Chi-restraints excluded: chain c residue 187 LEU Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 75 SER Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 132 LYS Chi-restraints excluded: chain d residue 167 VAL Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 65 LEU Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 117 SER Chi-restraints excluded: chain e residue 129 MET Chi-restraints excluded: chain e residue 142 TYR Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 146 ASP Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 76 ILE Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 148 ARG Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain i residue 85 ILE Chi-restraints excluded: chain i residue 121 ILE Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 70 THR Chi-restraints excluded: chain j residue 76 HIS Chi-restraints excluded: chain j residue 78 THR Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 13 ASN Chi-restraints excluded: chain k residue 25 LEU Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 73 ASP Chi-restraints excluded: chain k residue 79 PHE Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 47 ARG Chi-restraints excluded: chain l residue 100 ILE Chi-restraints excluded: chain l residue 103 ILE Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 82 MET Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 96 ILE Chi-restraints excluded: chain m residue 102 LEU Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain n residue 117 ASP Chi-restraints excluded: chain n residue 119 SER Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 58 ILE Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 90 VAL Chi-restraints excluded: chain o residue 106 LEU Chi-restraints excluded: chain p residue 19 PHE Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 64 SER Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 79 ILE Chi-restraints excluded: chain q residue 86 SER Chi-restraints excluded: chain q residue 93 ILE Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 83 TYR Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 13 SER Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 55 ILE Chi-restraints excluded: chain s residue 62 ASP Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain t residue 70 HIS Chi-restraints excluded: chain t residue 85 VAL Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 21 ARG Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 39 ASN Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain u residue 88 ASP Chi-restraints excluded: chain v residue 41 GLU Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 51 GLN Chi-restraints excluded: chain v residue 58 SER Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 32 ILE Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 66 GLU Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 75 GLU Chi-restraints excluded: chain y residue 4 LYS Chi-restraints excluded: chain y residue 50 VAL Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 3 THR Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 23 LEU Chi-restraints excluded: chain z residue 24 LEU Chi-restraints excluded: chain z residue 28 LEU Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 202 ASN Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 31 CYS Chi-restraints excluded: chain I residue 40 HIS Chi-restraints excluded: chain I residue 68 GLU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 59 ILE Chi-restraints excluded: chain J residue 60 GLN Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 14 ASP Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 80 ASN Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 14 LYS Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 69 GLU Chi-restraints excluded: chain Q residue 74 GLN Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 116 TYR Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain S residue 22 LYS Chi-restraints excluded: chain S residue 62 ARG Chi-restraints excluded: chain T residue 17 ASP Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 51 SER Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 81 ILE Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain U residue 18 GLN Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 46 HIS Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 63 CYS Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 5 LYS Chi-restraints excluded: chain X residue 13 HIS Chi-restraints excluded: chain X residue 14 LEU Chi-restraints excluded: chain X residue 36 ARG Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 73 PHE Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 8 LYS Chi-restraints excluded: chain Y residue 35 TYR Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 62 GLU Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 22 ASP Chi-restraints excluded: chain a residue 47 ASN Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 212 VAL Chi-restraints excluded: chain a residue 214 ILE Chi-restraints excluded: chain a residue 224 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1031 random chunks: chunk 922 optimal weight: 10.0000 chunk 608 optimal weight: 30.0000 chunk 979 optimal weight: 20.0000 chunk 597 optimal weight: 20.0000 chunk 464 optimal weight: 9.9990 chunk 680 optimal weight: 10.0000 chunk 1027 optimal weight: 20.0000 chunk 945 optimal weight: 20.0000 chunk 817 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 631 optimal weight: 10.0000 overall best weight: 8.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 HIS ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 ASN ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 19 HIS Y 60 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 160118 Z= 0.323 Angle : 0.739 11.037 239622 Z= 0.377 Chirality : 0.041 0.379 30641 Planarity : 0.005 0.082 12773 Dihedral : 23.929 178.961 80458 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.62 % Favored : 86.24 % Rotamer: Outliers : 7.76 % Allowed : 25.34 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.10), residues: 5743 helix: -0.77 (0.12), residues: 1824 sheet: -1.61 (0.16), residues: 979 loop : -2.75 (0.11), residues: 2940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.002 TRP G 103 HIS 0.009 0.001 HIS Y 19 PHE 0.037 0.002 PHE k 79 TYR 0.039 0.002 TYR I 75 ARG 0.013 0.001 ARG f 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1346 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 371 poor density : 975 time to evaluate : 6.779 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: c 83 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.6791 (ttt90) REVERT: d 132 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8164 (mtmm) REVERT: f 76 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8366 (mt) REVERT: f 148 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7722 (ttp80) REVERT: j 136 GLN cc_start: 0.8464 (mt0) cc_final: 0.8107 (mt0) REVERT: l 10 GLU cc_start: 0.8290 (pp20) cc_final: 0.7695 (pm20) REVERT: l 47 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7387 (ttp-110) REVERT: l 76 GLU cc_start: 0.7595 (pt0) cc_final: 0.7238 (pt0) REVERT: m 75 GLU cc_start: 0.7545 (pm20) cc_final: 0.6642 (pm20) REVERT: m 90 GLU cc_start: 0.7367 (pm20) cc_final: 0.6646 (pm20) REVERT: n 117 ASP cc_start: 0.7019 (OUTLIER) cc_final: 0.6421 (p0) REVERT: o 4 LYS cc_start: 0.8315 (ptmm) cc_final: 0.7739 (ptmm) REVERT: o 85 LYS cc_start: 0.8126 (mmpt) cc_final: 0.7830 (mmmm) REVERT: q 18 LYS cc_start: 0.8241 (mmmm) cc_final: 0.8021 (tptp) REVERT: r 10 LYS cc_start: 0.8865 (mmmt) cc_final: 0.8359 (mmtt) REVERT: r 13 ARG cc_start: 0.7964 (tmm-80) cc_final: 0.7649 (tmm-80) REVERT: r 60 LYS cc_start: 0.7470 (tppt) cc_final: 0.7074 (tptt) REVERT: s 1 MET cc_start: 0.6974 (ppp) cc_final: 0.6536 (ppp) REVERT: s 62 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7342 (p0) REVERT: t 32 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8781 (pp) REVERT: u 36 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7422 (pm20) REVERT: v 1 MET cc_start: 0.7040 (ppp) cc_final: 0.6539 (ppp) REVERT: v 12 GLN cc_start: 0.7816 (tt0) cc_final: 0.7353 (tt0) REVERT: v 35 GLU cc_start: 0.6980 (pm20) cc_final: 0.6747 (pm20) REVERT: v 44 HIS cc_start: 0.7023 (t-90) cc_final: 0.6588 (t-90) REVERT: v 51 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.6786 (pp30) REVERT: w 66 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6793 (mm-30) REVERT: y 4 LYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7177 (mttt) REVERT: A 44 PHE cc_start: 0.6507 (p90) cc_final: 0.6202 (p90) REVERT: C 34 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7320 (mt-10) REVERT: G 67 LEU cc_start: 0.8496 (tt) cc_final: 0.8006 (mt) REVERT: G 224 ARG cc_start: 0.5101 (OUTLIER) cc_final: 0.4614 (pmt-80) REVERT: H 19 SER cc_start: 0.8322 (m) cc_final: 0.7741 (p) REVERT: H 24 ASN cc_start: 0.8299 (m-40) cc_final: 0.8069 (m-40) REVERT: H 79 LYS cc_start: 0.6039 (mptt) cc_final: 0.5226 (mmmt) REVERT: H 129 PHE cc_start: 0.7843 (p90) cc_final: 0.7507 (p90) REVERT: I 4 LEU cc_start: 0.6281 (OUTLIER) cc_final: 0.5851 (mt) REVERT: I 134 TYR cc_start: 0.7658 (t80) cc_final: 0.7352 (t80) REVERT: I 170 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.6666 (pp) REVERT: J 59 ILE cc_start: 0.9473 (OUTLIER) cc_final: 0.9244 (mp) REVERT: J 60 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8156 (pm20) REVERT: L 53 SER cc_start: 0.6736 (t) cc_final: 0.6315 (m) REVERT: L 142 ARG cc_start: 0.6553 (ptm160) cc_final: 0.6346 (ppt170) REVERT: M 72 GLU cc_start: 0.7515 (pt0) cc_final: 0.7311 (pt0) REVERT: N 21 LYS cc_start: 0.7857 (tttt) cc_final: 0.7433 (ttmm) REVERT: N 129 ARG cc_start: 0.6882 (mtm-85) cc_final: 0.6520 (mtm-85) REVERT: O 8 ILE cc_start: 0.7845 (mt) cc_final: 0.7599 (mp) REVERT: O 19 ASP cc_start: 0.9047 (t0) cc_final: 0.8718 (t70) REVERT: O 47 GLU cc_start: 0.6761 (mp0) cc_final: 0.6510 (mp0) REVERT: O 71 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8235 (pt) REVERT: R 30 LYS cc_start: 0.7948 (tppt) cc_final: 0.6590 (ptpp) REVERT: S 22 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.6771 (pttp) REVERT: S 62 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.6772 (ptp-170) REVERT: W 47 ARG cc_start: 0.6754 (mpt180) cc_final: 0.6180 (mpt180) REVERT: X 13 HIS cc_start: 0.5974 (OUTLIER) cc_final: 0.5573 (t70) REVERT: X 36 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7351 (ptm160) REVERT: X 55 GLN cc_start: 0.7834 (mp10) cc_final: 0.7498 (pm20) REVERT: X 72 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7476 (mm-30) REVERT: Y 12 GLN cc_start: 0.8429 (tm-30) cc_final: 0.8217 (tm-30) REVERT: Y 35 TYR cc_start: 0.7739 (OUTLIER) cc_final: 0.4829 (t80) REVERT: Y 81 GLN cc_start: 0.8562 (mm-40) cc_final: 0.8150 (mm-40) REVERT: Z 62 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6146 (pp20) outliers start: 371 outliers final: 331 residues processed: 1210 average time/residue: 1.2117 time to fit residues: 2605.0475 Evaluate side-chains 1312 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 356 poor density : 956 time to evaluate : 6.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 59 GLN Chi-restraints excluded: chain b residue 87 SER Chi-restraints excluded: chain b residue 97 ASP Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 156 SER Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 204 LEU Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 251 THR Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 21 SER Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 83 ARG Chi-restraints excluded: chain c residue 91 THR Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 133 THR Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 173 GLN Chi-restraints excluded: chain c residue 178 VAL Chi-restraints excluded: chain c residue 187 LEU Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 75 SER Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 132 LYS Chi-restraints excluded: chain d residue 167 VAL Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 7 TYR Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 65 LEU Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 117 SER Chi-restraints excluded: chain e residue 129 MET Chi-restraints excluded: chain e residue 142 TYR Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 146 ASP Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 76 ILE Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 148 ARG Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain i residue 85 ILE Chi-restraints excluded: chain i residue 121 ILE Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 70 THR Chi-restraints excluded: chain j residue 76 HIS Chi-restraints excluded: chain j residue 78 THR Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 13 ASN Chi-restraints excluded: chain k residue 25 LEU Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 73 ASP Chi-restraints excluded: chain k residue 79 PHE Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 47 ARG Chi-restraints excluded: chain l residue 100 ILE Chi-restraints excluded: chain l residue 103 ILE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 96 ILE Chi-restraints excluded: chain m residue 102 LEU Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain n residue 117 ASP Chi-restraints excluded: chain n residue 119 SER Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 58 ILE Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 90 VAL Chi-restraints excluded: chain o residue 106 LEU Chi-restraints excluded: chain p residue 19 PHE Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 64 SER Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 79 ILE Chi-restraints excluded: chain q residue 86 SER Chi-restraints excluded: chain q residue 93 ILE Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 83 TYR Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 13 SER Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 55 ILE Chi-restraints excluded: chain s residue 62 ASP Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain t residue 70 HIS Chi-restraints excluded: chain t residue 85 VAL Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 21 ARG Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 39 ASN Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain u residue 88 ASP Chi-restraints excluded: chain v residue 41 GLU Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 51 GLN Chi-restraints excluded: chain v residue 58 SER Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 32 ILE Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 66 GLU Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 69 GLU Chi-restraints excluded: chain x residue 75 GLU Chi-restraints excluded: chain y residue 4 LYS Chi-restraints excluded: chain y residue 50 VAL Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 3 THR Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 23 LEU Chi-restraints excluded: chain z residue 24 LEU Chi-restraints excluded: chain z residue 28 LEU Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 202 ASN Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 31 CYS Chi-restraints excluded: chain I residue 40 HIS Chi-restraints excluded: chain I residue 68 GLU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 59 ILE Chi-restraints excluded: chain J residue 60 GLN Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 14 ASP Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 80 ASN Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 14 LYS Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 69 GLU Chi-restraints excluded: chain Q residue 74 GLN Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 116 TYR Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 57 ASP Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain S residue 22 LYS Chi-restraints excluded: chain S residue 62 ARG Chi-restraints excluded: chain T residue 17 ASP Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 51 SER Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain U residue 18 GLN Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 46 HIS Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 63 CYS Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 5 LYS Chi-restraints excluded: chain X residue 13 HIS Chi-restraints excluded: chain X residue 14 LEU Chi-restraints excluded: chain X residue 36 ARG Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 73 PHE Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 8 LYS Chi-restraints excluded: chain Y residue 35 TYR Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain Z residue 34 ARG Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 62 GLU Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 22 ASP Chi-restraints excluded: chain a residue 47 ASN Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 212 VAL Chi-restraints excluded: chain a residue 214 ILE Chi-restraints excluded: chain a residue 224 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1031 random chunks: chunk 501 optimal weight: 8.9990 chunk 649 optimal weight: 10.0000 chunk 871 optimal weight: 10.0000 chunk 250 optimal weight: 20.0000 chunk 754 optimal weight: 20.0000 chunk 120 optimal weight: 0.0370 chunk 227 optimal weight: 9.9990 chunk 819 optimal weight: 40.0000 chunk 342 optimal weight: 10.0000 chunk 841 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 overall best weight: 7.8070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 196 ASN ** b 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 169 HIS ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 HIS ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 ASN ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 55 GLN ** 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 = 0.3720 r_free = 0.3720 target = 0.077594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.065062 restraints weight = 649183.063| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.77 r_work: 0.3353 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 160118 Z= 0.306 Angle : 0.728 12.367 239622 Z= 0.371 Chirality : 0.041 0.370 30641 Planarity : 0.005 0.081 12773 Dihedral : 23.906 178.994 80458 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 14.59 % Favored : 85.29 % Rotamer: Outliers : 7.74 % Allowed : 25.70 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.10), residues: 5743 helix: -0.75 (0.12), residues: 1842 sheet: -1.60 (0.16), residues: 989 loop : -2.75 (0.11), residues: 2912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.095 0.003 TRP G 103 HIS 0.007 0.001 HIS a 172 PHE 0.037 0.002 PHE k 79 TYR 0.037 0.002 TYR I 75 ARG 0.014 0.001 ARG f 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 44258.17 seconds wall clock time: 771 minutes 16.35 seconds (46276.35 seconds total)