Starting phenix.real_space_refine on Sun Mar 24 02:49:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogf_20056/03_2024/6ogf_20056.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogf_20056/03_2024/6ogf_20056.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogf_20056/03_2024/6ogf_20056.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogf_20056/03_2024/6ogf_20056.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogf_20056/03_2024/6ogf_20056.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogf_20056/03_2024/6ogf_20056.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.481 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 4650 5.49 5 S 152 5.16 5 C 74487 2.51 5 N 27520 2.21 5 O 40924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b GLU 22": "OE1" <-> "OE2" Residue "b GLU 99": "OE1" <-> "OE2" Residue "b ASP 167": "OD1" <-> "OD2" Residue "b GLU 179": "OE1" <-> "OE2" Residue "b GLU 198": "OE1" <-> "OE2" Residue "c ARG 13": "NH1" <-> "NH2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c ARG 59": "NH1" <-> "NH2" Residue "c GLU 64": "OE1" <-> "OE2" Residue "c ARG 77": "NH1" <-> "NH2" Residue "c ARG 83": "NH1" <-> "NH2" Residue "c PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 169": "NH1" <-> "NH2" Residue "c ARG 184": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 49": "NH1" <-> "NH2" Residue "d ARG 61": "NH1" <-> "NH2" Residue "d ARG 88": "NH1" <-> "NH2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "d GLU 122": "OE1" <-> "OE2" Residue "d PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 162": "NH1" <-> "NH2" Residue "d ARG 170": "NH1" <-> "NH2" Residue "d ASP 171": "OD1" <-> "OD2" Residue "d ASP 191": "OD1" <-> "OD2" Residue "e ARG 70": "NH1" <-> "NH2" Residue "e ARG 79": "NH1" <-> "NH2" Residue "e ARG 91": "NH1" <-> "NH2" Residue "e ARG 101": "NH1" <-> "NH2" Residue "e ARG 109": "NH1" <-> "NH2" Residue "e ARG 111": "NH1" <-> "NH2" Residue "e ARG 114": "NH1" <-> "NH2" Residue "e ARG 132": "NH1" <-> "NH2" Residue "e GLU 133": "OE1" <-> "OE2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "f ASP 15": "OD1" <-> "OD2" Residue "f ARG 152": "NH1" <-> "NH2" Residue "f ARG 162": "NH1" <-> "NH2" Residue "f TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 169": "NH1" <-> "NH2" Residue "g GLU 45": "OE1" <-> "OE2" Residue "g GLU 55": "OE1" <-> "OE2" Residue "g GLU 87": "OE1" <-> "OE2" Residue "g GLU 109": "OE1" <-> "OE2" Residue "g GLU 114": "OE1" <-> "OE2" Residue "g GLU 129": "OE1" <-> "OE2" Residue "g GLU 137": "OE1" <-> "OE2" Residue "j GLU 9": "OE1" <-> "OE2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j ASP 71": "OD1" <-> "OD2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j GLU 98": "OE1" <-> "OE2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "k GLU 4": "OE1" <-> "OE2" Residue "k GLU 45": "OE1" <-> "OE2" Residue "k GLU 106": "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 GLU 51": "OE1" <-> "OE2" Residue "l ARG 60": "NH1" <-> "NH2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "l GLU 136": "OE1" <-> "OE2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 18": "NH1" <-> "NH2" Residue "m 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 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 111": "OE1" <-> "OE2" Residue "m ARG 114": "NH1" <-> "NH2" Residue "n ARG 8": "NH1" <-> "NH2" Residue "n ARG 12": "NH1" <-> "NH2" Residue "n ARG 17": "NH1" <-> "NH2" Residue "n ARG 22": "NH1" <-> "NH2" Residue "n ARG 46": "NH1" <-> "NH2" Residue "n ARG 63": "NH1" <-> "NH2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n ARG 69": "NH1" <-> "NH2" Residue "n ARG 71": "NH1" <-> "NH2" Residue "n ARG 96": "NH1" <-> "NH2" Residue "n ARG 118": "NH1" <-> "NH2" Residue "o ARG 10": "NH1" <-> "NH2" Residue "o ARG 16": "NH1" <-> "NH2" Residue "o ARG 25": "NH1" <-> "NH2" Residue "o ARG 81": "NH1" <-> "NH2" Residue "o ARG 94": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ASP 108": "OD1" <-> "OD2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "p PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 20": "NH1" <-> "NH2" Residue "p ARG 38": "NH1" <-> "NH2" Residue "p ARG 61": "NH1" <-> "NH2" Residue "p ASP 81": "OD1" <-> "OD2" Residue "p ARG 88": "NH1" <-> "NH2" 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 ARG 32": "NH1" <-> "NH2" Residue "q ARG 47": "NH1" <-> "NH2" Residue "q ASP 48": "OD1" <-> "OD2" Residue "q ARG 69": "NH1" <-> "NH2" Residue "q GLU 110": "OE1" <-> "OE2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r GLU 34": "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 22": "OD1" <-> "OD2" Residue "s GLU 52": "OE1" <-> "OE2" Residue "s ASP 65": "OD1" <-> "OD2" Residue "s ASP 68": "OD1" <-> "OD2" Residue "s GLU 78": "OE1" <-> "OE2" Residue "s ARG 84": "NH1" <-> "NH2" Residue "s ARG 88": "NH1" <-> "NH2" Residue "s ARG 95": "NH1" <-> "NH2" Residue "s ARG 110": "NH1" <-> "NH2" Residue "t GLU 5": "OE1" <-> "OE2" Residue "t ASP 37": "OD1" <-> "OD2" Residue "t GLU 42": "OE1" <-> "OE2" Residue "t ARG 73": "NH1" <-> "NH2" Residue "u ARG 5": "NH1" <-> "NH2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u ARG 81": "NH1" <-> "NH2" Residue "u ARG 85": "NH1" <-> "NH2" Residue "u ARG 93": "NH1" <-> "NH2" Residue "v GLU 35": "OE1" <-> "OE2" Residue "v ASP 76": "OD1" <-> "OD2" Residue "w PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 42": "OE1" <-> "OE2" Residue "y GLU 17": "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 "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 GLU 6": "OE1" <-> "OE2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 3": "NH1" <-> "NH2" Residue "D ARG 12": "NH1" <-> "NH2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D ARG 19": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 41": "NH1" <-> "NH2" Residue "E ARG 12": "NH1" <-> "NH2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "E ARG 41": "NH1" <-> "NH2" Residue "F ARG 12": "NH1" <-> "NH2" Residue "F ARG 24": "NH1" <-> "NH2" Residue "G ASP 7": "OD1" <-> "OD2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "G GLU 77": "OE1" <-> "OE2" Residue "G ASP 115": "OD1" <-> "OD2" Residue "G ASP 152": "OD1" <-> "OD2" Residue "G ASP 204": "OD1" <-> "OD2" Residue "G GLU 222": "OE1" <-> "OE2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "H GLU 27": "OE1" <-> "OE2" Residue "H ASP 35": "OD1" <-> "OD2" Residue "H GLU 81": "OE1" <-> "OE2" Residue "H GLU 84": "OE1" <-> "OE2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H ASP 117": "OD1" <-> "OD2" Residue "H GLU 124": "OE1" <-> "OE2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "I GLU 68": "OE1" <-> "OE2" Residue "I GLU 94": "OE1" <-> "OE2" Residue "I GLU 162": "OE1" <-> "OE2" Residue "J GLU 54": "OE1" <-> "OE2" Residue "J GLU 115": "OE1" <-> "OE2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "J GLU 161": "OE1" <-> "OE2" Residue "K GLU 40": "OE1" <-> "OE2" Residue "K TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 73": "OE1" <-> "OE2" Residue "K PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 20": "OE1" <-> "OE2" Residue "L GLU 73": "OE1" <-> "OE2" Residue "M PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 123": "OE1" <-> "OE2" Residue "N GLU 41": "OE1" <-> "OE2" Residue "N GLU 52": "OE1" <-> "OE2" Residue "N GLU 91": "OE1" <-> "OE2" Residue "N GLU 96": "OE1" <-> "OE2" Residue "N ASP 106": "OD1" <-> "OD2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "O ASP 14": "OD1" <-> "OD2" Residue "P ASP 17": "OD1" <-> "OD2" Residue "P ASP 71": "OD1" <-> "OD2" Residue "Q GLU 24": "OE1" <-> "OE2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q GLU 69": "OE1" <-> "OE2" Residue "Q ASP 88": "OD1" <-> "OD2" Residue "Q ASP 102": "OD1" <-> "OD2" Residue "R ASP 10": "OD1" <-> "OD2" Residue "S PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 25": "OE1" <-> "OE2" Residue "S GLU 38": "OE1" <-> "OE2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 53": "OD1" <-> "OD2" Residue "U ASP 55": "OD1" <-> "OD2" Residue "U GLU 77": "OE1" <-> "OE2" Residue "V GLU 17": "OE1" <-> "OE2" Residue "V PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "W GLU 19": "OE1" <-> "OE2" Residue "W ASP 24": "OD1" <-> "OD2" Residue "Z GLU 30": "OE1" <-> "OE2" Residue "Z ARG 66": "NH1" <-> "NH2" Residue "a ARG 7": "NH1" <-> "NH2" Residue "a ARG 12": "NH1" <-> "NH2" Residue "a ARG 162": "NH1" <-> "NH2" Residue "a GLU 190": "OE1" <-> "OE2" Residue "8 GLU 32": "OE1" <-> "OE2" Residue "8 GLU 35": "OE1" <-> "OE2" Residue "8 GLU 49": "OE1" <-> "OE2" Residue "8 ASP 79": "OD1" <-> "OD2" Residue "8 ASP 91": "OD1" <-> "OD2" Residue "8 ASP 92": "OD1" <-> "OD2" Residue "8 GLU 93": "OE1" <-> "OE2" Residue "8 ARG 213": "NH1" <-> "NH2" Residue "8 ASP 227": "OD1" <-> "OD2" Residue "8 ASP 238": "OD1" <-> "OD2" Residue "8 ASP 242": "OD1" <-> "OD2" Residue "8 ASP 312": "OD1" <-> "OD2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 147733 Number of models: 1 Model: "" Number of chains: 55 Chain: "b" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} 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: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "f" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "g" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "j" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "k" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} 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: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} 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: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "u" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "v" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "w" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "x" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "B" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "C" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} 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: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1756 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "H" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} 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: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1156 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "K" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 824 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "L" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} 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: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "P" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 869 Classifications: {'peptide': 116} 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: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} 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: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "W" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "X" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} 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: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 544 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "a" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1026 Classifications: {'peptide': 134} 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': 93, 'rna2p_pyr': 49, 'rna3p_pur': 781, 'rna3p_pyr': 616} Link IDs: {'rna2p': 142, 'rna3p': 1396} 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': 219, 'rna2p_pyr': 98, 'rna3p_pur': 1455, 'rna3p_pyr': 1131} Link IDs: {'rna2p': 317, 'rna3p': 2585} Chain: "2" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2568 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 61, 'rna3p_pyr': 53} Link IDs: {'rna2p': 6, 'rna3p': 113} Chain: "5" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1556 Classifications: {'RNA': 73} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 32, 'rna3p_pyr': 31} Link IDs: {'rna2p': 10, 'rna3p': 62} Chain: "4" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 437 Classifications: {'RNA': 20} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 14, 'rna3p_pyr': 3} Link IDs: {'rna2p': 3, 'rna3p': 16} Chain: "8" Number of atoms: 2860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2860 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 7, 'TRANS': 353} Time building chain proxies: 58.25, per 1000 atoms: 0.39 Number of scatterers: 147733 At special positions: 0 Unit cell: (236.118, 261.464, 268.134, 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 152 16.00 P 4650 15.00 O 40924 8.00 N 27520 7.00 C 74487 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 57.81 Conformation dependent library (CDL) restraints added in 8.6 seconds 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11242 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 73 sheets defined 34.8% alpha, 16.2% beta 1324 base pairs and 2588 stacking pairs defined. Time for finding SS restraints: 51.67 Creating SS restraints... Processing helix chain 'b' and resid 29 through 31 No H-bonds generated for 'chain 'b' and resid 29 through 31' Processing helix chain 'b' and resid 132 through 134 No H-bonds generated for 'chain 'b' and resid 132 through 134' Processing helix chain 'b' and resid 196 through 202 removed outlier: 4.062A pdb=" N MET b 200 " --> pdb=" O ALA b 197 " (cutoff:3.500A) Processing helix chain 'b' and resid 206 through 213 removed outlier: 3.981A pdb=" N ALA b 210 " --> pdb=" O LYS b 206 " (cutoff:3.500A) Processing helix chain 'b' and resid 262 through 264 No H-bonds generated for 'chain 'b' and resid 262 through 264' Processing helix chain 'c' and resid 61 through 72 removed outlier: 3.544A pdb=" N ALA c 71 " --> pdb=" O HIS c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 97 through 102 removed outlier: 3.876A pdb=" N LEU c 100 " --> pdb=" O SER c 97 " (cutoff:3.500A) Processing helix chain 'c' and resid 120 through 125 Processing helix chain 'd' and resid 15 through 20 removed outlier: 3.545A pdb=" N PHE d 19 " --> pdb=" O SER d 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 24 through 39 removed outlier: 3.673A pdb=" N VAL d 33 " --> pdb=" O HIS d 29 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 115 Processing helix chain 'd' and resid 130 through 141 removed outlier: 3.878A pdb=" N LEU d 134 " --> pdb=" O LYS d 130 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 161 removed outlier: 3.648A pdb=" N ALA d 160 " --> pdb=" O ASN d 156 " (cutoff:3.500A) Processing helix chain 'd' and resid 178 through 183 removed outlier: 3.657A pdb=" N PHE d 183 " --> pdb=" O SER d 179 " (cutoff:3.500A) Processing helix chain 'd' and resid 190 through 200 Processing helix chain 'e' and resid 2 through 10 Processing helix chain 'e' and resid 10 through 16 Processing helix chain 'e' and resid 23 through 27 Processing helix chain 'e' and resid 45 through 60 removed outlier: 3.674A pdb=" N LEU e 49 " --> pdb=" O ASP e 45 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU e 56 " --> pdb=" O ALA e 52 " (cutoff:3.500A) Processing helix chain 'e' and resid 93 through 104 removed outlier: 3.509A pdb=" N GLU e 97 " --> pdb=" O GLU e 93 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU e 100 " --> pdb=" O TRP e 96 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG e 101 " --> pdb=" O GLU e 97 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU e 102 " --> pdb=" O PHE e 98 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE e 103 " --> pdb=" O PHE e 99 " (cutoff:3.500A) Processing helix chain 'e' and resid 133 through 137 removed outlier: 3.875A pdb=" N ILE e 136 " --> pdb=" O GLU e 133 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE e 137 " --> pdb=" O GLN e 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 133 through 137' Processing helix chain 'e' and resid 161 through 170 removed outlier: 3.904A pdb=" N ALA e 167 " --> pdb=" O GLU e 163 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU e 168 " --> pdb=" O GLU e 164 " (cutoff:3.500A) Processing helix chain 'f' and resid 59 through 80 removed outlier: 3.753A pdb=" N ALA f 69 " --> pdb=" O GLY f 65 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR f 79 " --> pdb=" O VAL f 75 " (cutoff:3.500A) Processing helix chain 'f' and resid 136 through 149 Processing helix chain 'g' and resid 22 through 29 removed outlier: 3.537A pdb=" N ASN g 28 " --> pdb=" O GLY g 24 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE g 29 " --> pdb=" O TYR g 25 " (cutoff:3.500A) Processing helix chain 'g' and resid 40 through 50 removed outlier: 3.616A pdb=" N GLU g 45 " --> pdb=" O LYS g 41 " (cutoff:3.500A) Processing helix chain 'g' and resid 54 through 59 removed outlier: 3.606A pdb=" N LEU g 58 " --> pdb=" O LEU g 54 " (cutoff:3.500A) Processing helix chain 'g' and resid 60 through 72 removed outlier: 3.662A pdb=" N ALA g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE g 72 " --> pdb=" O ARG g 68 " (cutoff:3.500A) Processing helix chain 'g' and resid 96 through 104 removed outlier: 3.659A pdb=" N ALA g 100 " --> pdb=" O THR g 96 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR g 104 " --> pdb=" O ALA g 100 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 38 removed outlier: 3.609A pdb=" N GLU j 31 " --> pdb=" O ARG j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 58 through 62 removed outlier: 3.985A pdb=" N VAL j 62 " --> pdb=" O ALA j 59 " (cutoff:3.500A) Processing helix chain 'j' and resid 67 through 72 Processing helix chain 'j' and resid 88 through 96 Processing helix chain 'j' and resid 98 through 107 removed outlier: 3.543A pdb=" N GLU j 102 " --> pdb=" O GLU j 98 " (cutoff:3.500A) Processing helix chain 'j' and resid 112 through 120 removed outlier: 3.782A pdb=" N ARG j 120 " --> pdb=" O ARG j 116 " (cutoff:3.500A) Processing helix chain 'j' and resid 132 through 136 Processing helix chain 'k' and resid 104 through 108 removed outlier: 3.924A pdb=" N LEU k 107 " --> pdb=" O THR k 104 " (cutoff:3.500A) Processing helix chain 'k' and resid 109 through 111 No H-bonds generated for 'chain 'k' and resid 109 through 111' Processing helix chain 'k' and resid 112 through 117 removed outlier: 3.554A pdb=" N SER k 117 " --> pdb=" O MET k 113 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 6 removed outlier: 3.853A pdb=" N LEU l 6 " --> pdb=" O LEU l 3 " (cutoff:3.500A) Processing helix chain 'l' and resid 37 through 41 removed outlier: 3.518A pdb=" N ARG l 41 " --> pdb=" O GLN l 38 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 61 Processing helix chain 'l' and resid 128 through 138 Processing helix chain 'm' and resid 43 through 58 removed outlier: 3.795A pdb=" N ALA m 56 " --> pdb=" O ALA m 52 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL m 57 " --> pdb=" O MET m 53 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 122 removed outlier: 3.580A pdb=" N ALA m 120 " --> pdb=" O ALA m 116 " (cutoff:3.500A) Processing helix chain 'n' and resid 13 through 32 removed outlier: 3.505A pdb=" N ALA n 19 " --> pdb=" O SER n 15 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS n 31 " --> pdb=" O SER n 27 " (cutoff:3.500A) Processing helix chain 'n' and resid 38 through 57 removed outlier: 5.262A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Proline residue: n 50 - end of helix removed outlier: 4.227A pdb=" N THR n 57 " --> pdb=" O THR n 53 " (cutoff:3.500A) Processing helix chain 'n' and resid 59 through 69 Processing helix chain 'n' and resid 74 through 79 Processing helix chain 'n' and resid 82 through 87 Processing helix chain 'o' and resid 3 through 22 removed outlier: 4.759A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 60 Processing helix chain 'o' and resid 67 through 86 removed outlier: 3.688A pdb=" N ALA o 71 " --> pdb=" O ASN o 67 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA o 72 " --> pdb=" O LYS o 68 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA o 79 " --> pdb=" O GLY o 75 " (cutoff:3.500A) Processing helix chain 'o' and resid 101 through 114 removed outlier: 3.637A pdb=" N ALA o 110 " --> pdb=" O LEU o 106 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU o 112 " --> pdb=" O ASP o 108 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY o 114 " --> pdb=" O ALA o 110 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 10 removed outlier: 4.277A pdb=" N GLU p 10 " --> pdb=" O GLN p 6 " (cutoff:3.500A) Processing helix chain 'p' and resid 52 through 55 Processing helix chain 'p' and resid 96 through 101 removed outlier: 3.744A pdb=" N GLU p 101 " --> pdb=" O TYR p 98 " (cutoff:3.500A) Processing helix chain 'p' and resid 103 through 108 Processing helix chain 'q' and resid 6 through 18 Processing helix chain 'q' and resid 24 through 29 Processing helix chain 'q' and resid 30 through 70 removed outlier: 4.020A pdb=" N GLN q 36 " --> pdb=" O ARG q 32 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG q 50 " --> pdb=" O TYR q 46 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) Processing helix chain 'q' and resid 74 through 85 Processing helix chain 'q' and resid 90 through 100 removed outlier: 3.538A pdb=" N ASP q 96 " --> pdb=" O LYS q 92 " (cutoff:3.500A) Processing helix chain 'q' and resid 101 through 116 Processing helix chain 's' and resid 13 through 24 removed outlier: 3.909A pdb=" N VAL s 17 " --> pdb=" O SER s 13 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU s 19 " --> pdb=" O GLN s 15 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU s 23 " --> pdb=" O LEU s 19 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE s 24 " --> pdb=" O VAL s 20 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 37 removed outlier: 4.158A pdb=" N ASP s 34 " --> pdb=" O SER s 30 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE s 35 " --> pdb=" O GLN s 31 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 61 removed outlier: 3.610A pdb=" N VAL s 45 " --> pdb=" O LYS s 41 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU s 46 " --> pdb=" O LYS s 42 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) Processing helix chain 's' and resid 89 through 91 No H-bonds generated for 'chain 's' and resid 89 through 91' Processing helix chain 't' and resid 2 through 10 removed outlier: 3.737A pdb=" N LYS t 9 " --> pdb=" O GLU t 5 " (cutoff:3.500A) Processing helix chain 't' and resid 17 through 26 removed outlier: 3.510A pdb=" N SER t 21 " --> pdb=" O SER t 17 " (cutoff:3.500A) Processing helix chain 't' and resid 39 through 50 Processing helix chain 'v' and resid 13 through 21 Processing helix chain 'v' and resid 22 through 24 No H-bonds generated for 'chain 'v' and resid 22 through 24' Processing helix chain 'v' and resid 43 through 52 removed outlier: 3.969A pdb=" N VAL v 47 " --> pdb=" O ASP v 43 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA v 52 " --> pdb=" O MET v 48 " (cutoff:3.500A) Processing helix chain 'v' and resid 53 through 57 Processing helix chain 'x' and resid 52 through 61 removed outlier: 3.749A pdb=" N ARG x 56 " --> pdb=" O ALA x 52 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP x 59 " --> pdb=" O MET x 55 " (cutoff:3.500A) Processing helix chain 'x' and resid 62 through 73 Processing helix chain 'y' and resid 3 through 8 removed outlier: 3.566A pdb=" N ARG y 7 " --> pdb=" O ALA y 3 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU y 8 " --> pdb=" O LYS y 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 3 through 8' Processing helix chain 'y' and resid 9 through 23 removed outlier: 3.600A pdb=" N LEU y 21 " --> pdb=" O GLU y 17 " (cutoff:3.500A) Processing helix chain 'y' and resid 23 through 35 removed outlier: 3.823A pdb=" N ARG y 29 " --> pdb=" O GLN y 25 " (cutoff:3.500A) Processing helix chain 'y' and resid 39 through 61 removed outlier: 3.806A pdb=" N LEU y 43 " --> pdb=" O GLN y 39 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG y 47 " --> pdb=" O LEU y 43 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA y 51 " --> pdb=" O ARG y 47 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 27 Processing helix chain 'z' and resid 40 through 50 removed outlier: 3.509A pdb=" N VAL z 50 " --> pdb=" O MET z 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 16 Processing helix chain 'B' and resid 17 through 20 removed outlier: 3.735A pdb=" N ALA B 20 " --> pdb=" O SER B 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 17 through 20' Processing helix chain 'D' and resid 8 through 14 Processing helix chain 'D' and resid 17 through 23 Processing helix chain 'D' and resid 24 through 38 removed outlier: 3.653A pdb=" N ARG D 28 " --> pdb=" O THR D 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 11 Processing helix chain 'E' and resid 36 through 43 Processing helix chain 'E' and resid 53 through 61 Processing helix chain 'F' and resid 18 through 22 Processing helix chain 'G' and resid 33 through 37 removed outlier: 3.597A pdb=" N LYS G 36 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 62 Processing helix chain 'G' and resid 75 through 85 removed outlier: 3.696A pdb=" N VAL G 79 " --> pdb=" O ALA G 75 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS G 80 " --> pdb=" O SER G 76 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA G 83 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU G 84 " --> pdb=" O LYS G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 122 removed outlier: 4.241A pdb=" N GLN G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER G 120 " --> pdb=" O LEU G 116 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP G 122 " --> pdb=" O THR G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 146 removed outlier: 3.519A pdb=" N ASN G 145 " --> pdb=" O GLU G 141 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER G 146 " --> pdb=" O LYS G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 153 removed outlier: 3.543A pdb=" N LYS G 151 " --> pdb=" O GLY G 148 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP G 152 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 177 removed outlier: 3.868A pdb=" N ILE G 172 " --> pdb=" O GLU G 168 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN G 177 " --> pdb=" O LYS G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 224 removed outlier: 3.904A pdb=" N ALA G 215 " --> pdb=" O LEU G 211 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA G 218 " --> pdb=" O GLY G 214 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR G 219 " --> pdb=" O ALA G 215 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL G 220 " --> pdb=" O VAL G 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 10 removed outlier: 4.148A pdb=" N ARG H 10 " --> pdb=" O PRO H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 47 removed outlier: 3.601A pdb=" N ASN H 31 " --> pdb=" O GLU H 27 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS H 44 " --> pdb=" O GLN H 40 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU H 45 " --> pdb=" O TYR H 41 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA H 47 " --> pdb=" O THR H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 77 removed outlier: 3.835A pdb=" N VAL H 75 " --> pdb=" O ARG H 71 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE H 76 " --> pdb=" O PRO H 72 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY H 77 " --> pdb=" O GLY H 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 71 through 77' Processing helix chain 'H' and resid 80 through 95 removed outlier: 3.582A pdb=" N ALA H 91 " --> pdb=" O ARG H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 125 removed outlier: 3.887A pdb=" N SER H 118 " --> pdb=" O LEU H 114 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG H 125 " --> pdb=" O SER H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 142 removed outlier: 3.739A pdb=" N ARG H 135 " --> pdb=" O ARG H 131 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA H 136 " --> pdb=" O ALA H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 159 Processing helix chain 'I' and resid 8 through 15 removed outlier: 3.596A pdb=" N ARG I 12 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG I 13 " --> pdb=" O LYS I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 65 Processing helix chain 'I' and resid 67 through 81 Processing helix chain 'I' and resid 84 through 96 removed outlier: 4.079A pdb=" N LEU I 90 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA I 91 " --> pdb=" O GLU I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 104 removed outlier: 3.515A pdb=" N TYR I 102 " --> pdb=" O ASP I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 118 removed outlier: 3.798A pdb=" N GLN I 115 " --> pdb=" O ALA I 111 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU I 116 " --> pdb=" O GLU I 112 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL I 117 " --> pdb=" O ALA I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 160 removed outlier: 3.808A pdb=" N GLU I 159 " --> pdb=" O LYS I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 164 Processing helix chain 'I' and resid 196 through 203 removed outlier: 3.533A pdb=" N TYR I 203 " --> pdb=" O ILE I 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 68 removed outlier: 3.964A pdb=" N LYS J 65 " --> pdb=" O LYS J 61 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG J 68 " --> pdb=" O GLU J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 118 removed outlier: 3.574A pdb=" N VAL J 113 " --> pdb=" O ALA J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 146 removed outlier: 3.709A pdb=" N VAL J 136 " --> pdb=" O PRO J 132 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG J 137 " --> pdb=" O ILE J 133 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA J 138 " --> pdb=" O ASN J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 156 Processing helix chain 'K' and resid 11 through 16 removed outlier: 4.171A pdb=" N GLU K 16 " --> pdb=" O PRO K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 31 Processing helix chain 'K' and resid 67 through 79 removed outlier: 3.995A pdb=" N ILE K 71 " --> pdb=" O PRO K 67 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP K 72 " --> pdb=" O GLN K 68 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU K 73 " --> pdb=" O GLU K 69 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR K 76 " --> pdb=" O ASP K 72 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 30 Processing helix chain 'L' and resid 34 through 54 removed outlier: 3.717A pdb=" N SER L 40 " --> pdb=" O SER L 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 64 removed outlier: 3.632A pdb=" N ALA L 60 " --> pdb=" O SER L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 109 removed outlier: 3.681A pdb=" N ASN L 96 " --> pdb=" O PRO L 92 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA L 97 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL L 104 " --> pdb=" O MET L 100 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS L 109 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 128 removed outlier: 3.923A pdb=" N ALA L 120 " --> pdb=" O ALA L 116 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN L 121 " --> pdb=" O LEU L 117 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU L 122 " --> pdb=" O ARG L 118 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU L 128 " --> pdb=" O SER L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 146 removed outlier: 3.838A pdb=" N LYS L 135 " --> pdb=" O GLY L 131 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG L 137 " --> pdb=" O ALA L 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 20 removed outlier: 3.562A pdb=" N GLN M 17 " --> pdb=" O ILE M 13 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA M 18 " --> pdb=" O ARG M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 43 removed outlier: 3.664A pdb=" N VAL M 38 " --> pdb=" O ALA M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 91 removed outlier: 3.717A pdb=" N LEU M 91 " --> pdb=" O LYS M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 117 Processing helix chain 'N' and resid 10 through 14 removed outlier: 3.953A pdb=" N SER N 13 " --> pdb=" O ARG N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 33 through 38 removed outlier: 3.846A pdb=" N PHE N 38 " --> pdb=" O LEU N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 53 removed outlier: 3.597A pdb=" N LEU N 53 " --> pdb=" O PRO N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 84 removed outlier: 3.853A pdb=" N ALA N 77 " --> pdb=" O GLY N 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 90 through 99 removed outlier: 3.785A pdb=" N ARG N 94 " --> pdb=" O ASP N 90 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU N 96 " --> pdb=" O SER N 92 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 19 Processing helix chain 'O' and resid 20 through 31 removed outlier: 3.794A pdb=" N GLU O 24 " --> pdb=" O GLN O 20 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE O 25 " --> pdb=" O ALA O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 85 removed outlier: 3.577A pdb=" N ASP O 85 " --> pdb=" O GLU O 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 50 removed outlier: 3.624A pdb=" N GLY P 50 " --> pdb=" O GLY P 47 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 57 removed outlier: 3.907A pdb=" N ARG P 55 " --> pdb=" O ARG P 52 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS P 56 " --> pdb=" O GLY P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 58 through 71 removed outlier: 3.898A pdb=" N GLU P 67 " --> pdb=" O GLN P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 101 removed outlier: 3.885A pdb=" N SER P 94 " --> pdb=" O PRO P 90 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE P 96 " --> pdb=" O ARG P 92 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 9 Processing helix chain 'Q' and resid 114 through 118 removed outlier: 4.201A pdb=" N VAL Q 118 " --> pdb=" O LYS Q 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 20 Processing helix chain 'R' and resid 25 through 36 removed outlier: 4.444A pdb=" N ALA R 31 " --> pdb=" O THR R 27 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE R 32 " --> pdb=" O ARG R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 61 removed outlier: 3.719A pdb=" N ASP R 53 " --> pdb=" O GLU R 49 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N THR R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL R 59 " --> pdb=" O LEU R 55 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS R 61 " --> pdb=" O ASP R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 83 removed outlier: 3.725A pdb=" N ARG R 70 " --> pdb=" O GLY R 66 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU R 79 " --> pdb=" O SER R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 91 removed outlier: 3.571A pdb=" N HIS R 90 " --> pdb=" O ARG R 86 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 19 removed outlier: 3.605A pdb=" N GLU S 9 " --> pdb=" O MET S 5 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 29 Processing helix chain 'S' and resid 37 through 47 removed outlier: 3.639A pdb=" N LEU S 47 " --> pdb=" O ALA S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 90 Processing helix chain 'T' and resid 3 through 15 removed outlier: 3.628A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER T 12 " --> pdb=" O ALA T 8 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU T 13 " --> pdb=" O LYS T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 44 removed outlier: 3.895A pdb=" N GLY T 40 " --> pdb=" O ASN T 36 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N HIS T 41 " --> pdb=" O HIS T 37 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 73 removed outlier: 3.781A pdb=" N GLY T 54 " --> pdb=" O HIS T 50 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP T 67 " --> pdb=" O ARG T 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 84 removed outlier: 3.564A pdb=" N GLU T 82 " --> pdb=" O THR T 78 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 62 Processing helix chain 'U' and resid 68 through 78 Processing helix chain 'W' and resid 24 through 30 removed outlier: 3.854A pdb=" N ASN W 30 " --> pdb=" O ALA W 26 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 45 removed outlier: 3.673A pdb=" N THR W 44 " --> pdb=" O PRO W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 47 through 64 removed outlier: 3.610A pdb=" N ARG W 56 " --> pdb=" O ARG W 52 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA W 57 " --> pdb=" O GLN W 53 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS W 59 " --> pdb=" O ALA W 55 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 23 removed outlier: 3.619A pdb=" N LYS X 17 " --> pdb=" O HIS X 13 " (cutoff:3.500A) Processing helix chain 'X' and resid 69 through 74 Processing helix chain 'Y' and resid 5 through 41 removed outlier: 3.751A pdb=" N ILE Y 11 " --> pdb=" O LYS Y 7 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS Y 19 " --> pdb=" O LYS Y 15 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE Y 30 " --> pdb=" O MET Y 26 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 52 Processing helix chain 'Y' and resid 53 through 63 removed outlier: 3.592A pdb=" N ASP Y 58 " --> pdb=" O GLN Y 54 " (cutoff:3.500A) Processing helix chain 'Y' and resid 68 through 86 removed outlier: 3.803A pdb=" N THR Y 79 " --> pdb=" O LYS Y 75 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN Y 83 " --> pdb=" O THR Y 79 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS Y 84 " --> pdb=" O ALA Y 80 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA Y 86 " --> pdb=" O ILE Y 82 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 23 Processing helix chain 'Z' and resid 38 through 57 Processing helix chain 'a' and resid 5 through 15 removed outlier: 3.512A pdb=" N VAL a 10 " --> pdb=" O LYS a 6 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE a 11 " --> pdb=" O ARG a 7 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS a 14 " --> pdb=" O VAL a 10 " (cutoff:3.500A) Processing helix chain 'a' and resid 23 through 31 removed outlier: 3.871A pdb=" N ILE a 27 " --> pdb=" O ILE a 23 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA a 28 " --> pdb=" O ASN a 24 " (cutoff:3.500A) Processing helix chain 'a' and resid 181 through 198 removed outlier: 3.608A pdb=" N GLU a 187 " --> pdb=" O ASP a 183 " (cutoff:3.500A) Processing helix chain '8' and resid 5 through 22 removed outlier: 3.822A pdb=" N ARG 8 10 " --> pdb=" O PRO 8 6 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL 8 20 " --> pdb=" O GLU 8 16 " (cutoff:3.500A) Processing helix chain '8' and resid 26 through 40 removed outlier: 3.733A pdb=" N LYS 8 30 " --> pdb=" O ASP 8 26 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS 8 31 " --> pdb=" O TYR 8 27 " (cutoff:3.500A) Processing helix chain '8' and resid 45 through 48 removed outlier: 3.873A pdb=" N ASN 8 48 " --> pdb=" O ASP 8 45 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 45 through 48' Processing helix chain '8' and resid 49 through 64 removed outlier: 3.925A pdb=" N ALA 8 53 " --> pdb=" O GLU 8 49 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN 8 54 " --> pdb=" O PRO 8 50 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU 8 56 " --> pdb=" O ARG 8 52 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU 8 63 " --> pdb=" O GLU 8 59 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU 8 64 " --> pdb=" O ARG 8 60 " (cutoff:3.500A) Processing helix chain '8' and resid 66 through 90 removed outlier: 3.885A pdb=" N GLN 8 72 " --> pdb=" O ASP 8 68 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET 8 73 " --> pdb=" O THR 8 69 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU 8 85 " --> pdb=" O SER 8 81 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU 8 86 " --> pdb=" O GLY 8 82 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL 8 88 " --> pdb=" O LEU 8 84 " (cutoff:3.500A) Processing helix chain '8' and resid 93 through 119 removed outlier: 3.806A pdb=" N GLU 8 98 " --> pdb=" O GLU 8 94 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA 8 99 " --> pdb=" O THR 8 95 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLN 8 112 " --> pdb=" O GLU 8 108 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG 8 117 " --> pdb=" O LEU 8 113 " (cutoff:3.500A) Processing helix chain '8' and resid 138 through 159 Processing helix chain '8' and resid 187 through 193 Processing helix chain '8' and resid 279 through 314 removed outlier: 3.527A pdb=" N MET 8 300 " --> pdb=" O TYR 8 296 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA 8 309 " --> pdb=" O ALA 8 305 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET 8 310 " --> pdb=" O GLU 8 306 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU 8 311 " --> pdb=" O LYS 8 307 " (cutoff:3.500A) Processing helix chain '8' and resid 344 through 349 Processing helix chain '8' and resid 353 through 359 removed outlier: 3.648A pdb=" N ILE 8 357 " --> pdb=" O LEU 8 353 " (cutoff:3.500A) Processing helix chain '8' and resid 360 through 363 removed outlier: 3.857A pdb=" N ALA 8 363 " --> pdb=" O SER 8 360 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 360 through 363' Processing sheet with id=AA1, first strand: chain 'b' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'b' and resid 33 through 35 Processing sheet with id=AA3, first strand: chain 'b' and resid 100 through 104 removed outlier: 6.502A pdb=" N ILE b 90 " --> pdb=" O LEU b 80 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU b 80 " --> pdb=" O ILE b 90 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU b 92 " --> pdb=" O GLU b 78 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'b' and resid 128 through 130 removed outlier: 3.657A pdb=" N LEU b 129 " --> pdb=" O ALA b 189 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN b 162 " --> pdb=" O ARG b 174 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR b 172 " --> pdb=" O VAL b 164 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N MET b 180 " --> pdb=" O VAL b 267 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'c' and resid 4 through 15 removed outlier: 5.701A pdb=" N LYS c 8 " --> pdb=" O GLU c 28 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLU c 28 " --> pdb=" O LYS c 8 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLY c 10 " --> pdb=" O VAL c 26 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU c 186 " --> pdb=" O VAL c 180 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N VAL c 180 " --> pdb=" O LEU c 186 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU c 188 " --> pdb=" O VAL c 178 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ASP c 176 " --> pdb=" O LYS c 190 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL c 107 " --> pdb=" O SER c 174 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N THR c 112 " --> pdb=" O ASP c 200 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ASP c 200 " --> pdb=" O THR c 112 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU c 201 " --> pdb=" O GLY c 6 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'c' and resid 80 through 83 removed outlier: 6.563A pdb=" N ALA c 47 " --> pdb=" O VAL c 37 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N VAL c 37 " --> pdb=" O ALA c 47 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN c 49 " --> pdb=" O THR c 35 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'c' and resid 115 through 119 Processing sheet with id=AA8, first strand: chain 'd' and resid 2 through 3 Processing sheet with id=AA9, first strand: chain 'd' and resid 118 through 121 removed outlier: 6.991A pdb=" N LEU d 147 " --> pdb=" O VAL d 187 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N THR d 189 " --> pdb=" O LEU d 147 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ILE d 149 " --> pdb=" O THR d 189 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ARG d 170 " --> pdb=" O VAL d 146 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE d 148 " --> pdb=" O ARG d 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'e' and resid 65 through 68 removed outlier: 6.161A pdb=" N LEU e 65 " --> pdb=" O CYS e 86 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N CYS e 86 " --> pdb=" O LEU e 65 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N THR e 67 " --> pdb=" O ILE e 84 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'f' and resid 8 through 9 Processing sheet with id=AB3, first strand: chain 'f' and resid 15 through 19 removed outlier: 3.554A pdb=" N VAL f 22 " --> pdb=" O ASN f 19 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'f' and resid 121 through 126 removed outlier: 6.959A pdb=" N GLU f 129 " --> pdb=" O PRO f 125 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN f 87 " --> pdb=" O ARG f 162 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG f 162 " --> pdb=" O GLN f 87 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL f 89 " --> pdb=" O GLY f 160 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'f' and resid 94 through 98 removed outlier: 3.594A pdb=" N ARG f 94 " --> pdb=" O SER f 105 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER f 105 " --> pdb=" O ARG f 94 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'g' and resid 3 through 5 Processing sheet with id=AB7, first strand: chain 'g' and resid 77 through 78 removed outlier: 3.747A pdb=" N VAL g 78 " --> pdb=" O ILE g 143 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'j' and resid 123 through 124 removed outlier: 6.121A pdb=" N TYR j 16 " --> pdb=" O ILE j 55 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU j 57 " --> pdb=" O TYR j 16 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL j 18 " --> pdb=" O LEU j 57 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'j' and resid 76 through 77 Processing sheet with id=AC1, first strand: chain 'k' and resid 7 through 10 removed outlier: 5.883A pdb=" N ARG k 17 " --> pdb=" O VAL k 10 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA k 16 " --> pdb=" O ALA k 46 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA k 46 " --> pdb=" O ALA k 16 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ARG k 18 " --> pdb=" O LYS k 44 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET k 20 " --> pdb=" O THR k 42 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LYS k 40 " --> pdb=" O ILE k 22 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL k 24 " --> pdb=" O ILE k 38 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ILE k 38 " --> pdb=" O VAL k 24 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA k 83 " --> pdb=" O VAL k 63 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N CYS k 84 " --> pdb=" O MET k 7 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASN k 9 " --> pdb=" O CYS k 84 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU k 86 " --> pdb=" O ASN k 9 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'k' and resid 77 through 79 removed outlier: 4.172A pdb=" N ALA p 48 " --> pdb=" O THR p 59 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ARG p 61 " --> pdb=" O VAL p 46 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N VAL p 46 " --> pdb=" O ARG p 61 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N ILE p 63 " --> pdb=" O GLY p 44 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N GLY p 44 " --> pdb=" O ILE p 63 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER p 82 " --> pdb=" O LYS p 28 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'l' and resid 74 through 78 Processing sheet with id=AC4, first strand: chain 'l' and resid 89 through 90 Processing sheet with id=AC5, first strand: chain 'm' and resid 62 through 65 removed outlier: 5.884A pdb=" N VAL m 101 " --> pdb=" O ALA m 35 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ALA m 35 " --> pdb=" O VAL m 101 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR m 103 " --> pdb=" O LEU m 33 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'm' and resid 39 through 42 removed outlier: 5.599A pdb=" N VAL m 89 " --> pdb=" O GLU m 75 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLU m 75 " --> pdb=" O VAL m 89 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR m 91 " --> pdb=" O ILE m 73 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'n' and resid 33 through 37 Processing sheet with id=AC8, first strand: chain 'o' and resid 47 through 52 removed outlier: 6.652A pdb=" N VAL o 39 " --> pdb=" O LEU o 48 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ALA o 50 " --> pdb=" O ALA o 37 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ALA o 37 " --> pdb=" O ALA o 50 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N SER o 52 " --> pdb=" O ILE o 35 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE o 35 " --> pdb=" O SER o 52 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'r' and resid 11 through 14 removed outlier: 3.581A pdb=" N PHE r 5 " --> pdb=" O HIS r 12 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLN r 6 " --> pdb=" O VAL r 38 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL r 38 " --> pdb=" O GLN r 6 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'r' and resid 19 through 22 removed outlier: 6.800A pdb=" N PHE r 93 " --> pdb=" O HIS r 66 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N HIS r 66 " --> pdb=" O PHE r 93 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'r' and resid 74 through 78 removed outlier: 4.671A pdb=" N TYR r 83 " --> pdb=" O ARG r 78 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 's' and resid 4 through 10 removed outlier: 5.958A pdb=" N ILE s 4 " --> pdb=" O VAL s 107 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL s 107 " --> pdb=" O ILE s 4 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N LYS s 6 " --> pdb=" O VAL s 105 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL s 105 " --> pdb=" O LYS s 6 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ARG s 8 " --> pdb=" O ILE s 103 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE s 103 " --> pdb=" O ARG s 8 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASP s 94 " --> pdb=" O ARG s 84 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ARG s 84 " --> pdb=" O ASP s 94 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE s 96 " --> pdb=" O MET s 82 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N MET s 82 " --> pdb=" O ILE s 96 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LYS s 98 " --> pdb=" O PRO s 80 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N THR s 100 " --> pdb=" O GLU s 78 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N GLU s 78 " --> pdb=" O THR s 100 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N HIS s 102 " --> pdb=" O VAL s 76 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL s 76 " --> pdb=" O HIS s 102 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N THR s 104 " --> pdb=" O ILE s 74 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE s 74 " --> pdb=" O THR s 104 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL s 106 " --> pdb=" O THR s 72 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 't' and resid 11 through 14 removed outlier: 3.930A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LYS t 82 " --> pdb=" O THR t 60 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N THR t 60 " --> pdb=" O LYS t 82 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N TYR t 84 " --> pdb=" O VAL t 58 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL t 58 " --> pdb=" O TYR t 84 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N THR t 86 " --> pdb=" O GLU t 56 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 't' and resid 67 through 70 Processing sheet with id=AD6, first strand: chain 'u' and resid 64 through 65 removed outlier: 6.792A pdb=" N LYS u 32 " --> pdb=" O VAL u 27 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL u 27 " --> pdb=" O LYS u 32 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE u 34 " --> pdb=" O LYS u 25 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'u' and resid 40 through 44 Processing sheet with id=AD8, first strand: chain 'u' and resid 82 through 86 Processing sheet with id=AD9, first strand: chain 'v' and resid 3 through 8 removed outlier: 8.539A pdb=" N PHE v 91 " --> pdb=" O PRO v 27 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE v 29 " --> pdb=" O PHE v 91 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL v 92 " --> pdb=" O ALA v 74 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ALA v 74 " --> pdb=" O VAL v 92 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE v 4 " --> pdb=" O VAL v 64 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'w' and resid 18 through 19 removed outlier: 6.857A pdb=" N LEU w 55 " --> pdb=" O ILE w 33 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'w' and resid 61 through 68 Processing sheet with id=AE3, first strand: chain 'x' and resid 12 through 15 removed outlier: 3.593A pdb=" N VAL x 12 " --> pdb=" O PHE x 28 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'x' and resid 32 through 38 Processing sheet with id=AE5, first strand: chain 'z' and resid 34 through 38 removed outlier: 3.806A pdb=" N LYS z 5 " --> pdb=" O GLU z 57 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 27 through 29 Processing sheet with id=AE7, first strand: chain 'C' and resid 19 through 24 removed outlier: 3.779A pdb=" N THR C 22 " --> pdb=" O ILE C 8 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 14 through 15 Processing sheet with id=AE9, first strand: chain 'F' and resid 2 through 3 removed outlier: 6.690A pdb=" N LYS F 2 " --> pdb=" O ARG F 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'F' and resid 14 through 17 Processing sheet with id=AF2, first strand: chain 'G' and resid 67 through 69 removed outlier: 6.148A pdb=" N LEU G 67 " --> pdb=" O PHE G 161 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE G 163 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL G 69 " --> pdb=" O ILE G 163 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE G 197 " --> pdb=" O VAL G 182 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 19 through 20 Processing sheet with id=AF4, first strand: chain 'H' and resid 166 through 169 removed outlier: 3.811A pdb=" N GLY H 147 " --> pdb=" O PHE H 202 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASP H 180 " --> pdb=" O LYS H 203 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 127 through 128 Processing sheet with id=AF6, first strand: chain 'J' and resid 12 through 21 removed outlier: 5.145A pdb=" N GLU J 12 " --> pdb=" O GLY J 39 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLY J 39 " --> pdb=" O GLU J 12 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LEU J 14 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL J 37 " --> pdb=" O LEU J 14 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 84 through 85 Processing sheet with id=AF8, first strand: chain 'K' and resid 2 through 4 Processing sheet with id=AF9, first strand: chain 'K' and resid 43 through 45 removed outlier: 6.903A pdb=" N VAL K 7 " --> pdb=" O SER K 87 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N SER K 87 " --> pdb=" O VAL K 7 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 72 through 75 Processing sheet with id=AG2, first strand: chain 'M' and resid 73 through 76 removed outlier: 3.713A pdb=" N SER M 73 " --> pdb=" O ALA M 129 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M' and resid 73 through 76 removed outlier: 3.713A pdb=" N SER M 73 " --> pdb=" O ALA M 129 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL M 102 " --> pdb=" O ILE M 125 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N TYR M 127 " --> pdb=" O ILE M 100 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ILE M 100 " --> pdb=" O TYR M 127 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 5 through 7 removed outlier: 3.556A pdb=" N ALA N 15 " --> pdb=" O LYS N 67 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS N 67 " --> pdb=" O ALA N 15 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 45 through 46 removed outlier: 3.566A pdb=" N LYS O 11 " --> pdb=" O ASP O 97 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'O' and resid 49 through 52 Processing sheet with id=AG7, first strand: chain 'P' and resid 40 through 42 removed outlier: 7.089A pdb=" N GLY P 18 " --> pdb=" O GLU P 82 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N MET P 84 " --> pdb=" O GLY P 18 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ALA P 20 " --> pdb=" O MET P 84 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LYS P 86 " --> pdb=" O ALA P 20 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ILE P 22 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU P 81 " --> pdb=" O ILE P 106 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASN P 108 " --> pdb=" O LEU P 81 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Q' and resid 28 through 31 removed outlier: 4.619A pdb=" N TYR Q 94 " --> pdb=" O THR Q 63 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LYS Q 50 " --> pdb=" O ILE Q 66 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ARG Q 35 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'U' and resid 32 through 34 removed outlier: 7.409A pdb=" N PHE U 32 " --> pdb=" O ASP U 23 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ASP U 23 " --> pdb=" O PHE U 32 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU U 34 " --> pdb=" O VAL U 21 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL U 2 " --> pdb=" O THR U 66 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'U' and resid 9 through 11 Processing sheet with id=AH2, first strand: chain 'U' and resid 37 through 39 Processing sheet with id=AH3, first strand: chain 'V' and resid 10 through 13 removed outlier: 7.088A pdb=" N VAL V 21 " --> pdb=" O VAL V 12 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TRP V 72 " --> pdb=" O HIS V 44 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLU V 59 " --> pdb=" O VAL V 75 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N VAL V 77 " --> pdb=" O VAL V 57 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL V 57 " --> pdb=" O VAL V 77 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'X' and resid 49 through 51 Processing sheet with id=AH5, first strand: chain 'a' and resid 21 through 22 removed outlier: 6.004A pdb=" N TYR a 21 " --> pdb=" O ASP a 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'a' and resid 173 through 177 removed outlier: 4.293A pdb=" N ILE a 175 " --> pdb=" O VAL a 42 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL a 42 " --> pdb=" O ILE a 175 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP a 43 " --> pdb=" O SER a 215 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'a' and resid 46 through 47 removed outlier: 3.946A pdb=" N LYS a 211 " --> pdb=" O ASN a 47 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'a' and resid 60 through 64 removed outlier: 3.784A pdb=" N GLY a 61 " --> pdb=" O TYR a 163 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain '8' and resid 162 through 167 removed outlier: 3.573A pdb=" N LYS 8 162 " --> pdb=" O SER 8 184 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR 8 180 " --> pdb=" O ILE 8 166 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG 8 203 " --> pdb=" O HIS 8 214 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER 8 218 " --> pdb=" O HIS 8 199 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ARG 8 324 " --> pdb=" O VAL 8 198 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain '8' and resid 242 through 244 1717 hydrogen bonds defined for protein. 4812 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3267 hydrogen bonds 5366 hydrogen bond angles 0 basepair planarities 1324 basepair parallelities 2588 stacking parallelities Total time for adding SS restraints: 261.99 Time building geometry restraints manager: 63.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 29162 1.34 - 1.46: 62255 1.46 - 1.57: 59370 1.57 - 1.69: 9300 1.69 - 1.81: 274 Bond restraints: 160361 Sorted by residual: bond pdb=" CA VAL J 55 " pdb=" CB VAL J 55 " ideal model delta sigma weight residual 1.539 1.557 -0.018 5.40e-03 3.43e+04 1.07e+01 bond pdb=" CA VAL G 46 " pdb=" CB VAL G 46 " ideal model delta sigma weight residual 1.537 1.551 -0.014 5.00e-03 4.00e+04 8.26e+00 bond pdb=" N GLY H 1 " pdb=" CA GLY H 1 " ideal model delta sigma weight residual 1.451 1.488 -0.037 1.60e-02 3.91e+03 5.22e+00 bond pdb=" CA THR J 130 " pdb=" CB THR J 130 " ideal model delta sigma weight residual 1.523 1.549 -0.026 1.21e-02 6.83e+03 4.71e+00 bond pdb=" C3' C 2 88 " pdb=" O3' C 2 88 " ideal model delta sigma weight residual 1.417 1.449 -0.032 1.50e-02 4.44e+03 4.52e+00 ... (remaining 160356 not shown) Histogram of bond angle deviations from ideal: 95.25 - 103.00: 10282 103.00 - 110.75: 84034 110.75 - 118.49: 59272 118.49 - 126.24: 70773 126.24 - 133.98: 15205 Bond angle restraints: 239566 Sorted by residual: angle pdb=" N LEU P 99 " pdb=" CA LEU P 99 " pdb=" C LEU P 99 " ideal model delta sigma weight residual 113.41 102.07 11.34 1.22e+00 6.72e-01 8.64e+01 angle pdb=" N ARG Q 109 " pdb=" CA ARG Q 109 " pdb=" C ARG Q 109 " ideal model delta sigma weight residual 109.59 95.25 14.34 1.61e+00 3.86e-01 7.93e+01 angle pdb=" N ALA T 43 " pdb=" CA ALA T 43 " pdb=" C ALA T 43 " ideal model delta sigma weight residual 111.82 101.61 10.21 1.16e+00 7.43e-01 7.75e+01 angle pdb=" N GLN m 60 " pdb=" CA GLN m 60 " pdb=" C GLN m 60 " ideal model delta sigma weight residual 110.24 121.53 -11.29 1.30e+00 5.92e-01 7.54e+01 angle pdb=" N ARG Z 17 " pdb=" CA ARG Z 17 " pdb=" C ARG Z 17 " ideal model delta sigma weight residual 113.02 100.10 12.92 1.49e+00 4.50e-01 7.52e+01 ... (remaining 239561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 91742 35.90 - 71.80: 9705 71.80 - 107.70: 1197 107.70 - 143.61: 13 143.61 - 179.51: 17 Dihedral angle restraints: 102674 sinusoidal: 85248 harmonic: 17426 Sorted by residual: dihedral pdb=" O4' U 12580 " pdb=" C1' U 12580 " pdb=" N1 U 12580 " pdb=" C2 U 12580 " ideal model delta sinusoidal sigma weight residual 200.00 30.64 169.36 1 1.50e+01 4.44e-03 8.46e+01 dihedral pdb=" O4' U 12457 " pdb=" C1' U 12457 " pdb=" N1 U 12457 " pdb=" C2 U 12457 " ideal model delta sinusoidal sigma weight residual 200.00 31.31 168.69 1 1.50e+01 4.44e-03 8.45e+01 dihedral pdb=" O4' U 12552 " pdb=" C1' U 12552 " pdb=" N1 U 12552 " pdb=" C2 U 12552 " ideal model delta sinusoidal sigma weight residual 200.00 46.62 153.38 1 1.50e+01 4.44e-03 8.08e+01 ... (remaining 102671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 23521 0.094 - 0.188: 6506 0.188 - 0.282: 494 0.282 - 0.376: 35 0.376 - 0.471: 3 Chirality restraints: 30559 Sorted by residual: chirality pdb=" CA ASP r 55 " pdb=" N ASP r 55 " pdb=" C ASP r 55 " pdb=" CB ASP r 55 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.53e+00 chirality pdb=" C3' A 11020 " pdb=" C4' A 11020 " pdb=" O3' A 11020 " pdb=" C2' A 11020 " both_signs ideal model delta sigma weight residual False -2.74 -2.35 -0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CA ASN Z 8 " pdb=" N ASN Z 8 " pdb=" C ASN Z 8 " pdb=" CB ASN Z 8 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.75e+00 ... (remaining 30556 not shown) Planarity restraints: 13074 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 12061 " -0.087 2.00e-02 2.50e+03 3.65e-02 3.99e+01 pdb=" N9 G 12061 " 0.005 2.00e-02 2.50e+03 pdb=" C8 G 12061 " 0.040 2.00e-02 2.50e+03 pdb=" N7 G 12061 " 0.037 2.00e-02 2.50e+03 pdb=" C5 G 12061 " 0.016 2.00e-02 2.50e+03 pdb=" C6 G 12061 " -0.016 2.00e-02 2.50e+03 pdb=" O6 G 12061 " -0.057 2.00e-02 2.50e+03 pdb=" N1 G 12061 " -0.012 2.00e-02 2.50e+03 pdb=" C2 G 12061 " 0.010 2.00e-02 2.50e+03 pdb=" N2 G 12061 " 0.020 2.00e-02 2.50e+03 pdb=" N3 G 12061 " 0.021 2.00e-02 2.50e+03 pdb=" C4 G 12061 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 11328 " -0.080 2.00e-02 2.50e+03 3.47e-02 3.31e+01 pdb=" N9 A 11328 " 0.006 2.00e-02 2.50e+03 pdb=" C8 A 11328 " 0.033 2.00e-02 2.50e+03 pdb=" N7 A 11328 " 0.028 2.00e-02 2.50e+03 pdb=" C5 A 11328 " 0.013 2.00e-02 2.50e+03 pdb=" C6 A 11328 " -0.012 2.00e-02 2.50e+03 pdb=" N6 A 11328 " -0.054 2.00e-02 2.50e+03 pdb=" N1 A 11328 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A 11328 " 0.017 2.00e-02 2.50e+03 pdb=" N3 A 11328 " 0.028 2.00e-02 2.50e+03 pdb=" C4 A 11328 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 1 895 " -0.061 2.00e-02 2.50e+03 3.25e-02 2.38e+01 pdb=" N1 U 1 895 " 0.003 2.00e-02 2.50e+03 pdb=" C2 U 1 895 " 0.011 2.00e-02 2.50e+03 pdb=" O2 U 1 895 " 0.025 2.00e-02 2.50e+03 pdb=" N3 U 1 895 " 0.007 2.00e-02 2.50e+03 pdb=" C4 U 1 895 " 0.008 2.00e-02 2.50e+03 pdb=" O4 U 1 895 " -0.055 2.00e-02 2.50e+03 pdb=" C5 U 1 895 " 0.032 2.00e-02 2.50e+03 pdb=" C6 U 1 895 " 0.030 2.00e-02 2.50e+03 ... (remaining 13071 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 28361 2.78 - 3.31: 130349 3.31 - 3.84: 292589 3.84 - 4.37: 366249 4.37 - 4.90: 493753 Nonbonded interactions: 1311301 Sorted by model distance: nonbonded pdb=" OG SER N 72 " pdb=" OP1 U 31372 " model vdw 2.252 2.440 nonbonded pdb=" O ASN l 93 " pdb=" OG1 THR l 94 " model vdw 2.262 2.440 nonbonded pdb=" O GLY x 62 " pdb=" OG1 THR x 65 " model vdw 2.274 2.440 nonbonded pdb=" OG SER H 52 " pdb=" O HIS H 68 " model vdw 2.294 2.440 nonbonded pdb=" O GLU e 100 " pdb=" OG1 THR e 104 " model vdw 2.295 2.440 ... (remaining 1311296 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 0.090 Extract box with map and model: 12.510 Check model and map are aligned: 1.630 Set scattering table: 1.010 Process input model: 537.370 Find NCS groups from input model: 2.930 Set up NCS constraints: 0.370 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:2.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 559.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 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 : 0.006 0.072 160361 Z= 0.350 Angle : 0.924 14.336 239566 Z= 0.624 Chirality : 0.079 0.471 30559 Planarity : 0.006 0.069 13074 Dihedral : 22.085 179.508 91432 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 1.55 % Allowed : 12.41 % Favored : 86.04 % Rotamer: Outliers : 0.70 % Allowed : 5.47 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.77 (0.09), residues: 6011 helix: -3.40 (0.08), residues: 1740 sheet: -2.91 (0.14), residues: 1045 loop : -3.16 (0.09), residues: 3226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.006 TRP b 247 HIS 0.002 0.000 HIS J 88 PHE 0.025 0.004 PHE S 20 TYR 0.050 0.007 TYR T 68 ARG 0.005 0.001 ARG y 47 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1339 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1304 time to evaluate : 8.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 65 ASP cc_start: 0.9334 (t70) cc_final: 0.9040 (t0) REVERT: b 99 GLU cc_start: 0.6960 (mt-10) cc_final: 0.6650 (mt-10) REVERT: b 110 LYS cc_start: 0.9335 (tmmt) cc_final: 0.8947 (tmmt) REVERT: b 115 ILE cc_start: 0.9088 (pt) cc_final: 0.8599 (pt) REVERT: b 131 MET cc_start: 0.9329 (mmp) cc_final: 0.8963 (mmp) REVERT: b 145 MET cc_start: 0.8521 (ttm) cc_final: 0.8064 (mmm) REVERT: b 180 MET cc_start: 0.8755 (mmm) cc_final: 0.8451 (mmm) REVERT: b 184 GLU cc_start: 0.8164 (tp30) cc_final: 0.7821 (tp30) REVERT: b 186 ASP cc_start: 0.8570 (m-30) cc_final: 0.7996 (m-30) REVERT: b 202 ARG cc_start: 0.8741 (ttm170) cc_final: 0.8474 (ttm-80) REVERT: b 225 ASN cc_start: 0.8919 (OUTLIER) cc_final: 0.8622 (t0) REVERT: c 2 ILE cc_start: 0.8907 (tp) cc_final: 0.8401 (tp) REVERT: c 126 ASN cc_start: 0.8818 (m-40) cc_final: 0.8605 (m-40) REVERT: c 131 ASP cc_start: 0.7613 (t0) cc_final: 0.7140 (t0) REVERT: d 77 ILE cc_start: 0.9446 (pt) cc_final: 0.9245 (mm) REVERT: d 115 GLN cc_start: 0.9582 (tp-100) cc_final: 0.8655 (pt0) REVERT: d 138 LEU cc_start: 0.9562 (mt) cc_final: 0.9326 (pp) REVERT: e 37 MET cc_start: 0.8481 (mtp) cc_final: 0.8025 (ttm) REVERT: f 25 ILE cc_start: 0.8535 (mt) cc_final: 0.8266 (tp) REVERT: f 41 GLU cc_start: 0.9306 (tt0) cc_final: 0.8690 (tm-30) REVERT: f 57 TYR cc_start: 0.8012 (m-80) cc_final: 0.7414 (m-80) REVERT: f 61 TRP cc_start: 0.7500 (m100) cc_final: 0.7062 (m100) REVERT: f 100 ASN cc_start: 0.7447 (p0) cc_final: 0.6948 (p0) REVERT: f 142 GLN cc_start: 0.8595 (tt0) cc_final: 0.8216 (tp40) REVERT: g 1 MET cc_start: 0.8074 (ptp) cc_final: 0.7329 (pmm) REVERT: g 2 GLN cc_start: 0.8357 (mm-40) cc_final: 0.8113 (mm-40) REVERT: g 7 ASP cc_start: 0.9473 (t70) cc_final: 0.9175 (m-30) REVERT: g 28 ASN cc_start: 0.8956 (m-40) cc_final: 0.7152 (p0) REVERT: j 1 MET cc_start: 0.7748 (ptp) cc_final: 0.7097 (pmm) REVERT: j 14 ASP cc_start: 0.8713 (t70) cc_final: 0.7482 (t70) REVERT: j 36 LEU cc_start: 0.9729 (mt) cc_final: 0.9419 (mt) REVERT: j 75 TYR cc_start: 0.8595 (m-80) cc_final: 0.8286 (m-10) REVERT: j 96 ARG cc_start: 0.8520 (ttt180) cc_final: 0.8308 (ptm160) REVERT: j 102 GLU cc_start: 0.8665 (pt0) cc_final: 0.8435 (pt0) REVERT: j 103 ILE cc_start: 0.9701 (mt) cc_final: 0.9486 (mt) REVERT: j 108 MET cc_start: 0.9132 (mtm) cc_final: 0.8916 (mtm) REVERT: j 114 LEU cc_start: 0.9696 (tp) cc_final: 0.9243 (mt) REVERT: j 118 MET cc_start: 0.8760 (ptp) cc_final: 0.8293 (ptp) REVERT: k 7 MET cc_start: 0.9018 (mmm) cc_final: 0.8641 (mmm) REVERT: k 9 ASN cc_start: 0.8982 (m-40) cc_final: 0.8561 (m-40) REVERT: l 57 LEU cc_start: 0.9483 (tp) cc_final: 0.9078 (tp) REVERT: l 76 GLU cc_start: 0.8338 (pt0) cc_final: 0.7811 (mt-10) REVERT: m 90 GLU cc_start: 0.8262 (mm-30) cc_final: 0.8048 (tp30) REVERT: n 10 LEU cc_start: 0.9635 (mt) cc_final: 0.9416 (mp) REVERT: n 99 LYS cc_start: 0.9260 (mtmm) cc_final: 0.9043 (mttt) REVERT: o 20 GLU cc_start: 0.9466 (tt0) cc_final: 0.8859 (tm-30) REVERT: o 61 GLN cc_start: 0.8760 (tt0) cc_final: 0.8511 (pt0) REVERT: p 4 ILE cc_start: 0.9665 (OUTLIER) cc_final: 0.9413 (mp) REVERT: p 5 LYS cc_start: 0.9433 (mmmt) cc_final: 0.9172 (mmmt) REVERT: p 40 GLN cc_start: 0.8664 (tm-30) cc_final: 0.8133 (tm-30) REVERT: p 84 SER cc_start: 0.9235 (t) cc_final: 0.8606 (t) REVERT: p 98 TYR cc_start: 0.9027 (p90) cc_final: 0.8355 (p90) REVERT: q 16 ILE cc_start: 0.9853 (mm) cc_final: 0.9324 (mm) REVERT: q 23 TYR cc_start: 0.8848 (m-80) cc_final: 0.8556 (m-80) REVERT: q 39 ILE cc_start: 0.9795 (mt) cc_final: 0.9185 (mm) REVERT: q 48 ASP cc_start: 0.7481 (m-30) cc_final: 0.7041 (m-30) REVERT: q 51 GLN cc_start: 0.9275 (mm-40) cc_final: 0.8695 (mm110) REVERT: q 101 ASP cc_start: 0.8549 (t0) cc_final: 0.8076 (t0) REVERT: r 32 THR cc_start: 0.9078 (t) cc_final: 0.8730 (t) REVERT: r 34 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7464 (mm-30) REVERT: r 45 GLU cc_start: 0.9128 (tp30) cc_final: 0.8539 (tm-30) REVERT: r 78 ARG cc_start: 0.9094 (tpp80) cc_final: 0.8660 (mmt90) REVERT: r 86 GLN cc_start: 0.8913 (mm110) cc_final: 0.8608 (mm110) REVERT: r 95 ASP cc_start: 0.9082 (m-30) cc_final: 0.8666 (m-30) REVERT: s 2 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8860 (mm-30) REVERT: s 69 LEU cc_start: 0.9276 (tp) cc_final: 0.8812 (mt) REVERT: s 86 MET cc_start: 0.8894 (tpt) cc_final: 0.8057 (tpt) REVERT: s 88 ARG cc_start: 0.8659 (mmt180) cc_final: 0.8393 (mmm-85) REVERT: t 18 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8659 (tp30) REVERT: t 43 ILE cc_start: 0.9634 (mt) cc_final: 0.9388 (mt) REVERT: u 7 ASP cc_start: 0.9166 (m-30) cc_final: 0.8304 (t0) REVERT: u 13 LEU cc_start: 0.9509 (mt) cc_final: 0.9249 (mt) REVERT: u 45 GLN cc_start: 0.9382 (tp-100) cc_final: 0.9124 (tp-100) REVERT: v 75 GLN cc_start: 0.8306 (tp40) cc_final: 0.7614 (tm-30) REVERT: v 76 ASP cc_start: 0.8383 (m-30) cc_final: 0.7216 (m-30) REVERT: w 11 ASP cc_start: 0.7914 (t70) cc_final: 0.7520 (t70) REVERT: w 51 ARG cc_start: 0.8160 (ptm-80) cc_final: 0.7465 (ptm160) REVERT: w 54 THR cc_start: 0.9590 (m) cc_final: 0.9325 (p) REVERT: w 79 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8343 (mp0) REVERT: x 24 THR cc_start: 0.9341 (t) cc_final: 0.8985 (p) REVERT: x 25 LYS cc_start: 0.8837 (mmmm) cc_final: 0.8458 (mmmm) REVERT: x 35 HIS cc_start: 0.8217 (t-90) cc_final: 0.8006 (t-90) REVERT: x 50 VAL cc_start: 0.9416 (m) cc_final: 0.8959 (p) REVERT: x 59 ASP cc_start: 0.9139 (m-30) cc_final: 0.8827 (p0) REVERT: x 64 ASP cc_start: 0.9543 (m-30) cc_final: 0.9266 (m-30) REVERT: x 70 LEU cc_start: 0.9526 (mt) cc_final: 0.9247 (mt) REVERT: y 1 MET cc_start: 0.8956 (mmt) cc_final: 0.8665 (mmm) REVERT: y 4 LYS cc_start: 0.9426 (mttm) cc_final: 0.9157 (mmtm) REVERT: y 17 GLU cc_start: 0.9510 (tm-30) cc_final: 0.9163 (tm-30) REVERT: y 26 PHE cc_start: 0.9196 (t80) cc_final: 0.8919 (t80) REVERT: y 36 GLN cc_start: 0.9204 (mt0) cc_final: 0.8764 (pt0) REVERT: y 45 GLN cc_start: 0.8896 (pt0) cc_final: 0.8572 (pm20) REVERT: y 49 ASP cc_start: 0.8833 (m-30) cc_final: 0.8520 (m-30) REVERT: z 20 LYS cc_start: 0.9538 (mttt) cc_final: 0.9310 (mmtt) REVERT: B 6 LYS cc_start: 0.9040 (ttpp) cc_final: 0.8831 (ttmt) REVERT: B 14 MET cc_start: 0.8623 (mtm) cc_final: 0.8161 (mmm) REVERT: B 47 TYR cc_start: 0.8942 (m-80) cc_final: 0.8329 (m-10) REVERT: C 6 GLU cc_start: 0.7713 (pm20) cc_final: 0.7289 (pm20) REVERT: C 9 LYS cc_start: 0.9144 (tttt) cc_final: 0.8396 (tttp) REVERT: C 29 LYS cc_start: 0.8909 (mmmt) cc_final: 0.8644 (mmtp) REVERT: C 31 GLU cc_start: 0.8723 (pm20) cc_final: 0.8443 (pm20) REVERT: C 32 LYS cc_start: 0.8192 (ptmm) cc_final: 0.7977 (ptmt) REVERT: C 34 GLU cc_start: 0.7822 (mp0) cc_final: 0.7550 (mp0) REVERT: F 13 ASN cc_start: 0.9387 (m-40) cc_final: 0.8753 (p0) REVERT: F 36 ARG cc_start: 0.8087 (ptm-80) cc_final: 0.7492 (ptm-80) REVERT: G 7 ASP cc_start: 0.9005 (m-30) cc_final: 0.8686 (p0) REVERT: G 26 MET cc_start: 0.7979 (mmp) cc_final: 0.7646 (mmp) REVERT: G 27 LYS cc_start: 0.8940 (mmtp) cc_final: 0.8581 (mmmt) REVERT: G 153 MET cc_start: 0.8070 (mmm) cc_final: 0.7752 (mmm) REVERT: G 167 HIS cc_start: 0.7389 (t70) cc_final: 0.6908 (t-90) REVERT: H 28 PHE cc_start: 0.8882 (t80) cc_final: 0.8493 (t80) REVERT: H 68 HIS cc_start: 0.8987 (m90) cc_final: 0.8522 (m90) REVERT: H 166 TRP cc_start: 0.8982 (p-90) cc_final: 0.8495 (p-90) REVERT: I 50 TYR cc_start: 0.9135 (t80) cc_final: 0.8824 (t80) REVERT: I 64 TYR cc_start: 0.9251 (m-80) cc_final: 0.8730 (m-80) REVERT: I 74 TYR cc_start: 0.9529 (m-80) cc_final: 0.8693 (m-80) REVERT: I 104 MET cc_start: 0.8683 (mmt) cc_final: 0.7991 (mmm) REVERT: I 123 MET cc_start: 0.9264 (ttm) cc_final: 0.8781 (tmm) REVERT: I 134 TYR cc_start: 0.9208 (t80) cc_final: 0.8918 (t80) REVERT: J 22 LYS cc_start: 0.9264 (tttm) cc_final: 0.8809 (tptm) REVERT: J 28 ARG cc_start: 0.8601 (mtm-85) cc_final: 0.8107 (mtm110) REVERT: J 70 MET cc_start: 0.8485 (ttp) cc_final: 0.8280 (tpt) REVERT: J 110 MET cc_start: 0.9152 (ttm) cc_final: 0.8317 (tpp) REVERT: J 114 LEU cc_start: 0.9730 (mt) cc_final: 0.8711 (mt) REVERT: J 125 LYS cc_start: 0.9335 (tptm) cc_final: 0.8684 (tptp) REVERT: J 137 ARG cc_start: 0.8907 (mtp85) cc_final: 0.8434 (mtp85) REVERT: K 17 GLN cc_start: 0.8870 (pt0) cc_final: 0.8468 (pm20) REVERT: K 21 MET cc_start: 0.8496 (mtt) cc_final: 0.8074 (mtp) REVERT: K 22 ILE cc_start: 0.8752 (mt) cc_final: 0.8475 (mt) REVERT: K 25 TYR cc_start: 0.8967 (m-80) cc_final: 0.8663 (m-80) REVERT: K 56 LYS cc_start: 0.9478 (mptt) cc_final: 0.8947 (mmmt) REVERT: K 93 LYS cc_start: 0.9076 (mmtp) cc_final: 0.8763 (tttm) REVERT: K 94 HIS cc_start: 0.7262 (OUTLIER) cc_final: 0.6871 (p-80) REVERT: L 84 TYR cc_start: 0.4157 (OUTLIER) cc_final: 0.3721 (p90) REVERT: L 100 MET cc_start: 0.8151 (mtm) cc_final: 0.7314 (mtm) REVERT: L 143 MET cc_start: 0.9478 (mmm) cc_final: 0.9155 (mmm) REVERT: L 147 ASN cc_start: 0.7471 (t0) cc_final: 0.7031 (t0) REVERT: M 9 MET cc_start: 0.9288 (ttt) cc_final: 0.9049 (tmm) REVERT: M 13 ILE cc_start: 0.9727 (mt) cc_final: 0.9482 (mt) REVERT: M 26 MET cc_start: 0.9281 (ptp) cc_final: 0.8612 (ptm) REVERT: M 45 ILE cc_start: 0.8653 (pt) cc_final: 0.8399 (tp) REVERT: M 58 LEU cc_start: 0.9293 (tp) cc_final: 0.8722 (tp) REVERT: M 84 ILE cc_start: 0.9663 (mt) cc_final: 0.9091 (mt) REVERT: M 124 ILE cc_start: 0.8786 (mt) cc_final: 0.8288 (mt) REVERT: N 55 ASP cc_start: 0.9266 (m-30) cc_final: 0.8881 (t70) REVERT: N 87 MET cc_start: 0.8876 (ptm) cc_final: 0.8654 (ppp) REVERT: N 96 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8215 (tm-30) REVERT: N 128 LYS cc_start: 0.9113 (tppp) cc_final: 0.8845 (ttpp) REVERT: O 40 ILE cc_start: 0.6021 (mt) cc_final: 0.5790 (mt) REVERT: O 42 LEU cc_start: 0.7618 (mt) cc_final: 0.7165 (mt) REVERT: O 49 PHE cc_start: 0.8457 (m-80) cc_final: 0.8172 (m-80) REVERT: O 66 GLU cc_start: 0.8634 (pt0) cc_final: 0.8291 (pt0) REVERT: O 73 LEU cc_start: 0.7945 (mt) cc_final: 0.7682 (mt) REVERT: O 76 ILE cc_start: 0.6207 (OUTLIER) cc_final: 0.5898 (mm) REVERT: P 54 SER cc_start: 0.7659 (OUTLIER) cc_final: 0.7101 (p) REVERT: P 97 ARG cc_start: 0.9030 (mtp85) cc_final: 0.8414 (mtp85) REVERT: P 105 ARG cc_start: 0.8397 (ttt-90) cc_final: 0.8052 (tpt170) REVERT: Q 69 GLU cc_start: 0.8661 (pt0) cc_final: 0.8178 (pm20) REVERT: Q 80 LEU cc_start: 0.9478 (tp) cc_final: 0.9242 (mm) REVERT: R 10 ASP cc_start: 0.8975 (m-30) cc_final: 0.8717 (m-30) REVERT: R 65 GLU cc_start: 0.9295 (tt0) cc_final: 0.9002 (pp20) REVERT: R 71 GLU cc_start: 0.9218 (tm-30) cc_final: 0.9005 (tm-30) REVERT: R 99 GLN cc_start: 0.6858 (mt0) cc_final: 0.5780 (mp10) REVERT: S 73 LEU cc_start: 0.9561 (tt) cc_final: 0.9240 (mt) REVERT: S 78 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6548 (pp) REVERT: T 10 ILE cc_start: 0.9108 (mt) cc_final: 0.8860 (mm) REVERT: T 13 GLU cc_start: 0.9287 (tt0) cc_final: 0.8892 (mt-10) REVERT: T 24 THR cc_start: 0.9008 (p) cc_final: 0.8742 (p) REVERT: T 25 GLU cc_start: 0.8788 (pt0) cc_final: 0.8077 (mp0) REVERT: T 35 ILE cc_start: 0.9503 (mt) cc_final: 0.9255 (mt) REVERT: T 58 MET cc_start: 0.8878 (ptp) cc_final: 0.8591 (ptm) REVERT: U 6 LEU cc_start: 0.8943 (mt) cc_final: 0.8643 (mt) REVERT: U 14 ARG cc_start: 0.8869 (mmm-85) cc_final: 0.8303 (mmm160) REVERT: U 25 ARG cc_start: 0.9082 (mtm180) cc_final: 0.8587 (mtm180) REVERT: U 45 GLU cc_start: 0.8081 (pp20) cc_final: 0.7840 (pm20) REVERT: U 66 THR cc_start: 0.8412 (p) cc_final: 0.8192 (p) REVERT: U 77 GLU cc_start: 0.9536 (tp30) cc_final: 0.9197 (mm-30) REVERT: V 51 GLU cc_start: 0.7926 (pt0) cc_final: 0.6762 (pt0) REVERT: W 67 LEU cc_start: 0.9377 (mt) cc_final: 0.9167 (mp) REVERT: Y 12 GLN cc_start: 0.9202 (tt0) cc_final: 0.8905 (tt0) REVERT: Y 23 ARG cc_start: 0.9172 (mmm-85) cc_final: 0.8926 (mpt180) REVERT: Y 28 ARG cc_start: 0.9276 (mmt90) cc_final: 0.8919 (ttm110) REVERT: Y 31 ILE cc_start: 0.9604 (mt) cc_final: 0.9202 (mm) REVERT: Y 47 GLN cc_start: 0.9519 (tt0) cc_final: 0.8920 (tp-100) REVERT: Y 52 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8628 (mt-10) REVERT: Y 53 MET cc_start: 0.8746 (tmm) cc_final: 0.8475 (tmm) REVERT: Y 58 ASP cc_start: 0.9265 (m-30) cc_final: 0.8621 (p0) REVERT: Z 37 TYR cc_start: 0.8217 (t80) cc_final: 0.7928 (t80) REVERT: 8 73 MET cc_start: 0.3940 (tmm) cc_final: 0.3635 (tmm) REVERT: 8 186 ASP cc_start: 0.9308 (p0) cc_final: 0.8963 (t0) REVERT: 8 207 PHE cc_start: 0.8078 (m-80) cc_final: 0.7799 (m-80) REVERT: 8 288 MET cc_start: 0.9335 (tpp) cc_final: 0.9093 (tpp) outliers start: 35 outliers final: 13 residues processed: 1329 average time/residue: 1.4168 time to fit residues: 3246.7026 Evaluate side-chains 925 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 905 time to evaluate : 6.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 225 ASN Chi-restraints excluded: chain d residue 184 ASP Chi-restraints excluded: chain f residue 102 ILE Chi-restraints excluded: chain g residue 127 GLU Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 83 ILE Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 94 HIS Chi-restraints excluded: chain L residue 84 TYR Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain R residue 85 TYR Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain a residue 22 ASP Chi-restraints excluded: chain 8 residue 4 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1053 random chunks: chunk 889 optimal weight: 20.0000 chunk 798 optimal weight: 20.0000 chunk 442 optimal weight: 30.0000 chunk 272 optimal weight: 8.9990 chunk 538 optimal weight: 50.0000 chunk 426 optimal weight: 6.9990 chunk 825 optimal weight: 10.0000 chunk 319 optimal weight: 30.0000 chunk 501 optimal weight: 9.9990 chunk 614 optimal weight: 20.0000 chunk 956 optimal weight: 10.0000 overall best weight: 9.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 85 ASN b 89 ASN ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 196 ASN b 238 ASN c 32 ASN d 30 GLN d 62 GLN d 97 ASN e 4 HIS e 51 ASN e 80 GLN e 134 GLN ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 44 HIS g 18 GLN g 20 ASN j 40 HIS j 128 ASN k 5 GLN k 90 ASN l 54 GLN n 62 ASN n 81 ASN o 98 GLN p 65 ASN q 36 GLN ** q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 70 GLN ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 18 GLN s 15 GLN t 15 HIS u 68 ASN v 49 ASN v 87 GLN w 42 HIS w 53 HIS x 31 ASN y 15 ASN y 20 ASN y 36 GLN y 41 HIS y 45 GLN C 25 ASN F 35 GLN G 18 GLN G 50 ASN G 57 ASN G 108 GLN G 119 GLN H 184 ASN I 53 GLN I 88 ASN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 125 ASN I 139 ASN I 151 GLN I 195 ASN ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 121 ASN ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 ASN N 4 GLN N 74 GLN ** N 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 HIS O 70 HIS P 21 HIS P 118 ASN ** Q 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 13 HIS T 36 ASN T 49 HIS ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 ASN W 30 ASN Y 19 HIS Y 20 ASN Y 69 ASN ** Y 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 38 ASN 8 43 GLN 8 97 ASN 8 301 GLN 8 304 ASN 8 308 GLN ** 8 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 344 ASN Total number of N/Q/H flips: 77 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.148 160361 Z= 0.331 Angle : 0.726 10.733 239566 Z= 0.371 Chirality : 0.039 0.258 30559 Planarity : 0.006 0.067 13074 Dihedral : 22.930 174.512 79441 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.37 % Favored : 90.45 % Rotamer: Outliers : 3.38 % Allowed : 13.74 % Favored : 82.88 % 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: -3.49 (0.10), residues: 6011 helix: -1.63 (0.10), residues: 1895 sheet: -2.44 (0.14), residues: 1007 loop : -2.74 (0.10), residues: 3109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 103 HIS 0.013 0.002 HIS 8 265 PHE 0.034 0.003 PHE Z 18 TYR 0.038 0.002 TYR g 25 ARG 0.017 0.001 ARG y 7 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1185 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1016 time to evaluate : 6.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 110 LYS cc_start: 0.9285 (tmmt) cc_final: 0.8924 (tmmt) REVERT: b 131 MET cc_start: 0.9395 (mmp) cc_final: 0.9029 (mmp) REVERT: b 145 MET cc_start: 0.8448 (ttm) cc_final: 0.8111 (mmm) REVERT: b 184 GLU cc_start: 0.8148 (tp30) cc_final: 0.7880 (tp30) REVERT: b 202 ARG cc_start: 0.8809 (ttm170) cc_final: 0.8540 (tpp-160) REVERT: c 131 ASP cc_start: 0.7602 (t0) cc_final: 0.7258 (t0) REVERT: d 9 GLN cc_start: 0.8956 (mm-40) cc_final: 0.8543 (mm110) REVERT: d 136 GLN cc_start: 0.9458 (pt0) cc_final: 0.9207 (mm-40) REVERT: f 41 GLU cc_start: 0.9273 (tt0) cc_final: 0.8530 (tm-30) REVERT: f 57 TYR cc_start: 0.7958 (m-80) cc_final: 0.7480 (m-80) REVERT: f 61 TRP cc_start: 0.7648 (m100) cc_final: 0.7111 (m100) REVERT: f 82 PHE cc_start: 0.7296 (m-80) cc_final: 0.6968 (m-80) REVERT: f 100 ASN cc_start: 0.7566 (p0) cc_final: 0.6911 (p0) REVERT: f 115 GLN cc_start: 0.8934 (mm-40) cc_final: 0.8674 (tm-30) REVERT: f 123 GLU cc_start: 0.8763 (tp30) cc_final: 0.8154 (tp30) REVERT: f 142 GLN cc_start: 0.8629 (tt0) cc_final: 0.8358 (tp40) REVERT: g 2 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7985 (mm-40) REVERT: g 7 ASP cc_start: 0.9472 (t70) cc_final: 0.9219 (m-30) REVERT: g 28 ASN cc_start: 0.8986 (m-40) cc_final: 0.7530 (p0) REVERT: j 36 LEU cc_start: 0.9701 (mt) cc_final: 0.9468 (mt) REVERT: j 49 ASP cc_start: 0.8153 (t0) cc_final: 0.6878 (t0) REVERT: j 75 TYR cc_start: 0.8627 (m-80) cc_final: 0.8318 (m-10) REVERT: j 102 GLU cc_start: 0.8827 (pt0) cc_final: 0.8261 (pt0) REVERT: j 114 LEU cc_start: 0.9646 (tp) cc_final: 0.9236 (mt) REVERT: j 118 MET cc_start: 0.8585 (ptp) cc_final: 0.8236 (ptp) REVERT: k 73 ASP cc_start: 0.8746 (p0) cc_final: 0.8281 (p0) REVERT: k 90 ASN cc_start: 0.9275 (m-40) cc_final: 0.8969 (m110) REVERT: l 86 GLU cc_start: 0.8034 (pm20) cc_final: 0.7767 (pm20) REVERT: m 41 LEU cc_start: 0.9564 (mm) cc_final: 0.9301 (mm) REVERT: m 136 MET cc_start: 0.7680 (mtm) cc_final: 0.5724 (mmm) REVERT: n 99 LYS cc_start: 0.9378 (mtmm) cc_final: 0.9134 (mttt) REVERT: n 114 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7538 (pp20) REVERT: o 20 GLU cc_start: 0.9424 (tt0) cc_final: 0.8945 (tm-30) REVERT: o 56 LYS cc_start: 0.8952 (mmtt) cc_final: 0.8745 (mmtt) REVERT: o 61 GLN cc_start: 0.8733 (tt0) cc_final: 0.8525 (pt0) REVERT: p 4 ILE cc_start: 0.9593 (mp) cc_final: 0.9272 (tp) REVERT: p 10 GLU cc_start: 0.9254 (pt0) cc_final: 0.8531 (pm20) REVERT: p 67 GLU cc_start: 0.8110 (pm20) cc_final: 0.7842 (pm20) REVERT: p 84 SER cc_start: 0.9017 (t) cc_final: 0.8496 (p) REVERT: p 98 TYR cc_start: 0.8993 (p90) cc_final: 0.8656 (p90) REVERT: q 48 ASP cc_start: 0.7472 (m-30) cc_final: 0.7115 (m-30) REVERT: q 51 GLN cc_start: 0.9167 (mm-40) cc_final: 0.8595 (mm-40) REVERT: q 101 ASP cc_start: 0.8559 (t0) cc_final: 0.8268 (t0) REVERT: r 78 ARG cc_start: 0.9341 (tpp80) cc_final: 0.8869 (mmt90) REVERT: r 86 GLN cc_start: 0.8868 (mm110) cc_final: 0.8574 (mm110) REVERT: r 95 ASP cc_start: 0.9222 (m-30) cc_final: 0.8727 (m-30) REVERT: s 2 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8821 (mm-30) REVERT: s 19 LEU cc_start: 0.9644 (mt) cc_final: 0.9409 (mt) REVERT: s 40 ASN cc_start: 0.9233 (p0) cc_final: 0.8967 (p0) REVERT: s 69 LEU cc_start: 0.9215 (tp) cc_final: 0.8586 (mt) REVERT: t 7 LEU cc_start: 0.9505 (mt) cc_final: 0.9122 (pp) REVERT: u 13 LEU cc_start: 0.9596 (mt) cc_final: 0.9317 (mt) REVERT: u 38 ILE cc_start: 0.9270 (mm) cc_final: 0.9034 (mm) REVERT: u 39 ASN cc_start: 0.9484 (m-40) cc_final: 0.9172 (t0) REVERT: v 75 GLN cc_start: 0.8507 (tp40) cc_final: 0.7701 (tm-30) REVERT: v 76 ASP cc_start: 0.8482 (m-30) cc_final: 0.7193 (m-30) REVERT: w 62 LYS cc_start: 0.9308 (mtpp) cc_final: 0.8977 (mtpp) REVERT: w 79 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8499 (mt-10) REVERT: x 24 THR cc_start: 0.9496 (t) cc_final: 0.9237 (p) REVERT: x 25 LYS cc_start: 0.9107 (mmmm) cc_final: 0.8749 (mmmm) REVERT: x 59 ASP cc_start: 0.9189 (m-30) cc_final: 0.8765 (p0) REVERT: x 61 LYS cc_start: 0.8959 (ttmt) cc_final: 0.8689 (ttmm) REVERT: y 17 GLU cc_start: 0.9514 (tm-30) cc_final: 0.9187 (tm-30) REVERT: y 26 PHE cc_start: 0.9148 (t80) cc_final: 0.8866 (t80) REVERT: y 49 ASP cc_start: 0.9020 (m-30) cc_final: 0.8648 (m-30) REVERT: z 20 LYS cc_start: 0.9603 (mttt) cc_final: 0.9376 (mmtt) REVERT: z 36 GLU cc_start: 0.8774 (tt0) cc_final: 0.8226 (pm20) REVERT: B 47 TYR cc_start: 0.8827 (m-80) cc_final: 0.8576 (m-10) REVERT: C 6 GLU cc_start: 0.7442 (pm20) cc_final: 0.7112 (pm20) REVERT: C 9 LYS cc_start: 0.9114 (tttt) cc_final: 0.8802 (tttm) REVERT: C 24 LYS cc_start: 0.8731 (ptmt) cc_final: 0.8421 (tttp) REVERT: C 29 LYS cc_start: 0.8927 (mmmt) cc_final: 0.8718 (mmtp) REVERT: C 31 GLU cc_start: 0.8697 (pm20) cc_final: 0.8390 (pm20) REVERT: C 49 LYS cc_start: 0.8833 (mmmt) cc_final: 0.8616 (mmmm) REVERT: F 13 ASN cc_start: 0.9415 (m-40) cc_final: 0.8814 (p0) REVERT: F 14 CYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8180 (m) REVERT: F 36 ARG cc_start: 0.8164 (ptm-80) cc_final: 0.7622 (ptm-80) REVERT: G 8 MET cc_start: 0.6462 (mtm) cc_final: 0.6131 (mmm) REVERT: G 21 TYR cc_start: 0.9093 (m-80) cc_final: 0.8856 (m-80) REVERT: G 27 LYS cc_start: 0.8906 (mmtp) cc_final: 0.8644 (mmtp) REVERT: G 167 HIS cc_start: 0.7254 (t70) cc_final: 0.6778 (t-90) REVERT: H 28 PHE cc_start: 0.8681 (t80) cc_final: 0.8249 (t80) REVERT: H 166 TRP cc_start: 0.9138 (p-90) cc_final: 0.8321 (p-90) REVERT: I 43 ARG cc_start: 0.5486 (mtt180) cc_final: 0.5116 (mmt180) REVERT: I 74 TYR cc_start: 0.9509 (m-80) cc_final: 0.8808 (m-80) REVERT: I 134 TYR cc_start: 0.9163 (t80) cc_final: 0.8918 (t80) REVERT: J 28 ARG cc_start: 0.8607 (mtm-85) cc_final: 0.8113 (mtm110) REVERT: J 53 ARG cc_start: 0.8760 (mmm160) cc_final: 0.8428 (mmm160) REVERT: J 65 LYS cc_start: 0.9542 (mmmt) cc_final: 0.9316 (mmmm) REVERT: J 70 MET cc_start: 0.8381 (ttp) cc_final: 0.8088 (tpp) REVERT: J 92 ARG cc_start: 0.8185 (mtm180) cc_final: 0.7843 (mtm180) REVERT: J 125 LYS cc_start: 0.9408 (tptm) cc_final: 0.9060 (tptp) REVERT: J 137 ARG cc_start: 0.8906 (mtp85) cc_final: 0.8213 (mtp85) REVERT: J 144 GLU cc_start: 0.9082 (tp30) cc_final: 0.8683 (tp30) REVERT: K 22 ILE cc_start: 0.8496 (mt) cc_final: 0.8219 (mt) REVERT: K 25 TYR cc_start: 0.8893 (m-10) cc_final: 0.8563 (m-80) REVERT: K 39 LEU cc_start: 0.8909 (mt) cc_final: 0.8675 (mp) REVERT: K 56 LYS cc_start: 0.9170 (mptt) cc_final: 0.8582 (mmmt) REVERT: M 66 GLN cc_start: 0.8770 (mm-40) cc_final: 0.8468 (mp10) REVERT: M 72 GLU cc_start: 0.9219 (tp30) cc_final: 0.8975 (mm-30) REVERT: M 124 ILE cc_start: 0.8856 (mt) cc_final: 0.8509 (mm) REVERT: N 45 MET cc_start: 0.9151 (ppp) cc_final: 0.8864 (ptp) REVERT: N 55 ASP cc_start: 0.9190 (m-30) cc_final: 0.8788 (t70) REVERT: N 56 MET cc_start: 0.6706 (tmm) cc_final: 0.6340 (tmm) REVERT: N 87 MET cc_start: 0.8961 (ptm) cc_final: 0.8759 (ppp) REVERT: N 128 LYS cc_start: 0.9169 (tppp) cc_final: 0.8563 (tptt) REVERT: O 42 LEU cc_start: 0.7500 (mt) cc_final: 0.7143 (mt) REVERT: O 49 PHE cc_start: 0.8396 (m-80) cc_final: 0.8088 (m-80) REVERT: O 66 GLU cc_start: 0.8962 (pt0) cc_final: 0.8456 (pt0) REVERT: P 54 SER cc_start: 0.7368 (OUTLIER) cc_final: 0.7071 (p) REVERT: P 71 ASP cc_start: 0.9374 (t0) cc_final: 0.9155 (m-30) REVERT: P 105 ARG cc_start: 0.8479 (ttt-90) cc_final: 0.8034 (tpt170) REVERT: P 106 ILE cc_start: 0.5568 (mm) cc_final: 0.4844 (mp) REVERT: Q 69 GLU cc_start: 0.8653 (pt0) cc_final: 0.8165 (pm20) REVERT: R 10 ASP cc_start: 0.8959 (m-30) cc_final: 0.8723 (m-30) REVERT: T 9 LYS cc_start: 0.9500 (ttpt) cc_final: 0.9260 (ttpp) REVERT: T 10 ILE cc_start: 0.9225 (mt) cc_final: 0.8926 (mm) REVERT: T 13 GLU cc_start: 0.9179 (tt0) cc_final: 0.8798 (mt-10) REVERT: T 24 THR cc_start: 0.8871 (p) cc_final: 0.8555 (p) REVERT: T 25 GLU cc_start: 0.8866 (pt0) cc_final: 0.8253 (mp0) REVERT: T 44 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7813 (pt0) REVERT: T 77 TYR cc_start: 0.9179 (t80) cc_final: 0.8864 (t80) REVERT: U 25 ARG cc_start: 0.9068 (mtm180) cc_final: 0.8531 (mtm180) REVERT: U 46 LYS cc_start: 0.8848 (pttm) cc_final: 0.8230 (tttt) REVERT: U 51 ARG cc_start: 0.7424 (mtp180) cc_final: 0.7022 (mtt90) REVERT: U 66 THR cc_start: 0.8692 (p) cc_final: 0.6262 (p) REVERT: U 74 LEU cc_start: 0.9421 (mt) cc_final: 0.8662 (mp) REVERT: W 28 LEU cc_start: 0.8953 (pp) cc_final: 0.8471 (mp) REVERT: Y 12 GLN cc_start: 0.9161 (tt0) cc_final: 0.8769 (tt0) REVERT: Y 47 GLN cc_start: 0.9460 (tt0) cc_final: 0.9002 (tp-100) REVERT: Y 53 MET cc_start: 0.8812 (tmm) cc_final: 0.8554 (tmm) REVERT: Y 58 ASP cc_start: 0.9195 (m-30) cc_final: 0.8339 (p0) REVERT: Z 37 TYR cc_start: 0.8236 (t80) cc_final: 0.7951 (t80) REVERT: Z 38 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6954 (mm-30) REVERT: 8 186 ASP cc_start: 0.9307 (p0) cc_final: 0.8968 (t0) REVERT: 8 207 PHE cc_start: 0.8219 (m-80) cc_final: 0.8000 (m-80) REVERT: 8 217 PHE cc_start: 0.8645 (m-80) cc_final: 0.8381 (m-10) REVERT: 8 265 HIS cc_start: 0.8873 (t-90) cc_final: 0.8599 (t-170) REVERT: 8 288 MET cc_start: 0.9356 (tpp) cc_final: 0.8937 (tpt) REVERT: 8 300 MET cc_start: 0.8981 (mtm) cc_final: 0.8759 (ptp) outliers start: 169 outliers final: 89 residues processed: 1101 average time/residue: 1.2737 time to fit residues: 2431.8193 Evaluate side-chains 932 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 839 time to evaluate : 6.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 66 PHE Chi-restraints excluded: chain b residue 80 LEU Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 263 ASP Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 95 SER Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 184 ASP Chi-restraints excluded: chain f residue 51 PHE Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain j residue 47 HIS Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain k residue 17 ARG Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 102 LEU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 114 GLU Chi-restraints excluded: chain p residue 6 GLN Chi-restraints excluded: chain p residue 30 TRP Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 82 SER Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain t residue 42 GLU Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain u residue 65 GLN Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 78 GLN Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain z residue 18 LYS Chi-restraints excluded: chain z residue 43 ILE Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain F residue 14 CYS Chi-restraints excluded: chain G residue 38 HIS Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 192 TYR Chi-restraints excluded: chain I residue 173 ASP Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain N residue 5 TYR Chi-restraints excluded: chain N residue 30 ASN Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 69 CYS Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain R residue 85 TYR Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain S residue 17 ASP Chi-restraints excluded: chain T residue 44 GLU Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 60 ILE Chi-restraints excluded: chain X residue 55 GLN Chi-restraints excluded: chain Y residue 65 LEU Chi-restraints excluded: chain Z residue 55 HIS Chi-restraints excluded: chain a residue 22 ASP Chi-restraints excluded: chain 8 residue 266 ILE Chi-restraints excluded: chain 8 residue 281 HIS Chi-restraints excluded: chain 8 residue 285 ASP Chi-restraints excluded: chain 8 residue 316 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1053 random chunks: chunk 531 optimal weight: 30.0000 chunk 296 optimal weight: 40.0000 chunk 795 optimal weight: 30.0000 chunk 651 optimal weight: 40.0000 chunk 263 optimal weight: 20.0000 chunk 957 optimal weight: 10.0000 chunk 1034 optimal weight: 30.0000 chunk 853 optimal weight: 50.0000 chunk 949 optimal weight: 20.0000 chunk 326 optimal weight: 8.9990 chunk 768 optimal weight: 20.0000 overall best weight: 15.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 57 HIS ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 196 ASN c 130 GLN ** c 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 167 ASN d 94 GLN ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 142 GLN g 11 ASN ** g 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 119 ASN g 145 ASN j 128 ASN o 104 GLN q 70 GLN ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 31 GLN t 28 ASN ** t 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 15 ASN y 58 ASN ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 197 HIS J 11 GLN ** J 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 ASN K 17 GLN ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 4 ASN ** Q 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 7 ASN ** R 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 54 GLN Y 74 HIS ** Y 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 160361 Z= 0.508 Angle : 0.885 11.334 239566 Z= 0.448 Chirality : 0.045 0.514 30559 Planarity : 0.007 0.086 13074 Dihedral : 23.796 173.810 79414 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 35.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.38 % Favored : 87.49 % Rotamer: Outliers : 5.73 % Allowed : 16.78 % Favored : 77.49 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.10), residues: 6011 helix: -1.40 (0.11), residues: 1874 sheet: -2.32 (0.14), residues: 1059 loop : -2.66 (0.10), residues: 3078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP e 96 HIS 0.013 0.002 HIS y 41 PHE 0.042 0.003 PHE e 176 TYR 0.029 0.003 TYR b 170 ARG 0.022 0.001 ARG Q 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1153 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 287 poor density : 866 time to evaluate : 6.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 131 MET cc_start: 0.9417 (mmp) cc_final: 0.8776 (mmm) REVERT: b 145 MET cc_start: 0.8623 (ttm) cc_final: 0.8235 (tpp) REVERT: b 160 TYR cc_start: 0.9124 (p90) cc_final: 0.8848 (p90) REVERT: b 182 LYS cc_start: 0.9415 (mmmt) cc_final: 0.9154 (mmmm) REVERT: b 196 ASN cc_start: 0.9109 (OUTLIER) cc_final: 0.8891 (t0) REVERT: b 258 SER cc_start: 0.9180 (t) cc_final: 0.8964 (p) REVERT: c 180 VAL cc_start: 0.9123 (OUTLIER) cc_final: 0.8922 (m) REVERT: f 57 TYR cc_start: 0.7941 (m-80) cc_final: 0.7497 (m-80) REVERT: f 59 ASP cc_start: 0.6760 (OUTLIER) cc_final: 0.6430 (p0) REVERT: f 61 TRP cc_start: 0.7632 (m100) cc_final: 0.7190 (m100) REVERT: f 142 GLN cc_start: 0.8753 (tt0) cc_final: 0.8167 (tp40) REVERT: g 2 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7699 (mm-40) REVERT: g 7 ASP cc_start: 0.9539 (t70) cc_final: 0.9294 (m-30) REVERT: g 28 ASN cc_start: 0.8942 (m-40) cc_final: 0.7694 (p0) REVERT: j 1 MET cc_start: 0.7765 (ptp) cc_final: 0.7021 (pmm) REVERT: j 16 TYR cc_start: 0.9094 (m-80) cc_final: 0.8640 (m-80) REVERT: j 49 ASP cc_start: 0.8291 (t0) cc_final: 0.6898 (t0) REVERT: j 75 TYR cc_start: 0.8795 (m-80) cc_final: 0.8505 (m-10) REVERT: j 102 GLU cc_start: 0.8737 (pt0) cc_final: 0.8421 (pt0) REVERT: j 108 MET cc_start: 0.9202 (mtm) cc_final: 0.8789 (mtm) REVERT: j 114 LEU cc_start: 0.9698 (tp) cc_final: 0.8934 (tp) REVERT: j 118 MET cc_start: 0.8478 (ptp) cc_final: 0.7929 (ptp) REVERT: l 86 GLU cc_start: 0.8101 (pm20) cc_final: 0.7897 (pm20) REVERT: m 41 LEU cc_start: 0.9506 (mm) cc_final: 0.9281 (mm) REVERT: m 70 ASP cc_start: 0.8688 (OUTLIER) cc_final: 0.8448 (p0) REVERT: m 82 MET cc_start: 0.8660 (tpp) cc_final: 0.8423 (tpp) REVERT: m 136 MET cc_start: 0.7670 (mtm) cc_final: 0.5471 (mmt) REVERT: n 2 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7251 (tmt-80) REVERT: n 82 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7587 (tm-30) REVERT: n 99 LYS cc_start: 0.9452 (mtmm) cc_final: 0.9205 (mttt) REVERT: n 114 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7968 (pp20) REVERT: o 2 ASP cc_start: 0.8059 (m-30) cc_final: 0.7841 (m-30) REVERT: o 19 GLN cc_start: 0.9326 (tp-100) cc_final: 0.8802 (tp-100) REVERT: o 20 GLU cc_start: 0.9404 (tt0) cc_final: 0.9045 (tm-30) REVERT: o 112 GLU cc_start: 0.8764 (pm20) cc_final: 0.8561 (pm20) REVERT: p 43 GLU cc_start: 0.8265 (tp30) cc_final: 0.7453 (tp30) REVERT: p 98 TYR cc_start: 0.8926 (p90) cc_final: 0.8395 (p90) REVERT: q 51 GLN cc_start: 0.9277 (mm-40) cc_final: 0.8669 (mm-40) REVERT: q 56 PHE cc_start: 0.9257 (OUTLIER) cc_final: 0.8216 (m-10) REVERT: q 101 ASP cc_start: 0.8894 (t0) cc_final: 0.8509 (t0) REVERT: r 48 LYS cc_start: 0.8668 (ttmm) cc_final: 0.8392 (ttmm) REVERT: r 78 ARG cc_start: 0.9336 (tpp80) cc_final: 0.8575 (tpp80) REVERT: r 86 GLN cc_start: 0.8874 (mm110) cc_final: 0.8616 (mm110) REVERT: s 19 LEU cc_start: 0.9621 (mt) cc_final: 0.9417 (mt) REVERT: s 35 ILE cc_start: 0.9521 (mm) cc_final: 0.9268 (mm) REVERT: s 69 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8649 (mt) REVERT: u 13 LEU cc_start: 0.9620 (mt) cc_final: 0.9417 (mt) REVERT: u 39 ASN cc_start: 0.9258 (m-40) cc_final: 0.8998 (t0) REVERT: u 45 GLN cc_start: 0.9237 (tp40) cc_final: 0.8605 (tp40) REVERT: v 20 LEU cc_start: 0.9776 (tp) cc_final: 0.9453 (tp) REVERT: v 75 GLN cc_start: 0.8398 (tp40) cc_final: 0.7836 (tm-30) REVERT: w 15 LYS cc_start: 0.9476 (mmtt) cc_final: 0.9214 (mmtm) REVERT: w 79 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8550 (mp0) REVERT: x 25 LYS cc_start: 0.9236 (mmmm) cc_final: 0.8819 (mmmm) REVERT: x 55 MET cc_start: 0.9028 (mmm) cc_final: 0.8777 (mmm) REVERT: x 59 ASP cc_start: 0.9311 (m-30) cc_final: 0.8829 (p0) REVERT: x 61 LYS cc_start: 0.8991 (ttmt) cc_final: 0.8698 (mttm) REVERT: y 17 GLU cc_start: 0.9581 (tm-30) cc_final: 0.9324 (tm-30) REVERT: y 49 ASP cc_start: 0.9097 (m-30) cc_final: 0.8633 (m-30) REVERT: z 20 LYS cc_start: 0.9615 (mttt) cc_final: 0.9378 (mmtt) REVERT: C 6 GLU cc_start: 0.7092 (pm20) cc_final: 0.6610 (pm20) REVERT: C 7 LYS cc_start: 0.7671 (mtmt) cc_final: 0.7212 (mtmt) REVERT: C 9 LYS cc_start: 0.9229 (tttt) cc_final: 0.8807 (tttm) REVERT: C 24 LYS cc_start: 0.8594 (ptmt) cc_final: 0.8286 (ptmt) REVERT: C 31 GLU cc_start: 0.8726 (pm20) cc_final: 0.8352 (pm20) REVERT: F 13 ASN cc_start: 0.9388 (m-40) cc_final: 0.8634 (p0) REVERT: F 36 ARG cc_start: 0.8139 (ptm-80) cc_final: 0.7697 (ptm-80) REVERT: G 26 MET cc_start: 0.8049 (mmp) cc_final: 0.7267 (mmp) REVERT: H 99 GLN cc_start: 0.8595 (pt0) cc_final: 0.8228 (pm20) REVERT: H 166 TRP cc_start: 0.8950 (p-90) cc_final: 0.8379 (p-90) REVERT: I 43 ARG cc_start: 0.5277 (mtt180) cc_final: 0.4875 (mmm160) REVERT: I 74 TYR cc_start: 0.9461 (m-80) cc_final: 0.8715 (m-80) REVERT: I 104 MET cc_start: 0.8708 (mmt) cc_final: 0.7664 (mmm) REVERT: I 134 TYR cc_start: 0.9050 (t80) cc_final: 0.8741 (t80) REVERT: I 135 GLN cc_start: 0.8839 (tt0) cc_final: 0.8606 (tm-30) REVERT: J 53 ARG cc_start: 0.8860 (mmm160) cc_final: 0.8616 (mmm160) REVERT: J 65 LYS cc_start: 0.9609 (mmmt) cc_final: 0.9307 (mmmm) REVERT: J 70 MET cc_start: 0.8224 (ttp) cc_final: 0.8017 (tpp) REVERT: J 92 ARG cc_start: 0.8238 (mtm180) cc_final: 0.7846 (mtm180) REVERT: J 144 GLU cc_start: 0.9118 (tp30) cc_final: 0.8867 (tm-30) REVERT: J 151 MET cc_start: 0.9271 (ppp) cc_final: 0.8979 (ppp) REVERT: K 56 LYS cc_start: 0.9230 (mptt) cc_final: 0.8722 (mmmt) REVERT: L 4 ARG cc_start: 0.2848 (ppt170) cc_final: 0.0536 (ptm-80) REVERT: L 25 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.8148 (m-80) REVERT: L 102 TRP cc_start: 0.8484 (OUTLIER) cc_final: 0.8264 (m-10) REVERT: M 110 MET cc_start: 0.9266 (ptp) cc_final: 0.8910 (pmm) REVERT: N 45 MET cc_start: 0.8954 (ppp) cc_final: 0.8697 (ptp) REVERT: N 87 MET cc_start: 0.8856 (ptm) cc_final: 0.8564 (ppp) REVERT: N 128 LYS cc_start: 0.9223 (tppp) cc_final: 0.8667 (tptt) REVERT: O 66 GLU cc_start: 0.8816 (pt0) cc_final: 0.8357 (pt0) REVERT: P 71 ASP cc_start: 0.9349 (t0) cc_final: 0.9122 (m-30) REVERT: P 105 ARG cc_start: 0.8420 (ttt-90) cc_final: 0.8068 (tpt170) REVERT: Q 69 GLU cc_start: 0.8560 (pt0) cc_final: 0.8166 (pm20) REVERT: R 10 ASP cc_start: 0.8945 (m-30) cc_final: 0.8649 (m-30) REVERT: S 73 LEU cc_start: 0.9492 (tt) cc_final: 0.9146 (mt) REVERT: S 88 MET cc_start: 0.8671 (mmp) cc_final: 0.8371 (mmt) REVERT: T 25 GLU cc_start: 0.8632 (pt0) cc_final: 0.8036 (mp0) REVERT: T 77 TYR cc_start: 0.9403 (t80) cc_final: 0.8840 (t80) REVERT: U 25 ARG cc_start: 0.8981 (mtm180) cc_final: 0.8417 (mpp80) REVERT: U 46 LYS cc_start: 0.8806 (pttm) cc_final: 0.7890 (ttmm) REVERT: U 79 ASN cc_start: 0.9497 (t0) cc_final: 0.9224 (t0) REVERT: V 7 LEU cc_start: 0.9187 (tp) cc_final: 0.8895 (mt) REVERT: V 38 LYS cc_start: 0.8961 (pttt) cc_final: 0.8557 (ptpp) REVERT: X 16 LYS cc_start: 0.8332 (mtpp) cc_final: 0.7960 (mtmt) REVERT: Y 12 GLN cc_start: 0.9354 (tt0) cc_final: 0.9104 (tt0) REVERT: Y 23 ARG cc_start: 0.9473 (mmm-85) cc_final: 0.9140 (mmm-85) REVERT: Y 54 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8342 (tm-30) REVERT: Y 58 ASP cc_start: 0.9219 (m-30) cc_final: 0.8266 (p0) REVERT: Z 37 TYR cc_start: 0.8227 (t80) cc_final: 0.7995 (t80) REVERT: 8 147 MET cc_start: 0.9202 (ttp) cc_final: 0.8979 (ppp) REVERT: 8 168 GLU cc_start: 0.7152 (pp20) cc_final: 0.6740 (pp20) REVERT: 8 186 ASP cc_start: 0.9217 (OUTLIER) cc_final: 0.8954 (t0) REVERT: 8 265 HIS cc_start: 0.8956 (t-90) cc_final: 0.8677 (t-90) REVERT: 8 288 MET cc_start: 0.9273 (tpp) cc_final: 0.8727 (tpt) outliers start: 287 outliers final: 183 residues processed: 1061 average time/residue: 1.2476 time to fit residues: 2320.4484 Evaluate side-chains 964 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 769 time to evaluate : 6.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 15 VAL Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 66 PHE Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 196 ASN Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 224 MET Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 263 ASP Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 88 GLU Chi-restraints excluded: chain c residue 95 SER Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 184 ASP Chi-restraints excluded: chain e residue 113 PHE Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain f residue 51 PHE Chi-restraints excluded: chain f residue 55 ASP Chi-restraints excluded: chain f residue 59 ASP Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 42 LYS Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 47 HIS Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain k residue 17 ARG Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 45 GLU Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 84 CYS Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 100 PHE Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 20 LEU Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 80 VAL Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 2 ARG Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 48 VAL Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 114 GLU Chi-restraints excluded: chain n residue 117 ASP Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain p residue 6 GLN Chi-restraints excluded: chain p residue 24 THR Chi-restraints excluded: chain p residue 27 VAL Chi-restraints excluded: chain p residue 30 TRP Chi-restraints excluded: chain p residue 62 LYS Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain q residue 56 PHE Chi-restraints excluded: chain q residue 70 GLN Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain r residue 25 LEU Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 84 ARG Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain s residue 105 VAL Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 42 GLU Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 61 LEU Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 7 ASP Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 34 ILE Chi-restraints excluded: chain v residue 71 LYS Chi-restraints excluded: chain v residue 78 GLN Chi-restraints excluded: chain w residue 55 LEU Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain x residue 6 VAL Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 21 LEU Chi-restraints excluded: chain x residue 29 LEU Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 18 LEU Chi-restraints excluded: chain y residue 59 GLU Chi-restraints excluded: chain z residue 18 LYS Chi-restraints excluded: chain z residue 35 VAL Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain z residue 53 MET Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain F residue 14 CYS Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain G residue 38 HIS Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain H residue 2 GLN Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 192 TYR Chi-restraints excluded: chain I residue 102 TYR Chi-restraints excluded: chain I residue 173 ASP Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 94 HIS Chi-restraints excluded: chain L residue 25 PHE Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 102 TRP Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 26 MET Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain N residue 5 TYR Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 123 ARG Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain P residue 69 CYS Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain R residue 8 ILE Chi-restraints excluded: chain R residue 85 TYR Chi-restraints excluded: chain T residue 44 GLU Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain V residue 8 GLN Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 51 GLU Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 60 ILE Chi-restraints excluded: chain W residue 34 GLU Chi-restraints excluded: chain W residue 67 LEU Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 54 GLN Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 22 ASP Chi-restraints excluded: chain 8 residue 186 ASP Chi-restraints excluded: chain 8 residue 229 ASP Chi-restraints excluded: chain 8 residue 281 HIS Chi-restraints excluded: chain 8 residue 285 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1053 random chunks: chunk 946 optimal weight: 20.0000 chunk 720 optimal weight: 20.0000 chunk 497 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 chunk 457 optimal weight: 30.0000 chunk 643 optimal weight: 10.0000 chunk 961 optimal weight: 10.0000 chunk 1017 optimal weight: 5.9990 chunk 502 optimal weight: 10.0000 chunk 911 optimal weight: 5.9990 chunk 274 optimal weight: 3.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 126 ASN c 134 HIS d 97 ASN ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 72 ASN ** f 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 20 ASN g 73 ASN l 104 GLN ** q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 12 HIS u 53 GLN y 36 GLN G 88 GLN ** H 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 GLN ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 ASN ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 ASN Q 4 ASN ** Q 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 160361 Z= 0.248 Angle : 0.623 10.532 239566 Z= 0.320 Chirality : 0.035 0.288 30559 Planarity : 0.005 0.061 13074 Dihedral : 23.709 171.387 79413 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 21.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.27 % Favored : 90.65 % Rotamer: Outliers : 4.81 % Allowed : 19.65 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.78 (0.10), residues: 6011 helix: -0.84 (0.11), residues: 1875 sheet: -2.06 (0.15), residues: 1024 loop : -2.44 (0.10), residues: 3112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 103 HIS 0.008 0.001 HIS B 37 PHE 0.034 0.002 PHE N 38 TYR 0.017 0.002 TYR I 75 ARG 0.009 0.001 ARG t 73 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1127 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 886 time to evaluate : 6.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 131 MET cc_start: 0.9417 (mmp) cc_final: 0.8934 (mmm) REVERT: b 184 GLU cc_start: 0.8105 (tp30) cc_final: 0.7602 (tp30) REVERT: b 250 GLN cc_start: 0.8385 (tm-30) cc_final: 0.8006 (tp-100) REVERT: d 158 PHE cc_start: 0.8831 (m-80) cc_final: 0.8494 (m-80) REVERT: e 37 MET cc_start: 0.8408 (ptp) cc_final: 0.7912 (pmm) REVERT: e 47 LYS cc_start: 0.9399 (pttt) cc_final: 0.9132 (tppt) REVERT: f 57 TYR cc_start: 0.7954 (m-80) cc_final: 0.7445 (m-80) REVERT: f 61 TRP cc_start: 0.7633 (m100) cc_final: 0.7246 (m100) REVERT: f 123 GLU cc_start: 0.8710 (tp30) cc_final: 0.8063 (tm-30) REVERT: f 129 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8379 (tp30) REVERT: f 142 GLN cc_start: 0.8565 (tt0) cc_final: 0.7965 (tp40) REVERT: f 172 GLU cc_start: 0.8058 (pt0) cc_final: 0.7775 (pt0) REVERT: g 2 GLN cc_start: 0.8130 (mm-40) cc_final: 0.7894 (mm-40) REVERT: g 7 ASP cc_start: 0.9497 (t70) cc_final: 0.9294 (m-30) REVERT: j 16 TYR cc_start: 0.9075 (m-80) cc_final: 0.8812 (m-80) REVERT: j 49 ASP cc_start: 0.8181 (t0) cc_final: 0.7374 (t0) REVERT: j 75 TYR cc_start: 0.8733 (m-80) cc_final: 0.8468 (m-10) REVERT: j 108 MET cc_start: 0.9014 (mtm) cc_final: 0.8664 (mtm) REVERT: j 118 MET cc_start: 0.8455 (ptp) cc_final: 0.8047 (ptm) REVERT: k 73 ASP cc_start: 0.8606 (p0) cc_final: 0.8341 (p0) REVERT: m 136 MET cc_start: 0.7742 (mtm) cc_final: 0.5628 (mmt) REVERT: n 82 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7701 (tm-30) REVERT: n 114 GLU cc_start: 0.8224 (pt0) cc_final: 0.7942 (pp20) REVERT: o 19 GLN cc_start: 0.9279 (tp-100) cc_final: 0.8748 (tp-100) REVERT: o 20 GLU cc_start: 0.9407 (tt0) cc_final: 0.8982 (tm-30) REVERT: o 61 GLN cc_start: 0.8820 (tt0) cc_final: 0.8344 (mp10) REVERT: o 76 LYS cc_start: 0.9640 (tmmt) cc_final: 0.9229 (tppt) REVERT: o 116 GLN cc_start: 0.9389 (mm-40) cc_final: 0.9069 (mp10) REVERT: p 10 GLU cc_start: 0.9169 (OUTLIER) cc_final: 0.8696 (pm20) REVERT: p 98 TYR cc_start: 0.8958 (p90) cc_final: 0.8599 (p90) REVERT: q 51 GLN cc_start: 0.9194 (mm-40) cc_final: 0.8600 (mm-40) REVERT: q 101 ASP cc_start: 0.8749 (t0) cc_final: 0.8421 (t0) REVERT: r 78 ARG cc_start: 0.9355 (tpp80) cc_final: 0.8548 (tpp80) REVERT: r 86 GLN cc_start: 0.8816 (mm110) cc_final: 0.8565 (mm110) REVERT: s 2 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8738 (mm-30) REVERT: s 78 GLU cc_start: 0.8132 (pp20) cc_final: 0.7579 (pp20) REVERT: t 7 LEU cc_start: 0.9399 (mt) cc_final: 0.8900 (pp) REVERT: t 8 LEU cc_start: 0.9772 (mt) cc_final: 0.9496 (mt) REVERT: t 37 ASP cc_start: 0.8666 (p0) cc_final: 0.8334 (p0) REVERT: u 7 ASP cc_start: 0.9227 (m-30) cc_final: 0.8070 (t0) REVERT: u 13 LEU cc_start: 0.9621 (mt) cc_final: 0.9351 (mt) REVERT: u 45 GLN cc_start: 0.9266 (tp40) cc_final: 0.8601 (tp40) REVERT: v 75 GLN cc_start: 0.8354 (tp40) cc_final: 0.7873 (tm-30) REVERT: w 15 LYS cc_start: 0.9407 (mmtt) cc_final: 0.9151 (mmtm) REVERT: w 42 HIS cc_start: 0.8462 (OUTLIER) cc_final: 0.8247 (m-70) REVERT: w 62 LYS cc_start: 0.9319 (mtpp) cc_final: 0.9003 (mtpp) REVERT: w 79 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8531 (mt-10) REVERT: x 55 MET cc_start: 0.9037 (mmm) cc_final: 0.8727 (mmm) REVERT: x 59 ASP cc_start: 0.9256 (m-30) cc_final: 0.8751 (p0) REVERT: x 61 LYS cc_start: 0.8980 (ttmt) cc_final: 0.8579 (mttm) REVERT: y 8 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7028 (mp0) REVERT: y 17 GLU cc_start: 0.9552 (tm-30) cc_final: 0.9294 (tm-30) REVERT: y 49 ASP cc_start: 0.8999 (m-30) cc_final: 0.8539 (m-30) REVERT: z 20 LYS cc_start: 0.9607 (mttt) cc_final: 0.9323 (mmtt) REVERT: B 27 LEU cc_start: 0.9203 (mm) cc_final: 0.8988 (mm) REVERT: C 24 LYS cc_start: 0.8820 (ptmt) cc_final: 0.8361 (ptmt) REVERT: F 4 ARG cc_start: 0.7549 (mtm180) cc_final: 0.7225 (mtm-85) REVERT: F 13 ASN cc_start: 0.9376 (m-40) cc_final: 0.8671 (p0) REVERT: F 36 ARG cc_start: 0.8008 (ptm-80) cc_final: 0.7602 (ptm-80) REVERT: G 26 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7221 (mmp) REVERT: G 167 HIS cc_start: 0.7250 (t70) cc_final: 0.6755 (t70) REVERT: H 166 TRP cc_start: 0.8997 (p-90) cc_final: 0.8297 (p-90) REVERT: I 43 ARG cc_start: 0.5584 (mtt180) cc_final: 0.5018 (mmm160) REVERT: I 64 TYR cc_start: 0.9257 (m-80) cc_final: 0.8992 (m-80) REVERT: I 74 TYR cc_start: 0.9443 (m-80) cc_final: 0.8651 (m-80) REVERT: I 134 TYR cc_start: 0.9155 (t80) cc_final: 0.8938 (t80) REVERT: J 22 LYS cc_start: 0.9067 (tttt) cc_final: 0.8357 (tppt) REVERT: J 28 ARG cc_start: 0.8611 (mtm-85) cc_final: 0.7925 (mtm110) REVERT: J 70 MET cc_start: 0.8195 (ttp) cc_final: 0.7961 (tpp) REVERT: J 125 LYS cc_start: 0.9424 (tptm) cc_final: 0.9012 (tptp) REVERT: J 144 GLU cc_start: 0.9120 (tp30) cc_final: 0.8680 (tp30) REVERT: K 39 LEU cc_start: 0.8943 (mt) cc_final: 0.8679 (mp) REVERT: K 54 LEU cc_start: 0.8987 (tp) cc_final: 0.8714 (tp) REVERT: K 56 LYS cc_start: 0.9145 (mptt) cc_final: 0.8862 (mmtm) REVERT: K 88 MET cc_start: 0.7829 (ptm) cc_final: 0.7275 (ttp) REVERT: L 102 TRP cc_start: 0.8549 (OUTLIER) cc_final: 0.8255 (m-10) REVERT: L 150 PHE cc_start: 0.7514 (m-80) cc_final: 0.7138 (m-80) REVERT: M 65 PHE cc_start: 0.9148 (t80) cc_final: 0.8769 (t80) REVERT: M 117 GLN cc_start: 0.9311 (mm-40) cc_final: 0.9053 (mp10) REVERT: N 55 ASP cc_start: 0.9218 (m-30) cc_final: 0.8725 (t70) REVERT: N 87 MET cc_start: 0.8918 (ptm) cc_final: 0.8709 (ppp) REVERT: N 128 LYS cc_start: 0.9191 (tppp) cc_final: 0.8668 (tptt) REVERT: O 66 GLU cc_start: 0.8811 (pt0) cc_final: 0.8308 (pt0) REVERT: P 105 ARG cc_start: 0.8386 (ttt-90) cc_final: 0.8035 (tpt170) REVERT: Q 69 GLU cc_start: 0.8618 (pt0) cc_final: 0.8147 (pm20) REVERT: Q 111 GLN cc_start: 0.8494 (mm-40) cc_final: 0.7756 (mp10) REVERT: R 10 ASP cc_start: 0.8807 (m-30) cc_final: 0.8474 (m-30) REVERT: R 71 GLU cc_start: 0.9195 (tm-30) cc_final: 0.8858 (tm-30) REVERT: S 5 MET cc_start: 0.6364 (ttt) cc_final: 0.5516 (tpp) REVERT: S 73 LEU cc_start: 0.9479 (tt) cc_final: 0.9207 (mt) REVERT: T 44 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8060 (pt0) REVERT: T 77 TYR cc_start: 0.9235 (t80) cc_final: 0.8972 (t80) REVERT: U 6 LEU cc_start: 0.8984 (mt) cc_final: 0.8440 (mt) REVERT: U 25 ARG cc_start: 0.8977 (mtm180) cc_final: 0.8433 (mtm180) REVERT: U 46 LYS cc_start: 0.9003 (pttm) cc_final: 0.8487 (tttm) REVERT: U 79 ASN cc_start: 0.9491 (t0) cc_final: 0.9164 (t0) REVERT: V 7 LEU cc_start: 0.9258 (tp) cc_final: 0.9030 (tp) REVERT: V 38 LYS cc_start: 0.8853 (pttt) cc_final: 0.8283 (ptpp) REVERT: W 28 LEU cc_start: 0.8873 (pp) cc_final: 0.8404 (mp) REVERT: X 16 LYS cc_start: 0.8528 (mtpp) cc_final: 0.8188 (ptpt) REVERT: Y 12 GLN cc_start: 0.9358 (tt0) cc_final: 0.9021 (tt0) REVERT: Y 23 ARG cc_start: 0.9501 (mmm-85) cc_final: 0.8870 (mmm-85) REVERT: Y 26 MET cc_start: 0.8713 (ptp) cc_final: 0.8122 (ptp) REVERT: Y 47 GLN cc_start: 0.9369 (tt0) cc_final: 0.8797 (tp-100) REVERT: Z 53 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8589 (pttm) REVERT: 8 147 MET cc_start: 0.9021 (ttp) cc_final: 0.8636 (ppp) REVERT: 8 151 MET cc_start: 0.8911 (ppp) cc_final: 0.8628 (ppp) REVERT: 8 168 GLU cc_start: 0.7042 (pp20) cc_final: 0.6579 (pp20) REVERT: 8 186 ASP cc_start: 0.9257 (OUTLIER) cc_final: 0.8979 (t0) REVERT: 8 265 HIS cc_start: 0.8966 (t-90) cc_final: 0.8710 (t-170) REVERT: 8 288 MET cc_start: 0.9316 (tpp) cc_final: 0.8921 (tpt) outliers start: 241 outliers final: 153 residues processed: 1037 average time/residue: 1.2714 time to fit residues: 2319.0929 Evaluate side-chains 959 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 799 time to evaluate : 6.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 66 PHE Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 263 ASP Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain d residue 184 ASP Chi-restraints excluded: chain e residue 113 PHE Chi-restraints excluded: chain f residue 51 PHE Chi-restraints excluded: chain f residue 55 ASP Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 42 LYS Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain j residue 47 HIS Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 141 ASP Chi-restraints excluded: chain k residue 17 ARG Chi-restraints excluded: chain k residue 45 GLU Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 100 PHE Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 20 LEU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 80 VAL Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 102 LEU Chi-restraints excluded: chain m residue 119 LEU Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain p residue 2 ASN Chi-restraints excluded: chain p residue 6 GLN Chi-restraints excluded: chain p residue 10 GLU Chi-restraints excluded: chain p residue 30 TRP Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 82 SER Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain q residue 3 VAL Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain r residue 25 LEU Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain r residue 98 ILE Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain s residue 105 VAL Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 42 GLU Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 34 ILE Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain u residue 65 GLN Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 78 GLN Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 42 HIS Chi-restraints excluded: chain w residue 55 LEU Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain y residue 18 LEU Chi-restraints excluded: chain z residue 18 LYS Chi-restraints excluded: chain z residue 43 ILE Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain z residue 53 MET Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain F residue 14 CYS Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 26 MET Chi-restraints excluded: chain G residue 38 HIS Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 192 TYR Chi-restraints excluded: chain I residue 102 TYR Chi-restraints excluded: chain I residue 173 ASP Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 94 HIS Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 102 TRP Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain N residue 5 TYR Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 123 ARG Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 23 HIS Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 69 CYS Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain R residue 8 ILE Chi-restraints excluded: chain R residue 57 ASP Chi-restraints excluded: chain R residue 85 TYR Chi-restraints excluded: chain S residue 17 ASP Chi-restraints excluded: chain T residue 44 GLU Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 12 LYS Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain W residue 67 LEU Chi-restraints excluded: chain X residue 55 GLN Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain Z residue 53 LYS Chi-restraints excluded: chain Z residue 55 HIS Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 22 ASP Chi-restraints excluded: chain 8 residue 186 ASP Chi-restraints excluded: chain 8 residue 232 ILE Chi-restraints excluded: chain 8 residue 281 HIS Chi-restraints excluded: chain 8 residue 285 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1053 random chunks: chunk 847 optimal weight: 40.0000 chunk 577 optimal weight: 20.0000 chunk 14 optimal weight: 0.9990 chunk 757 optimal weight: 10.0000 chunk 419 optimal weight: 0.9980 chunk 868 optimal weight: 10.0000 chunk 703 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 519 optimal weight: 0.0010 chunk 913 optimal weight: 10.0000 chunk 256 optimal weight: 30.0000 overall best weight: 4.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 196 ASN ** d 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 44 HIS f 72 ASN f 127 GLN ** f 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 31 GLN t 28 ASN ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 197 HIS J 11 GLN ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 ASN ** Q 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 GLN U 9 HIS ** Y 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 301 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 160361 Z= 0.182 Angle : 0.577 9.993 239566 Z= 0.295 Chirality : 0.033 0.293 30559 Planarity : 0.004 0.062 13074 Dihedral : 23.601 170.233 79411 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.42 % Favored : 90.50 % Rotamer: Outliers : 4.85 % Allowed : 20.77 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.10), residues: 6011 helix: -0.59 (0.11), residues: 1897 sheet: -1.93 (0.15), residues: 1024 loop : -2.29 (0.11), residues: 3090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP G 103 HIS 0.005 0.001 HIS o 100 PHE 0.023 0.002 PHE N 38 TYR 0.020 0.001 TYR I 75 ARG 0.010 0.001 ARG y 7 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1158 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 915 time to evaluate : 5.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 99 GLU cc_start: 0.8696 (tp30) cc_final: 0.8411 (tp30) REVERT: b 131 MET cc_start: 0.9441 (mmp) cc_final: 0.8934 (mmm) REVERT: b 182 LYS cc_start: 0.9505 (mmmt) cc_final: 0.9301 (mmmt) REVERT: b 184 GLU cc_start: 0.7980 (tp30) cc_final: 0.7561 (tp30) REVERT: b 196 ASN cc_start: 0.9113 (OUTLIER) cc_final: 0.8814 (t0) REVERT: b 257 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8294 (tmt-80) REVERT: d 115 GLN cc_start: 0.9498 (tp40) cc_final: 0.9052 (tm-30) REVERT: d 158 PHE cc_start: 0.8850 (m-80) cc_final: 0.8505 (m-80) REVERT: d 188 MET cc_start: 0.8882 (tpp) cc_final: 0.8411 (tpp) REVERT: e 37 MET cc_start: 0.8415 (ptp) cc_final: 0.7910 (pmm) REVERT: e 47 LYS cc_start: 0.9397 (pttt) cc_final: 0.9149 (tppt) REVERT: e 95 MET cc_start: 0.9334 (tmm) cc_final: 0.8594 (ppp) REVERT: f 54 ARG cc_start: 0.8632 (ttm170) cc_final: 0.8288 (ttm110) REVERT: f 57 TYR cc_start: 0.8132 (m-80) cc_final: 0.7640 (m-80) REVERT: f 61 TRP cc_start: 0.7559 (m100) cc_final: 0.7174 (m100) REVERT: f 123 GLU cc_start: 0.8699 (tp30) cc_final: 0.8039 (tm-30) REVERT: f 129 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8182 (tp30) REVERT: f 142 GLN cc_start: 0.8505 (tt0) cc_final: 0.8053 (tp40) REVERT: f 148 ARG cc_start: 0.9164 (ptm-80) cc_final: 0.8822 (ptt180) REVERT: g 2 GLN cc_start: 0.7955 (mm-40) cc_final: 0.7697 (mm-40) REVERT: j 75 TYR cc_start: 0.8735 (m-80) cc_final: 0.8501 (m-10) REVERT: j 108 MET cc_start: 0.8901 (mtm) cc_final: 0.8646 (mtp) REVERT: j 118 MET cc_start: 0.8517 (ptp) cc_final: 0.7860 (ptp) REVERT: k 39 ILE cc_start: 0.9626 (pt) cc_final: 0.9254 (pt) REVERT: k 73 ASP cc_start: 0.8609 (p0) cc_final: 0.8331 (p0) REVERT: m 41 LEU cc_start: 0.9379 (mm) cc_final: 0.8937 (mm) REVERT: m 110 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8094 (tm-30) REVERT: m 136 MET cc_start: 0.7723 (mtm) cc_final: 0.5735 (mmt) REVERT: n 24 MET cc_start: 0.9102 (ttm) cc_final: 0.8576 (tpt) REVERT: n 82 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7694 (tm-30) REVERT: n 114 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.8000 (pp20) REVERT: o 20 GLU cc_start: 0.9355 (tt0) cc_final: 0.8908 (tm-30) REVERT: o 61 GLN cc_start: 0.8763 (tt0) cc_final: 0.8359 (mp10) REVERT: o 116 GLN cc_start: 0.9360 (mm-40) cc_final: 0.9044 (mp10) REVERT: p 10 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8188 (pm20) REVERT: p 40 GLN cc_start: 0.8659 (tp40) cc_final: 0.8199 (tm-30) REVERT: p 84 SER cc_start: 0.8884 (t) cc_final: 0.8666 (p) REVERT: p 98 TYR cc_start: 0.8988 (p90) cc_final: 0.8652 (p90) REVERT: q 48 ASP cc_start: 0.7590 (m-30) cc_final: 0.7359 (m-30) REVERT: q 51 GLN cc_start: 0.9176 (mm-40) cc_final: 0.8592 (mm-40) REVERT: q 101 ASP cc_start: 0.8679 (t0) cc_final: 0.8379 (t0) REVERT: r 37 GLU cc_start: 0.8712 (pm20) cc_final: 0.8498 (pm20) REVERT: r 46 GLU cc_start: 0.8299 (mp0) cc_final: 0.7996 (pm20) REVERT: r 78 ARG cc_start: 0.9287 (tpp80) cc_final: 0.8651 (mmt90) REVERT: r 86 GLN cc_start: 0.8746 (mm110) cc_final: 0.8505 (mm110) REVERT: s 52 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8760 (mp0) REVERT: s 78 GLU cc_start: 0.8027 (pp20) cc_final: 0.7486 (pp20) REVERT: t 7 LEU cc_start: 0.9375 (mt) cc_final: 0.8900 (pp) REVERT: t 8 LEU cc_start: 0.9727 (mt) cc_final: 0.9461 (mt) REVERT: u 13 LEU cc_start: 0.9608 (mt) cc_final: 0.9330 (mt) REVERT: u 39 ASN cc_start: 0.9243 (t0) cc_final: 0.8991 (t0) REVERT: u 45 GLN cc_start: 0.9261 (tp40) cc_final: 0.8548 (tp40) REVERT: v 75 GLN cc_start: 0.8302 (tp40) cc_final: 0.7498 (tm-30) REVERT: v 76 ASP cc_start: 0.8473 (m-30) cc_final: 0.7426 (m-30) REVERT: v 87 GLN cc_start: 0.8754 (mt0) cc_final: 0.8247 (mt0) REVERT: w 15 LYS cc_start: 0.9369 (mmtt) cc_final: 0.9083 (mmtm) REVERT: w 79 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8603 (mp0) REVERT: x 24 THR cc_start: 0.9455 (t) cc_final: 0.9251 (p) REVERT: x 55 MET cc_start: 0.9037 (mmm) cc_final: 0.8797 (mmm) REVERT: x 59 ASP cc_start: 0.9218 (m-30) cc_final: 0.8775 (p0) REVERT: x 61 LYS cc_start: 0.8990 (ttmt) cc_final: 0.8623 (mttm) REVERT: y 17 GLU cc_start: 0.9486 (tm-30) cc_final: 0.9221 (tm-30) REVERT: y 36 GLN cc_start: 0.9249 (mp10) cc_final: 0.8930 (pm20) REVERT: y 49 ASP cc_start: 0.9017 (m-30) cc_final: 0.8572 (m-30) REVERT: z 20 LYS cc_start: 0.9594 (mttt) cc_final: 0.9325 (mmtt) REVERT: z 36 GLU cc_start: 0.8661 (tt0) cc_final: 0.8237 (pm20) REVERT: B 16 ARG cc_start: 0.9010 (mtm-85) cc_final: 0.7872 (mtm-85) REVERT: C 6 GLU cc_start: 0.7061 (pm20) cc_final: 0.6664 (pm20) REVERT: C 9 LYS cc_start: 0.9141 (tttt) cc_final: 0.8629 (tttm) REVERT: C 24 LYS cc_start: 0.8687 (ptmt) cc_final: 0.8267 (ptmt) REVERT: C 31 GLU cc_start: 0.8834 (pm20) cc_final: 0.8573 (pm20) REVERT: C 32 LYS cc_start: 0.8518 (mmmt) cc_final: 0.8288 (ptmt) REVERT: D 29 GLN cc_start: 0.9525 (tp40) cc_final: 0.8949 (mm-40) REVERT: E 43 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9071 (mm) REVERT: F 13 ASN cc_start: 0.9330 (m-40) cc_final: 0.8646 (p0) REVERT: F 36 ARG cc_start: 0.7883 (ptm-80) cc_final: 0.7533 (ptm-80) REVERT: G 26 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.7068 (mmp) REVERT: G 99 MET cc_start: 0.9312 (tpp) cc_final: 0.8944 (tpp) REVERT: G 167 HIS cc_start: 0.7232 (t70) cc_final: 0.6703 (t70) REVERT: H 166 TRP cc_start: 0.8910 (p-90) cc_final: 0.8220 (p-90) REVERT: I 43 ARG cc_start: 0.5520 (mtt180) cc_final: 0.4964 (mmm160) REVERT: I 58 GLN cc_start: 0.8788 (tm-30) cc_final: 0.8435 (mm-40) REVERT: I 64 TYR cc_start: 0.9272 (m-80) cc_final: 0.9015 (m-80) REVERT: I 74 TYR cc_start: 0.9465 (m-80) cc_final: 0.8799 (m-80) REVERT: I 104 MET cc_start: 0.8717 (mmt) cc_final: 0.8434 (mmp) REVERT: J 13 LYS cc_start: 0.9557 (mmmt) cc_final: 0.8969 (mmtm) REVERT: J 22 LYS cc_start: 0.9060 (tttt) cc_final: 0.8395 (tppt) REVERT: J 28 ARG cc_start: 0.8667 (mtm-85) cc_final: 0.8030 (mtm110) REVERT: J 123 LEU cc_start: 0.9315 (mt) cc_final: 0.9103 (mm) REVERT: J 125 LYS cc_start: 0.9379 (tptm) cc_final: 0.8909 (tptp) REVERT: J 144 GLU cc_start: 0.9123 (tp30) cc_final: 0.8653 (tp30) REVERT: J 151 MET cc_start: 0.9147 (ppp) cc_final: 0.8891 (ppp) REVERT: K 39 LEU cc_start: 0.8925 (mt) cc_final: 0.8608 (mp) REVERT: K 56 LYS cc_start: 0.9264 (mptt) cc_final: 0.8546 (mmmt) REVERT: L 4 ARG cc_start: 0.3013 (ptt180) cc_final: 0.0757 (ptm-80) REVERT: L 150 PHE cc_start: 0.7463 (m-80) cc_final: 0.7089 (m-80) REVERT: M 110 MET cc_start: 0.9249 (ptp) cc_final: 0.9024 (pmm) REVERT: M 117 GLN cc_start: 0.9326 (mm-40) cc_final: 0.9083 (mp10) REVERT: N 31 GLN cc_start: 0.9085 (mp10) cc_final: 0.8870 (mp10) REVERT: N 45 MET cc_start: 0.9001 (ptp) cc_final: 0.8736 (pmm) REVERT: N 55 ASP cc_start: 0.9267 (m-30) cc_final: 0.8774 (t70) REVERT: N 87 MET cc_start: 0.8865 (ptm) cc_final: 0.8646 (ppp) REVERT: N 128 LYS cc_start: 0.9187 (tppp) cc_final: 0.8598 (tptt) REVERT: O 66 GLU cc_start: 0.8988 (pt0) cc_final: 0.8569 (pt0) REVERT: P 105 ARG cc_start: 0.8371 (ttt-90) cc_final: 0.8019 (tpt170) REVERT: Q 69 GLU cc_start: 0.8571 (pt0) cc_final: 0.8041 (pm20) REVERT: Q 80 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9128 (mm) REVERT: Q 111 GLN cc_start: 0.8664 (mm-40) cc_final: 0.8030 (mp10) REVERT: R 10 ASP cc_start: 0.8782 (m-30) cc_final: 0.8412 (m-30) REVERT: R 71 GLU cc_start: 0.9095 (tm-30) cc_final: 0.8781 (tm-30) REVERT: S 5 MET cc_start: 0.6310 (ttt) cc_final: 0.6021 (ttt) REVERT: T 13 GLU cc_start: 0.9132 (tt0) cc_final: 0.8848 (tm-30) REVERT: T 25 GLU cc_start: 0.8620 (pt0) cc_final: 0.7998 (pp20) REVERT: T 44 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.7817 (pt0) REVERT: T 77 TYR cc_start: 0.9146 (t80) cc_final: 0.8852 (t80) REVERT: T 88 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.8020 (tmm160) REVERT: U 6 LEU cc_start: 0.8925 (mt) cc_final: 0.8407 (mt) REVERT: U 14 ARG cc_start: 0.9059 (mmm-85) cc_final: 0.8628 (mmm160) REVERT: U 25 ARG cc_start: 0.8972 (mtm180) cc_final: 0.8455 (mtm180) REVERT: U 46 LYS cc_start: 0.9005 (pttm) cc_final: 0.8453 (tttm) REVERT: U 51 ARG cc_start: 0.7991 (mtp180) cc_final: 0.7766 (ptp-170) REVERT: V 7 LEU cc_start: 0.9202 (tp) cc_final: 0.8952 (tp) REVERT: V 10 ARG cc_start: 0.8515 (tpp80) cc_final: 0.8303 (tpp80) REVERT: V 16 MET cc_start: 0.7608 (mmm) cc_final: 0.7383 (mmm) REVERT: V 27 PHE cc_start: 0.9000 (OUTLIER) cc_final: 0.8745 (m-80) REVERT: W 28 LEU cc_start: 0.8812 (pp) cc_final: 0.8286 (mp) REVERT: X 16 LYS cc_start: 0.8499 (mtpp) cc_final: 0.8198 (ptpt) REVERT: X 43 MET cc_start: 0.6077 (tpp) cc_final: 0.5383 (tpp) REVERT: Y 12 GLN cc_start: 0.9315 (tt0) cc_final: 0.8954 (tt0) REVERT: Y 23 ARG cc_start: 0.9481 (mmm-85) cc_final: 0.8681 (mmm-85) REVERT: Y 26 MET cc_start: 0.8507 (ptp) cc_final: 0.7955 (ptp) REVERT: Y 47 GLN cc_start: 0.9327 (tt0) cc_final: 0.8858 (tp-100) REVERT: Z 53 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8545 (pttm) REVERT: 8 151 MET cc_start: 0.8901 (ppp) cc_final: 0.8672 (ppp) REVERT: 8 168 GLU cc_start: 0.7082 (pp20) cc_final: 0.6609 (pp20) REVERT: 8 186 ASP cc_start: 0.9268 (OUTLIER) cc_final: 0.8975 (t0) REVERT: 8 265 HIS cc_start: 0.8837 (t-90) cc_final: 0.8518 (t-170) REVERT: 8 288 MET cc_start: 0.9299 (tpp) cc_final: 0.8882 (tpt) outliers start: 243 outliers final: 162 residues processed: 1068 average time/residue: 1.2360 time to fit residues: 2313.3138 Evaluate side-chains 993 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 818 time to evaluate : 6.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 66 PHE Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 196 ASN Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 257 ARG Chi-restraints excluded: chain b residue 263 ASP Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 184 ASP Chi-restraints excluded: chain e residue 113 PHE Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain f residue 55 ASP Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 42 LYS Chi-restraints excluded: chain g residue 119 ASN Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain j residue 47 HIS Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 141 ASP Chi-restraints excluded: chain k residue 17 ARG Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 45 GLU Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 88 ASN Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 100 PHE Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 20 LEU Chi-restraints excluded: chain m residue 63 ILE Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 119 LEU Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 114 GLU Chi-restraints excluded: chain o residue 87 ILE Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain p residue 6 GLN Chi-restraints excluded: chain p residue 10 GLU Chi-restraints excluded: chain p residue 27 VAL Chi-restraints excluded: chain p residue 30 TRP Chi-restraints excluded: chain p residue 82 SER Chi-restraints excluded: chain q residue 3 VAL Chi-restraints excluded: chain q residue 103 VAL Chi-restraints excluded: chain r residue 25 LEU Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 52 GLU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain t residue 42 GLU Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 34 ILE Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain u residue 65 GLN Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 71 LYS Chi-restraints excluded: chain v residue 78 GLN Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 55 LEU Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain z residue 18 LYS Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain F residue 14 CYS Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 26 MET Chi-restraints excluded: chain G residue 38 HIS Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 192 TYR Chi-restraints excluded: chain I residue 102 TYR Chi-restraints excluded: chain I residue 173 ASP Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 94 HIS Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 5 TYR Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 123 ARG Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain R residue 8 ILE Chi-restraints excluded: chain R residue 57 ASP Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 85 TYR Chi-restraints excluded: chain S residue 37 ASP Chi-restraints excluded: chain S residue 54 SER Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 44 GLU Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 51 GLU Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain Z residue 53 LYS Chi-restraints excluded: chain Z residue 55 HIS Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 22 ASP Chi-restraints excluded: chain 8 residue 186 ASP Chi-restraints excluded: chain 8 residue 229 ASP Chi-restraints excluded: chain 8 residue 232 ILE Chi-restraints excluded: chain 8 residue 266 ILE Chi-restraints excluded: chain 8 residue 277 ASP Chi-restraints excluded: chain 8 residue 281 HIS Chi-restraints excluded: chain 8 residue 285 ASP Chi-restraints excluded: chain 8 residue 349 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1053 random chunks: chunk 342 optimal weight: 10.0000 chunk 916 optimal weight: 50.0000 chunk 201 optimal weight: 6.9990 chunk 597 optimal weight: 30.0000 chunk 251 optimal weight: 20.0000 chunk 1018 optimal weight: 4.9990 chunk 845 optimal weight: 20.0000 chunk 471 optimal weight: 30.0000 chunk 84 optimal weight: 50.0000 chunk 337 optimal weight: 6.9990 chunk 534 optimal weight: 7.9990 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 196 ASN c 167 ASN ** d 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 44 HIS ** f 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 20 ASN j 40 HIS ** j 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 8 GLN ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 197 HIS J 11 GLN J 69 ASN ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 ASN ** Q 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 301 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 160361 Z= 0.257 Angle : 0.611 13.455 239566 Z= 0.313 Chirality : 0.034 0.273 30559 Planarity : 0.004 0.065 13074 Dihedral : 23.645 171.434 79411 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 22.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.58 % Favored : 90.30 % Rotamer: Outliers : 5.25 % Allowed : 21.77 % Favored : 72.98 % 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: -2.41 (0.10), residues: 6011 helix: -0.50 (0.12), residues: 1887 sheet: -1.87 (0.15), residues: 1041 loop : -2.22 (0.11), residues: 3083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP G 103 HIS 0.009 0.001 HIS b 199 PHE 0.021 0.002 PHE x 45 TYR 0.019 0.002 TYR B 47 ARG 0.008 0.001 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1103 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 840 time to evaluate : 6.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 99 GLU cc_start: 0.8727 (tp30) cc_final: 0.8481 (tp30) REVERT: b 131 MET cc_start: 0.9457 (mmp) cc_final: 0.8887 (mmm) REVERT: b 184 GLU cc_start: 0.7980 (tp30) cc_final: 0.7624 (tp30) REVERT: b 196 ASN cc_start: 0.9124 (OUTLIER) cc_final: 0.8920 (t0) REVERT: b 250 GLN cc_start: 0.8323 (tm-30) cc_final: 0.7837 (tp40) REVERT: d 115 GLN cc_start: 0.9491 (tp40) cc_final: 0.9080 (tm-30) REVERT: d 158 PHE cc_start: 0.8881 (m-80) cc_final: 0.8510 (m-80) REVERT: d 188 MET cc_start: 0.8845 (tpp) cc_final: 0.8443 (tpp) REVERT: e 37 MET cc_start: 0.8388 (ptp) cc_final: 0.7964 (pmm) REVERT: e 47 LYS cc_start: 0.9391 (pttt) cc_final: 0.9150 (tppt) REVERT: e 95 MET cc_start: 0.9354 (tmm) cc_final: 0.8782 (ppp) REVERT: e 168 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8670 (mm) REVERT: f 57 TYR cc_start: 0.8099 (m-80) cc_final: 0.7597 (m-80) REVERT: f 61 TRP cc_start: 0.7643 (m100) cc_final: 0.7200 (m100) REVERT: f 123 GLU cc_start: 0.8690 (tp30) cc_final: 0.8032 (tm-30) REVERT: f 129 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8171 (tp30) REVERT: f 142 GLN cc_start: 0.8348 (tt0) cc_final: 0.7970 (tp40) REVERT: f 148 ARG cc_start: 0.9130 (ptm-80) cc_final: 0.8779 (ptt180) REVERT: g 2 GLN cc_start: 0.8040 (mm-40) cc_final: 0.7834 (mm-40) REVERT: j 75 TYR cc_start: 0.8787 (m-80) cc_final: 0.8423 (m-10) REVERT: j 108 MET cc_start: 0.8950 (mtm) cc_final: 0.8601 (mtm) REVERT: j 118 MET cc_start: 0.8548 (ptp) cc_final: 0.8051 (ptp) REVERT: k 73 ASP cc_start: 0.8592 (p0) cc_final: 0.8356 (p0) REVERT: m 41 LEU cc_start: 0.9441 (mm) cc_final: 0.9175 (mm) REVERT: m 136 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.5895 (mmt) REVERT: n 24 MET cc_start: 0.9114 (ttm) cc_final: 0.8586 (tpt) REVERT: n 82 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7909 (tm-30) REVERT: n 114 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7914 (pp20) REVERT: o 20 GLU cc_start: 0.9304 (tt0) cc_final: 0.8834 (tm-30) REVERT: o 61 GLN cc_start: 0.8825 (tt0) cc_final: 0.8379 (mp10) REVERT: p 10 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.8283 (pm20) REVERT: p 40 GLN cc_start: 0.8574 (tp40) cc_final: 0.8171 (tm-30) REVERT: p 70 GLU cc_start: 0.7951 (tp30) cc_final: 0.7649 (tp30) REVERT: p 98 TYR cc_start: 0.9073 (p90) cc_final: 0.8696 (p90) REVERT: q 48 ASP cc_start: 0.7626 (m-30) cc_final: 0.7378 (m-30) REVERT: q 51 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8626 (mm-40) REVERT: q 101 ASP cc_start: 0.8742 (t0) cc_final: 0.8413 (t0) REVERT: r 46 GLU cc_start: 0.8247 (mp0) cc_final: 0.7995 (pm20) REVERT: r 78 ARG cc_start: 0.9307 (tpp80) cc_final: 0.8796 (tpp-160) REVERT: r 86 GLN cc_start: 0.8812 (mm110) cc_final: 0.8564 (mm110) REVERT: s 78 GLU cc_start: 0.8174 (pp20) cc_final: 0.7456 (pp20) REVERT: s 94 ASP cc_start: 0.7343 (p0) cc_final: 0.7020 (p0) REVERT: u 13 LEU cc_start: 0.9606 (mt) cc_final: 0.9344 (mt) REVERT: u 36 GLU cc_start: 0.8422 (pm20) cc_final: 0.7625 (pm20) REVERT: v 75 GLN cc_start: 0.8320 (tp40) cc_final: 0.7897 (tm-30) REVERT: v 78 GLN cc_start: 0.9213 (OUTLIER) cc_final: 0.8540 (mp10) REVERT: w 15 LYS cc_start: 0.9434 (mmtt) cc_final: 0.9176 (mmtp) REVERT: w 79 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8506 (mt-10) REVERT: x 45 PHE cc_start: 0.8531 (m-80) cc_final: 0.7990 (t80) REVERT: x 55 MET cc_start: 0.9109 (mmm) cc_final: 0.8830 (mmm) REVERT: x 59 ASP cc_start: 0.9226 (m-30) cc_final: 0.8784 (p0) REVERT: x 61 LYS cc_start: 0.9019 (ttmt) cc_final: 0.8570 (mttm) REVERT: y 17 GLU cc_start: 0.9486 (tm-30) cc_final: 0.9204 (tm-30) REVERT: y 26 PHE cc_start: 0.8936 (t80) cc_final: 0.8012 (t80) REVERT: y 45 GLN cc_start: 0.8727 (pt0) cc_final: 0.8279 (pt0) REVERT: y 49 ASP cc_start: 0.9066 (m-30) cc_final: 0.8641 (m-30) REVERT: z 20 LYS cc_start: 0.9604 (mttt) cc_final: 0.9339 (mmtt) REVERT: z 36 GLU cc_start: 0.8740 (tt0) cc_final: 0.8264 (pm20) REVERT: B 27 LEU cc_start: 0.9263 (mm) cc_final: 0.9008 (mm) REVERT: C 9 LYS cc_start: 0.9169 (tttt) cc_final: 0.8703 (tttm) REVERT: C 24 LYS cc_start: 0.8716 (ptmt) cc_final: 0.8214 (ptmt) REVERT: D 29 GLN cc_start: 0.9567 (tp40) cc_final: 0.8981 (mm-40) REVERT: E 43 LEU cc_start: 0.9348 (mm) cc_final: 0.9091 (mm) REVERT: F 13 ASN cc_start: 0.9345 (m-40) cc_final: 0.8638 (p0) REVERT: F 36 ARG cc_start: 0.7885 (ptm-80) cc_final: 0.7461 (ptm-80) REVERT: G 26 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7328 (mmp) REVERT: G 167 HIS cc_start: 0.7253 (t70) cc_final: 0.6713 (t70) REVERT: H 166 TRP cc_start: 0.8908 (p-90) cc_final: 0.8209 (p-90) REVERT: I 43 ARG cc_start: 0.5493 (mtt180) cc_final: 0.4948 (mmm160) REVERT: I 55 ARG cc_start: 0.8884 (mmm160) cc_final: 0.8445 (mmm160) REVERT: I 58 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8335 (mm-40) REVERT: I 64 TYR cc_start: 0.9346 (m-80) cc_final: 0.9142 (m-80) REVERT: I 104 MET cc_start: 0.8885 (mmt) cc_final: 0.8035 (mmm) REVERT: J 13 LYS cc_start: 0.9556 (mmmt) cc_final: 0.8968 (mmtm) REVERT: J 28 ARG cc_start: 0.8635 (mtm-85) cc_final: 0.7997 (mtm110) REVERT: J 125 LYS cc_start: 0.9362 (tptm) cc_final: 0.8876 (tptp) REVERT: J 144 GLU cc_start: 0.9119 (tp30) cc_final: 0.8644 (tp30) REVERT: K 56 LYS cc_start: 0.9323 (mptt) cc_final: 0.8621 (mmmt) REVERT: K 91 ARG cc_start: 0.8682 (tpm170) cc_final: 0.8172 (tpm170) REVERT: L 102 TRP cc_start: 0.8484 (OUTLIER) cc_final: 0.8282 (m-10) REVERT: L 150 PHE cc_start: 0.7432 (m-80) cc_final: 0.7021 (m-80) REVERT: M 110 MET cc_start: 0.9242 (ptp) cc_final: 0.8899 (pmm) REVERT: N 55 ASP cc_start: 0.9295 (m-30) cc_final: 0.8724 (t70) REVERT: N 128 LYS cc_start: 0.9159 (tppp) cc_final: 0.8551 (tptt) REVERT: O 66 GLU cc_start: 0.8957 (pt0) cc_final: 0.8496 (pt0) REVERT: P 105 ARG cc_start: 0.8388 (ttt-90) cc_final: 0.8028 (tpt170) REVERT: Q 69 GLU cc_start: 0.8567 (pt0) cc_final: 0.8153 (mp0) REVERT: Q 111 GLN cc_start: 0.8646 (mm-40) cc_final: 0.7992 (mp10) REVERT: R 10 ASP cc_start: 0.8794 (m-30) cc_final: 0.8416 (m-30) REVERT: R 30 LYS cc_start: 0.7979 (mmmt) cc_final: 0.7737 (mmtm) REVERT: R 71 GLU cc_start: 0.9086 (tm-30) cc_final: 0.8783 (tm-30) REVERT: S 5 MET cc_start: 0.6186 (ttt) cc_final: 0.5844 (ttt) REVERT: S 23 ARG cc_start: 0.9711 (ttt90) cc_final: 0.9441 (ttm-80) REVERT: T 13 GLU cc_start: 0.9223 (tt0) cc_final: 0.8928 (tm-30) REVERT: T 25 GLU cc_start: 0.8656 (pt0) cc_final: 0.7997 (pp20) REVERT: T 44 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.7879 (pt0) REVERT: T 77 TYR cc_start: 0.9137 (t80) cc_final: 0.8875 (t80) REVERT: U 6 LEU cc_start: 0.8982 (mt) cc_final: 0.8467 (mt) REVERT: U 12 LYS cc_start: 0.9299 (pttt) cc_final: 0.9011 (mtmt) REVERT: U 25 ARG cc_start: 0.8988 (mtm180) cc_final: 0.8462 (mtm180) REVERT: U 46 LYS cc_start: 0.8925 (pttm) cc_final: 0.8433 (tttm) REVERT: V 7 LEU cc_start: 0.9205 (tp) cc_final: 0.8992 (tp) REVERT: V 10 ARG cc_start: 0.8545 (tpp80) cc_final: 0.8327 (tpp80) REVERT: V 16 MET cc_start: 0.7660 (mmm) cc_final: 0.7414 (mmm) REVERT: V 27 PHE cc_start: 0.9041 (OUTLIER) cc_final: 0.8721 (m-80) REVERT: X 16 LYS cc_start: 0.8593 (mtpp) cc_final: 0.8188 (mtmt) REVERT: X 43 MET cc_start: 0.5989 (tpp) cc_final: 0.5309 (tpp) REVERT: X 55 GLN cc_start: 0.8941 (pm20) cc_final: 0.8292 (pp30) REVERT: Y 12 GLN cc_start: 0.9334 (tt0) cc_final: 0.9022 (tt0) REVERT: Y 23 ARG cc_start: 0.9465 (mmm-85) cc_final: 0.8644 (mmm-85) REVERT: Y 26 MET cc_start: 0.8540 (ptp) cc_final: 0.8057 (ptp) REVERT: Y 47 GLN cc_start: 0.9235 (tt0) cc_final: 0.8851 (tp-100) REVERT: Z 53 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8630 (pttm) REVERT: 8 151 MET cc_start: 0.8952 (ppp) cc_final: 0.8746 (ppp) REVERT: 8 186 ASP cc_start: 0.9266 (OUTLIER) cc_final: 0.8981 (t0) REVERT: 8 265 HIS cc_start: 0.8837 (t-90) cc_final: 0.8491 (t-170) REVERT: 8 288 MET cc_start: 0.9293 (tpp) cc_final: 0.8868 (tpt) REVERT: 8 310 MET cc_start: 0.9326 (mmp) cc_final: 0.8995 (mpp) outliers start: 263 outliers final: 197 residues processed: 1005 average time/residue: 1.2708 time to fit residues: 2258.5953 Evaluate side-chains 1001 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 792 time to evaluate : 6.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 66 PHE Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 196 ASN Chi-restraints excluded: chain b residue 200 MET Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 263 ASP Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 95 SER Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 184 ASP Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain f residue 55 ASP Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 42 LYS Chi-restraints excluded: chain g residue 119 ASN Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain j residue 47 HIS Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 138 GLN Chi-restraints excluded: chain j residue 141 ASP Chi-restraints excluded: chain k residue 17 ARG Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 88 ASN Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 100 PHE Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 6 ARG Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 20 LEU Chi-restraints excluded: chain m residue 63 ILE Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 80 VAL Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 102 LEU Chi-restraints excluded: chain m residue 119 LEU Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain m residue 136 MET Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 114 GLU Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain p residue 2 ASN Chi-restraints excluded: chain p residue 6 GLN Chi-restraints excluded: chain p residue 10 GLU Chi-restraints excluded: chain p residue 30 TRP Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 82 SER Chi-restraints excluded: chain q residue 3 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain q residue 103 VAL Chi-restraints excluded: chain r residue 25 LEU Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 84 ARG Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain r residue 98 ILE Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 82 MET Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain s residue 105 VAL Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 42 GLU Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 34 ILE Chi-restraints excluded: chain u residue 65 GLN Chi-restraints excluded: chain v residue 1 MET Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 71 LYS Chi-restraints excluded: chain v residue 78 GLN Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain x residue 29 LEU Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain y residue 14 LEU Chi-restraints excluded: chain y residue 18 LEU Chi-restraints excluded: chain y residue 59 GLU Chi-restraints excluded: chain z residue 18 LYS Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain z residue 53 MET Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain F residue 14 CYS Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 26 MET Chi-restraints excluded: chain G residue 38 HIS Chi-restraints excluded: chain G residue 104 LYS Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 192 TYR Chi-restraints excluded: chain I residue 102 TYR Chi-restraints excluded: chain I residue 173 ASP Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain J residue 11 GLN Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 90 MET Chi-restraints excluded: chain K residue 94 HIS Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 102 TRP Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 48 PHE Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain N residue 5 TYR Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 123 ARG Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 23 HIS Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain R residue 8 ILE Chi-restraints excluded: chain R residue 57 ASP Chi-restraints excluded: chain R residue 85 TYR Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 54 SER Chi-restraints excluded: chain T residue 44 GLU Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 51 GLU Chi-restraints excluded: chain X residue 14 LEU Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain Z residue 53 LYS Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 22 ASP Chi-restraints excluded: chain 8 residue 186 ASP Chi-restraints excluded: chain 8 residue 229 ASP Chi-restraints excluded: chain 8 residue 232 ILE Chi-restraints excluded: chain 8 residue 266 ILE Chi-restraints excluded: chain 8 residue 277 ASP Chi-restraints excluded: chain 8 residue 281 HIS Chi-restraints excluded: chain 8 residue 285 ASP Chi-restraints excluded: chain 8 residue 349 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1053 random chunks: chunk 982 optimal weight: 20.0000 chunk 114 optimal weight: 50.0000 chunk 580 optimal weight: 20.0000 chunk 744 optimal weight: 20.0000 chunk 576 optimal weight: 20.0000 chunk 857 optimal weight: 50.0000 chunk 568 optimal weight: 30.0000 chunk 1014 optimal weight: 50.0000 chunk 635 optimal weight: 20.0000 chunk 618 optimal weight: 30.0000 chunk 468 optimal weight: 0.1980 overall best weight: 16.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 196 ASN ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 93 GLN ** o 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 71 ASN ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 9 HIS ** y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 ASN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 139 ASN I 197 HIS ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 42 ASN ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 ASN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 ASN Q 4 ASN ** Q 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 46 HIS ** Y 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 322 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.5492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.134 160361 Z= 0.501 Angle : 0.842 14.413 239566 Z= 0.423 Chirality : 0.043 0.303 30559 Planarity : 0.006 0.082 13074 Dihedral : 24.089 176.802 79411 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 36.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.43 % Favored : 87.49 % Rotamer: Outliers : 6.33 % Allowed : 22.03 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.78 (0.10), residues: 6011 helix: -0.92 (0.11), residues: 1889 sheet: -2.14 (0.14), residues: 1076 loop : -2.33 (0.11), residues: 3046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP G 103 HIS 0.009 0.002 HIS K 3 PHE 0.026 0.003 PHE e 174 TYR 0.023 0.003 TYR H 183 ARG 0.012 0.001 ARG N 17 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1077 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 317 poor density : 760 time to evaluate : 6.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 131 MET cc_start: 0.9479 (mmp) cc_final: 0.8879 (mmm) REVERT: b 160 TYR cc_start: 0.8776 (p90) cc_final: 0.8392 (p90) REVERT: b 196 ASN cc_start: 0.9110 (OUTLIER) cc_final: 0.8805 (t0) REVERT: d 115 GLN cc_start: 0.9509 (tp40) cc_final: 0.9120 (tm-30) REVERT: d 141 MET cc_start: 0.9047 (mmm) cc_final: 0.8778 (mpp) REVERT: d 158 PHE cc_start: 0.8881 (m-80) cc_final: 0.8459 (m-80) REVERT: d 188 MET cc_start: 0.9055 (tpp) cc_final: 0.8683 (tpp) REVERT: e 47 LYS cc_start: 0.9412 (pttt) cc_final: 0.9176 (tppt) REVERT: e 168 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8564 (mm) REVERT: f 57 TYR cc_start: 0.8023 (m-80) cc_final: 0.7557 (m-80) REVERT: f 59 ASP cc_start: 0.7048 (OUTLIER) cc_final: 0.6785 (p0) REVERT: f 61 TRP cc_start: 0.7643 (m100) cc_final: 0.7305 (m100) REVERT: f 123 GLU cc_start: 0.8666 (tp30) cc_final: 0.8130 (tm-30) REVERT: f 129 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8731 (mm-30) REVERT: f 142 GLN cc_start: 0.8505 (tt0) cc_final: 0.8052 (tp40) REVERT: f 148 ARG cc_start: 0.9258 (ptm-80) cc_final: 0.8781 (ptt180) REVERT: g 7 ASP cc_start: 0.9493 (m-30) cc_final: 0.9247 (m-30) REVERT: j 75 TYR cc_start: 0.8844 (m-80) cc_final: 0.8440 (m-10) REVERT: j 108 MET cc_start: 0.9078 (mtm) cc_final: 0.8685 (mtm) REVERT: j 118 MET cc_start: 0.8571 (ptp) cc_final: 0.7969 (ptp) REVERT: m 41 LEU cc_start: 0.9508 (mm) cc_final: 0.9200 (mm) REVERT: m 136 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.5809 (mmt) REVERT: n 82 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7884 (tm-30) REVERT: n 114 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7978 (pp20) REVERT: o 20 GLU cc_start: 0.9352 (tt0) cc_final: 0.8903 (tm-30) REVERT: o 116 GLN cc_start: 0.9494 (mm-40) cc_final: 0.9163 (mm-40) REVERT: p 10 GLU cc_start: 0.9214 (OUTLIER) cc_final: 0.8387 (pm20) REVERT: p 40 GLN cc_start: 0.8549 (tp40) cc_final: 0.8154 (tm-30) REVERT: p 98 TYR cc_start: 0.9142 (p90) cc_final: 0.8723 (p90) REVERT: q 51 GLN cc_start: 0.9312 (mm-40) cc_final: 0.8706 (mm-40) REVERT: q 56 PHE cc_start: 0.9224 (OUTLIER) cc_final: 0.8324 (m-80) REVERT: q 58 GLN cc_start: 0.9316 (OUTLIER) cc_final: 0.8196 (pp30) REVERT: q 101 ASP cc_start: 0.8987 (t0) cc_final: 0.8695 (t0) REVERT: r 46 GLU cc_start: 0.8339 (mp0) cc_final: 0.7970 (pm20) REVERT: r 78 ARG cc_start: 0.9393 (tpp80) cc_final: 0.8922 (tpp-160) REVERT: r 86 GLN cc_start: 0.8929 (mm110) cc_final: 0.8699 (mm110) REVERT: s 52 GLU cc_start: 0.9038 (mp0) cc_final: 0.8699 (pm20) REVERT: s 95 ARG cc_start: 0.8905 (mtp-110) cc_final: 0.8619 (tpp80) REVERT: t 7 LEU cc_start: 0.9364 (mt) cc_final: 0.9160 (mm) REVERT: t 37 ASP cc_start: 0.8585 (p0) cc_final: 0.8198 (p0) REVERT: t 76 ARG cc_start: 0.9127 (ttm-80) cc_final: 0.8002 (ppt170) REVERT: u 13 LEU cc_start: 0.9620 (mt) cc_final: 0.9368 (mt) REVERT: u 100 GLU cc_start: 0.8651 (pm20) cc_final: 0.8282 (pm20) REVERT: v 20 LEU cc_start: 0.9785 (tp) cc_final: 0.9468 (tp) REVERT: v 75 GLN cc_start: 0.8331 (tp40) cc_final: 0.7858 (tm-30) REVERT: w 15 LYS cc_start: 0.9465 (mmtt) cc_final: 0.9191 (mmtm) REVERT: w 79 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8465 (mt-10) REVERT: x 55 MET cc_start: 0.9142 (mmm) cc_final: 0.8837 (mmm) REVERT: x 59 ASP cc_start: 0.9348 (m-30) cc_final: 0.8876 (p0) REVERT: x 61 LYS cc_start: 0.9020 (ttmt) cc_final: 0.8617 (mmtp) REVERT: y 13 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8404 (mm-30) REVERT: y 17 GLU cc_start: 0.9565 (tm-30) cc_final: 0.9353 (tm-30) REVERT: y 49 ASP cc_start: 0.9137 (m-30) cc_final: 0.8729 (m-30) REVERT: z 8 GLN cc_start: 0.8216 (pt0) cc_final: 0.8004 (pt0) REVERT: z 20 LYS cc_start: 0.9616 (mttt) cc_final: 0.9380 (mmtt) REVERT: z 36 GLU cc_start: 0.8833 (tt0) cc_final: 0.8373 (pm20) REVERT: B 14 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8402 (tpp) REVERT: C 6 GLU cc_start: 0.6498 (pm20) cc_final: 0.6206 (pm20) REVERT: C 9 LYS cc_start: 0.9222 (tttt) cc_final: 0.8728 (tttm) REVERT: C 24 LYS cc_start: 0.8707 (ptmt) cc_final: 0.8375 (ptmt) REVERT: E 43 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9184 (mm) REVERT: E 53 ASP cc_start: 0.8724 (OUTLIER) cc_final: 0.8505 (m-30) REVERT: F 36 ARG cc_start: 0.8037 (ptm-80) cc_final: 0.7619 (ptm-80) REVERT: G 26 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7222 (mmp) REVERT: G 167 HIS cc_start: 0.7427 (t70) cc_final: 0.6830 (t70) REVERT: H 166 TRP cc_start: 0.8940 (p-90) cc_final: 0.8369 (p-90) REVERT: I 43 ARG cc_start: 0.5529 (mtt180) cc_final: 0.5155 (mmt180) REVERT: I 64 TYR cc_start: 0.9318 (m-80) cc_final: 0.9077 (m-80) REVERT: I 89 LEU cc_start: 0.9656 (mt) cc_final: 0.9440 (mp) REVERT: I 104 MET cc_start: 0.9061 (mmt) cc_final: 0.8275 (mmm) REVERT: J 22 LYS cc_start: 0.8963 (tptt) cc_final: 0.8298 (tppt) REVERT: J 28 ARG cc_start: 0.8633 (mtm-85) cc_final: 0.7995 (mtm110) REVERT: J 110 MET cc_start: 0.8918 (tpp) cc_final: 0.8685 (tpp) REVERT: J 125 LYS cc_start: 0.9466 (tptm) cc_final: 0.9019 (tptp) REVERT: J 144 GLU cc_start: 0.9138 (tp30) cc_final: 0.8906 (tm-30) REVERT: J 151 MET cc_start: 0.9086 (ppp) cc_final: 0.8872 (ppp) REVERT: K 56 LYS cc_start: 0.9333 (mptt) cc_final: 0.8766 (mmmt) REVERT: L 150 PHE cc_start: 0.7572 (m-80) cc_final: 0.7150 (m-80) REVERT: N 31 GLN cc_start: 0.9083 (mp10) cc_final: 0.8882 (mp10) REVERT: N 55 ASP cc_start: 0.9267 (m-30) cc_final: 0.8693 (t70) REVERT: N 128 LYS cc_start: 0.9108 (tppp) cc_final: 0.8580 (tptt) REVERT: O 66 GLU cc_start: 0.8814 (pt0) cc_final: 0.8324 (pt0) REVERT: P 105 ARG cc_start: 0.8397 (ttt-90) cc_final: 0.8052 (tpt170) REVERT: Q 69 GLU cc_start: 0.8606 (pt0) cc_final: 0.8146 (pm20) REVERT: Q 111 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8245 (mm110) REVERT: R 10 ASP cc_start: 0.8765 (m-30) cc_final: 0.8510 (m-30) REVERT: R 71 GLU cc_start: 0.9080 (tm-30) cc_final: 0.8858 (tm-30) REVERT: S 5 MET cc_start: 0.6261 (ttt) cc_final: 0.5660 (tpp) REVERT: T 13 GLU cc_start: 0.9178 (tt0) cc_final: 0.8859 (tm-30) REVERT: T 25 GLU cc_start: 0.8698 (pt0) cc_final: 0.8390 (pp20) REVERT: T 77 TYR cc_start: 0.9264 (t80) cc_final: 0.9035 (t80) REVERT: T 88 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7751 (tmm160) REVERT: U 46 LYS cc_start: 0.8939 (pttm) cc_final: 0.8386 (tttt) REVERT: V 80 LYS cc_start: 0.8168 (tppt) cc_final: 0.7937 (tppt) REVERT: X 16 LYS cc_start: 0.8484 (mtpp) cc_final: 0.8279 (ptpt) REVERT: X 43 MET cc_start: 0.5959 (tpp) cc_final: 0.5399 (tpp) REVERT: Y 12 GLN cc_start: 0.9399 (tt0) cc_final: 0.9105 (tt0) REVERT: Y 23 ARG cc_start: 0.9427 (mmm-85) cc_final: 0.8744 (mmm-85) REVERT: Y 26 MET cc_start: 0.8838 (ptp) cc_final: 0.8275 (ptp) REVERT: Y 47 GLN cc_start: 0.9375 (tt0) cc_final: 0.8934 (tp-100) REVERT: Y 58 ASP cc_start: 0.9167 (m-30) cc_final: 0.8356 (p0) REVERT: 8 151 MET cc_start: 0.9048 (ppp) cc_final: 0.8669 (ppp) REVERT: 8 168 GLU cc_start: 0.7078 (pp20) cc_final: 0.6682 (pp20) REVERT: 8 265 HIS cc_start: 0.8886 (t-90) cc_final: 0.8669 (t-90) REVERT: 8 288 MET cc_start: 0.9274 (tpp) cc_final: 0.8877 (tpt) outliers start: 317 outliers final: 238 residues processed: 968 average time/residue: 1.3438 time to fit residues: 2312.1134 Evaluate side-chains 977 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 726 time to evaluate : 6.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 66 PHE Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 196 ASN Chi-restraints excluded: chain b residue 200 MET Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 258 SER Chi-restraints excluded: chain b residue 263 ASP Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 88 GLU Chi-restraints excluded: chain c residue 95 SER Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 110 ILE Chi-restraints excluded: chain e residue 124 ARG Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain f residue 55 ASP Chi-restraints excluded: chain f residue 59 ASP Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 42 LYS Chi-restraints excluded: chain g residue 119 ASN Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain g residue 145 ASN Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 47 HIS Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain j residue 138 GLN Chi-restraints excluded: chain j residue 141 ASP Chi-restraints excluded: chain k residue 17 ARG Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 25 LEU Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 45 GLU Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 88 ASN Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 100 PHE Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 6 ARG Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 20 LEU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 63 ILE Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 102 LEU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain m residue 136 MET Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 114 GLU Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain p residue 2 ASN Chi-restraints excluded: chain p residue 6 GLN Chi-restraints excluded: chain p residue 10 GLU Chi-restraints excluded: chain p residue 24 THR Chi-restraints excluded: chain p residue 30 TRP Chi-restraints excluded: chain p residue 43 GLU Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 82 SER Chi-restraints excluded: chain q residue 3 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 56 PHE Chi-restraints excluded: chain q residue 58 GLN Chi-restraints excluded: chain r residue 25 LEU Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 84 ARG Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 22 ASP Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 82 MET Chi-restraints excluded: chain s residue 85 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 42 GLU Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 7 ASP Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 65 GLN Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 49 ASN Chi-restraints excluded: chain v residue 71 LYS Chi-restraints excluded: chain v residue 78 GLN Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 55 LEU Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain x residue 29 LEU Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain y residue 14 LEU Chi-restraints excluded: chain y residue 18 LEU Chi-restraints excluded: chain y residue 59 GLU Chi-restraints excluded: chain z residue 18 LYS Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain z residue 53 MET Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 14 CYS Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 26 MET Chi-restraints excluded: chain G residue 38 HIS Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 104 LYS Chi-restraints excluded: chain G residue 121 GLN Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 192 TYR Chi-restraints excluded: chain I residue 102 TYR Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 173 ASP Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 95 MET 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 143 LEU Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 90 MET Chi-restraints excluded: chain K residue 94 HIS Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 48 PHE Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain N residue 5 TYR Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 30 ASN Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 123 ARG Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 11 LYS Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 23 HIS Chi-restraints excluded: chain P residue 69 CYS Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain R residue 8 ILE Chi-restraints excluded: chain R residue 57 ASP Chi-restraints excluded: chain R residue 85 TYR Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain S residue 17 ASP Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 54 SER Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 44 GLU Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 51 GLU Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 60 ILE Chi-restraints excluded: chain X residue 14 LEU Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 22 ASP Chi-restraints excluded: chain a residue 23 ILE Chi-restraints excluded: chain 8 residue 84 LEU Chi-restraints excluded: chain 8 residue 229 ASP Chi-restraints excluded: chain 8 residue 232 ILE Chi-restraints excluded: chain 8 residue 277 ASP Chi-restraints excluded: chain 8 residue 281 HIS Chi-restraints excluded: chain 8 residue 285 ASP Chi-restraints excluded: chain 8 residue 349 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1053 random chunks: chunk 627 optimal weight: 30.0000 chunk 405 optimal weight: 20.0000 chunk 606 optimal weight: 20.0000 chunk 305 optimal weight: 7.9990 chunk 199 optimal weight: 9.9990 chunk 196 optimal weight: 5.9990 chunk 645 optimal weight: 20.0000 chunk 691 optimal weight: 20.0000 chunk 501 optimal weight: 20.0000 chunk 94 optimal weight: 5.9990 chunk 797 optimal weight: 10.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 196 ASN ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 44 HIS ** f 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 20 ASN ** j 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 71 ASN ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 8 GLN ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 197 HIS ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 GLN ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 ASN Q 4 ASN ** Q 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 19 ASN ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.5372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 160361 Z= 0.271 Angle : 0.650 12.258 239566 Z= 0.331 Chirality : 0.036 0.312 30559 Planarity : 0.004 0.062 13074 Dihedral : 24.002 175.511 79409 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 25.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.95 % Favored : 89.97 % Rotamer: Outliers : 5.09 % Allowed : 23.55 % Favored : 71.36 % 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: -2.51 (0.10), residues: 6011 helix: -0.64 (0.12), residues: 1882 sheet: -1.99 (0.15), residues: 1058 loop : -2.21 (0.11), residues: 3071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP L 102 HIS 0.006 0.001 HIS p 76 PHE 0.026 0.002 PHE K 8 TYR 0.023 0.002 TYR Z 37 ARG 0.009 0.001 ARG J 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1058 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 803 time to evaluate : 6.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 131 MET cc_start: 0.9461 (mmp) cc_final: 0.8876 (mmm) REVERT: b 160 TYR cc_start: 0.8630 (p90) cc_final: 0.8410 (p90) REVERT: b 184 GLU cc_start: 0.7963 (tp30) cc_final: 0.7740 (tp30) REVERT: b 196 ASN cc_start: 0.9070 (OUTLIER) cc_final: 0.8712 (t0) REVERT: b 250 GLN cc_start: 0.8342 (tm-30) cc_final: 0.7856 (tp40) REVERT: d 115 GLN cc_start: 0.9471 (tp40) cc_final: 0.9072 (tm-30) REVERT: d 158 PHE cc_start: 0.8830 (m-80) cc_final: 0.8429 (m-80) REVERT: d 188 MET cc_start: 0.9170 (tpp) cc_final: 0.8845 (tpt) REVERT: e 37 MET cc_start: 0.7973 (ptp) cc_final: 0.7542 (pmm) REVERT: e 47 LYS cc_start: 0.9390 (pttt) cc_final: 0.9166 (tppt) REVERT: e 168 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8731 (mm) REVERT: f 57 TYR cc_start: 0.7852 (m-80) cc_final: 0.7426 (m-80) REVERT: f 61 TRP cc_start: 0.7626 (m100) cc_final: 0.7148 (m100) REVERT: f 123 GLU cc_start: 0.8668 (tp30) cc_final: 0.8060 (tm-30) REVERT: f 129 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8759 (mm-30) REVERT: f 142 GLN cc_start: 0.8380 (tt0) cc_final: 0.8018 (tp40) REVERT: f 148 ARG cc_start: 0.9164 (ptm-80) cc_final: 0.8743 (ptt180) REVERT: j 75 TYR cc_start: 0.8833 (m-80) cc_final: 0.8370 (m-10) REVERT: j 108 MET cc_start: 0.8951 (mtm) cc_final: 0.8628 (mtm) REVERT: j 118 MET cc_start: 0.8583 (ptp) cc_final: 0.8087 (ptp) REVERT: k 73 ASP cc_start: 0.8518 (p0) cc_final: 0.8303 (p0) REVERT: m 41 LEU cc_start: 0.9472 (mm) cc_final: 0.9120 (mm) REVERT: m 136 MET cc_start: 0.7543 (mtm) cc_final: 0.5831 (mmt) REVERT: n 82 GLU cc_start: 0.8359 (tm-30) cc_final: 0.7950 (tm-30) REVERT: n 114 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7928 (pp20) REVERT: o 20 GLU cc_start: 0.9346 (tt0) cc_final: 0.8885 (tm-30) REVERT: o 116 GLN cc_start: 0.9377 (mm-40) cc_final: 0.9103 (mm-40) REVERT: p 10 GLU cc_start: 0.9212 (OUTLIER) cc_final: 0.8388 (pm20) REVERT: p 40 GLN cc_start: 0.8542 (tp40) cc_final: 0.8197 (tm-30) REVERT: p 98 TYR cc_start: 0.9117 (p90) cc_final: 0.8726 (p90) REVERT: q 51 GLN cc_start: 0.9249 (mm-40) cc_final: 0.8494 (mm-40) REVERT: q 58 GLN cc_start: 0.9250 (OUTLIER) cc_final: 0.8242 (pp30) REVERT: q 101 ASP cc_start: 0.8815 (t0) cc_final: 0.8487 (t0) REVERT: r 46 GLU cc_start: 0.8312 (mp0) cc_final: 0.8013 (pm20) REVERT: r 60 LYS cc_start: 0.9021 (mmtp) cc_final: 0.8710 (mmtm) REVERT: r 78 ARG cc_start: 0.9314 (tpp80) cc_final: 0.8826 (tpp-160) REVERT: r 86 GLN cc_start: 0.8751 (mm110) cc_final: 0.8516 (mm110) REVERT: s 52 GLU cc_start: 0.9025 (mp0) cc_final: 0.8728 (pm20) REVERT: s 78 GLU cc_start: 0.8089 (pp20) cc_final: 0.7226 (pp20) REVERT: t 76 ARG cc_start: 0.9002 (ttm-80) cc_final: 0.8027 (ppt170) REVERT: u 13 LEU cc_start: 0.9617 (mt) cc_final: 0.9407 (mt) REVERT: u 36 GLU cc_start: 0.8482 (pm20) cc_final: 0.7440 (pm20) REVERT: v 75 GLN cc_start: 0.8318 (tp40) cc_final: 0.7849 (tm-30) REVERT: w 15 LYS cc_start: 0.9424 (mmtt) cc_final: 0.9114 (mmtm) REVERT: w 79 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8553 (mp0) REVERT: x 55 MET cc_start: 0.9120 (mmm) cc_final: 0.8831 (mmm) REVERT: x 59 ASP cc_start: 0.9267 (m-30) cc_final: 0.8807 (p0) REVERT: x 61 LYS cc_start: 0.8975 (ttmt) cc_final: 0.8596 (mttm) REVERT: y 13 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8529 (mm-30) REVERT: y 17 GLU cc_start: 0.9486 (tm-30) cc_final: 0.9188 (tm-30) REVERT: y 45 GLN cc_start: 0.8780 (pt0) cc_final: 0.8262 (pt0) REVERT: y 49 ASP cc_start: 0.9088 (m-30) cc_final: 0.8651 (m-30) REVERT: z 5 LYS cc_start: 0.9414 (mmmm) cc_final: 0.8814 (mmmm) REVERT: z 8 GLN cc_start: 0.8158 (pt0) cc_final: 0.7927 (pt0) REVERT: z 20 LYS cc_start: 0.9607 (mttt) cc_final: 0.9346 (mmtt) REVERT: C 6 GLU cc_start: 0.6574 (pm20) cc_final: 0.5932 (pm20) REVERT: C 9 LYS cc_start: 0.9194 (tttt) cc_final: 0.8749 (tttm) REVERT: C 24 LYS cc_start: 0.8651 (ptmt) cc_final: 0.8096 (ptmt) REVERT: C 31 GLU cc_start: 0.8625 (pm20) cc_final: 0.8350 (pm20) REVERT: E 43 LEU cc_start: 0.9379 (mm) cc_final: 0.9117 (mm) REVERT: E 53 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8444 (m-30) REVERT: F 36 ARG cc_start: 0.7919 (ptm-80) cc_final: 0.7323 (ptm-80) REVERT: G 26 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7290 (mmp) REVERT: G 167 HIS cc_start: 0.7399 (t70) cc_final: 0.6793 (t70) REVERT: H 166 TRP cc_start: 0.8993 (p-90) cc_final: 0.8252 (p-90) REVERT: I 43 ARG cc_start: 0.5751 (mtt180) cc_final: 0.5170 (mmm160) REVERT: I 55 ARG cc_start: 0.8846 (mmm160) cc_final: 0.8582 (mmm160) REVERT: I 104 MET cc_start: 0.8970 (mmt) cc_final: 0.8118 (mmm) REVERT: I 123 MET cc_start: 0.8828 (mmm) cc_final: 0.8352 (mmm) REVERT: I 135 GLN cc_start: 0.8511 (tm-30) cc_final: 0.8295 (tm-30) REVERT: J 12 GLU cc_start: 0.8596 (mp0) cc_final: 0.8335 (mp0) REVERT: J 13 LYS cc_start: 0.9588 (mmmt) cc_final: 0.8826 (mmtm) REVERT: J 22 LYS cc_start: 0.9002 (tptt) cc_final: 0.8320 (tppt) REVERT: J 28 ARG cc_start: 0.8620 (mtm-85) cc_final: 0.7702 (mtm110) REVERT: J 70 MET cc_start: 0.8041 (tpt) cc_final: 0.7795 (tpt) REVERT: J 110 MET cc_start: 0.9155 (tpp) cc_final: 0.8904 (tpp) REVERT: J 125 LYS cc_start: 0.9476 (tptm) cc_final: 0.8945 (tptp) REVERT: J 144 GLU cc_start: 0.9097 (tp30) cc_final: 0.8877 (tm-30) REVERT: K 9 MET cc_start: 0.8187 (mmm) cc_final: 0.7953 (mmm) REVERT: K 56 LYS cc_start: 0.9233 (mptt) cc_final: 0.8679 (mmmt) REVERT: K 91 ARG cc_start: 0.8621 (tpm170) cc_final: 0.8311 (tpm170) REVERT: L 150 PHE cc_start: 0.7519 (m-80) cc_final: 0.7083 (m-80) REVERT: M 110 MET cc_start: 0.9253 (ptp) cc_final: 0.8959 (pmm) REVERT: N 31 GLN cc_start: 0.9069 (mp10) cc_final: 0.8819 (mp10) REVERT: N 55 ASP cc_start: 0.9217 (m-30) cc_final: 0.8675 (t70) REVERT: N 128 LYS cc_start: 0.9147 (tppp) cc_final: 0.8626 (tptt) REVERT: O 66 GLU cc_start: 0.8921 (pt0) cc_final: 0.8514 (pt0) REVERT: P 29 THR cc_start: 0.8826 (m) cc_final: 0.8619 (p) REVERT: P 105 ARG cc_start: 0.8371 (ttt-90) cc_final: 0.8064 (tpt170) REVERT: Q 69 GLU cc_start: 0.8660 (pt0) cc_final: 0.8176 (pm20) REVERT: Q 80 LEU cc_start: 0.9230 (mm) cc_final: 0.8893 (mm) REVERT: Q 111 GLN cc_start: 0.8577 (mm-40) cc_final: 0.8217 (mm110) REVERT: R 10 ASP cc_start: 0.8705 (m-30) cc_final: 0.8429 (m-30) REVERT: R 71 GLU cc_start: 0.9091 (tm-30) cc_final: 0.8792 (tm-30) REVERT: S 5 MET cc_start: 0.6257 (ttt) cc_final: 0.5639 (tpp) REVERT: T 13 GLU cc_start: 0.9256 (tt0) cc_final: 0.8969 (tm-30) REVERT: T 25 GLU cc_start: 0.8631 (pt0) cc_final: 0.8020 (pp20) REVERT: T 44 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.7831 (pt0) REVERT: T 77 TYR cc_start: 0.9123 (t80) cc_final: 0.8815 (t80) REVERT: T 88 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7786 (tmm160) REVERT: U 6 LEU cc_start: 0.9016 (mt) cc_final: 0.8785 (mt) REVERT: U 14 ARG cc_start: 0.9127 (mmm-85) cc_final: 0.8193 (mtt180) REVERT: U 25 ARG cc_start: 0.8949 (mtm180) cc_final: 0.8465 (mpp80) REVERT: U 46 LYS cc_start: 0.8941 (pttm) cc_final: 0.8526 (tttm) REVERT: V 7 LEU cc_start: 0.9232 (tp) cc_final: 0.8741 (mp) REVERT: V 16 MET cc_start: 0.7584 (mmm) cc_final: 0.6937 (mmm) REVERT: X 14 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8025 (mt) REVERT: X 16 LYS cc_start: 0.8512 (mtpp) cc_final: 0.8308 (ptpt) REVERT: X 43 MET cc_start: 0.6252 (tpp) cc_final: 0.5647 (tpp) REVERT: Y 23 ARG cc_start: 0.9388 (mmm-85) cc_final: 0.8645 (mmm-85) REVERT: Y 26 MET cc_start: 0.8696 (ptp) cc_final: 0.8270 (ptp) REVERT: Y 47 GLN cc_start: 0.9282 (tt0) cc_final: 0.8842 (tp-100) REVERT: Y 58 ASP cc_start: 0.9075 (m-30) cc_final: 0.8066 (p0) REVERT: 8 17 ARG cc_start: 0.3460 (tpt170) cc_final: 0.3007 (tpt170) REVERT: 8 151 MET cc_start: 0.8936 (ppp) cc_final: 0.8673 (ppp) REVERT: 8 168 GLU cc_start: 0.7035 (pp20) cc_final: 0.6641 (pp20) REVERT: 8 262 ARG cc_start: 0.7155 (ttm170) cc_final: 0.6812 (ttp-170) REVERT: 8 265 HIS cc_start: 0.8864 (t-90) cc_final: 0.8628 (t-170) REVERT: 8 288 MET cc_start: 0.9282 (tpp) cc_final: 0.8995 (tpp) outliers start: 255 outliers final: 201 residues processed: 966 average time/residue: 1.3351 time to fit residues: 2291.9565 Evaluate side-chains 974 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 763 time to evaluate : 6.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 66 PHE Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 196 ASN Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 258 SER Chi-restraints excluded: chain b residue 263 ASP Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 95 SER Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain e residue 124 ARG Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain f residue 55 ASP Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 42 LYS Chi-restraints excluded: chain g residue 119 ASN Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain g residue 145 ASN Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 47 HIS Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 141 ASP Chi-restraints excluded: chain k residue 17 ARG Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 45 GLU Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 88 ASN Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 100 PHE Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 20 LEU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 63 ILE Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 102 LEU Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 114 GLU Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain p residue 2 ASN Chi-restraints excluded: chain p residue 6 GLN Chi-restraints excluded: chain p residue 10 GLU Chi-restraints excluded: chain p residue 24 THR Chi-restraints excluded: chain p residue 30 TRP Chi-restraints excluded: chain p residue 43 GLU Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 82 SER Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain q residue 58 GLN Chi-restraints excluded: chain q residue 103 VAL Chi-restraints excluded: chain q residue 116 LEU Chi-restraints excluded: chain r residue 25 LEU Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 84 ARG Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 82 MET Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 42 GLU Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 61 GLU Chi-restraints excluded: chain u residue 65 GLN Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 71 LYS Chi-restraints excluded: chain v residue 78 GLN Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 29 LEU Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain y residue 9 LYS Chi-restraints excluded: chain y residue 14 LEU Chi-restraints excluded: chain y residue 18 LEU Chi-restraints excluded: chain z residue 18 LYS Chi-restraints excluded: chain z residue 43 ILE Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain z residue 53 MET Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 14 CYS Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 26 MET Chi-restraints excluded: chain G residue 38 HIS Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 192 TYR Chi-restraints excluded: chain I residue 102 TYR Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 173 ASP Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 90 MET Chi-restraints excluded: chain K residue 94 HIS Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain N residue 5 TYR Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 123 ARG Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 11 LYS Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 23 HIS Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 57 ASP Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 85 TYR Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain S residue 17 ASP Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain T residue 44 GLU Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain X residue 14 LEU Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain Z residue 55 HIS Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 22 ASP Chi-restraints excluded: chain 8 residue 84 LEU Chi-restraints excluded: chain 8 residue 229 ASP Chi-restraints excluded: chain 8 residue 232 ILE Chi-restraints excluded: chain 8 residue 266 ILE Chi-restraints excluded: chain 8 residue 277 ASP Chi-restraints excluded: chain 8 residue 281 HIS Chi-restraints excluded: chain 8 residue 285 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1053 random chunks: chunk 923 optimal weight: 50.0000 chunk 972 optimal weight: 30.0000 chunk 887 optimal weight: 10.0000 chunk 945 optimal weight: 20.0000 chunk 569 optimal weight: 30.0000 chunk 412 optimal weight: 30.0000 chunk 742 optimal weight: 40.0000 chunk 290 optimal weight: 7.9990 chunk 854 optimal weight: 50.0000 chunk 894 optimal weight: 30.0000 chunk 942 optimal weight: 20.0000 overall best weight: 17.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 152 GLN b 196 ASN ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 72 ASN ** f 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 71 ASN ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 28 ASN ** y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 130 ASN I 197 HIS ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 ASN N 36 GLN Q 4 ASN ** Q 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 83 ASN Z 55 HIS ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.5956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.102 160361 Z= 0.545 Angle : 0.874 12.629 239566 Z= 0.437 Chirality : 0.045 0.321 30559 Planarity : 0.006 0.094 13074 Dihedral : 24.307 179.188 79409 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 38.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.96 % Favored : 86.96 % Rotamer: Outliers : 5.39 % Allowed : 24.09 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 6011 helix: -0.99 (0.11), residues: 1868 sheet: -2.11 (0.14), residues: 1083 loop : -2.41 (0.11), residues: 3060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP G 103 HIS 0.012 0.002 HIS p 76 PHE 0.027 0.003 PHE e 174 TYR 0.023 0.003 TYR k 32 ARG 0.015 0.001 ARG x 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1006 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 736 time to evaluate : 6.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 131 MET cc_start: 0.9470 (mmp) cc_final: 0.8837 (mmm) REVERT: b 160 TYR cc_start: 0.8686 (p90) cc_final: 0.8278 (p90) REVERT: b 196 ASN cc_start: 0.8964 (OUTLIER) cc_final: 0.8603 (t0) REVERT: d 115 GLN cc_start: 0.9493 (tp40) cc_final: 0.9096 (tm-30) REVERT: d 158 PHE cc_start: 0.8873 (m-80) cc_final: 0.8410 (m-80) REVERT: d 188 MET cc_start: 0.9249 (tpp) cc_final: 0.8951 (tpt) REVERT: e 37 MET cc_start: 0.8052 (ptp) cc_final: 0.7558 (pmm) REVERT: e 47 LYS cc_start: 0.9409 (pttt) cc_final: 0.9179 (tppt) REVERT: e 168 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8703 (mm) REVERT: f 57 TYR cc_start: 0.7795 (m-80) cc_final: 0.7375 (m-80) REVERT: f 61 TRP cc_start: 0.7622 (m100) cc_final: 0.7147 (m100) REVERT: f 123 GLU cc_start: 0.8664 (tp30) cc_final: 0.8123 (tm-30) REVERT: f 129 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8332 (mm-30) REVERT: f 142 GLN cc_start: 0.8485 (tt0) cc_final: 0.8048 (tp40) REVERT: j 75 TYR cc_start: 0.8832 (m-80) cc_final: 0.8446 (m-10) REVERT: j 108 MET cc_start: 0.9063 (mtm) cc_final: 0.8686 (mtm) REVERT: k 8 LEU cc_start: 0.9596 (mm) cc_final: 0.9365 (mm) REVERT: m 41 LEU cc_start: 0.9563 (mm) cc_final: 0.9222 (mm) REVERT: n 82 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7888 (tm-30) REVERT: n 114 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7993 (pp20) REVERT: o 20 GLU cc_start: 0.9349 (tt0) cc_final: 0.8914 (tm-30) REVERT: o 116 GLN cc_start: 0.9469 (mm-40) cc_final: 0.9138 (mm-40) REVERT: p 6 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.7950 (mp10) REVERT: p 10 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8420 (pm20) REVERT: p 40 GLN cc_start: 0.8550 (tp40) cc_final: 0.8243 (tm-30) REVERT: p 98 TYR cc_start: 0.9183 (p90) cc_final: 0.8657 (p90) REVERT: q 48 ASP cc_start: 0.7679 (m-30) cc_final: 0.7476 (m-30) REVERT: q 51 GLN cc_start: 0.9315 (mm-40) cc_final: 0.8717 (mm-40) REVERT: q 58 GLN cc_start: 0.9328 (OUTLIER) cc_final: 0.8192 (pp30) REVERT: q 101 ASP cc_start: 0.9000 (t0) cc_final: 0.8749 (t0) REVERT: r 46 GLU cc_start: 0.8263 (mp0) cc_final: 0.7892 (pm20) REVERT: r 60 LYS cc_start: 0.8956 (mmtp) cc_final: 0.8655 (mmtm) REVERT: r 78 ARG cc_start: 0.9404 (tpp80) cc_final: 0.8934 (tpp-160) REVERT: r 86 GLN cc_start: 0.8853 (mm110) cc_final: 0.8617 (mm110) REVERT: s 52 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8806 (pm20) REVERT: s 78 GLU cc_start: 0.7963 (pp20) cc_final: 0.7016 (pp20) REVERT: s 95 ARG cc_start: 0.8810 (mtp85) cc_final: 0.8456 (mmm-85) REVERT: t 37 ASP cc_start: 0.8599 (p0) cc_final: 0.8221 (p0) REVERT: t 76 ARG cc_start: 0.9138 (ttm-80) cc_final: 0.8035 (ppt170) REVERT: u 13 LEU cc_start: 0.9622 (mt) cc_final: 0.9365 (mt) REVERT: v 20 LEU cc_start: 0.9794 (tp) cc_final: 0.9481 (tp) REVERT: v 75 GLN cc_start: 0.8215 (tp40) cc_final: 0.7665 (tm-30) REVERT: w 15 LYS cc_start: 0.9465 (mmtt) cc_final: 0.9238 (mmtm) REVERT: w 79 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8443 (mt-10) REVERT: y 13 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8376 (mm-30) REVERT: y 17 GLU cc_start: 0.9549 (tm-30) cc_final: 0.9275 (tm-30) REVERT: y 49 ASP cc_start: 0.9146 (m-30) cc_final: 0.8734 (m-30) REVERT: z 5 LYS cc_start: 0.9439 (mmmm) cc_final: 0.9168 (mmmt) REVERT: z 20 LYS cc_start: 0.9617 (mttt) cc_final: 0.9382 (mmtt) REVERT: B 14 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8320 (tpp) REVERT: B 36 LYS cc_start: 0.9320 (tptp) cc_final: 0.8938 (tptp) REVERT: C 9 LYS cc_start: 0.9259 (tttt) cc_final: 0.8766 (tttm) REVERT: C 24 LYS cc_start: 0.8639 (ptmt) cc_final: 0.8152 (ptmt) REVERT: C 31 GLU cc_start: 0.8533 (pm20) cc_final: 0.8236 (pm20) REVERT: E 43 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9182 (mm) REVERT: E 53 ASP cc_start: 0.8770 (OUTLIER) cc_final: 0.8537 (m-30) REVERT: F 36 ARG cc_start: 0.8020 (ptm-80) cc_final: 0.7422 (ptm-80) REVERT: G 26 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7273 (mmp) REVERT: G 167 HIS cc_start: 0.7639 (t70) cc_final: 0.7053 (t70) REVERT: H 166 TRP cc_start: 0.8980 (p-90) cc_final: 0.8481 (p-90) REVERT: I 43 ARG cc_start: 0.5862 (mtt180) cc_final: 0.5303 (mmm160) REVERT: I 55 ARG cc_start: 0.8943 (mmm160) cc_final: 0.8490 (mmm160) REVERT: I 58 GLN cc_start: 0.8780 (tm-30) cc_final: 0.8317 (mm-40) REVERT: I 104 MET cc_start: 0.9137 (mmt) cc_final: 0.8399 (mmm) REVERT: I 123 MET cc_start: 0.8926 (mmm) cc_final: 0.8489 (mmm) REVERT: J 110 MET cc_start: 0.9280 (tpp) cc_final: 0.8972 (tpp) REVERT: J 125 LYS cc_start: 0.9171 (tptm) cc_final: 0.8866 (tptp) REVERT: J 144 GLU cc_start: 0.9165 (tp30) cc_final: 0.8935 (tm-30) REVERT: K 56 LYS cc_start: 0.9099 (mptt) cc_final: 0.8579 (mmmt) REVERT: L 150 PHE cc_start: 0.7614 (m-80) cc_final: 0.7179 (m-80) REVERT: M 110 MET cc_start: 0.9219 (ptp) cc_final: 0.8827 (pmm) REVERT: N 31 GLN cc_start: 0.9106 (mp10) cc_final: 0.8856 (mp10) REVERT: N 55 ASP cc_start: 0.9202 (m-30) cc_final: 0.8629 (t70) REVERT: N 128 LYS cc_start: 0.9110 (tppp) cc_final: 0.8575 (tptt) REVERT: O 66 GLU cc_start: 0.8803 (pt0) cc_final: 0.8344 (pt0) REVERT: P 105 ARG cc_start: 0.8217 (ttt-90) cc_final: 0.7922 (tpt170) REVERT: Q 69 GLU cc_start: 0.8577 (pt0) cc_final: 0.8194 (pm20) REVERT: Q 80 LEU cc_start: 0.9264 (mm) cc_final: 0.8851 (mm) REVERT: Q 111 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8161 (mm110) REVERT: R 10 ASP cc_start: 0.8730 (m-30) cc_final: 0.8474 (m-30) REVERT: R 71 GLU cc_start: 0.9062 (tm-30) cc_final: 0.8767 (tm-30) REVERT: S 5 MET cc_start: 0.6226 (ttt) cc_final: 0.5631 (tpp) REVERT: T 13 GLU cc_start: 0.9227 (tt0) cc_final: 0.8928 (tm-30) REVERT: T 25 GLU cc_start: 0.8692 (pt0) cc_final: 0.8384 (pp20) REVERT: T 88 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7787 (tmm160) REVERT: U 14 ARG cc_start: 0.9213 (mmm-85) cc_final: 0.8686 (mmm160) REVERT: U 46 LYS cc_start: 0.8927 (pttm) cc_final: 0.8397 (tttm) REVERT: X 16 LYS cc_start: 0.8495 (mtpp) cc_final: 0.8244 (ptpt) REVERT: X 43 MET cc_start: 0.5932 (tpp) cc_final: 0.5464 (tpp) REVERT: Y 23 ARG cc_start: 0.9332 (mmm-85) cc_final: 0.8727 (mmm-85) REVERT: Y 26 MET cc_start: 0.8889 (ptp) cc_final: 0.8300 (ptp) REVERT: Y 47 GLN cc_start: 0.9373 (tt0) cc_final: 0.8917 (tp-100) REVERT: Y 58 ASP cc_start: 0.9223 (m-30) cc_final: 0.8445 (p0) REVERT: a 8 MET cc_start: -0.1874 (mpp) cc_final: -0.2711 (ttp) REVERT: 8 151 MET cc_start: 0.9053 (ppp) cc_final: 0.8731 (ppp) REVERT: 8 168 GLU cc_start: 0.7111 (pp20) cc_final: 0.6719 (pp20) REVERT: 8 262 ARG cc_start: 0.7230 (ttm170) cc_final: 0.6869 (ttp-170) REVERT: 8 288 MET cc_start: 0.9307 (tpp) cc_final: 0.9069 (tpp) outliers start: 270 outliers final: 230 residues processed: 920 average time/residue: 1.2458 time to fit residues: 2022.6265 Evaluate side-chains 965 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 723 time to evaluate : 6.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 66 PHE Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 196 ASN Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 263 ASP Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 95 SER Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain e residue 110 ILE Chi-restraints excluded: chain e residue 124 ARG Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain f residue 51 PHE Chi-restraints excluded: chain f residue 55 ASP Chi-restraints excluded: chain f residue 72 ASN Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 42 LYS Chi-restraints excluded: chain g residue 119 ASN Chi-restraints excluded: chain g residue 121 VAL Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain g residue 145 ASN Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 47 HIS Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 141 ASP Chi-restraints excluded: chain k residue 17 ARG Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 25 LEU Chi-restraints excluded: chain k residue 45 GLU Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 88 ASN Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 100 PHE Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 20 LEU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 102 LEU Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 114 GLU Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain p residue 2 ASN Chi-restraints excluded: chain p residue 6 GLN Chi-restraints excluded: chain p residue 10 GLU Chi-restraints excluded: chain p residue 24 THR Chi-restraints excluded: chain p residue 30 TRP Chi-restraints excluded: chain p residue 43 GLU Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 82 SER Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 58 GLN Chi-restraints excluded: chain q residue 103 VAL Chi-restraints excluded: chain q residue 116 LEU Chi-restraints excluded: chain r residue 25 LEU Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 84 ARG Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 7 HIS Chi-restraints excluded: chain s residue 52 GLU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 42 GLU Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 61 GLU Chi-restraints excluded: chain u residue 65 GLN Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 71 LYS Chi-restraints excluded: chain v residue 78 GLN Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain x residue 6 VAL Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 29 LEU Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 9 LYS Chi-restraints excluded: chain y residue 14 LEU Chi-restraints excluded: chain y residue 18 LEU Chi-restraints excluded: chain z residue 18 LYS Chi-restraints excluded: chain z residue 43 ILE Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain z residue 53 MET Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 14 CYS Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 26 MET Chi-restraints excluded: chain G residue 38 HIS Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 104 LYS Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 192 TYR Chi-restraints excluded: chain I residue 102 TYR Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 173 ASP Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 197 HIS Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 90 MET Chi-restraints excluded: chain K residue 94 HIS Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain N residue 5 TYR Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 123 ARG Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 23 HIS Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain R residue 8 ILE Chi-restraints excluded: chain R residue 57 ASP Chi-restraints excluded: chain R residue 85 TYR Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain S residue 17 ASP Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 54 SER Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 44 GLU Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 59 HIS Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 51 GLU Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain X residue 14 LEU Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 22 ASP Chi-restraints excluded: chain a residue 23 ILE Chi-restraints excluded: chain 8 residue 84 LEU Chi-restraints excluded: chain 8 residue 229 ASP Chi-restraints excluded: chain 8 residue 232 ILE Chi-restraints excluded: chain 8 residue 277 ASP Chi-restraints excluded: chain 8 residue 281 HIS Chi-restraints excluded: chain 8 residue 285 ASP Chi-restraints excluded: chain 8 residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1053 random chunks: chunk 621 optimal weight: 30.0000 chunk 1000 optimal weight: 30.0000 chunk 610 optimal weight: 10.0000 chunk 474 optimal weight: 9.9990 chunk 695 optimal weight: 10.0000 chunk 1049 optimal weight: 6.9990 chunk 965 optimal weight: 10.0000 chunk 835 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 645 optimal weight: 20.0000 chunk 512 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 196 ASN ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 92 HIS ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 20 ASN ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 139 ASN I 195 ASN ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 ASN Q 4 ASN ** Q 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 54 GLN ** Y 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 322 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.5767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 160361 Z= 0.264 Angle : 0.666 16.603 239566 Z= 0.338 Chirality : 0.037 0.342 30559 Planarity : 0.005 0.060 13074 Dihedral : 24.162 177.633 79409 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 25.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.50 % Favored : 90.42 % Rotamer: Outliers : 4.37 % Allowed : 25.26 % Favored : 70.36 % 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: -2.54 (0.10), residues: 6011 helix: -0.73 (0.11), residues: 1894 sheet: -1.88 (0.15), residues: 1005 loop : -2.25 (0.11), residues: 3112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP G 103 HIS 0.011 0.001 HIS P 21 PHE 0.023 0.002 PHE H 36 TYR 0.029 0.002 TYR T 77 ARG 0.010 0.001 ARG J 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1007 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 788 time to evaluate : 6.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 131 MET cc_start: 0.9436 (mmp) cc_final: 0.8784 (mmm) REVERT: b 145 MET cc_start: 0.8657 (mtt) cc_final: 0.8290 (mmm) REVERT: b 160 TYR cc_start: 0.8627 (p90) cc_final: 0.8361 (p90) REVERT: b 184 GLU cc_start: 0.7947 (tp30) cc_final: 0.7743 (tp30) REVERT: b 196 ASN cc_start: 0.9131 (OUTLIER) cc_final: 0.8747 (t0) REVERT: b 250 GLN cc_start: 0.8248 (tm-30) cc_final: 0.7865 (tp40) REVERT: d 115 GLN cc_start: 0.9467 (tp40) cc_final: 0.9060 (tm-30) REVERT: d 158 PHE cc_start: 0.8854 (m-80) cc_final: 0.8607 (m-80) REVERT: d 188 MET cc_start: 0.9179 (tpp) cc_final: 0.8872 (tpt) REVERT: e 37 MET cc_start: 0.8000 (ptp) cc_final: 0.7666 (pmm) REVERT: e 47 LYS cc_start: 0.9389 (pttt) cc_final: 0.9172 (tppt) REVERT: e 168 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8674 (mm) REVERT: f 57 TYR cc_start: 0.7839 (m-80) cc_final: 0.7471 (m-80) REVERT: f 61 TRP cc_start: 0.7612 (m100) cc_final: 0.7129 (m100) REVERT: f 123 GLU cc_start: 0.8748 (tp30) cc_final: 0.8100 (tm-30) REVERT: f 129 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8611 (mm-30) REVERT: f 142 GLN cc_start: 0.8424 (tt0) cc_final: 0.8146 (tp40) REVERT: f 148 ARG cc_start: 0.9170 (ptm-80) cc_final: 0.8753 (ptt180) REVERT: j 75 TYR cc_start: 0.8833 (m-80) cc_final: 0.8380 (m-10) REVERT: j 108 MET cc_start: 0.8956 (mtm) cc_final: 0.8642 (mtm) REVERT: m 41 LEU cc_start: 0.9518 (mm) cc_final: 0.9171 (mm) REVERT: n 82 GLU cc_start: 0.8315 (tm-30) cc_final: 0.7923 (tm-30) REVERT: n 114 GLU cc_start: 0.8212 (pt0) cc_final: 0.7935 (pp20) REVERT: o 20 GLU cc_start: 0.9364 (tt0) cc_final: 0.8860 (tm-30) REVERT: o 116 GLN cc_start: 0.9375 (mm-40) cc_final: 0.9112 (mm-40) REVERT: p 10 GLU cc_start: 0.9267 (OUTLIER) cc_final: 0.8452 (pm20) REVERT: p 40 GLN cc_start: 0.8557 (tp40) cc_final: 0.8176 (tm-30) REVERT: p 98 TYR cc_start: 0.9135 (p90) cc_final: 0.8744 (p90) REVERT: q 51 GLN cc_start: 0.9235 (mm-40) cc_final: 0.8621 (mm-40) REVERT: q 58 GLN cc_start: 0.9247 (OUTLIER) cc_final: 0.8233 (pp30) REVERT: q 101 ASP cc_start: 0.8832 (t0) cc_final: 0.8617 (t0) REVERT: r 46 GLU cc_start: 0.8444 (mp0) cc_final: 0.8063 (pm20) REVERT: r 48 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8471 (tppp) REVERT: r 78 ARG cc_start: 0.9303 (tpp80) cc_final: 0.8875 (tpp-160) REVERT: r 86 GLN cc_start: 0.8782 (mm110) cc_final: 0.8535 (mm110) REVERT: s 52 GLU cc_start: 0.9045 (OUTLIER) cc_final: 0.8771 (pm20) REVERT: s 69 LEU cc_start: 0.9136 (tp) cc_final: 0.8333 (mt) REVERT: s 78 GLU cc_start: 0.8079 (pp20) cc_final: 0.7190 (pp20) REVERT: t 76 ARG cc_start: 0.8942 (ttm-80) cc_final: 0.7987 (ppt170) REVERT: u 13 LEU cc_start: 0.9626 (mt) cc_final: 0.9385 (mt) REVERT: v 50 MET cc_start: 0.8442 (ptm) cc_final: 0.7755 (tmm) REVERT: v 75 GLN cc_start: 0.8291 (tp40) cc_final: 0.7858 (tm-30) REVERT: w 15 LYS cc_start: 0.9404 (mmtt) cc_final: 0.9163 (mmtm) REVERT: w 79 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8472 (mt-10) REVERT: x 61 LYS cc_start: 0.9090 (mttt) cc_final: 0.8799 (mmtp) REVERT: y 13 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8536 (mm-30) REVERT: y 17 GLU cc_start: 0.9500 (tm-30) cc_final: 0.9199 (tm-30) REVERT: y 45 GLN cc_start: 0.8765 (pt0) cc_final: 0.8244 (pt0) REVERT: y 49 ASP cc_start: 0.9091 (m-30) cc_final: 0.8692 (m-30) REVERT: z 5 LYS cc_start: 0.9408 (mmmm) cc_final: 0.9146 (mmmt) REVERT: z 20 LYS cc_start: 0.9607 (mttt) cc_final: 0.9341 (mmtt) REVERT: B 14 MET cc_start: 0.8741 (tpp) cc_final: 0.8453 (tpp) REVERT: C 9 LYS cc_start: 0.9199 (tttt) cc_final: 0.8739 (tttm) REVERT: C 24 LYS cc_start: 0.8746 (ptmt) cc_final: 0.8521 (mmtm) REVERT: C 31 GLU cc_start: 0.8640 (pm20) cc_final: 0.8393 (pm20) REVERT: E 43 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9113 (mm) REVERT: E 53 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8386 (m-30) REVERT: F 36 ARG cc_start: 0.7920 (ptm-80) cc_final: 0.7314 (ptm-80) REVERT: G 26 MET cc_start: 0.7757 (mmp) cc_final: 0.7245 (mmp) REVERT: G 99 MET cc_start: 0.9403 (tpp) cc_final: 0.9056 (mpp) REVERT: G 167 HIS cc_start: 0.7627 (t70) cc_final: 0.7028 (t70) REVERT: H 166 TRP cc_start: 0.9023 (p-90) cc_final: 0.8317 (p-90) REVERT: I 43 ARG cc_start: 0.5910 (mtt180) cc_final: 0.5254 (mmm160) REVERT: I 55 ARG cc_start: 0.8846 (mmm160) cc_final: 0.8496 (mmm160) REVERT: I 104 MET cc_start: 0.9035 (mmt) cc_final: 0.8259 (mmm) REVERT: I 123 MET cc_start: 0.8842 (mmm) cc_final: 0.8341 (mmm) REVERT: I 135 GLN cc_start: 0.8569 (tm-30) cc_final: 0.8327 (tm-30) REVERT: J 28 ARG cc_start: 0.8379 (mtm-85) cc_final: 0.7730 (ptp-110) REVERT: J 70 MET cc_start: 0.8251 (tpt) cc_final: 0.8029 (tpt) REVERT: J 110 MET cc_start: 0.9238 (tpp) cc_final: 0.8949 (tpp) REVERT: J 125 LYS cc_start: 0.9461 (tptm) cc_final: 0.8929 (tptp) REVERT: J 144 GLU cc_start: 0.9136 (tp30) cc_final: 0.8890 (tm-30) REVERT: K 56 LYS cc_start: 0.9273 (mptt) cc_final: 0.8739 (mmmt) REVERT: L 51 GLN cc_start: 0.8566 (mm-40) cc_final: 0.8136 (pp30) REVERT: L 150 PHE cc_start: 0.7537 (m-80) cc_final: 0.7099 (m-80) REVERT: M 95 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8653 (ttm) REVERT: M 110 MET cc_start: 0.9234 (ptp) cc_final: 0.8973 (pmm) REVERT: N 31 GLN cc_start: 0.9075 (mp10) cc_final: 0.8816 (mp10) REVERT: N 55 ASP cc_start: 0.9191 (m-30) cc_final: 0.8666 (t70) REVERT: N 128 LYS cc_start: 0.9132 (tppp) cc_final: 0.8578 (tptt) REVERT: O 66 GLU cc_start: 0.8971 (pt0) cc_final: 0.8572 (pt0) REVERT: P 76 TYR cc_start: 0.7398 (m-80) cc_final: 0.7189 (t80) REVERT: P 105 ARG cc_start: 0.8220 (ttt-90) cc_final: 0.7933 (tpt170) REVERT: Q 69 GLU cc_start: 0.8593 (pt0) cc_final: 0.8110 (pm20) REVERT: Q 80 LEU cc_start: 0.9282 (mm) cc_final: 0.8971 (mm) REVERT: Q 111 GLN cc_start: 0.8584 (mm-40) cc_final: 0.8212 (mm-40) REVERT: R 10 ASP cc_start: 0.8671 (m-30) cc_final: 0.8379 (m-30) REVERT: R 71 GLU cc_start: 0.9084 (tm-30) cc_final: 0.8776 (tm-30) REVERT: R 103 THR cc_start: 0.7918 (p) cc_final: 0.7632 (p) REVERT: S 5 MET cc_start: 0.6207 (ttt) cc_final: 0.5582 (tpp) REVERT: T 13 GLU cc_start: 0.9262 (tt0) cc_final: 0.8941 (tm-30) REVERT: T 25 GLU cc_start: 0.8623 (pt0) cc_final: 0.7992 (mp0) REVERT: T 44 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7856 (pt0) REVERT: T 88 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7874 (tmm160) REVERT: U 14 ARG cc_start: 0.9156 (mmm-85) cc_final: 0.8660 (mmm160) REVERT: U 46 LYS cc_start: 0.8917 (pttm) cc_final: 0.8501 (tttm) REVERT: X 14 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.8006 (mt) REVERT: X 16 LYS cc_start: 0.8481 (mtpp) cc_final: 0.8231 (ptpt) REVERT: X 43 MET cc_start: 0.6254 (tpp) cc_final: 0.5633 (tpp) REVERT: Y 23 ARG cc_start: 0.9347 (mmm-85) cc_final: 0.8679 (mmm-85) REVERT: Y 26 MET cc_start: 0.8737 (ptp) cc_final: 0.8221 (ptp) REVERT: Y 47 GLN cc_start: 0.9281 (tt0) cc_final: 0.8843 (tp-100) REVERT: Y 54 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8148 (tm-30) REVERT: Y 58 ASP cc_start: 0.9095 (m-30) cc_final: 0.8301 (p0) REVERT: 8 17 ARG cc_start: 0.3483 (tpt-90) cc_final: 0.3132 (tpt170) REVERT: 8 151 MET cc_start: 0.8948 (ppp) cc_final: 0.8732 (ppp) REVERT: 8 168 GLU cc_start: 0.6990 (pp20) cc_final: 0.6537 (pp20) REVERT: 8 262 ARG cc_start: 0.7179 (ttm170) cc_final: 0.6828 (ttp-170) REVERT: 8 281 HIS cc_start: 0.6464 (OUTLIER) cc_final: 0.5968 (m90) REVERT: 8 288 MET cc_start: 0.9276 (tpp) cc_final: 0.9001 (tpp) outliers start: 219 outliers final: 185 residues processed: 933 average time/residue: 1.2687 time to fit residues: 2088.8576 Evaluate side-chains 962 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 763 time to evaluate : 6.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 66 PHE Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 196 ASN Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 263 ASP Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 95 SER Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain e residue 110 ILE Chi-restraints excluded: chain e residue 124 ARG Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain f residue 55 ASP Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 42 LYS Chi-restraints excluded: chain g residue 119 ASN Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain g residue 145 ASN Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 47 HIS Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 118 MET Chi-restraints excluded: chain j residue 141 ASP Chi-restraints excluded: chain k residue 17 ARG Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 25 LEU Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 88 ASN Chi-restraints excluded: chain k residue 100 PHE Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 20 LEU Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 102 LEU Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain p residue 2 ASN Chi-restraints excluded: chain p residue 6 GLN Chi-restraints excluded: chain p residue 10 GLU Chi-restraints excluded: chain p residue 24 THR Chi-restraints excluded: chain p residue 30 TRP Chi-restraints excluded: chain p residue 43 GLU Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 82 SER Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain q residue 58 GLN Chi-restraints excluded: chain q residue 103 VAL Chi-restraints excluded: chain q residue 116 LEU Chi-restraints excluded: chain r residue 25 LEU Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 48 LYS Chi-restraints excluded: chain r residue 84 ARG Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 52 GLU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 42 GLU Chi-restraints excluded: chain t residue 51 PHE Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 65 GLN Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 71 LYS Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 29 LEU Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain y residue 9 LYS Chi-restraints excluded: chain y residue 18 LEU Chi-restraints excluded: chain z residue 18 LYS Chi-restraints excluded: chain z residue 43 ILE Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain z residue 53 MET Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 14 CYS Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 38 HIS Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 104 LYS Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 192 TYR Chi-restraints excluded: chain I residue 102 TYR Chi-restraints excluded: chain I residue 139 ASN Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 173 ASP Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 90 MET Chi-restraints excluded: chain K residue 94 HIS Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 95 MET Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain N residue 5 TYR Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 123 ARG Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain R residue 57 ASP Chi-restraints excluded: chain R residue 85 TYR Chi-restraints excluded: chain R residue 102 LYS Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 54 SER Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 44 GLU Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain X residue 14 LEU Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 54 GLN Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 22 ASP Chi-restraints excluded: chain 8 residue 229 ASP Chi-restraints excluded: chain 8 residue 232 ILE Chi-restraints excluded: chain 8 residue 266 ILE Chi-restraints excluded: chain 8 residue 281 HIS Chi-restraints excluded: chain 8 residue 285 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1053 random chunks: chunk 663 optimal weight: 40.0000 chunk 889 optimal weight: 20.0000 chunk 255 optimal weight: 7.9990 chunk 770 optimal weight: 20.0000 chunk 123 optimal weight: 9.9990 chunk 232 optimal weight: 8.9990 chunk 836 optimal weight: 20.0000 chunk 350 optimal weight: 40.0000 chunk 859 optimal weight: 50.0000 chunk 105 optimal weight: 0.1980 chunk 154 optimal weight: 9.9990 overall best weight: 7.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 196 ASN ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 36 GLN ** q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 72 GLN ** y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 197 HIS ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 81 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 = 0.3447 r_free = 0.3447 target = 0.055612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.035978 restraints weight = 1148221.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 85)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.036065 restraints weight = 436715.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.036571 restraints weight = 270277.956| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.5776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.259 160361 Z= 0.289 Angle : 0.694 59.200 239566 Z= 0.359 Chirality : 0.039 1.784 30559 Planarity : 0.005 0.161 13074 Dihedral : 24.157 177.709 79409 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 26.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.77 % Favored : 90.15 % Rotamer: Outliers : 4.49 % Allowed : 25.36 % Favored : 70.14 % Cbeta Deviations : 0.04 % 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: -2.53 (0.10), residues: 6011 helix: -0.71 (0.11), residues: 1894 sheet: -1.86 (0.15), residues: 1006 loop : -2.25 (0.11), residues: 3111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP G 103 HIS 0.048 0.001 HIS P 21 PHE 0.026 0.002 PHE K 8 TYR 0.078 0.002 TYR S 19 ARG 0.021 0.001 ARG J 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33846.46 seconds wall clock time: 596 minutes 38.79 seconds (35798.79 seconds total)