Starting phenix.real_space_refine on Mon Mar 25 22:57:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdi_21637/03_2024/6wdi_21637_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdi_21637/03_2024/6wdi_21637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdi_21637/03_2024/6wdi_21637.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdi_21637/03_2024/6wdi_21637.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdi_21637/03_2024/6wdi_21637_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdi_21637/03_2024/6wdi_21637_updated.pdb" } resolution = 4.0 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= 0.128 sd= 0.905 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 4800 5.49 5 S 151 5.16 5 C 75111 2.51 5 N 27863 2.21 5 O 41703 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b GLU 34": "OE1" <-> "OE2" Residue "b GLU 198": "OE1" <-> "OE2" Residue "c ARG 13": "NH1" <-> "NH2" Residue "c PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 169": "NH1" <-> "NH2" Residue "c ARG 184": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ASP 22": "OD1" <-> "OD2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 49": "NH1" <-> "NH2" Residue "d ARG 61": "NH1" <-> "NH2" Residue "d ARG 88": "NH1" <-> "NH2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "d GLU 155": "OE1" <-> "OE2" Residue "d ARG 162": "NH1" <-> "NH2" Residue "d ARG 170": "NH1" <-> "NH2" Residue "d ASP 171": "OD1" <-> "OD2" Residue "d ASP 184": "OD1" <-> "OD2" Residue "e ASP 5": "OD1" <-> "OD2" Residue "e GLU 18": "OE1" <-> "OE2" Residue "e PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 70": "NH1" <-> "NH2" Residue "e ARG 79": "NH1" <-> "NH2" Residue "e ARG 91": "NH1" <-> "NH2" Residue "e GLU 100": "OE1" <-> "OE2" 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 TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 152": "OD1" <-> "OD2" Residue "e PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "f ASP 15": "OD1" <-> "OD2" Residue "f GLU 31": "OE1" <-> "OE2" Residue "f ASP 38": "OD1" <-> "OD2" Residue "f ASP 59": "OD1" <-> "OD2" Residue "f ARG 152": "NH1" <-> "NH2" Residue "f GLU 154": "OE1" <-> "OE2" Residue "f ARG 162": "NH1" <-> "NH2" Residue "f GLU 166": "OE1" <-> "OE2" Residue "f ARG 169": "NH1" <-> "NH2" Residue "g GLU 45": "OE1" <-> "OE2" Residue "g ASP 86": "OD1" <-> "OD2" Residue "g ASP 98": "OD1" <-> "OD2" Residue "g ASP 101": "OD1" <-> "OD2" Residue "g GLU 114": "OE1" <-> "OE2" Residue "g GLU 127": "OE1" <-> "OE2" Residue "g PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 36": "OD1" <-> "OD2" Residue "h TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 9": "OE1" <-> "OE2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j ASP 14": "OD1" <-> "OD2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j GLU 90": "OE1" <-> "OE2" 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 92": "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 TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 60": "NH1" <-> "NH2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l GLU 106": "OE1" <-> "OE2" Residue "l GLU 115": "OE1" <-> "OE2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 18": "NH1" <-> "NH2" Residue "m ARG 40": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m GLU 47": "OE1" <-> "OE2" Residue "m ARG 50": "NH1" <-> "NH2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m ARG 59": "NH1" <-> "NH2" Residue "m GLU 75": "OE1" <-> "OE2" Residue "m TYR 91": "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 GLU 49": "OE1" <-> "OE2" Residue "n ASP 58": "OD1" <-> "OD2" 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 ASP 72": "OD1" <-> "OD2" Residue "n GLU 82": "OE1" <-> "OE2" 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 ASP 69": "OD1" <-> "OD2" Residue "o ARG 81": "NH1" <-> "NH2" Residue "o ARG 94": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ASP 108": "OD1" <-> "OD2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "p ARG 20": "NH1" <-> "NH2" Residue "p ARG 38": "NH1" <-> "NH2" Residue "p ARG 61": "NH1" <-> "NH2" Residue "p GLU 70": "OE1" <-> "OE2" Residue "p ARG 88": "NH1" <-> "NH2" Residue "p ARG 100": "NH1" <-> "NH2" Residue "p GLU 101": "OE1" <-> "OE2" Residue "p ARG 108": "NH1" <-> "NH2" Residue "q ARG 2": "NH1" <-> "NH2" Residue "q ARG 5": "NH1" <-> "NH2" Residue "q ARG 12": "NH1" <-> "NH2" Residue "q ARG 32": "NH1" <-> "NH2" Residue "q ARG 47": "NH1" <-> "NH2" Residue "q ARG 69": "NH1" <-> "NH2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r ASP 26": "OD1" <-> "OD2" Residue "r GLU 34": "OE1" <-> "OE2" Residue "r GLU 37": "OE1" <-> "OE2" Residue "r GLU 62": "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 "r ASP 95": "OD1" <-> "OD2" Residue "s ARG 84": "NH1" <-> "NH2" Residue "s ARG 88": "NH1" <-> "NH2" Residue "s ASP 94": "OD1" <-> "OD2" Residue "s ARG 95": "NH1" <-> "NH2" Residue "s ARG 110": "NH1" <-> "NH2" Residue "t GLU 4": "OE1" <-> "OE2" Residue "t GLU 52": "OE1" <-> "OE2" Residue "t ARG 73": "NH1" <-> "NH2" Residue "t TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 5": "NH1" <-> "NH2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u ASP 8": "OD1" <-> "OD2" Residue "u ASP 80": "OD1" <-> "OD2" Residue "u ARG 81": "NH1" <-> "NH2" Residue "u ARG 85": "NH1" <-> "NH2" Residue "u ARG 93": "NH1" <-> "NH2" Residue "w ASP 52": "OD1" <-> "OD2" Residue "x GLU 42": "OE1" <-> "OE2" Residue "x ASP 59": "OD1" <-> "OD2" Residue "x GLU 75": "OE1" <-> "OE2" Residue "x TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 13": "OE1" <-> "OE2" Residue "y GLU 24": "OE1" <-> "OE2" Residue "y ARG 29": "NH1" <-> "NH2" Residue "y ARG 47": "NH1" <-> "NH2" Residue "y ARG 52": "NH1" <-> "NH2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 29": "NH1" <-> "NH2" Residue "z ARG 44": "NH1" <-> "NH2" Residue "z GLU 57": "OE1" <-> "OE2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "C ASP 39": "OD1" <-> "OD2" 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 ASP 20": "OD1" <-> "OD2" Residue "F ARG 24": "NH1" <-> "NH2" Residue "G ASP 7": "OD1" <-> "OD2" Residue "G PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 77": "OE1" <-> "OE2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 132": "OE1" <-> "OE2" Residue "G PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 196": "OD1" <-> "OD2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "H ASP 33": "OD1" <-> "OD2" Residue "H TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 45": "OE1" <-> "OE2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "H GLU 151": "OE1" <-> "OE2" Residue "H GLU 205": "OE1" <-> "OE2" Residue "I ASP 17": "OD1" <-> "OD2" Residue "I ASP 140": "OD1" <-> "OD2" Residue "I GLU 162": "OE1" <-> "OE2" Residue "J PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 54": "OE1" <-> "OE2" Residue "J GLU 115": "OE1" <-> "OE2" Residue "J ASP 141": "OD1" <-> "OD2" Residue "J GLU 150": "OE1" <-> "OE2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "J GLU 162": "OE1" <-> "OE2" Residue "K GLU 69": "OE1" <-> "OE2" Residue "L PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "M ASP 47": "OD1" <-> "OD2" Residue "N GLU 91": "OE1" <-> "OE2" Residue "N GLU 96": "OE1" <-> "OE2" Residue "N GLU 111": "OE1" <-> "OE2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "O TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 66": "OE1" <-> "OE2" Residue "O ASP 97": "OD1" <-> "OD2" Residue "P ASP 17": "OD1" <-> "OD2" Residue "P GLU 67": "OE1" <-> "OE2" Residue "P TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 24": "OE1" <-> "OE2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "R GLU 40": "OE1" <-> "OE2" Residue "R ASP 57": "OD1" <-> "OD2" Residue "R ASP 67": "OD1" <-> "OD2" Residue "S ASP 17": "OD1" <-> "OD2" Residue "S PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 85": "OE1" <-> "OE2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U GLU 34": "OE1" <-> "OE2" Residue "U ASP 53": "OD1" <-> "OD2" Residue "U ASP 55": "OD1" <-> "OD2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "W ASP 24": "OD1" <-> "OD2" Residue "W TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 11": "OD1" <-> "OD2" Residue "Z GLU 9": "OE1" <-> "OE2" Residue "Z GLU 23": "OE1" <-> "OE2" Residue "Z GLU 30": "OE1" <-> "OE2" Residue "Z GLU 43": "OE1" <-> "OE2" Residue "Z ARG 66": "NH1" <-> "NH2" Residue "a ARG 7": "NH1" <-> "NH2" Residue "a ARG 12": "NH1" <-> "NH2" Residue "a ARG 162": "NH1" <-> "NH2" Residue "a ASP 179": "OD1" <-> "OD2" Residue "a TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 149628 Number of models: 1 Model: "" Number of chains: 59 Chain: "b" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "c" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "d" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "e" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "f" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "g" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "h" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 989 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "i" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 511 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "j" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "k" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "l" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "m" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "n" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 961 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "o" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "p" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "r" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "s" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "t" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 739 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "u" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "v" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "w" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "x" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "B" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "C" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 410 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "D" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "E" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "F" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "G" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1757 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "H" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1625 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "I" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "J" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1157 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "K" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 818 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "L" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1182 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "M" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "N" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "O" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 787 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "P" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 870 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "Q" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "R" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 884 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "S" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "T" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "U" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "V" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "W" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 536 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "X" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "Y" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "Z" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 545 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "a" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1027 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 1 Chain: "3" Number of atoms: 33012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33012 Classifications: {'RNA': 1539} Modifications used: {'5*END': 1, 'rna2p_pur': 91, 'rna2p_pyr': 49, 'rna3p_pur': 783, 'rna3p_pyr': 616} Link IDs: {'rna2p': 140, 'rna3p': 1398} Chain: "1" Number of atoms: 62317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62317 Classifications: {'RNA': 2903} Modifications used: {'5*END': 1, 'rna2p_pur': 211, 'rna2p_pyr': 92, 'rna3p_pur': 1463, 'rna3p_pyr': 1137} Link IDs: {'rna2p': 303, 'rna3p': 2599} Chain: "2" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2568 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 61, 'rna3p_pyr': 53} Link IDs: {'rna2p': 6, 'rna3p': 113} Chain: "5" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 33, 'rna3p_pyr': 34} Link IDs: {'rna2p': 9, 'rna3p': 67} Chain: "6" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 34, 'rna3p_pyr': 34} Link IDs: {'rna2p': 9, 'rna3p': 67} Chain: "4" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 388 Classifications: {'RNA': 18} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 12, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "7" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1557 Classifications: {'RNA': 73} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 32, 'rna3p_pyr': 28} Link IDs: {'rna2p': 13, 'rna3p': 59} Chain: "5" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 60.56, per 1000 atoms: 0.40 Number of scatterers: 149628 At special positions: 0 Unit cell: (278.597, 265.267, 245.272, 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 151 16.00 P 4800 15.00 O 41703 8.00 N 27863 7.00 C 75111 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 62.51 Conformation dependent library (CDL) restraints added in 7.2 seconds 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10944 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 176 helices and 70 sheets defined 38.0% alpha, 16.2% beta 1376 base pairs and 2968 stacking pairs defined. Time for finding SS restraints: 80.59 Creating SS restraints... Processing helix chain 'b' and resid 9 through 16 removed outlier: 7.023A pdb=" N HIS b 14 " --> pdb=" O PRO b 10 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL b 15 " --> pdb=" O GLY b 11 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL b 16 " --> pdb=" O ARG b 12 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 135 Proline residue: b 135 - end of helix Processing helix chain 'b' and resid 198 through 203 removed outlier: 3.687A pdb=" N ARG b 202 " --> pdb=" O GLU b 198 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N VAL b 203 " --> pdb=" O HIS b 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 198 through 203' Processing helix chain 'b' and resid 206 through 214 removed outlier: 4.281A pdb=" N ALA b 210 " --> pdb=" O LYS b 206 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG b 213 " --> pdb=" O ALA b 209 " (cutoff:3.500A) Processing helix chain 'b' and resid 259 through 264 removed outlier: 6.039A pdb=" N ASP b 263 " --> pdb=" O ASN b 259 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LYS b 264 " --> pdb=" O LYS b 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 259 through 264' Processing helix chain 'c' and resid 61 through 72 removed outlier: 3.780A pdb=" N HIS c 67 " --> pdb=" O PRO c 63 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA c 71 " --> pdb=" O HIS c 67 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY c 72 " --> pdb=" O PHE c 68 " (cutoff:3.500A) Processing helix chain 'c' and resid 98 through 103 removed outlier: 4.961A pdb=" N ASP c 103 " --> pdb=" O GLU c 99 " (cutoff:3.500A) Processing helix chain 'c' and resid 120 through 125 removed outlier: 3.884A pdb=" N ARG c 124 " --> pdb=" O GLY c 120 " (cutoff:3.500A) Processing helix chain 'd' and resid 15 through 20 removed outlier: 3.548A pdb=" N GLY d 20 " --> pdb=" O GLU d 16 " (cutoff:3.500A) Processing helix chain 'd' and resid 24 through 41 removed outlier: 3.622A pdb=" N VAL d 31 " --> pdb=" O LEU d 27 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N GLN d 41 " --> pdb=" O ALA d 37 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 116 removed outlier: 3.696A pdb=" N ARG d 114 " --> pdb=" O SER d 110 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 142 removed outlier: 3.554A pdb=" N LEU d 134 " --> pdb=" O LYS d 130 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET d 141 " --> pdb=" O LYS d 137 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 162 removed outlier: 4.489A pdb=" N ARG d 162 " --> pdb=" O PHE d 158 " (cutoff:3.500A) Processing helix chain 'd' and resid 176 through 183 removed outlier: 3.569A pdb=" N LEU d 180 " --> pdb=" O ASP d 176 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 201 removed outlier: 3.545A pdb=" N LYS d 194 " --> pdb=" O ALA d 190 " (cutoff:3.500A) Processing helix chain 'e' and resid 1 through 20 removed outlier: 3.702A pdb=" N ASP e 5 " --> pdb=" O ALA e 1 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N VAL e 12 " --> pdb=" O LYS e 8 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR e 17 " --> pdb=" O LYS e 13 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU e 18 " --> pdb=" O LYS e 14 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN e 20 " --> pdb=" O MET e 16 " (cutoff:3.500A) Processing helix chain 'e' and resid 39 through 46 removed outlier: 6.995A pdb=" N ILE e 43 " --> pdb=" O VAL e 39 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ALA e 44 " --> pdb=" O GLY e 40 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS e 46 " --> pdb=" O ALA e 42 " (cutoff:3.500A) Processing helix chain 'e' and resid 47 through 61 removed outlier: 4.677A pdb=" N GLY e 61 " --> pdb=" O ALA e 57 " (cutoff:3.500A) Processing helix chain 'e' and resid 92 through 110 removed outlier: 4.859A pdb=" N TRP e 96 " --> pdb=" O GLY e 92 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU e 97 " --> pdb=" O GLU e 93 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE e 99 " --> pdb=" O MET e 95 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR e 104 " --> pdb=" O GLU e 100 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE e 105 " --> pdb=" O ARG e 101 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N VAL e 107 " --> pdb=" O ILE e 103 " (cutoff:3.500A) Proline residue: e 108 - end of helix Processing helix chain 'e' and resid 161 through 173 removed outlier: 4.908A pdb=" N ALA e 167 " --> pdb=" O GLU e 163 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU e 168 " --> pdb=" O GLU e 164 " (cutoff:3.500A) Processing helix chain 'e' and resid 133 through 138 removed outlier: 4.505A pdb=" N ILE e 136 " --> pdb=" O GLU e 133 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE e 137 " --> pdb=" O GLN e 134 " (cutoff:3.500A) Proline residue: e 138 - end of helix No H-bonds generated for 'chain 'e' and resid 133 through 138' Processing helix chain 'f' and resid 1 through 7 removed outlier: 3.598A pdb=" N ALA f 6 " --> pdb=" O ARG f 2 " (cutoff:3.500A) Proline residue: f 7 - end of helix Processing helix chain 'f' and resid 59 through 80 removed outlier: 3.650A pdb=" N GLY f 65 " --> pdb=" O TRP f 61 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR f 79 " --> pdb=" O VAL f 75 " (cutoff:3.500A) Processing helix chain 'f' and resid 136 through 152 removed outlier: 3.693A pdb=" N GLN f 142 " --> pdb=" O GLN f 138 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG f 151 " --> pdb=" O LEU f 147 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG f 152 " --> pdb=" O ARG f 148 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 28 Processing helix chain 'g' and resid 29 through 34 removed outlier: 3.532A pdb=" N GLN g 33 " --> pdb=" O PHE g 29 " (cutoff:3.500A) Processing helix chain 'g' and resid 40 through 50 removed outlier: 3.900A pdb=" N ARG g 50 " --> pdb=" O PHE g 46 " (cutoff:3.500A) Processing helix chain 'g' and resid 51 through 73 removed outlier: 5.267A pdb=" N ALA g 56 " --> pdb=" O ALA g 52 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LYS g 57 " --> pdb=" O GLU g 53 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU g 60 " --> pdb=" O ALA g 56 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL g 61 " --> pdb=" O LYS g 57 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS g 71 " --> pdb=" O ALA g 67 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE g 72 " --> pdb=" O ARG g 68 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ASN g 73 " --> pdb=" O ALA g 69 " (cutoff:3.500A) Processing helix chain 'g' and resid 96 through 107 removed outlier: 3.535A pdb=" N ALA g 105 " --> pdb=" O ASP g 101 " (cutoff:3.500A) Processing helix chain 'g' and resid 111 through 116 removed outlier: 3.931A pdb=" N VAL g 115 " --> pdb=" O ALA g 111 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ARG g 116 " --> pdb=" O LYS g 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 111 through 116' Processing helix chain 'h' and resid 3 through 22 removed outlier: 3.880A pdb=" N ASP h 7 " --> pdb=" O LEU h 3 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS h 20 " --> pdb=" O SER h 16 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ALA h 22 " --> pdb=" O VAL h 18 " (cutoff:3.500A) Processing helix chain 'h' and resid 33 through 48 removed outlier: 3.860A pdb=" N LYS h 37 " --> pdb=" O VAL h 33 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET h 38 " --> pdb=" O THR h 34 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR h 39 " --> pdb=" O VAL h 35 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ARG h 42 " --> pdb=" O MET h 38 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA h 44 " --> pdb=" O GLU h 40 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY h 45 " --> pdb=" O LEU h 41 " (cutoff:3.500A) Processing helix chain 'h' and resid 62 through 68 removed outlier: 3.550A pdb=" N GLY h 66 " --> pdb=" O ARG h 62 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR h 67 " --> pdb=" O ALA h 63 " (cutoff:3.500A) Proline residue: h 68 - end of helix No H-bonds generated for 'chain 'h' and resid 62 through 68' Processing helix chain 'h' and resid 73 through 78 removed outlier: 4.688A pdb=" N VAL h 77 " --> pdb=" O LYS h 73 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLY h 78 " --> pdb=" O ASP h 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 73 through 78' Processing helix chain 'h' and resid 94 through 106 removed outlier: 3.719A pdb=" N PHE h 99 " --> pdb=" O LEU h 95 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA h 100 " --> pdb=" O PHE h 96 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA h 104 " --> pdb=" O ALA h 100 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LYS h 105 " --> pdb=" O LYS h 101 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N PHE h 106 " --> pdb=" O ALA h 102 " (cutoff:3.500A) Processing helix chain 'h' and resid 109 through 114 removed outlier: 6.229A pdb=" N ALA h 112 " --> pdb=" O LYS h 109 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU h 114 " --> pdb=" O ALA h 111 " (cutoff:3.500A) Processing helix chain 'i' and resid 74 through 84 removed outlier: 3.585A pdb=" N LYS i 81 " --> pdb=" O VAL i 77 " (cutoff:3.500A) Processing helix chain 'i' and resid 103 through 114 removed outlier: 3.552A pdb=" N ILE i 108 " --> pdb=" O GLN i 104 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR i 111 " --> pdb=" O GLU i 107 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA i 114 " --> pdb=" O GLN i 110 " (cutoff:3.500A) Processing helix chain 'i' and resid 120 through 136 removed outlier: 3.533A pdb=" N GLY i 130 " --> pdb=" O ARG i 126 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR i 131 " --> pdb=" O SER i 127 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 38 Processing helix chain 'j' and resid 67 through 72 Processing helix chain 'j' and resid 88 through 96 Processing helix chain 'j' and resid 97 through 109 removed outlier: 4.395A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU j 102 " --> pdb=" O GLU j 98 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA j 104 " --> pdb=" O VAL j 100 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N MET j 108 " --> pdb=" O ALA j 104 " (cutoff:3.500A) Processing helix chain 'j' and resid 112 through 123 removed outlier: 3.834A pdb=" N LYS j 121 " --> pdb=" O ALA j 117 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU j 122 " --> pdb=" O MET j 118 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LYS j 123 " --> pdb=" O PHE j 119 " (cutoff:3.500A) Processing helix chain 'k' and resid 112 through 120 Proline residue: k 120 - end of helix Processing helix chain 'k' and resid 104 through 109 removed outlier: 4.500A pdb=" N SER k 109 " --> pdb=" O GLU k 106 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 62 removed outlier: 3.637A pdb=" N LEU l 61 " --> pdb=" O LEU l 57 " (cutoff:3.500A) Proline residue: l 62 - end of helix Processing helix chain 'l' and resid 68 through 74 removed outlier: 3.885A pdb=" N ALA l 72 " --> pdb=" O SER l 68 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE l 73 " --> pdb=" O ARG l 69 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR l 74 " --> pdb=" O LYS l 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 68 through 74' Processing helix chain 'l' and resid 78 through 83 removed outlier: 3.861A pdb=" N LEU l 82 " --> pdb=" O ARG l 78 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ALA l 83 " --> pdb=" O LEU l 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 78 through 83' Processing helix chain 'l' and resid 93 through 99 removed outlier: 6.461A pdb=" N ALA l 97 " --> pdb=" O ASN l 93 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA l 98 " --> pdb=" O THR l 94 " (cutoff:3.500A) Processing helix chain 'l' and resid 128 through 139 removed outlier: 3.706A pdb=" N ARG l 132 " --> pdb=" O THR l 128 " (cutoff:3.500A) Processing helix chain 'm' and resid 42 through 57 removed outlier: 3.502A pdb=" N ALA m 48 " --> pdb=" O ARG m 44 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG m 55 " --> pdb=" O ARG m 51 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA m 56 " --> pdb=" O ALA m 52 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 125 removed outlier: 3.571A pdb=" N ALA m 122 " --> pdb=" O LYS m 118 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS m 123 " --> pdb=" O LEU m 119 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU m 124 " --> pdb=" O ALA m 120 " (cutoff:3.500A) Proline residue: m 125 - end of helix Processing helix chain 'n' and resid 13 through 32 removed outlier: 3.662A pdb=" N ARG n 22 " --> pdb=" O GLN n 18 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN n 23 " --> pdb=" O ALA n 19 " (cutoff:3.500A) Processing helix chain 'n' and resid 37 through 57 removed outlier: 3.593A pdb=" N LYS n 42 " --> pdb=" O LEU n 38 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU n 43 " --> pdb=" O PRO n 39 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU n 44 " --> pdb=" O LYS n 40 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG n 45 " --> pdb=" O ALA n 41 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Proline residue: n 50 - end of helix removed outlier: 4.330A pdb=" N THR n 57 " --> pdb=" O THR n 53 " (cutoff:3.500A) Processing helix chain 'n' and resid 59 through 71 removed outlier: 3.974A pdb=" N ARG n 63 " --> pdb=" O SER n 59 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N THR n 70 " --> pdb=" O ALA n 66 " (cutoff:3.500A) Processing helix chain 'n' and resid 72 through 81 removed outlier: 3.557A pdb=" N VAL n 76 " --> pdb=" O ASP n 72 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N PHE n 80 " --> pdb=" O VAL n 76 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASN n 81 " --> pdb=" O ALA n 77 " (cutoff:3.500A) Processing helix chain 'n' and resid 82 through 89 removed outlier: 4.500A pdb=" N ARG n 86 " --> pdb=" O GLU n 82 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE n 87 " --> pdb=" O LEU n 83 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N SER n 89 " --> pdb=" O PRO n 85 " (cutoff:3.500A) Processing helix chain 'o' and resid 2 through 22 removed outlier: 3.742A pdb=" N ALA o 6 " --> pdb=" O ASP o 2 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU o 18 " --> pdb=" O ALA o 14 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU o 21 " --> pdb=" O LYS o 17 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 63 removed outlier: 4.876A pdb=" N GLN o 61 " --> pdb=" O ALA o 57 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU o 62 " --> pdb=" O ILE o 58 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LYS o 63 " --> pdb=" O ALA o 59 " (cutoff:3.500A) Processing helix chain 'o' and resid 67 through 86 removed outlier: 3.646A pdb=" N ARG o 81 " --> pdb=" O ALA o 77 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA o 82 " --> pdb=" O VAL o 78 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU o 83 " --> pdb=" O ALA o 79 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU o 84 " --> pdb=" O GLU o 80 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS o 85 " --> pdb=" O ARG o 81 " (cutoff:3.500A) Processing helix chain 'o' and resid 101 through 114 removed outlier: 3.579A pdb=" N ASP o 108 " --> pdb=" O GLN o 104 " (cutoff:3.500A) Processing helix chain 'p' and resid 1 through 13 removed outlier: 3.762A pdb=" N LEU p 7 " --> pdb=" O ILE p 3 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N GLN p 11 " --> pdb=" O LEU p 7 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N MET p 12 " --> pdb=" O GLU p 8 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LYS p 13 " --> pdb=" O GLN p 9 " (cutoff:3.500A) Processing helix chain 'p' and resid 96 through 101 removed outlier: 3.626A pdb=" N LEU p 99 " --> pdb=" O LEU p 96 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG p 100 " --> pdb=" O TYR p 97 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLU p 101 " --> pdb=" O TYR p 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 96 through 101' Processing helix chain 'q' and resid 5 through 21 removed outlier: 4.524A pdb=" N ALA q 9 " --> pdb=" O ARG q 5 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA q 11 " --> pdb=" O VAL q 7 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN q 19 " --> pdb=" O LYS q 15 " (cutoff:3.500A) Processing helix chain 'q' and resid 25 through 30 removed outlier: 4.510A pdb=" N ARG q 29 " --> pdb=" O GLY q 25 " (cutoff:3.500A) Processing helix chain 'q' and resid 35 through 72 removed outlier: 3.522A pdb=" N ASP q 48 " --> pdb=" O TYR q 44 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ARG q 50 " --> pdb=" O TYR q 46 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LYS q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA q 62 " --> pdb=" O GLN q 58 " (cutoff:3.500A) Processing helix chain 'q' and resid 74 through 86 removed outlier: 3.537A pdb=" N LYS q 84 " --> pdb=" O ASN q 80 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA q 85 " --> pdb=" O GLY q 81 " (cutoff:3.500A) Processing helix chain 'q' and resid 90 through 101 removed outlier: 3.639A pdb=" N ALA q 98 " --> pdb=" O LEU q 94 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL q 99 " --> pdb=" O ALA q 95 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE q 100 " --> pdb=" O ASP q 96 " (cutoff:3.500A) Processing helix chain 'q' and resid 102 through 117 removed outlier: 3.593A pdb=" N ALA q 107 " --> pdb=" O VAL q 103 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU q 108 " --> pdb=" O ALA q 104 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL q 109 " --> pdb=" O PHE q 105 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU q 110 " --> pdb=" O THR q 106 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA q 117 " --> pdb=" O LYS q 113 " (cutoff:3.500A) Processing helix chain 's' and resid 13 through 25 removed outlier: 4.004A pdb=" N VAL s 17 " --> pdb=" O SER s 13 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LEU s 23 " --> pdb=" O LEU s 19 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE s 24 " --> pdb=" O VAL s 20 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG s 25 " --> pdb=" O ALA s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 39 removed outlier: 3.686A pdb=" N ILE s 35 " --> pdb=" O GLN s 31 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR s 38 " --> pdb=" O ASP s 34 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 61 removed outlier: 3.600A pdb=" N LYS s 48 " --> pdb=" O ALA s 44 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS s 49 " --> pdb=" O VAL s 45 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) Processing helix chain 't' and resid 1 through 11 removed outlier: 4.983A pdb=" N GLU t 5 " --> pdb=" O MET t 1 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG t 6 " --> pdb=" O ILE t 2 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU t 7 " --> pdb=" O ARG t 3 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU t 8 " --> pdb=" O GLU t 4 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LYS t 9 " --> pdb=" O GLU t 5 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL t 10 " --> pdb=" O ARG t 6 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N LEU t 11 " --> pdb=" O LEU t 7 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 1 through 11' Processing helix chain 't' and resid 17 through 26 Processing helix chain 't' and resid 39 through 51 removed outlier: 3.827A pdb=" N ALA t 45 " --> pdb=" O ALA t 41 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS t 49 " --> pdb=" O ALA t 45 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE t 51 " --> pdb=" O VAL t 47 " (cutoff:3.500A) Processing helix chain 'v' and resid 13 through 24 removed outlier: 3.691A pdb=" N SER v 17 " --> pdb=" O GLY v 13 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG v 18 " --> pdb=" O LYS v 14 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA v 22 " --> pdb=" O ARG v 18 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALA v 23 " --> pdb=" O ARG v 19 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN v 24 " --> pdb=" O LEU v 20 " (cutoff:3.500A) Processing helix chain 'v' and resid 43 through 54 removed outlier: 4.343A pdb=" N VAL v 47 " --> pdb=" O ASP v 43 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET v 48 " --> pdb=" O HIS v 44 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN v 49 " --> pdb=" O ASP v 45 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA v 52 " --> pdb=" O MET v 48 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS v 53 " --> pdb=" O ASN v 49 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ALA v 54 " --> pdb=" O MET v 50 " (cutoff:3.500A) Processing helix chain 'x' and resid 51 through 61 Processing helix chain 'x' and resid 62 through 74 removed outlier: 3.864A pdb=" N GLY x 74 " --> pdb=" O LEU x 70 " (cutoff:3.500A) Processing helix chain 'y' and resid 1 through 8 removed outlier: 3.884A pdb=" N LEU y 6 " --> pdb=" O LYS y 2 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ARG y 7 " --> pdb=" O ALA y 3 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N GLU y 8 " --> pdb=" O LYS y 4 " (cutoff:3.500A) Processing helix chain 'y' and resid 9 through 35 removed outlier: 3.531A pdb=" N ASN y 15 " --> pdb=" O VAL y 11 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR y 16 " --> pdb=" O GLU y 12 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU y 17 " --> pdb=" O GLU y 13 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU y 21 " --> pdb=" O GLU y 17 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG y 23 " --> pdb=" O LEU y 19 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU y 24 " --> pdb=" O ASN y 20 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLN y 25 " --> pdb=" O LEU y 21 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N PHE y 26 " --> pdb=" O LEU y 22 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG y 29 " --> pdb=" O GLN y 25 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY y 35 " --> pdb=" O GLN y 31 " (cutoff:3.500A) Processing helix chain 'y' and resid 39 through 63 removed outlier: 4.825A pdb=" N LEU y 43 " --> pdb=" O GLN y 39 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG y 48 " --> pdb=" O LYS y 44 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N GLY y 62 " --> pdb=" O ASN y 58 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ALA y 63 " --> pdb=" O GLU y 59 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 27 Processing helix chain 'z' and resid 40 through 51 removed outlier: 3.735A pdb=" N MET z 46 " --> pdb=" O ALA z 42 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA z 49 " --> pdb=" O GLY z 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 18 removed outlier: 3.567A pdb=" N ARG B 16 " --> pdb=" O ARG B 12 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER B 17 " --> pdb=" O GLY B 13 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N HIS B 18 " --> pdb=" O MET B 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 16 Processing helix chain 'D' and resid 17 through 24 removed outlier: 5.403A pdb=" N THR D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 38 removed outlier: 3.800A pdb=" N GLN D 29 " --> pdb=" O LYS D 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.523A pdb=" N ALA E 10 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG E 12 " --> pdb=" O GLY E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 45 removed outlier: 3.618A pdb=" N HIS E 42 " --> pdb=" O LYS E 38 " (cutoff:3.500A) Proline residue: E 45 - end of helix Processing helix chain 'E' and resid 50 through 61 removed outlier: 4.860A pdb=" N GLY E 55 " --> pdb=" O LYS E 51 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LEU E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 35 removed outlier: 4.356A pdb=" N LYS F 34 " --> pdb=" O GLU F 30 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N GLN F 35 " --> pdb=" O PRO F 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 30 through 35' Processing helix chain 'G' and resid 4 through 12 removed outlier: 4.032A pdb=" N MET G 8 " --> pdb=" O SER G 4 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS G 10 " --> pdb=" O ARG G 6 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA G 11 " --> pdb=" O ASP G 7 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY G 12 " --> pdb=" O MET G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 63 removed outlier: 3.582A pdb=" N VAL G 46 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Proline residue: G 47 - end of helix removed outlier: 3.892A pdb=" N GLU G 51 " --> pdb=" O PRO G 47 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA G 52 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 87 removed outlier: 3.683A pdb=" N LYS G 80 " --> pdb=" O SER G 76 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA G 82 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA G 83 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU G 84 " --> pdb=" O LYS G 80 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 123 removed outlier: 5.656A pdb=" N GLN G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER G 109 " --> pdb=" O THR G 105 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN G 119 " --> pdb=" O ASP G 115 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP G 122 " --> pdb=" O THR G 118 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLY G 123 " --> pdb=" O GLN G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 129 removed outlier: 3.644A pdb=" N LEU G 128 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N THR G 129 " --> pdb=" O PHE G 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 124 through 129' Processing helix chain 'G' and resid 130 through 147 removed outlier: 3.548A pdb=" N LEU G 134 " --> pdb=" O LYS G 130 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU G 139 " --> pdb=" O MET G 135 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU G 140 " --> pdb=" O ARG G 136 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS G 142 " --> pdb=" O ARG G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 169 removed outlier: 3.595A pdb=" N GLU G 168 " --> pdb=" O ASP G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 179 removed outlier: 3.510A pdb=" N ASN G 177 " --> pdb=" O LYS G 173 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU G 178 " --> pdb=" O GLU G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 225 removed outlier: 3.643A pdb=" N THR G 219 " --> pdb=" O ALA G 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 11 removed outlier: 3.609A pdb=" N ILE H 9 " --> pdb=" O HIS H 5 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ARG H 10 " --> pdb=" O PRO H 6 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU H 11 " --> pdb=" O ASN H 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 5 through 11' Processing helix chain 'H' and resid 27 through 46 removed outlier: 3.668A pdb=" N SER H 34 " --> pdb=" O ASP H 30 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS H 44 " --> pdb=" O GLN H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 77 removed outlier: 3.602A pdb=" N VAL H 75 " --> pdb=" O ARG H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 95 removed outlier: 3.550A pdb=" N LYS H 88 " --> pdb=" O GLU H 84 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA H 91 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP H 92 " --> pdb=" O LYS H 88 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE H 93 " --> pdb=" O VAL H 89 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA H 94 " --> pdb=" O VAL H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 112 removed outlier: 3.612A pdb=" N ASP H 111 " --> pdb=" O LYS H 107 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ALA H 112 " --> pdb=" O PRO H 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 107 through 112' Processing helix chain 'H' and resid 113 through 126 Processing helix chain 'H' and resid 128 through 144 removed outlier: 3.503A pdb=" N VAL H 137 " --> pdb=" O MET H 133 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU H 143 " --> pdb=" O ASN H 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 15 removed outlier: 4.160A pdb=" N LEU I 10 " --> pdb=" O PRO I 6 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER I 11 " --> pdb=" O LYS I 7 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU I 14 " --> pdb=" O LEU I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 65 removed outlier: 3.506A pdb=" N GLN I 53 " --> pdb=" O ASP I 49 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS I 59 " --> pdb=" O ARG I 55 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE I 63 " --> pdb=" O LYS I 59 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR I 64 " --> pdb=" O VAL I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 82 removed outlier: 5.898A pdb=" N LYS I 82 " --> pdb=" O ALA I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 96 Processing helix chain 'I' and resid 97 through 105 Processing helix chain 'I' and resid 109 through 120 removed outlier: 3.827A pdb=" N HIS I 119 " --> pdb=" O GLN I 115 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LYS I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 165 removed outlier: 6.653A pdb=" N LYS I 155 " --> pdb=" O GLN I 151 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ALA I 156 " --> pdb=" O SER I 152 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA I 157 " --> pdb=" O ARG I 153 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA I 161 " --> pdb=" O ALA I 157 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU I 162 " --> pdb=" O LEU I 158 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLN I 163 " --> pdb=" O GLU I 159 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG I 164 " --> pdb=" O LEU I 160 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N GLU I 165 " --> pdb=" O ALA I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 205 removed outlier: 4.439A pdb=" N ILE I 199 " --> pdb=" O ASN I 195 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS I 205 " --> pdb=" O GLU I 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 70 removed outlier: 3.532A pdb=" N ALA J 58 " --> pdb=" O GLU J 54 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET J 63 " --> pdb=" O ILE J 59 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG J 68 " --> pdb=" O GLU J 64 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN J 69 " --> pdb=" O LYS J 65 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET J 70 " --> pdb=" O ALA J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 118 removed outlier: 6.789A pdb=" N ALA J 112 " --> pdb=" O GLY J 108 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL J 113 " --> pdb=" O ALA J 109 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU J 114 " --> pdb=" O MET J 110 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL J 116 " --> pdb=" O ALA J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 146 removed outlier: 3.782A pdb=" N VAL J 136 " --> pdb=" O PRO J 132 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG J 137 " --> pdb=" O ILE J 133 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA J 138 " --> pdb=" O ASN J 134 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE J 140 " --> pdb=" O VAL J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 156 removed outlier: 3.846A pdb=" N ALA J 154 " --> pdb=" O GLU J 150 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS J 155 " --> pdb=" O MET J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 165 removed outlier: 3.981A pdb=" N ILE J 163 " --> pdb=" O SER J 159 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU J 164 " --> pdb=" O VAL J 160 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY J 165 " --> pdb=" O GLU J 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 159 through 165' Processing helix chain 'K' and resid 11 through 19 removed outlier: 3.968A pdb=" N GLU K 16 " --> pdb=" O PRO K 12 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLN K 17 " --> pdb=" O ASP K 13 " (cutoff:3.500A) Proline residue: K 19 - end of helix Processing helix chain 'K' and resid 20 through 31 removed outlier: 3.635A pdb=" N THR K 26 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA K 28 " --> pdb=" O ARG K 24 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE K 29 " --> pdb=" O TYR K 25 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY K 31 " --> pdb=" O ALA K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 81 removed outlier: 3.701A pdb=" N ASP K 72 " --> pdb=" O GLN K 68 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU K 75 " --> pdb=" O ILE K 71 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR K 76 " --> pdb=" O ASP K 72 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN K 81 " --> pdb=" O THR K 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 31 removed outlier: 3.524A pdb=" N ASN L 27 " --> pdb=" O ALA L 23 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N VAL L 31 " --> pdb=" O ASN L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 53 removed outlier: 3.625A pdb=" N ALA L 38 " --> pdb=" O LYS L 34 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU L 47 " --> pdb=" O TYR L 43 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU L 49 " --> pdb=" O ALA L 45 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA L 50 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 69 removed outlier: 4.109A pdb=" N ALA L 64 " --> pdb=" O ALA L 60 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN L 67 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL L 68 " --> pdb=" O ALA L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 111 removed outlier: 3.666A pdb=" N ASN L 96 " --> pdb=" O PRO L 92 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA L 97 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE L 103 " --> pdb=" O ALA L 99 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL L 104 " --> pdb=" O MET L 100 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG L 108 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS L 109 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ARG L 110 " --> pdb=" O ALA L 106 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N GLY L 111 " --> pdb=" O ALA L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 129 removed outlier: 3.846A pdb=" N ALA L 120 " --> pdb=" O ALA L 116 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU L 128 " --> pdb=" O SER L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 146 removed outlier: 4.419A pdb=" N ALA L 146 " --> pdb=" O ARG L 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 20 Processing helix chain 'M' and resid 29 through 43 removed outlier: 3.569A pdb=" N GLU M 41 " --> pdb=" O ASN M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 93 through 98 removed outlier: 4.718A pdb=" N GLY M 97 " --> pdb=" O LYS M 93 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 119 removed outlier: 3.856A pdb=" N GLN M 117 " --> pdb=" O ARG M 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 33 through 38 Processing helix chain 'N' and resid 45 through 55 Proline residue: N 50 - end of helix removed outlier: 4.194A pdb=" N LEU N 53 " --> pdb=" O GLN N 49 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL N 54 " --> pdb=" O PRO N 50 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ASP N 55 " --> pdb=" O LEU N 51 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 87 removed outlier: 3.541A pdb=" N ALA N 77 " --> pdb=" O GLY N 73 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR N 83 " --> pdb=" O ARG N 79 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N MET N 87 " --> pdb=" O THR N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 91 through 101 removed outlier: 5.518A pdb=" N GLU N 96 " --> pdb=" O SER N 92 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS N 99 " --> pdb=" O SER N 95 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA N 100 " --> pdb=" O GLU N 96 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY N 101 " --> pdb=" O LEU N 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 32 removed outlier: 3.501A pdb=" N ILE O 18 " --> pdb=" O ASP O 14 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU O 27 " --> pdb=" O ALA O 23 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR O 28 " --> pdb=" O GLU O 24 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA O 29 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG O 31 " --> pdb=" O GLU O 27 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N THR O 32 " --> pdb=" O THR O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 91 removed outlier: 3.629A pdb=" N VAL O 84 " --> pdb=" O THR O 80 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP O 85 " --> pdb=" O GLU O 81 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ALA O 86 " --> pdb=" O LYS O 82 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N MET O 88 " --> pdb=" O VAL O 84 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ARG O 89 " --> pdb=" O ASP O 85 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU O 90 " --> pdb=" O ALA O 86 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP O 91 " --> pdb=" O LEU O 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 50 removed outlier: 3.829A pdb=" N SER P 49 " --> pdb=" O THR P 45 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLY P 50 " --> pdb=" O ALA P 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 45 through 50' Processing helix chain 'P' and resid 58 through 74 removed outlier: 3.766A pdb=" N ASP P 71 " --> pdb=" O GLU P 67 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ALA P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N VAL P 73 " --> pdb=" O CYS P 69 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LYS P 74 " --> pdb=" O ALA P 70 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 103 removed outlier: 5.705A pdb=" N THR P 95 " --> pdb=" O GLY P 91 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE P 96 " --> pdb=" O ARG P 92 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG P 97 " --> pdb=" O GLU P 93 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU P 99 " --> pdb=" O THR P 95 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 10 Proline residue: Q 10 - end of helix Processing helix chain 'R' and resid 13 through 21 removed outlier: 4.411A pdb=" N ILE R 21 " --> pdb=" O ALA R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 37 removed outlier: 3.644A pdb=" N LYS R 30 " --> pdb=" O LYS R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 48 removed outlier: 5.481A pdb=" N SER R 48 " --> pdb=" O ILE R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 63 removed outlier: 3.792A pdb=" N ASP R 53 " --> pdb=" O GLU R 49 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N THR R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LYS R 61 " --> pdb=" O ASP R 57 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N PHE R 62 " --> pdb=" O GLU R 58 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL R 63 " --> pdb=" O VAL R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 83 Processing helix chain 'R' and resid 84 through 93 Processing helix chain 'R' and resid 105 through 110 removed outlier: 3.694A pdb=" N LYS R 109 " --> pdb=" O ALA R 105 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 20 removed outlier: 3.719A pdb=" N LYS S 6 " --> pdb=" O LYS S 2 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA S 14 " --> pdb=" O VAL S 10 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N PHE S 20 " --> pdb=" O ALA S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 50 removed outlier: 3.689A pdb=" N VAL S 44 " --> pdb=" O ARG S 40 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN S 48 " --> pdb=" O VAL S 44 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR S 49 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU S 50 " --> pdb=" O LYS S 46 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 90 removed outlier: 3.939A pdb=" N ARG S 84 " --> pdb=" O ARG S 80 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU S 85 " --> pdb=" O ILE S 81 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARG S 89 " --> pdb=" O GLU S 85 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 15 removed outlier: 3.502A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE T 10 " --> pdb=" O ALA T 6 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER T 12 " --> pdb=" O ALA T 8 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE T 14 " --> pdb=" O ILE T 10 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 43 removed outlier: 3.749A pdb=" N ASN T 36 " --> pdb=" O THR T 32 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY T 40 " --> pdb=" O ASN T 36 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N HIS T 41 " --> pdb=" O HIS T 37 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 73 removed outlier: 3.592A pdb=" N ARG T 63 " --> pdb=" O VAL T 59 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS T 64 " --> pdb=" O SER T 60 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 85 removed outlier: 3.683A pdb=" N GLN T 79 " --> pdb=" O ALA T 75 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 64 removed outlier: 3.737A pdb=" N ILE U 57 " --> pdb=" O ASP U 53 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS U 59 " --> pdb=" O ASP U 55 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL U 61 " --> pdb=" O ILE U 57 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY U 62 " --> pdb=" O ALA U 58 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN U 63 " --> pdb=" O HIS U 59 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY U 64 " --> pdb=" O TRP U 60 " (cutoff:3.500A) Processing helix chain 'U' and resid 68 through 79 removed outlier: 3.530A pdb=" N ALA U 73 " --> pdb=" O ASP U 69 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU U 74 " --> pdb=" O ARG U 70 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS U 76 " --> pdb=" O ALA U 72 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN U 79 " --> pdb=" O ILE U 75 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 17 removed outlier: 4.487A pdb=" N GLY W 16 " --> pdb=" O PHE W 12 " (cutoff:3.500A) Processing helix chain 'W' and resid 24 through 33 removed outlier: 4.131A pdb=" N LEU W 28 " --> pdb=" O ASP W 24 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN W 30 " --> pdb=" O ALA W 26 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TYR W 31 " --> pdb=" O THR W 27 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE W 32 " --> pdb=" O LEU W 28 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N THR W 33 " --> pdb=" O LYS W 29 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 45 removed outlier: 3.519A pdb=" N THR W 44 " --> pdb=" O PRO W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 47 through 65 removed outlier: 3.901A pdb=" N ARG W 56 " --> pdb=" O ARG W 52 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 25 removed outlier: 3.739A pdb=" N SER X 24 " --> pdb=" O LYS X 20 " (cutoff:3.500A) Processing helix chain 'X' and resid 69 through 75 removed outlier: 4.319A pdb=" N PHE X 73 " --> pdb=" O LYS X 69 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA X 74 " --> pdb=" O LEU X 70 " (cutoff:3.500A) Proline residue: X 75 - end of helix No H-bonds generated for 'chain 'X' and resid 69 through 75' Processing helix chain 'Y' and resid 5 through 41 removed outlier: 4.666A pdb=" N ARG Y 9 " --> pdb=" O SER Y 5 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA Y 10 " --> pdb=" O ALA Y 6 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE Y 11 " --> pdb=" O LYS Y 7 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS Y 19 " --> pdb=" O LYS Y 15 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE Y 31 " --> pdb=" O MET Y 27 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL Y 34 " --> pdb=" O PHE Y 30 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA Y 37 " --> pdb=" O LYS Y 33 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 64 Proline residue: Y 55 - end of helix removed outlier: 3.502A pdb=" N ASP Y 58 " --> pdb=" O GLN Y 54 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA Y 61 " --> pdb=" O VAL Y 57 " (cutoff:3.500A) Processing helix chain 'Y' and resid 67 through 86 removed outlier: 6.257A pdb=" N ALA Y 71 " --> pdb=" O HIS Y 67 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR Y 79 " --> pdb=" O LYS Y 75 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS Y 84 " --> pdb=" O ALA Y 80 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 23 removed outlier: 4.436A pdb=" N ARG Z 20 " --> pdb=" O ARG Z 16 " (cutoff:3.500A) Processing helix chain 'Z' and resid 26 through 32 removed outlier: 5.031A pdb=" N GLU Z 30 " --> pdb=" O GLY Z 26 " (cutoff:3.500A) Processing helix chain 'Z' and resid 36 through 61 Proline residue: Z 40 - end of helix removed outlier: 3.701A pdb=" N ARG Z 44 " --> pdb=" O PRO Z 40 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA Z 49 " --> pdb=" O LYS Z 45 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS Z 53 " --> pdb=" O ALA Z 49 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 16 removed outlier: 3.666A pdb=" N VAL a 15 " --> pdb=" O ILE a 11 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ASP a 16 " --> pdb=" O ARG a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 23 through 35 removed outlier: 3.847A pdb=" N ILE a 27 " --> pdb=" O ILE a 23 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ALA a 28 " --> pdb=" O ASN a 24 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LYS a 31 " --> pdb=" O ILE a 27 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLU a 32 " --> pdb=" O ALA a 28 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU a 33 " --> pdb=" O LEU a 29 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA a 34 " --> pdb=" O LEU a 30 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N THR a 35 " --> pdb=" O LYS a 31 " (cutoff:3.500A) Processing helix chain 'a' and resid 181 through 200 removed outlier: 3.685A pdb=" N ALA a 195 " --> pdb=" O ALA a 191 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS a 198 " --> pdb=" O VAL a 194 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS a 200 " --> pdb=" O LEU a 196 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'b' and resid 32 through 35 No H-bonds generated for sheet with id= 1 Processing sheet with id= 2, first strand: chain 'b' and resid 71 through 77 removed outlier: 7.342A pdb=" N ASP b 71 " --> pdb=" O GLY b 118 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N GLY b 118 " --> pdb=" O ASP b 71 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE b 73 " --> pdb=" O GLN b 116 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLN b 116 " --> pdb=" O ILE b 73 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA b 75 " --> pdb=" O GLN b 114 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLN b 114 " --> pdb=" O ALA b 75 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N VAL b 77 " --> pdb=" O GLY b 112 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'b' and resid 79 through 82 removed outlier: 3.685A pdb=" N ARG b 79 " --> pdb=" O LEU b 92 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLU b 99 " --> pdb=" O TYR b 95 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'b' and resid 161 through 164 removed outlier: 6.373A pdb=" N THR b 172 " --> pdb=" O VAL b 164 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'c' and resid 11 through 17 removed outlier: 3.568A pdb=" N ILE c 22 " --> pdb=" O ILE c 14 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL c 20 " --> pdb=" O THR c 16 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL c 26 " --> pdb=" O VAL c 9 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASP c 200 " --> pdb=" O THR c 112 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N THR c 112 " --> pdb=" O ASP c 200 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU c 168 " --> pdb=" O SER c 113 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'c' and resid 32 through 35 removed outlier: 6.411A pdb=" N GLN c 49 " --> pdb=" O THR c 35 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN c 36 " --> pdb=" O GLN c 49 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'c' and resid 179 through 182 removed outlier: 3.629A pdb=" N ARG c 179 " --> pdb=" O LEU c 188 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP c 181 " --> pdb=" O LEU c 186 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU c 186 " --> pdb=" O ASP c 181 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'c' and resid 24 through 28 No H-bonds generated for sheet with id= 8 Processing sheet with id= 9, first strand: chain 'c' and resid 46 through 51 removed outlier: 6.880A pdb=" N ARG c 46 " --> pdb=" O LEU c 84 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'c' and resid 105 through 108 removed outlier: 6.939A pdb=" N LYS c 105 " --> pdb=" O VAL c 177 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'd' and resid 1 through 5 No H-bonds generated for sheet with id= 11 Processing sheet with id= 12, first strand: chain 'd' and resid 117 through 120 removed outlier: 5.809A pdb=" N ARG d 117 " --> pdb=" O ASP d 184 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL d 146 " --> pdb=" O LYS d 166 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP d 168 " --> pdb=" O VAL d 146 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE d 148 " --> pdb=" O ASP d 168 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'e' and resid 64 through 67 removed outlier: 3.584A pdb=" N ILE e 33 " --> pdb=" O LEU e 90 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY e 38 " --> pdb=" O GLY e 150 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N GLY e 150 " --> pdb=" O GLY e 38 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'f' and resid 15 through 18 Processing sheet with id= 15, first strand: chain 'f' and resid 40 through 44 Processing sheet with id= 16, first strand: chain 'f' and resid 81 through 88 removed outlier: 7.009A pdb=" N THR f 128 " --> pdb=" O LEU f 88 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS f 133 " --> pdb=" O THR f 121 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR f 121 " --> pdb=" O LYS f 133 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N GLY f 119 " --> pdb=" O ALA f 135 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'f' and resid 93 through 97 Processing sheet with id= 18, first strand: chain 'g' and resid 1 through 6 removed outlier: 4.304A pdb=" N MET g 1 " --> pdb=" O ASN g 20 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN g 20 " --> pdb=" O MET g 1 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N VAL g 3 " --> pdb=" O GLN g 18 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLN g 18 " --> pdb=" O VAL g 3 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LEU g 5 " --> pdb=" O GLY g 16 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'g' and resid 76 through 80 removed outlier: 5.959A pdb=" N GLU g 76 " --> pdb=" O LYS g 141 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE g 80 " --> pdb=" O ASN g 145 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL g 142 " --> pdb=" O VAL g 130 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL g 130 " --> pdb=" O VAL g 142 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL g 146 " --> pdb=" O GLY g 126 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY g 126 " --> pdb=" O VAL g 146 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'h' and resid 24 through 28 removed outlier: 3.847A pdb=" N ALA h 25 " --> pdb=" O SER h 85 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER h 85 " --> pdb=" O ALA h 25 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL h 27 " --> pdb=" O ALA h 83 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'i' and resid 98 through 102 removed outlier: 4.233A pdb=" N ARG i 102 " --> pdb=" O GLU i 140 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'j' and resid 14 through 19 Processing sheet with id= 23, first strand: chain 'k' and resid 17 through 21 removed outlier: 6.665A pdb=" N ARG k 17 " --> pdb=" O VAL k 10 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR k 6 " --> pdb=" O CYS k 21 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ASN k 82 " --> pdb=" O MET k 7 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'l' and resid 88 through 91 Processing sheet with id= 25, first strand: chain 'm' and resid 37 through 40 No H-bonds generated for sheet with id= 25 Processing sheet with id= 26, first strand: chain 'm' and resid 62 through 65 removed outlier: 4.129A pdb=" N TYR m 103 " --> pdb=" O LEU m 33 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU m 33 " --> pdb=" O LEU m 102 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS m 100 " --> pdb=" O ALA m 35 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'm' and resid 30 through 36 removed outlier: 7.352A pdb=" N SER m 30 " --> pdb=" O LYS m 133 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LYS m 127 " --> pdb=" O VAL m 36 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'n' and resid 95 through 100 removed outlier: 3.705A pdb=" N CYS n 100 " --> pdb=" O MET n 110 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N MET n 110 " --> pdb=" O CYS n 100 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'o' and resid 49 through 53 removed outlier: 4.003A pdb=" N VAL o 49 " --> pdb=" O VAL o 39 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA o 51 " --> pdb=" O ALA o 37 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA o 37 " --> pdb=" O ALA o 51 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR o 53 " --> pdb=" O ILE o 35 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE o 35 " --> pdb=" O THR o 53 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG o 25 " --> pdb=" O ILE o 40 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP o 93 " --> pdb=" O LEU o 26 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL o 28 " --> pdb=" O ASP o 93 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'p' and resid 41 through 44 Processing sheet with id= 31, first strand: chain 'p' and resid 48 through 52 removed outlier: 4.030A pdb=" N ALA p 48 " --> pdb=" O THR p 59 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ARG p 52 " --> pdb=" O HIS p 55 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N SER p 56 " --> pdb=" O THR p 75 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'r' and resid 19 through 23 removed outlier: 6.277A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'r' and resid 39 through 42 removed outlier: 9.096A pdb=" N LEU r 39 " --> pdb=" O ILE r 49 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE r 49 " --> pdb=" O LEU r 39 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE r 41 " --> pdb=" O VAL r 47 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'r' and resid 65 through 68 Processing sheet with id= 35, first strand: chain 'r' and resid 71 through 78 removed outlier: 4.020A pdb=" N ARG r 78 " --> pdb=" O TYR r 83 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYR r 83 " --> pdb=" O ARG r 78 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 's' and resid 2 through 8 removed outlier: 4.655A pdb=" N THR s 3 " --> pdb=" O VAL s 107 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL s 107 " --> pdb=" O THR s 3 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N THR s 100 " --> pdb=" O GLY s 79 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS s 73 " --> pdb=" O VAL s 106 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 't' and resid 29 through 34 removed outlier: 4.157A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N SER t 78 " --> pdb=" O GLY t 65 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY t 65 " --> pdb=" O SER t 78 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL t 57 " --> pdb=" O THR t 86 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'u' and resid 39 through 44 removed outlier: 4.462A pdb=" N ASN u 39 " --> pdb=" O ALA u 62 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL u 58 " --> pdb=" O LYS u 43 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'u' and resid 81 through 86 removed outlier: 5.255A pdb=" N ARG u 81 " --> pdb=" O LYS u 96 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'v' and resid 2 through 5 removed outlier: 3.531A pdb=" N ILE v 4 " --> pdb=" O THR v 62 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'v' and resid 37 through 41 removed outlier: 4.650A pdb=" N ILE v 89 " --> pdb=" O PRO v 27 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE v 29 " --> pdb=" O ILE v 89 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'w' and resid 47 through 50 removed outlier: 6.410A pdb=" N GLY w 48 " --> pdb=" O LEU w 55 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU w 55 " --> pdb=" O GLY w 48 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N GLY w 50 " --> pdb=" O HIS w 53 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'w' and resid 62 through 67 Processing sheet with id= 44, first strand: chain 'x' and resid 11 through 18 removed outlier: 3.697A pdb=" N THR x 24 " --> pdb=" O ASN x 16 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASN x 22 " --> pdb=" O SER x 18 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'x' and resid 34 through 37 Processing sheet with id= 46, first strand: chain 'z' and resid 4 through 8 Processing sheet with id= 47, first strand: chain 'C' and resid 19 through 25 removed outlier: 4.018A pdb=" N GLU C 6 " --> pdb=" O LYS C 24 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS C 9 " --> pdb=" O ALA C 51 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ILE C 47 " --> pdb=" O SER C 13 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'F' and resid 13 through 19 removed outlier: 8.846A pdb=" N ASN F 13 " --> pdb=" O SER F 28 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER F 28 " --> pdb=" O ASN F 13 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL F 17 " --> pdb=" O ARG F 24 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG F 19 " --> pdb=" O VAL F 22 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'G' and resid 14 through 17 removed outlier: 4.740A pdb=" N HIS G 14 " --> pdb=" O ILE G 40 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N HIS G 38 " --> pdb=" O GLY G 16 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'G' and resid 89 through 92 removed outlier: 3.778A pdb=" N PHE G 89 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ILE G 163 " --> pdb=" O VAL G 69 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'H' and resid 53 through 58 removed outlier: 3.649A pdb=" N ILE H 67 " --> pdb=" O ASN H 101 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'H' and resid 163 through 169 removed outlier: 3.665A pdb=" N ILE H 148 " --> pdb=" O GLU H 169 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY H 147 " --> pdb=" O PHE H 202 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY H 193 " --> pdb=" O THR H 190 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASP H 180 " --> pdb=" O LYS H 203 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'I' and resid 139 through 143 Processing sheet with id= 54, first strand: chain 'J' and resid 16 through 21 removed outlier: 3.866A pdb=" N ALA J 16 " --> pdb=" O LEU J 35 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLY J 50 " --> pdb=" O ALA J 34 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ARG J 44 " --> pdb=" O ASP J 40 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'J' and resid 82 through 87 removed outlier: 7.644A pdb=" N HIS J 82 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N VAL J 93 " --> pdb=" O GLY J 86 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ARG J 92 " --> pdb=" O TYR J 127 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N TYR J 127 " --> pdb=" O ARG J 92 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLN J 96 " --> pdb=" O LEU J 123 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU J 123 " --> pdb=" O GLN J 96 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA J 98 " --> pdb=" O ASN J 121 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ASN J 121 " --> pdb=" O ALA J 98 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'K' and resid 38 through 43 removed outlier: 3.683A pdb=" N ARG K 38 " --> pdb=" O ASN K 63 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASN K 63 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU K 40 " --> pdb=" O LEU K 61 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU K 61 " --> pdb=" O GLU K 40 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR K 59 " --> pdb=" O TRP K 42 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS K 58 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL K 60 " --> pdb=" O PHE K 8 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE K 6 " --> pdb=" O MET K 62 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N HIS K 3 " --> pdb=" O THR K 92 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'L' and resid 72 through 77 removed outlier: 3.528A pdb=" N TYR L 84 " --> pdb=" O ARG L 77 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'M' and resid 22 through 28 removed outlier: 7.020A pdb=" N ALA M 22 " --> pdb=" O LEU M 62 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU M 62 " --> pdb=" O ALA M 22 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL M 24 " --> pdb=" O LEU M 60 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU M 60 " --> pdb=" O VAL M 24 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU M 51 " --> pdb=" O GLU M 57 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'M' and resid 73 through 76 removed outlier: 3.780A pdb=" N GLN M 75 " --> pdb=" O TYR M 127 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR M 127 " --> pdb=" O GLN M 75 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N CYS M 126 " --> pdb=" O VAL M 102 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'N' and resid 4 through 10 removed outlier: 4.934A pdb=" N GLY N 9 " --> pdb=" O ALA N 16 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'O' and resid 42 through 52 removed outlier: 4.845A pdb=" N LEU O 71 " --> pdb=" O PRO O 43 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG O 45 " --> pdb=" O THR O 69 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR O 69 " --> pdb=" O ARG O 45 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE O 8 " --> pdb=" O VAL O 74 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'P' and resid 41 through 44 removed outlier: 3.807A pdb=" N GLY P 42 " --> pdb=" O ILE P 33 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN P 108 " --> pdb=" O LEU P 81 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N GLY P 87 " --> pdb=" O VAL P 112 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'Q' and resid 28 through 32 removed outlier: 5.391A pdb=" N LEU Q 80 " --> pdb=" O VAL Q 97 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ARG Q 93 " --> pdb=" O GLY Q 84 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'Q' and resid 34 through 40 removed outlier: 4.658A pdb=" N ARG Q 35 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'U' and resid 16 through 20 removed outlier: 3.531A pdb=" N GLY U 37 " --> pdb=" O VAL U 19 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLY U 49 " --> pdb=" O ASN U 40 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'V' and resid 6 through 10 removed outlier: 3.502A pdb=" N GLY V 9 " --> pdb=" O VAL V 58 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLU V 59 " --> pdb=" O VAL V 75 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'V' and resid 19 through 29 No H-bonds generated for sheet with id= 67 Processing sheet with id= 68, first strand: chain 'X' and resid 46 through 49 removed outlier: 5.039A pdb=" N LEU X 46 " --> pdb=" O VAL X 61 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE X 48 " --> pdb=" O VAL X 59 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'a' and resid 59 through 65 removed outlier: 6.632A pdb=" N VAL a 59 " --> pdb=" O ASN a 165 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLY a 159 " --> pdb=" O LEU a 65 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'a' and resid 169 through 174 removed outlier: 6.200A pdb=" N GLY a 169 " --> pdb=" O LEU a 48 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR a 173 " --> pdb=" O VAL a 44 " (cutoff:3.500A) 1548 hydrogen bonds defined for protein. 4587 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3387 hydrogen bonds 5594 hydrogen bond angles 0 basepair planarities 1376 basepair parallelities 2968 stacking parallelities Total time for adding SS restraints: 287.74 Time building geometry restraints manager: 68.01 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: 32124 1.34 - 1.46: 66185 1.46 - 1.59: 54424 1.59 - 1.71: 9600 1.71 - 1.83: 273 Bond restraints: 162606 Sorted by residual: bond pdb=" CA VAL G 46 " pdb=" CB VAL G 46 " ideal model delta sigma weight residual 1.539 1.565 -0.026 5.40e-03 3.43e+04 2.29e+01 bond pdb=" CA PRO i 73 " pdb=" C PRO i 73 " ideal model delta sigma weight residual 1.514 1.532 -0.017 5.50e-03 3.31e+04 1.01e+01 bond pdb=" CA ILE j 84 " pdb=" CB ILE j 84 " ideal model delta sigma weight residual 1.530 1.556 -0.026 1.05e-02 9.07e+03 6.12e+00 bond pdb=" N GLY a 159 " pdb=" CA GLY a 159 " ideal model delta sigma weight residual 1.451 1.488 -0.037 1.60e-02 3.91e+03 5.42e+00 bond pdb=" N GLY C 3 " pdb=" CA GLY C 3 " ideal model delta sigma weight residual 1.451 1.488 -0.037 1.60e-02 3.91e+03 5.39e+00 ... (remaining 162601 not shown) Histogram of bond angle deviations from ideal: 99.58 - 106.47: 30259 106.47 - 113.36: 94187 113.36 - 120.25: 60891 120.25 - 127.15: 46448 127.15 - 134.04: 11571 Bond angle restraints: 243356 Sorted by residual: angle pdb=" N VAL G 220 " pdb=" CA VAL G 220 " pdb=" C VAL G 220 " ideal model delta sigma weight residual 111.81 103.56 8.25 8.60e-01 1.35e+00 9.20e+01 angle pdb=" N VAL L 79 " pdb=" CA VAL L 79 " pdb=" C VAL L 79 " ideal model delta sigma weight residual 113.53 104.62 8.91 9.80e-01 1.04e+00 8.27e+01 angle pdb=" N ALA J 117 " pdb=" CA ALA J 117 " pdb=" C ALA J 117 " ideal model delta sigma weight residual 113.23 103.20 10.03 1.24e+00 6.50e-01 6.55e+01 angle pdb=" N PHE b 239 " pdb=" CA PHE b 239 " pdb=" C PHE b 239 " ideal model delta sigma weight residual 112.12 101.46 10.66 1.34e+00 5.57e-01 6.33e+01 angle pdb=" N GLY r 50 " pdb=" CA GLY r 50 " pdb=" C GLY r 50 " ideal model delta sigma weight residual 112.50 103.42 9.08 1.16e+00 7.43e-01 6.12e+01 ... (remaining 243351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 93374 35.65 - 71.29: 9598 71.29 - 106.94: 1273 106.94 - 142.59: 9 142.59 - 178.23: 19 Dihedral angle restraints: 104273 sinusoidal: 87315 harmonic: 16958 Sorted by residual: dihedral pdb=" O4' C 2 12 " pdb=" C1' C 2 12 " pdb=" N1 C 2 12 " pdb=" C2 C 2 12 " ideal model delta sinusoidal sigma weight residual 200.00 34.75 165.25 1 1.50e+01 4.44e-03 8.39e+01 dihedral pdb=" O4' U 11915 " pdb=" C1' U 11915 " pdb=" N1 U 11915 " pdb=" C2 U 11915 " ideal model delta sinusoidal sigma weight residual 200.00 43.25 156.75 1 1.50e+01 4.44e-03 8.19e+01 dihedral pdb=" O4' U 5 55 " pdb=" C1' U 5 55 " pdb=" N1 U 5 55 " pdb=" C2 U 5 55 " ideal model delta sinusoidal sigma weight residual 200.00 44.64 155.36 1 1.50e+01 4.44e-03 8.14e+01 ... (remaining 104270 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 19854 0.086 - 0.172: 10459 0.172 - 0.257: 737 0.257 - 0.343: 73 0.343 - 0.429: 12 Chirality restraints: 31135 Sorted by residual: chirality pdb=" CA LYS P 125 " pdb=" N LYS P 125 " pdb=" C LYS P 125 " pdb=" CB LYS P 125 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.60e+00 chirality pdb=" CA PRO O 41 " pdb=" N PRO O 41 " pdb=" C PRO O 41 " pdb=" CB PRO O 41 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.87e+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 -2.36 -0.39 2.00e-01 2.50e+01 3.72e+00 ... (remaining 31132 not shown) Planarity restraints: 12986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 12061 " -0.090 2.00e-02 2.50e+03 3.67e-02 4.05e+01 pdb=" N9 G 12061 " 0.007 2.00e-02 2.50e+03 pdb=" C8 G 12061 " 0.039 2.00e-02 2.50e+03 pdb=" N7 G 12061 " 0.033 2.00e-02 2.50e+03 pdb=" C5 G 12061 " 0.015 2.00e-02 2.50e+03 pdb=" C6 G 12061 " -0.018 2.00e-02 2.50e+03 pdb=" O6 G 12061 " -0.052 2.00e-02 2.50e+03 pdb=" N1 G 12061 " -0.016 2.00e-02 2.50e+03 pdb=" C2 G 12061 " 0.010 2.00e-02 2.50e+03 pdb=" N2 G 12061 " 0.014 2.00e-02 2.50e+03 pdb=" N3 G 12061 " 0.030 2.00e-02 2.50e+03 pdb=" C4 G 12061 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 1 615 " 0.070 2.00e-02 2.50e+03 3.99e-02 3.58e+01 pdb=" N1 U 1 615 " -0.002 2.00e-02 2.50e+03 pdb=" C2 U 1 615 " -0.014 2.00e-02 2.50e+03 pdb=" O2 U 1 615 " -0.024 2.00e-02 2.50e+03 pdb=" N3 U 1 615 " -0.017 2.00e-02 2.50e+03 pdb=" C4 U 1 615 " -0.018 2.00e-02 2.50e+03 pdb=" O4 U 1 615 " 0.075 2.00e-02 2.50e+03 pdb=" C5 U 1 615 " -0.039 2.00e-02 2.50e+03 pdb=" C6 U 1 615 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 11647 " 0.069 2.00e-02 2.50e+03 3.93e-02 3.48e+01 pdb=" N1 U 11647 " -0.001 2.00e-02 2.50e+03 pdb=" C2 U 11647 " -0.013 2.00e-02 2.50e+03 pdb=" O2 U 11647 " -0.025 2.00e-02 2.50e+03 pdb=" N3 U 11647 " -0.016 2.00e-02 2.50e+03 pdb=" C4 U 11647 " -0.016 2.00e-02 2.50e+03 pdb=" O4 U 11647 " 0.073 2.00e-02 2.50e+03 pdb=" C5 U 11647 " -0.039 2.00e-02 2.50e+03 pdb=" C6 U 11647 " -0.032 2.00e-02 2.50e+03 ... (remaining 12983 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 33479 2.80 - 3.33: 126544 3.33 - 3.85: 296929 3.85 - 4.38: 367584 4.38 - 4.90: 489991 Nonbonded interactions: 1314527 Sorted by model distance: nonbonded pdb=" OG1 THR P 34 " pdb=" O ASN P 39 " model vdw 2.280 2.440 nonbonded pdb=" O ARG F 36 " pdb=" O GLN F 37 " model vdw 2.337 3.040 nonbonded pdb=" O PRO O 41 " pdb=" O LEU O 42 " model vdw 2.338 3.040 nonbonded pdb=" O ARG n 69 " pdb=" OG1 THR n 70 " model vdw 2.342 2.440 nonbonded pdb=" O GLY J 90 " pdb=" OG SER J 129 " model vdw 2.352 2.440 ... (remaining 1314522 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '5' and resid 1 through 76) selection = chain '6' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.52 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: 2.030 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: 0.160 Extract box with map and model: 11.710 Check model and map are aligned: 1.710 Set scattering table: 1.070 Process input model: 603.210 Find NCS groups from input model: 3.330 Set up NCS constraints: 0.540 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: 0.030 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 626.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 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 0.041 162606 Z= 0.355 Angle : 0.981 13.735 243356 Z= 0.644 Chirality : 0.082 0.429 31135 Planarity : 0.007 0.074 12986 Dihedral : 21.915 178.234 93329 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 1.59 % Allowed : 12.51 % Favored : 85.90 % Rotamer: Outliers : 0.49 % Allowed : 6.14 % Favored : 93.36 % 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: -4.84 (0.09), residues: 5849 helix: -3.63 (0.08), residues: 1676 sheet: -2.84 (0.15), residues: 851 loop : -3.17 (0.09), residues: 3322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.006 TRP b 247 HIS 0.002 0.000 HIS t 70 PHE 0.032 0.004 PHE Z 36 TYR 0.044 0.006 TYR M 127 ARG 0.006 0.001 ARG m 59 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1756 residues out of total 4852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1732 time to evaluate : 6.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 81 GLU cc_start: 0.7448 (tp30) cc_final: 0.7109 (tp30) REVERT: b 89 ASN cc_start: 0.7143 (m110) cc_final: 0.6892 (m110) REVERT: b 97 ASP cc_start: 0.6582 (p0) cc_final: 0.6041 (p0) REVERT: b 229 HIS cc_start: 0.7086 (t-90) cc_final: 0.6525 (t-170) REVERT: b 249 VAL cc_start: 0.9255 (t) cc_final: 0.8821 (p) REVERT: b 269 ARG cc_start: 0.3386 (tpt170) cc_final: 0.2917 (mmm160) REVERT: c 39 ASP cc_start: 0.8551 (t70) cc_final: 0.8330 (t70) REVERT: c 52 THR cc_start: 0.7212 (t) cc_final: 0.6812 (t) REVERT: c 59 ARG cc_start: 0.7585 (tpp-160) cc_final: 0.7307 (tpp-160) REVERT: c 139 SER cc_start: 0.8456 (t) cc_final: 0.8166 (p) REVERT: c 146 ILE cc_start: 0.8462 (mp) cc_final: 0.7968 (tp) REVERT: d 1 MET cc_start: 0.7234 (tpp) cc_final: 0.6933 (mmm) REVERT: d 48 THR cc_start: 0.8556 (p) cc_final: 0.8327 (t) REVERT: d 67 ARG cc_start: 0.8448 (mtp85) cc_final: 0.8212 (mtm-85) REVERT: e 3 LEU cc_start: 0.8765 (pp) cc_final: 0.8364 (pp) REVERT: e 6 TYR cc_start: 0.8753 (t80) cc_final: 0.8454 (t80) REVERT: e 56 LEU cc_start: 0.8660 (mt) cc_final: 0.8215 (mt) REVERT: e 96 TRP cc_start: 0.7295 (m100) cc_final: 0.6801 (m-90) REVERT: e 100 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8656 (mt-10) REVERT: e 112 ASP cc_start: 0.4996 (m-30) cc_final: 0.4194 (m-30) REVERT: e 129 MET cc_start: 0.8506 (tmm) cc_final: 0.8091 (tmm) REVERT: f 106 LEU cc_start: 0.7515 (mt) cc_final: 0.7265 (mt) REVERT: f 142 GLN cc_start: 0.8793 (tt0) cc_final: 0.8430 (tt0) REVERT: g 43 ASN cc_start: 0.8344 (m-40) cc_final: 0.7944 (p0) REVERT: i 116 MET cc_start: 0.2335 (mmp) cc_final: 0.0827 (ttm) REVERT: j 15 TRP cc_start: 0.7680 (m100) cc_final: 0.7477 (m100) REVERT: j 16 TYR cc_start: 0.8072 (m-80) cc_final: 0.7753 (m-10) REVERT: j 48 VAL cc_start: 0.7291 (t) cc_final: 0.6925 (p) REVERT: j 86 GLN cc_start: 0.8019 (pt0) cc_final: 0.7794 (pp30) REVERT: j 92 MET cc_start: 0.6949 (tpt) cc_final: 0.6733 (tpt) REVERT: k 64 ARG cc_start: 0.6967 (mtm-85) cc_final: 0.6120 (ttm-80) REVERT: k 82 ASN cc_start: 0.7375 (m-40) cc_final: 0.7144 (m110) REVERT: k 102 PRO cc_start: 0.7805 (Cg_endo) cc_final: 0.6932 (Cg_exo) REVERT: k 105 ARG cc_start: 0.6959 (mmt180) cc_final: 0.4823 (ttp80) REVERT: l 38 GLN cc_start: 0.7917 (tt0) cc_final: 0.7186 (tt0) REVERT: l 78 ARG cc_start: 0.7851 (mtp180) cc_final: 0.7569 (mtm180) REVERT: m 65 ILE cc_start: 0.8218 (mt) cc_final: 0.7778 (pt) REVERT: m 104 GLU cc_start: 0.8748 (mt-10) cc_final: 0.7882 (tt0) REVERT: n 10 LEU cc_start: 0.8226 (mm) cc_final: 0.7990 (mm) REVERT: n 17 ARG cc_start: 0.8961 (ttp-110) cc_final: 0.8498 (ttp-110) REVERT: n 20 MET cc_start: 0.8226 (mtm) cc_final: 0.7812 (mmm) REVERT: n 35 LYS cc_start: 0.8909 (tttm) cc_final: 0.8590 (tttm) REVERT: n 106 ASP cc_start: 0.7026 (p0) cc_final: 0.6632 (p0) REVERT: n 107 ASN cc_start: 0.7993 (t0) cc_final: 0.7324 (t0) REVERT: n 110 MET cc_start: 0.6391 (mtt) cc_final: 0.5878 (mtt) REVERT: o 16 ARG cc_start: 0.7859 (mmt-90) cc_final: 0.7535 (mmm160) REVERT: o 18 LEU cc_start: 0.8453 (mm) cc_final: 0.7922 (mm) REVERT: o 43 ASN cc_start: 0.8561 (p0) cc_final: 0.8212 (p0) REVERT: o 67 ASN cc_start: 0.8736 (p0) cc_final: 0.7628 (m-40) REVERT: o 76 LYS cc_start: 0.9056 (tttt) cc_final: 0.8425 (mmtm) REVERT: o 99 TYR cc_start: 0.7500 (t80) cc_final: 0.7222 (t80) REVERT: o 102 ARG cc_start: 0.7585 (mtm180) cc_final: 0.6662 (ttm110) REVERT: p 67 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6210 (mm-30) REVERT: p 99 LEU cc_start: 0.8439 (mp) cc_final: 0.8038 (tp) REVERT: q 15 LYS cc_start: 0.8131 (ttpt) cc_final: 0.7415 (tptp) REVERT: q 23 TYR cc_start: 0.8006 (m-10) cc_final: 0.7745 (m-80) REVERT: q 27 ARG cc_start: 0.7153 (mtt180) cc_final: 0.6933 (mtp85) REVERT: q 32 ARG cc_start: 0.6990 (ttm170) cc_final: 0.6580 (ptp-110) REVERT: q 55 GLN cc_start: 0.8582 (mt0) cc_final: 0.8187 (mm-40) REVERT: q 70 GLN cc_start: 0.8458 (tt0) cc_final: 0.8027 (tp40) REVERT: r 24 LYS cc_start: 0.7016 (ttpt) cc_final: 0.6233 (tptt) REVERT: r 45 GLU cc_start: 0.7884 (tp30) cc_final: 0.7371 (tm-30) REVERT: r 70 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7914 (mm-30) REVERT: r 98 ILE cc_start: 0.8325 (mm) cc_final: 0.8081 (tp) REVERT: s 28 LYS cc_start: 0.6891 (mmtt) cc_final: 0.5847 (mmtt) REVERT: s 38 TYR cc_start: 0.8690 (m-80) cc_final: 0.8232 (m-10) REVERT: s 40 ASN cc_start: 0.8298 (m-40) cc_final: 0.7709 (p0) REVERT: s 82 MET cc_start: 0.7110 (mtm) cc_final: 0.6809 (mmt) REVERT: s 86 MET cc_start: 0.7505 (tpt) cc_final: 0.7278 (mtt) REVERT: s 100 THR cc_start: 0.7336 (p) cc_final: 0.6661 (t) REVERT: t 1 MET cc_start: 0.2209 (mmt) cc_final: 0.1278 (mmt) REVERT: t 6 ARG cc_start: 0.8656 (tpm170) cc_final: 0.8326 (tpm170) REVERT: t 9 LYS cc_start: 0.7998 (mtpt) cc_final: 0.7727 (mttp) REVERT: t 19 LYS cc_start: 0.8249 (tttt) cc_final: 0.7971 (tptt) REVERT: t 24 MET cc_start: 0.6309 (tpp) cc_final: 0.6095 (tpp) REVERT: t 56 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7365 (tp30) REVERT: u 68 ASN cc_start: 0.7586 (m110) cc_final: 0.7234 (m110) REVERT: v 7 GLU cc_start: 0.6702 (tm-30) cc_final: 0.6243 (tm-30) REVERT: v 55 GLU cc_start: 0.9143 (mp0) cc_final: 0.8837 (mp0) REVERT: w 15 LYS cc_start: 0.7693 (tppt) cc_final: 0.7318 (ptpp) REVERT: w 25 GLU cc_start: 0.4615 (tt0) cc_final: 0.4257 (tt0) REVERT: w 33 ILE cc_start: 0.8913 (mt) cc_final: 0.8648 (mm) REVERT: w 63 VAL cc_start: 0.8798 (t) cc_final: 0.8566 (t) REVERT: x 15 ASN cc_start: 0.7267 (m110) cc_final: 0.6990 (m110) REVERT: y 39 GLN cc_start: 0.7836 (mt0) cc_final: 0.6978 (mt0) REVERT: y 49 ASP cc_start: 0.8032 (t70) cc_final: 0.7673 (t0) REVERT: y 55 THR cc_start: 0.8990 (t) cc_final: 0.8729 (m) REVERT: z 5 LYS cc_start: 0.7182 (mtpp) cc_final: 0.6952 (mptt) REVERT: B 2 VAL cc_start: 0.8535 (t) cc_final: 0.8172 (p) REVERT: D 12 ARG cc_start: 0.8248 (ttt90) cc_final: 0.7621 (ttp80) REVERT: D 22 MET cc_start: 0.8003 (tpp) cc_final: 0.7360 (tmm) REVERT: D 26 ASN cc_start: 0.7951 (p0) cc_final: 0.7743 (p0) REVERT: D 29 GLN cc_start: 0.5532 (tt0) cc_final: 0.5229 (tt0) REVERT: D 41 ARG cc_start: 0.7906 (tpt-90) cc_final: 0.7648 (tpt-90) REVERT: E 4 LYS cc_start: 0.5984 (tppt) cc_final: 0.3618 (tppt) REVERT: E 15 LYS cc_start: 0.7959 (tptt) cc_final: 0.7698 (tptt) REVERT: F 1 MET cc_start: 0.3160 (ptm) cc_final: 0.2781 (ptm) REVERT: F 24 ARG cc_start: 0.7836 (mmt90) cc_final: 0.7550 (ttm170) REVERT: G 34 ARG cc_start: 0.8322 (mmt-90) cc_final: 0.7914 (mmt180) REVERT: G 59 ILE cc_start: 0.9171 (mt) cc_final: 0.8763 (mt) REVERT: G 62 ARG cc_start: 0.6157 (ptt90) cc_final: 0.5827 (mmp80) REVERT: G 107 ARG cc_start: 0.7085 (ptt90) cc_final: 0.6738 (ptt90) REVERT: G 137 THR cc_start: 0.8909 (t) cc_final: 0.8662 (p) REVERT: G 138 ARG cc_start: 0.8523 (mtm110) cc_final: 0.7759 (mtp85) REVERT: G 142 LYS cc_start: 0.8822 (ttpt) cc_final: 0.8371 (mttt) REVERT: G 151 LYS cc_start: 0.8364 (ptmt) cc_final: 0.7765 (ptmt) REVERT: G 157 PRO cc_start: 0.7209 (Cg_endo) cc_final: 0.6961 (Cg_exo) REVERT: G 180 ILE cc_start: 0.8990 (mt) cc_final: 0.8542 (tt) REVERT: H 5 HIS cc_start: 0.8183 (t-90) cc_final: 0.7822 (t70) REVERT: H 68 HIS cc_start: 0.8079 (m90) cc_final: 0.7436 (m90) REVERT: H 85 LYS cc_start: 0.5815 (tmmt) cc_final: 0.5148 (tptt) REVERT: H 161 ILE cc_start: 0.7243 (mm) cc_final: 0.6930 (mm) REVERT: H 163 ARG cc_start: 0.7911 (pmt170) cc_final: 0.7653 (pmt170) REVERT: I 102 TYR cc_start: 0.6431 (t80) cc_final: 0.5896 (t80) REVERT: I 104 MET cc_start: 0.8788 (mmt) cc_final: 0.8414 (mmt) REVERT: I 127 ARG cc_start: 0.7853 (ttt180) cc_final: 0.6954 (ttt180) REVERT: I 162 GLU cc_start: 0.8976 (tp30) cc_final: 0.8508 (pp20) REVERT: J 42 ASN cc_start: 0.7536 (t0) cc_final: 0.7278 (p0) REVERT: J 51 LYS cc_start: 0.7620 (ptmm) cc_final: 0.7248 (tptt) REVERT: J 70 MET cc_start: 0.7144 (tpp) cc_final: 0.6703 (tpp) REVERT: J 80 LEU cc_start: 0.8421 (mp) cc_final: 0.8129 (mp) REVERT: J 131 ASN cc_start: 0.7996 (m110) cc_final: 0.7098 (m110) REVERT: J 163 ILE cc_start: 0.6234 (mm) cc_final: 0.5659 (mm) REVERT: K 25 TYR cc_start: 0.7079 (m-80) cc_final: 0.6862 (m-80) REVERT: L 28 ILE cc_start: 0.7932 (mt) cc_final: 0.7532 (mt) REVERT: L 30 MET cc_start: 0.6832 (ttm) cc_final: 0.6150 (mtp) REVERT: L 84 TYR cc_start: 0.7227 (p90) cc_final: 0.6384 (p90) REVERT: L 94 ARG cc_start: 0.8334 (ttt90) cc_final: 0.7553 (ptm-80) REVERT: L 115 MET cc_start: 0.8220 (tpp) cc_final: 0.7909 (tpp) REVERT: M 2 MET cc_start: 0.6429 (ptt) cc_final: 0.5590 (tpt) REVERT: M 30 LYS cc_start: 0.7868 (ttpt) cc_final: 0.7664 (ptpt) REVERT: M 32 LYS cc_start: 0.8368 (mttm) cc_final: 0.8083 (mttt) REVERT: M 72 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8393 (mm-30) REVERT: M 86 LYS cc_start: 0.7627 (mmmm) cc_final: 0.7158 (mmmm) REVERT: N 11 ARG cc_start: 0.8359 (tpt90) cc_final: 0.7736 (tpt170) REVERT: N 60 LEU cc_start: 0.8900 (pt) cc_final: 0.8301 (tt) REVERT: N 89 TYR cc_start: 0.6186 (m-10) cc_final: 0.5978 (m-10) REVERT: P 58 THR cc_start: 0.5359 (p) cc_final: 0.5018 (p) REVERT: P 68 ARG cc_start: 0.8639 (ttt180) cc_final: 0.8002 (tmt-80) REVERT: P 93 GLU cc_start: 0.5398 (mm-30) cc_final: 0.5070 (mm-30) REVERT: P 106 ILE cc_start: 0.6948 (mm) cc_final: 0.6230 (mt) REVERT: Q 4 ASN cc_start: 0.7519 (t0) cc_final: 0.6993 (t0) REVERT: Q 9 LYS cc_start: 0.9019 (ttpp) cc_final: 0.8819 (ttpp) REVERT: Q 82 ARG cc_start: 0.7748 (ptt-90) cc_final: 0.7388 (ptt-90) REVERT: R 54 THR cc_start: 0.7663 (p) cc_final: 0.7437 (p) REVERT: S 42 ASN cc_start: 0.8956 (m-40) cc_final: 0.8639 (m-40) REVERT: V 61 ARG cc_start: 0.8118 (ptt90) cc_final: 0.7741 (ptm-80) REVERT: W 62 ARG cc_start: 0.7380 (mtt180) cc_final: 0.7153 (mtt180) REVERT: X 80 ARG cc_start: 0.2371 (mtt-85) cc_final: 0.1214 (mmt180) REVERT: Y 7 LYS cc_start: 0.8963 (ptpt) cc_final: 0.8754 (ptmm) REVERT: Y 53 MET cc_start: 0.8023 (ppp) cc_final: 0.7783 (ppp) REVERT: Z 61 ARG cc_start: 0.8188 (ppt170) cc_final: 0.7854 (pmt-80) REVERT: a 8 MET cc_start: 0.1413 (mpp) cc_final: 0.0677 (mpp) outliers start: 24 outliers final: 8 residues processed: 1750 average time/residue: 1.6016 time to fit residues: 4698.4556 Evaluate side-chains 1261 residues out of total 4852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1253 time to evaluate : 6.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain p residue 69 VAL Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain K residue 58 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 886 optimal weight: 10.0000 chunk 795 optimal weight: 10.0000 chunk 441 optimal weight: 6.9990 chunk 271 optimal weight: 7.9990 chunk 536 optimal weight: 4.9990 chunk 425 optimal weight: 30.0000 chunk 822 optimal weight: 10.0000 chunk 318 optimal weight: 10.0000 chunk 500 optimal weight: 9.9990 chunk 612 optimal weight: 20.0000 chunk 953 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 20 ASN ** b 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 89 ASN ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 196 ASN b 238 ASN b 259 ASN ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 94 GLN c 126 ASN ** c 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 150 GLN c 164 GLN d 29 HIS d 97 ASN ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 126 ASN f 29 ASN f 37 ASN f 63 GLN f 142 GLN g 11 ASN g 66 ASN i 110 GLN k 3 GLN k 5 GLN l 38 GLN ** l 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 11 ASN ** n 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 23 ASN n 62 ASN o 100 HIS p 6 GLN ** p 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 114 ASN ** q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 82 HIS r 86 GLN ** r 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 28 ASN t 92 ASN u 39 ASN u 44 HIS u 45 GLN u 65 GLN v 12 GLN ** v 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 72 ASN x 15 ASN ** y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 HIS ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 HIS G 38 HIS ** G 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 145 ASN G 169 HIS G 189 ASN H 31 ASN ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN I 35 GLN I 40 HIS ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 ASN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 139 ASN J 42 ASN ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 134 ASN ** K 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 ASN ** K 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 GLN L 121 ASN L 129 ASN L 147 ASN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 GLN N 49 GLN N 109 GLN O 64 GLN P 23 HIS P 27 ASN R 7 ASN R 104 ASN ** S 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 42 ASN T 27 GLN T 39 GLN T 41 HIS ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 30 HIS V 44 HIS W 51 GLN ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 47 GLN Y 51 ASN Y 69 ASN ** a 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 ASN a 188 ASN a 203 GLN Total number of N/Q/H flips: 79 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 162606 Z= 0.361 Angle : 0.888 13.245 243356 Z= 0.454 Chirality : 0.049 0.313 31135 Planarity : 0.007 0.069 12986 Dihedral : 22.931 179.796 81661 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 28.17 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.58 % Favored : 89.18 % Rotamer: Outliers : 4.86 % Allowed : 17.42 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.84 (0.09), residues: 5849 helix: -2.14 (0.10), residues: 1759 sheet: -2.57 (0.16), residues: 826 loop : -2.85 (0.10), residues: 3264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP b 247 HIS 0.013 0.003 HIS x 35 PHE 0.025 0.003 PHE e 99 TYR 0.031 0.003 TYR W 69 ARG 0.010 0.001 ARG H 64 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1591 residues out of total 4852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1355 time to evaluate : 6.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 97 ASP cc_start: 0.7038 (p0) cc_final: 0.6663 (p0) REVERT: b 131 MET cc_start: 0.8559 (mpp) cc_final: 0.8115 (mpp) REVERT: b 181 ARG cc_start: 0.5345 (OUTLIER) cc_final: 0.3831 (ttp80) REVERT: b 200 MET cc_start: 0.7679 (ptt) cc_final: 0.7434 (ptp) REVERT: b 269 ARG cc_start: 0.4241 (tpt170) cc_final: 0.3300 (mmm160) REVERT: c 128 ARG cc_start: 0.7083 (mtt-85) cc_final: 0.6842 (mtt180) REVERT: c 164 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7891 (mm-40) REVERT: d 1 MET cc_start: 0.7795 (tpp) cc_final: 0.7328 (mpp) REVERT: d 187 VAL cc_start: 0.8574 (t) cc_final: 0.8258 (p) REVERT: e 3 LEU cc_start: 0.8441 (pp) cc_final: 0.8168 (pp) REVERT: e 6 TYR cc_start: 0.8769 (t80) cc_final: 0.8505 (t80) REVERT: e 96 TRP cc_start: 0.7607 (m100) cc_final: 0.6806 (m-90) REVERT: e 97 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8645 (tm-30) REVERT: e 100 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8867 (mp0) REVERT: e 129 MET cc_start: 0.7852 (tmm) cc_final: 0.7480 (tmm) REVERT: e 135 ILE cc_start: 0.8743 (mp) cc_final: 0.8284 (mm) REVERT: f 68 ARG cc_start: 0.8593 (tmt170) cc_final: 0.8213 (ttp80) REVERT: g 25 TYR cc_start: 0.7819 (t80) cc_final: 0.7432 (t80) REVERT: g 33 GLN cc_start: 0.8479 (mp10) cc_final: 0.8206 (mp10) REVERT: i 116 MET cc_start: 0.3869 (mmp) cc_final: 0.1076 (ttt) REVERT: j 35 ARG cc_start: 0.8184 (mpp80) cc_final: 0.7980 (mpp80) REVERT: j 48 VAL cc_start: 0.7521 (t) cc_final: 0.7248 (p) REVERT: j 85 LYS cc_start: 0.7147 (mttt) cc_final: 0.6760 (mttt) REVERT: j 86 GLN cc_start: 0.8048 (pt0) cc_final: 0.7699 (pp30) REVERT: j 96 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6952 (mpp80) REVERT: k 112 PHE cc_start: 0.8182 (m-10) cc_final: 0.7699 (m-10) REVERT: l 59 ARG cc_start: 0.8761 (mtp180) cc_final: 0.8158 (tpp80) REVERT: l 92 LEU cc_start: 0.7738 (mt) cc_final: 0.7501 (mp) REVERT: l 135 ILE cc_start: 0.8863 (mm) cc_final: 0.8478 (tp) REVERT: m 10 ARG cc_start: 0.7248 (mtm-85) cc_final: 0.6864 (mtm-85) REVERT: m 44 ARG cc_start: 0.8493 (ttm110) cc_final: 0.7920 (tpm170) REVERT: m 65 ILE cc_start: 0.8314 (mt) cc_final: 0.7763 (pt) REVERT: m 68 PHE cc_start: 0.7529 (t80) cc_final: 0.7166 (t80) REVERT: m 104 GLU cc_start: 0.8531 (mt-10) cc_final: 0.7682 (mt-10) REVERT: n 8 ARG cc_start: 0.8147 (ttm-80) cc_final: 0.7846 (ttm-80) REVERT: n 17 ARG cc_start: 0.9017 (ttp-110) cc_final: 0.8483 (ttp-110) REVERT: n 35 LYS cc_start: 0.9107 (tttm) cc_final: 0.8525 (tttm) REVERT: n 62 ASN cc_start: 0.8535 (m-40) cc_final: 0.8075 (m-40) REVERT: n 106 ASP cc_start: 0.7642 (p0) cc_final: 0.7340 (p0) REVERT: n 107 ASN cc_start: 0.8300 (t0) cc_final: 0.7630 (t0) REVERT: o 16 ARG cc_start: 0.7903 (mmt-90) cc_final: 0.7438 (mmm160) REVERT: o 18 LEU cc_start: 0.8740 (mm) cc_final: 0.8435 (mm) REVERT: o 36 TYR cc_start: 0.7604 (m-80) cc_final: 0.7190 (m-80) REVERT: o 43 ASN cc_start: 0.8563 (p0) cc_final: 0.8277 (p0) REVERT: o 67 ASN cc_start: 0.8851 (p0) cc_final: 0.7680 (m-40) REVERT: o 76 LYS cc_start: 0.9038 (tttt) cc_final: 0.8423 (mmtm) REVERT: o 98 GLN cc_start: 0.8131 (tp-100) cc_final: 0.7848 (tp-100) REVERT: o 102 ARG cc_start: 0.7456 (mtm180) cc_final: 0.6520 (ttm110) REVERT: p 67 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7071 (mm-30) REVERT: q 19 GLN cc_start: 0.8354 (mt0) cc_final: 0.8141 (mt0) REVERT: q 27 ARG cc_start: 0.7198 (mtt180) cc_final: 0.6872 (ttm110) REVERT: q 32 ARG cc_start: 0.6902 (ttm170) cc_final: 0.6682 (ptp-110) REVERT: q 55 GLN cc_start: 0.8680 (mt0) cc_final: 0.8311 (mm-40) REVERT: r 24 LYS cc_start: 0.6952 (ttpt) cc_final: 0.6103 (tptt) REVERT: r 45 GLU cc_start: 0.7504 (tp30) cc_final: 0.7034 (tm-30) REVERT: r 54 VAL cc_start: 0.3366 (OUTLIER) cc_final: 0.3130 (m) REVERT: r 70 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7825 (mm-30) REVERT: r 72 VAL cc_start: 0.8867 (OUTLIER) cc_final: 0.8576 (t) REVERT: s 28 LYS cc_start: 0.6949 (mmtt) cc_final: 0.6325 (mmtt) REVERT: s 40 ASN cc_start: 0.8254 (m-40) cc_final: 0.7661 (p0) REVERT: s 86 MET cc_start: 0.7548 (tpt) cc_final: 0.7235 (mtt) REVERT: t 6 ARG cc_start: 0.8742 (tpm170) cc_final: 0.8242 (tpm170) REVERT: t 19 LYS cc_start: 0.8334 (tttt) cc_final: 0.7969 (tptt) REVERT: t 24 MET cc_start: 0.6398 (tpp) cc_final: 0.5986 (tpp) REVERT: u 21 ARG cc_start: 0.7677 (mtm-85) cc_final: 0.7299 (mtt180) REVERT: u 95 PHE cc_start: 0.6588 (m-10) cc_final: 0.6026 (m-10) REVERT: v 7 GLU cc_start: 0.7183 (tm-30) cc_final: 0.6900 (tm-30) REVERT: v 55 GLU cc_start: 0.9167 (mp0) cc_final: 0.8844 (mp0) REVERT: v 56 PHE cc_start: 0.8718 (t80) cc_final: 0.8513 (t80) REVERT: w 15 LYS cc_start: 0.7914 (tppt) cc_final: 0.7363 (ptpp) REVERT: w 40 LYS cc_start: 0.7441 (pttt) cc_final: 0.7081 (pttt) REVERT: w 63 VAL cc_start: 0.8930 (t) cc_final: 0.8636 (t) REVERT: x 15 ASN cc_start: 0.7132 (m-40) cc_final: 0.6714 (m-40) REVERT: x 17 ARG cc_start: 0.7446 (mmm-85) cc_final: 0.6978 (mmm-85) REVERT: y 23 ARG cc_start: 0.7788 (mmt-90) cc_final: 0.7427 (mmm-85) REVERT: z 46 MET cc_start: 0.7831 (mtp) cc_final: 0.7429 (mtp) REVERT: B 2 VAL cc_start: 0.8834 (OUTLIER) cc_final: 0.8399 (p) REVERT: D 1 MET cc_start: 0.6062 (tpt) cc_final: 0.5771 (tpt) REVERT: D 21 ARG cc_start: 0.7806 (mmt180) cc_final: 0.7458 (mmt180) REVERT: D 22 MET cc_start: 0.8140 (tpp) cc_final: 0.7756 (tmm) REVERT: E 4 LYS cc_start: 0.6673 (tppt) cc_final: 0.5483 (pttt) REVERT: F 1 MET cc_start: 0.3447 (ptm) cc_final: 0.3106 (ptm) REVERT: F 24 ARG cc_start: 0.7666 (mmt90) cc_final: 0.7368 (ttm170) REVERT: G 55 GLU cc_start: 0.9035 (tp30) cc_final: 0.8589 (pp20) REVERT: G 56 LEU cc_start: 0.8615 (tt) cc_final: 0.8376 (tt) REVERT: G 59 ILE cc_start: 0.9056 (mt) cc_final: 0.8549 (mm) REVERT: G 67 LEU cc_start: 0.7478 (tp) cc_final: 0.6567 (mm) REVERT: G 103 TRP cc_start: 0.6873 (t-100) cc_final: 0.6652 (t-100) REVERT: G 107 ARG cc_start: 0.7130 (ptt90) cc_final: 0.6549 (ptt90) REVERT: G 135 MET cc_start: 0.7895 (mmm) cc_final: 0.7317 (mmp) REVERT: G 136 ARG cc_start: 0.8442 (mtm-85) cc_final: 0.7462 (mtm180) REVERT: G 138 ARG cc_start: 0.8221 (mtm110) cc_final: 0.7164 (mtp85) REVERT: G 142 LYS cc_start: 0.8899 (ttpt) cc_final: 0.8451 (mttt) REVERT: G 151 LYS cc_start: 0.8455 (ptmt) cc_final: 0.8232 (ptmt) REVERT: G 153 MET cc_start: 0.6076 (mtp) cc_final: 0.5789 (mtm) REVERT: G 180 ILE cc_start: 0.8934 (mt) cc_final: 0.8299 (tt) REVERT: G 204 ASP cc_start: 0.5634 (m-30) cc_final: 0.5342 (m-30) REVERT: H 5 HIS cc_start: 0.8263 (t-90) cc_final: 0.7969 (t70) REVERT: H 55 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8280 (m) REVERT: H 104 GLU cc_start: 0.8778 (pt0) cc_final: 0.8307 (pm20) REVERT: H 161 ILE cc_start: 0.7489 (mm) cc_final: 0.7127 (mm) REVERT: H 163 ARG cc_start: 0.7196 (pmt170) cc_final: 0.6924 (pmt170) REVERT: H 202 PHE cc_start: 0.7197 (t80) cc_final: 0.6863 (t80) REVERT: I 74 TYR cc_start: 0.8437 (m-80) cc_final: 0.8001 (m-80) REVERT: I 123 MET cc_start: 0.7445 (mtp) cc_final: 0.6831 (tpp) REVERT: I 124 VAL cc_start: 0.9022 (t) cc_final: 0.8811 (p) REVERT: I 162 GLU cc_start: 0.8835 (tp30) cc_final: 0.8507 (pp20) REVERT: J 42 ASN cc_start: 0.7963 (t0) cc_final: 0.7345 (p0) REVERT: J 70 MET cc_start: 0.7477 (tpp) cc_final: 0.6762 (tpp) REVERT: J 93 VAL cc_start: 0.4199 (OUTLIER) cc_final: 0.3838 (p) REVERT: J 110 MET cc_start: 0.6528 (tpp) cc_final: 0.5907 (mmm) REVERT: J 131 ASN cc_start: 0.7817 (m110) cc_final: 0.7149 (m110) REVERT: K 5 GLU cc_start: 0.7305 (mt-10) cc_final: 0.6853 (tp30) REVERT: K 36 ILE cc_start: 0.6672 (OUTLIER) cc_final: 0.6015 (mp) REVERT: K 41 ASP cc_start: 0.4698 (m-30) cc_final: 0.4060 (m-30) REVERT: K 90 MET cc_start: 0.8089 (mmm) cc_final: 0.7235 (mmm) REVERT: L 84 TYR cc_start: 0.6361 (p90) cc_final: 0.5565 (p90) REVERT: L 94 ARG cc_start: 0.7945 (ttt90) cc_final: 0.7275 (ptm160) REVERT: M 39 LEU cc_start: 0.7025 (OUTLIER) cc_final: 0.6823 (tp) REVERT: M 72 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8117 (mm-30) REVERT: M 86 LYS cc_start: 0.7853 (mmmm) cc_final: 0.7429 (mmmm) REVERT: M 107 LYS cc_start: 0.7227 (mmtp) cc_final: 0.6928 (tppt) REVERT: M 110 MET cc_start: 0.7387 (ptt) cc_final: 0.7124 (ptt) REVERT: N 11 ARG cc_start: 0.8475 (tpt90) cc_final: 0.7970 (tpt170) REVERT: N 45 MET cc_start: 0.7511 (ptm) cc_final: 0.7264 (ptt) REVERT: N 60 LEU cc_start: 0.8762 (pt) cc_final: 0.8184 (tt) REVERT: N 79 ARG cc_start: 0.9132 (ttm110) cc_final: 0.8905 (mtm-85) REVERT: N 94 ARG cc_start: 0.8263 (tpp80) cc_final: 0.7684 (ttm170) REVERT: N 103 VAL cc_start: 0.5051 (m) cc_final: 0.4284 (t) REVERT: N 108 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7712 (mtp85) REVERT: N 109 GLN cc_start: 0.8363 (mm-40) cc_final: 0.7997 (mt0) REVERT: P 19 VAL cc_start: 0.8858 (t) cc_final: 0.8538 (m) REVERT: P 58 THR cc_start: 0.4808 (p) cc_final: 0.4516 (p) REVERT: P 63 GLN cc_start: 0.8921 (tt0) cc_final: 0.8594 (pt0) REVERT: P 68 ARG cc_start: 0.8619 (ttt180) cc_final: 0.8363 (tmt-80) REVERT: P 93 GLU cc_start: 0.5377 (mm-30) cc_final: 0.5049 (mm-30) REVERT: Q 28 GLN cc_start: 0.8533 (mm-40) cc_final: 0.7884 (mm-40) REVERT: R 2 ARG cc_start: 0.9142 (ttt180) cc_final: 0.8550 (tpt170) REVERT: R 80 MET cc_start: 0.9295 (mtt) cc_final: 0.8945 (ptp) REVERT: R 90 HIS cc_start: 0.8475 (m-70) cc_final: 0.8227 (m170) REVERT: S 89 ARG cc_start: 0.8587 (tpm170) cc_final: 0.7894 (tpm170) REVERT: V 27 PHE cc_start: 0.3067 (OUTLIER) cc_final: 0.1777 (t80) REVERT: V 30 HIS cc_start: 0.7335 (t-90) cc_final: 0.7071 (t70) REVERT: V 70 LYS cc_start: 0.5694 (OUTLIER) cc_final: 0.5431 (ttpp) REVERT: X 80 ARG cc_start: 0.2292 (mtt-85) cc_final: 0.1338 (mmt180) REVERT: Y 7 LYS cc_start: 0.9006 (ptpt) cc_final: 0.8772 (ptmm) REVERT: Y 39 GLU cc_start: 0.8089 (pp20) cc_final: 0.7841 (pp20) REVERT: Z 45 LYS cc_start: 0.8760 (tppt) cc_final: 0.8469 (tppt) outliers start: 236 outliers final: 149 residues processed: 1471 average time/residue: 1.3955 time to fit residues: 3450.3297 Evaluate side-chains 1347 residues out of total 4852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1185 time to evaluate : 6.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 145 MET Chi-restraints excluded: chain b residue 181 ARG Chi-restraints excluded: chain b residue 196 ASN Chi-restraints excluded: chain b residue 225 ASN Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 101 PHE Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 164 GLN Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 178 VAL Chi-restraints excluded: chain c residue 193 VAL Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 100 MET Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 178 VAL Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain d residue 193 VAL Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 49 LEU Chi-restraints excluded: chain e residue 80 GLN Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 18 ILE Chi-restraints excluded: chain f residue 46 ASP Chi-restraints excluded: chain f residue 113 ASP Chi-restraints excluded: chain f residue 148 ARG Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 21 VAL Chi-restraints excluded: chain g residue 108 VAL Chi-restraints excluded: chain h residue 86 MET Chi-restraints excluded: chain h residue 119 PRO Chi-restraints excluded: chain i residue 124 MET Chi-restraints excluded: chain j residue 2 LYS Chi-restraints excluded: chain j residue 3 THR Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 36 LEU Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 70 THR Chi-restraints excluded: chain j residue 78 THR Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 96 ARG Chi-restraints excluded: chain k residue 7 MET Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain l residue 61 LEU Chi-restraints excluded: chain l residue 110 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 72 ASP Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 69 VAL Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 43 GLN Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 66 VAL Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain x residue 33 HIS Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain y residue 17 GLU Chi-restraints excluded: chain y residue 26 PHE Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 149 LYS Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 70 GLN Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain N residue 5 TYR Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain N residue 108 ARG Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 76 TYR Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain P residue 113 THR Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 45 GLU Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain U residue 59 HIS Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 70 LYS Chi-restraints excluded: chain X residue 5 LYS Chi-restraints excluded: chain X residue 20 LYS Chi-restraints excluded: chain X residue 65 MET Chi-restraints excluded: chain X residue 72 GLU Chi-restraints excluded: chain Z residue 12 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 529 optimal weight: 8.9990 chunk 295 optimal weight: 0.9980 chunk 793 optimal weight: 9.9990 chunk 649 optimal weight: 10.0000 chunk 263 optimal weight: 6.9990 chunk 955 optimal weight: 10.0000 chunk 1031 optimal weight: 20.0000 chunk 850 optimal weight: 9.9990 chunk 947 optimal weight: 10.0000 chunk 325 optimal weight: 8.9990 chunk 766 optimal weight: 10.0000 overall best weight: 7.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 20 ASN ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 196 ASN ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 126 ASN c 173 GLN d 94 GLN ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 3 GLN ** l 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 23 ASN ** o 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN ** p 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 55 GLN r 43 ASN ** r 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 12 GLN ** v 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 31 ASN ** y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 GLN ** G 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 ASN ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 GLN ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 ASN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN L 67 ASN ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 GLN N 4 GLN N 49 GLN O 58 ASN ** P 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 111 GLN ** S 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 19 ASN ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 56 HIS Y 19 HIS ** a 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 188 ASN a 203 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.164 162606 Z= 0.327 Angle : 0.787 14.927 243356 Z= 0.404 Chirality : 0.043 0.371 31135 Planarity : 0.006 0.078 12986 Dihedral : 23.442 178.934 81657 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 28.21 Ramachandran Plot: Outliers : 0.19 % Allowed : 12.10 % Favored : 87.71 % Rotamer: Outliers : 6.22 % Allowed : 20.57 % Favored : 73.21 % 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: -3.52 (0.10), residues: 5849 helix: -1.71 (0.11), residues: 1776 sheet: -2.39 (0.16), residues: 830 loop : -2.76 (0.10), residues: 3243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP U 60 HIS 0.017 0.003 HIS p 76 PHE 0.030 0.003 PHE Z 18 TYR 0.029 0.003 TYR t 84 ARG 0.030 0.001 ARG n 12 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1556 residues out of total 4852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 302 poor density : 1254 time to evaluate : 6.437 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: b 99 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7490 (tm-30) REVERT: b 131 MET cc_start: 0.8516 (mpp) cc_final: 0.8166 (mpp) REVERT: b 269 ARG cc_start: 0.4625 (tpt170) cc_final: 0.3669 (mmm160) REVERT: c 33 ARG cc_start: 0.7870 (mpp80) cc_final: 0.7235 (mpp80) REVERT: c 82 PHE cc_start: 0.8292 (m-80) cc_final: 0.8005 (m-80) REVERT: c 164 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7927 (mm-40) REVERT: c 167 ASN cc_start: 0.8919 (t0) cc_final: 0.8652 (t0) REVERT: d 1 MET cc_start: 0.7612 (tpp) cc_final: 0.7284 (mmm) REVERT: d 95 LYS cc_start: 0.7544 (tttt) cc_final: 0.7270 (tmtt) REVERT: d 100 MET cc_start: 0.7758 (tpp) cc_final: 0.7180 (mpp) REVERT: d 187 VAL cc_start: 0.8667 (t) cc_final: 0.8365 (p) REVERT: d 195 GLN cc_start: 0.8711 (tp40) cc_final: 0.8476 (tp40) REVERT: e 3 LEU cc_start: 0.8758 (pp) cc_final: 0.8419 (pp) REVERT: e 6 TYR cc_start: 0.8899 (t80) cc_final: 0.8639 (t80) REVERT: e 56 LEU cc_start: 0.7791 (mt) cc_final: 0.7499 (mt) REVERT: e 65 LEU cc_start: 0.9088 (tt) cc_final: 0.8652 (tp) REVERT: e 86 CYS cc_start: 0.6645 (OUTLIER) cc_final: 0.5568 (p) REVERT: e 95 MET cc_start: 0.8028 (ptm) cc_final: 0.7240 (mtm) REVERT: e 96 TRP cc_start: 0.7262 (m100) cc_final: 0.5788 (m100) REVERT: e 97 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8611 (tm-30) REVERT: e 129 MET cc_start: 0.7644 (tmm) cc_final: 0.7429 (tmm) REVERT: e 152 ASP cc_start: 0.4829 (OUTLIER) cc_final: 0.4531 (p0) REVERT: f 136 ASP cc_start: 0.8319 (t0) cc_final: 0.8055 (t0) REVERT: g 25 TYR cc_start: 0.7590 (t80) cc_final: 0.7199 (t80) REVERT: g 33 GLN cc_start: 0.8438 (mp10) cc_final: 0.8053 (mp10) REVERT: i 116 MET cc_start: 0.4289 (mmp) cc_final: 0.1955 (ttt) REVERT: j 13 ARG cc_start: 0.7192 (OUTLIER) cc_final: 0.6954 (mmt-90) REVERT: j 48 VAL cc_start: 0.7662 (t) cc_final: 0.7443 (p) REVERT: j 57 LEU cc_start: 0.8816 (pp) cc_final: 0.8417 (pp) REVERT: j 85 LYS cc_start: 0.7144 (mttt) cc_final: 0.6766 (mttt) REVERT: j 86 GLN cc_start: 0.7967 (pt0) cc_final: 0.7452 (pp30) REVERT: k 45 GLU cc_start: 0.6850 (mp0) cc_final: 0.6618 (mp0) REVERT: k 87 LEU cc_start: 0.7376 (mt) cc_final: 0.6944 (mt) REVERT: l 59 ARG cc_start: 0.8659 (mtp180) cc_final: 0.8152 (tpp80) REVERT: l 135 ILE cc_start: 0.8842 (mm) cc_final: 0.8622 (tp) REVERT: m 10 ARG cc_start: 0.7375 (mtm-85) cc_final: 0.7064 (mtm-85) REVERT: m 44 ARG cc_start: 0.8637 (ttm110) cc_final: 0.8294 (tpm170) REVERT: m 65 ILE cc_start: 0.8304 (mt) cc_final: 0.7883 (pt) REVERT: m 84 LYS cc_start: 0.8292 (mmtt) cc_final: 0.8057 (mmtt) REVERT: m 104 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7719 (mt-10) REVERT: m 111 GLU cc_start: 0.8357 (tm-30) cc_final: 0.7472 (tm-30) REVERT: m 115 GLU cc_start: 0.8349 (pt0) cc_final: 0.8112 (pt0) REVERT: n 8 ARG cc_start: 0.8079 (ttm-80) cc_final: 0.7817 (ttm-80) REVERT: n 9 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.7601 (mm-40) REVERT: n 35 LYS cc_start: 0.9063 (tttm) cc_final: 0.8526 (tttm) REVERT: n 62 ASN cc_start: 0.8418 (m-40) cc_final: 0.7997 (m-40) REVERT: n 106 ASP cc_start: 0.7239 (p0) cc_final: 0.5952 (t0) REVERT: n 107 ASN cc_start: 0.8229 (t0) cc_final: 0.7427 (t0) REVERT: o 16 ARG cc_start: 0.7805 (mmt-90) cc_final: 0.7266 (mmm160) REVERT: o 18 LEU cc_start: 0.8806 (mm) cc_final: 0.8467 (mm) REVERT: o 36 TYR cc_start: 0.7606 (m-80) cc_final: 0.7279 (m-80) REVERT: o 98 GLN cc_start: 0.8036 (tp-100) cc_final: 0.7663 (tp40) REVERT: o 102 ARG cc_start: 0.7490 (mtm180) cc_final: 0.6370 (ttm170) REVERT: p 9 GLN cc_start: 0.6766 (OUTLIER) cc_final: 0.6523 (mp10) REVERT: p 12 MET cc_start: 0.7347 (mmp) cc_final: 0.7012 (mmp) REVERT: p 67 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7086 (mm-30) REVERT: p 97 TYR cc_start: 0.7010 (m-80) cc_final: 0.6566 (m-80) REVERT: q 27 ARG cc_start: 0.6755 (mtt180) cc_final: 0.6471 (ttm110) REVERT: q 49 ARG cc_start: 0.9016 (mmt90) cc_final: 0.8811 (mmt90) REVERT: q 50 ARG cc_start: 0.8542 (mtm-85) cc_final: 0.8168 (mtm-85) REVERT: q 61 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8737 (tt) REVERT: r 16 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6445 (mm-30) REVERT: r 24 LYS cc_start: 0.7340 (ttpt) cc_final: 0.6086 (tptt) REVERT: r 45 GLU cc_start: 0.7338 (tp30) cc_final: 0.6922 (tm-30) REVERT: r 53 PHE cc_start: 0.7207 (OUTLIER) cc_final: 0.6948 (m-80) REVERT: r 70 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7693 (mm-30) REVERT: r 82 HIS cc_start: 0.7706 (t-90) cc_final: 0.7378 (t-90) REVERT: s 28 LYS cc_start: 0.7032 (mmtt) cc_final: 0.6282 (mmtt) REVERT: s 40 ASN cc_start: 0.8182 (m-40) cc_final: 0.7836 (p0) REVERT: t 1 MET cc_start: 0.2321 (mmt) cc_final: 0.1938 (mmt) REVERT: t 6 ARG cc_start: 0.8675 (tpm170) cc_final: 0.8105 (tpm170) REVERT: t 19 LYS cc_start: 0.8388 (tttt) cc_final: 0.7970 (tptt) REVERT: v 7 GLU cc_start: 0.7089 (tm-30) cc_final: 0.6885 (tm-30) REVERT: v 55 GLU cc_start: 0.9345 (mp0) cc_final: 0.9049 (mp0) REVERT: v 56 PHE cc_start: 0.8750 (t80) cc_final: 0.8463 (t80) REVERT: v 76 ASP cc_start: 0.7431 (t70) cc_final: 0.6776 (t70) REVERT: v 83 LYS cc_start: 0.8258 (ptpp) cc_final: 0.7859 (ptpp) REVERT: w 15 LYS cc_start: 0.8029 (tppt) cc_final: 0.7477 (ptpp) REVERT: w 40 LYS cc_start: 0.7364 (pttt) cc_final: 0.6831 (pttt) REVERT: w 63 VAL cc_start: 0.8919 (t) cc_final: 0.8647 (t) REVERT: w 65 PHE cc_start: 0.6473 (m-80) cc_final: 0.6238 (m-80) REVERT: w 74 LYS cc_start: 0.8425 (mmmt) cc_final: 0.8175 (mmmt) REVERT: x 15 ASN cc_start: 0.6856 (m-40) cc_final: 0.6629 (m-40) REVERT: y 23 ARG cc_start: 0.7945 (mmt-90) cc_final: 0.7462 (mmm-85) REVERT: z 30 ARG cc_start: 0.8746 (pmt170) cc_final: 0.8216 (pmt170) REVERT: z 33 HIS cc_start: 0.6209 (t-170) cc_final: 0.5971 (t-170) REVERT: z 36 GLU cc_start: 0.8573 (pm20) cc_final: 0.8222 (mp0) REVERT: C 9 LYS cc_start: 0.7334 (OUTLIER) cc_final: 0.7108 (pttm) REVERT: E 4 LYS cc_start: 0.7027 (tppt) cc_final: 0.4242 (tppt) REVERT: F 24 ARG cc_start: 0.7605 (mmt90) cc_final: 0.6401 (tpt170) REVERT: G 5 MET cc_start: 0.6393 (mmm) cc_final: 0.6161 (mmm) REVERT: G 26 MET cc_start: 0.6330 (tpp) cc_final: 0.6108 (mmt) REVERT: G 55 GLU cc_start: 0.9012 (tp30) cc_final: 0.8605 (pp20) REVERT: G 57 ASN cc_start: 0.7539 (m-40) cc_final: 0.7254 (m110) REVERT: G 67 LEU cc_start: 0.7662 (tp) cc_final: 0.6845 (mm) REVERT: G 103 TRP cc_start: 0.7336 (t-100) cc_final: 0.7084 (t-100) REVERT: G 107 ARG cc_start: 0.7116 (ptt90) cc_final: 0.6491 (ptt90) REVERT: G 114 LYS cc_start: 0.9212 (mmtm) cc_final: 0.8953 (mmmt) REVERT: G 142 LYS cc_start: 0.8880 (ttpt) cc_final: 0.8422 (mtmt) REVERT: G 153 MET cc_start: 0.6091 (mtp) cc_final: 0.5294 (mtp) REVERT: G 180 ILE cc_start: 0.8794 (mt) cc_final: 0.8392 (tt) REVERT: H 5 HIS cc_start: 0.8422 (t-90) cc_final: 0.8091 (t70) REVERT: H 161 ILE cc_start: 0.6630 (mm) cc_final: 0.6275 (mm) REVERT: H 163 ARG cc_start: 0.7072 (pmt170) cc_final: 0.6702 (pmt170) REVERT: I 74 TYR cc_start: 0.8366 (m-80) cc_final: 0.7999 (m-80) REVERT: I 102 TYR cc_start: 0.6670 (t80) cc_final: 0.5969 (t80) REVERT: I 123 MET cc_start: 0.7193 (mtp) cc_final: 0.6565 (mmt) REVERT: I 124 VAL cc_start: 0.9007 (t) cc_final: 0.8794 (p) REVERT: I 127 ARG cc_start: 0.7762 (ttt180) cc_final: 0.7007 (ttt-90) REVERT: I 162 GLU cc_start: 0.8895 (tp30) cc_final: 0.8686 (pp20) REVERT: J 42 ASN cc_start: 0.7817 (t0) cc_final: 0.7072 (p0) REVERT: J 70 MET cc_start: 0.7807 (tpp) cc_final: 0.6045 (pmm) REVERT: J 131 ASN cc_start: 0.8125 (m110) cc_final: 0.7777 (m110) REVERT: K 5 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6761 (tp30) REVERT: K 90 MET cc_start: 0.8376 (mmm) cc_final: 0.7785 (mmm) REVERT: L 94 ARG cc_start: 0.7921 (ttt180) cc_final: 0.7522 (ttt180) REVERT: L 115 MET cc_start: 0.8017 (tpp) cc_final: 0.7606 (tpp) REVERT: M 14 ARG cc_start: 0.8380 (ttm110) cc_final: 0.8117 (ptp-110) REVERT: M 72 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8016 (mm-30) REVERT: M 107 LYS cc_start: 0.7243 (mmtp) cc_final: 0.6932 (tppt) REVERT: M 113 ARG cc_start: 0.6931 (OUTLIER) cc_final: 0.5950 (ttp-110) REVERT: N 11 ARG cc_start: 0.8649 (tpt90) cc_final: 0.8325 (tpt170) REVERT: N 108 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7727 (mtp85) REVERT: N 109 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7813 (mt0) REVERT: P 19 VAL cc_start: 0.8718 (t) cc_final: 0.8515 (m) REVERT: P 58 THR cc_start: 0.5314 (p) cc_final: 0.5009 (p) REVERT: P 63 GLN cc_start: 0.8877 (tt0) cc_final: 0.8632 (pt0) REVERT: P 68 ARG cc_start: 0.8339 (ttt180) cc_final: 0.8114 (tmt-80) REVERT: P 86 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.6945 (ptpp) REVERT: P 93 GLU cc_start: 0.6280 (mm-30) cc_final: 0.5918 (mm-30) REVERT: Q 28 GLN cc_start: 0.8436 (mm-40) cc_final: 0.7744 (mm-40) REVERT: Q 80 LEU cc_start: 0.7897 (tp) cc_final: 0.7509 (mt) REVERT: Q 95 HIS cc_start: 0.8357 (OUTLIER) cc_final: 0.8017 (t-90) REVERT: R 2 ARG cc_start: 0.9031 (ttt180) cc_final: 0.8366 (tpt170) REVERT: R 90 HIS cc_start: 0.8486 (m-70) cc_final: 0.8249 (m170) REVERT: R 99 GLN cc_start: 0.7210 (mp10) cc_final: 0.6728 (mp10) REVERT: S 89 ARG cc_start: 0.8548 (tpm170) cc_final: 0.7685 (tpm170) REVERT: T 48 ASP cc_start: 0.8527 (t0) cc_final: 0.8239 (t0) REVERT: U 60 TRP cc_start: 0.8707 (m100) cc_final: 0.7855 (t-100) REVERT: V 27 PHE cc_start: 0.3520 (OUTLIER) cc_final: 0.2179 (t80) REVERT: V 30 HIS cc_start: 0.7432 (t-90) cc_final: 0.7221 (t70) REVERT: W 32 ILE cc_start: 0.6441 (OUTLIER) cc_final: 0.6117 (pt) REVERT: X 80 ARG cc_start: 0.2299 (mtt-85) cc_final: 0.1212 (mtt-85) REVERT: Y 7 LYS cc_start: 0.8916 (ptpt) cc_final: 0.8640 (ptmm) REVERT: Y 12 GLN cc_start: 0.8736 (mt0) cc_final: 0.8528 (mp10) REVERT: Y 18 LYS cc_start: 0.9300 (mtmm) cc_final: 0.9055 (mtmm) REVERT: Y 39 GLU cc_start: 0.8352 (pp20) cc_final: 0.8123 (pp20) REVERT: a 8 MET cc_start: 0.1276 (mpp) cc_final: 0.0617 (mpp) outliers start: 302 outliers final: 198 residues processed: 1427 average time/residue: 1.3567 time to fit residues: 3269.3369 Evaluate side-chains 1347 residues out of total 4852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 1132 time to evaluate : 6.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 78 GLU Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 172 THR Chi-restraints excluded: chain b residue 231 HIS Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 101 PHE Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 164 GLN Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 178 VAL Chi-restraints excluded: chain c residue 203 VAL Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 178 VAL Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 49 LEU Chi-restraints excluded: chain e residue 86 CYS Chi-restraints excluded: chain e residue 120 SER Chi-restraints excluded: chain e residue 152 ASP Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 18 ILE Chi-restraints excluded: chain f residue 46 ASP Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 113 ASP Chi-restraints excluded: chain f residue 148 ARG Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 19 VAL Chi-restraints excluded: chain g residue 20 ASN Chi-restraints excluded: chain h residue 86 MET Chi-restraints excluded: chain j residue 3 THR Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 13 ARG Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 36 LEU Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 70 THR Chi-restraints excluded: chain j residue 78 THR Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 130 HIS Chi-restraints excluded: chain k residue 52 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain l residue 61 LEU Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 110 VAL Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain n residue 9 GLN Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 38 GLN Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 68 LYS Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain p residue 9 GLN Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 55 HIS Chi-restraints excluded: chain p residue 69 VAL Chi-restraints excluded: chain p residue 83 ILE Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain p residue 93 LYS Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 43 GLN Chi-restraints excluded: chain q residue 61 ILE Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain r residue 16 GLU Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain r residue 98 ILE Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 83 LYS Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain u residue 7 ASP Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 40 LEU Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 12 GLN Chi-restraints excluded: chain v residue 19 ARG Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 49 ASN Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain x residue 29 LEU Chi-restraints excluded: chain x residue 33 HIS Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain y residue 17 GLU Chi-restraints excluded: chain y residue 26 PHE Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 29 ARG Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 136 ARG Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 120 LYS Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 173 ASP Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 58 HIS Chi-restraints excluded: chain K residue 59 TYR Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 113 ARG Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain N residue 108 ARG Chi-restraints excluded: chain N residue 109 GLN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 76 TYR Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 95 HIS Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 53 ASP Chi-restraints excluded: chain S residue 2 LYS Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain T residue 39 GLN Chi-restraints excluded: chain T residue 55 LEU Chi-restraints excluded: chain T residue 59 VAL Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 45 GLU Chi-restraints excluded: chain U residue 59 HIS Chi-restraints excluded: chain V residue 7 LEU Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 71 ASP Chi-restraints excluded: chain X residue 13 HIS Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 72 GLU Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain a residue 16 ASP Chi-restraints excluded: chain a residue 202 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 943 optimal weight: 40.0000 chunk 718 optimal weight: 20.0000 chunk 495 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 455 optimal weight: 20.0000 chunk 641 optimal weight: 20.0000 chunk 958 optimal weight: 10.9990 chunk 1014 optimal weight: 10.0000 chunk 500 optimal weight: 20.0000 chunk 908 optimal weight: 9.9990 chunk 273 optimal weight: 7.9990 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 20 ASN ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 196 ASN c 36 GLN c 126 ASN ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 57 ASN ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 3 GLN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 23 ASN ** o 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN ** o 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 6 GLN ** p 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 89 HIS ** s 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 49 ASN ** v 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN B 4 GLN ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 ASN ** K 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 56 HIS ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 172 HIS ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.225 162606 Z= 0.371 Angle : 0.846 13.081 243356 Z= 0.430 Chirality : 0.045 0.359 31135 Planarity : 0.007 0.160 12986 Dihedral : 23.785 178.400 81655 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 34.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.28 % Favored : 87.57 % Rotamer: Outliers : 8.08 % Allowed : 21.81 % Favored : 70.12 % 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: -3.45 (0.10), residues: 5849 helix: -1.54 (0.11), residues: 1764 sheet: -2.43 (0.17), residues: 798 loop : -2.76 (0.10), residues: 3287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP t 80 HIS 0.014 0.002 HIS p 76 PHE 0.025 0.003 PHE I 71 TYR 0.027 0.003 TYR t 84 ARG 0.025 0.001 ARG Y 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1588 residues out of total 4852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 392 poor density : 1196 time to evaluate : 6.671 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: b 83 ASP cc_start: 0.8743 (t0) cc_final: 0.8135 (t0) REVERT: b 99 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7394 (tm-30) REVERT: b 131 MET cc_start: 0.8537 (mpp) cc_final: 0.8186 (mpp) REVERT: b 176 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.7040 (mmm-85) REVERT: b 181 ARG cc_start: 0.6384 (OUTLIER) cc_final: 0.4676 (ttt90) REVERT: b 200 MET cc_start: 0.7661 (ptt) cc_final: 0.7347 (ptp) REVERT: b 269 ARG cc_start: 0.4682 (tpt170) cc_final: 0.3800 (mmm160) REVERT: c 33 ARG cc_start: 0.8061 (mpp80) cc_final: 0.7139 (mpp80) REVERT: c 82 PHE cc_start: 0.8360 (m-80) cc_final: 0.8103 (m-80) REVERT: c 157 LYS cc_start: 0.6842 (mttt) cc_final: 0.6253 (tttt) REVERT: c 167 ASN cc_start: 0.9004 (t0) cc_final: 0.8641 (t0) REVERT: d 18 THR cc_start: 0.8648 (m) cc_final: 0.8259 (p) REVERT: d 139 LYS cc_start: 0.9217 (ptpp) cc_final: 0.8947 (tppt) REVERT: d 187 VAL cc_start: 0.8677 (t) cc_final: 0.8342 (p) REVERT: e 3 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.7909 (pp) REVERT: e 87 LYS cc_start: 0.7691 (mtmt) cc_final: 0.7446 (ptpp) REVERT: e 96 TRP cc_start: 0.7020 (OUTLIER) cc_final: 0.6637 (m-90) REVERT: e 129 MET cc_start: 0.7573 (tmm) cc_final: 0.7079 (tmm) REVERT: f 68 ARG cc_start: 0.8524 (tmt170) cc_final: 0.8126 (tmm160) REVERT: f 74 MET cc_start: 0.7161 (ttt) cc_final: 0.5205 (tpt) REVERT: g 25 TYR cc_start: 0.7144 (t80) cc_final: 0.6600 (t80) REVERT: g 33 GLN cc_start: 0.8551 (mp10) cc_final: 0.8169 (mp10) REVERT: i 116 MET cc_start: 0.4485 (mmp) cc_final: 0.3762 (mmm) REVERT: j 34 ARG cc_start: 0.8520 (ttm170) cc_final: 0.8178 (mtp85) REVERT: j 78 THR cc_start: 0.9216 (OUTLIER) cc_final: 0.9011 (t) REVERT: j 85 LYS cc_start: 0.7534 (mttt) cc_final: 0.7235 (mttt) REVERT: j 86 GLN cc_start: 0.8043 (pt0) cc_final: 0.7406 (pp30) REVERT: j 135 GLN cc_start: 0.8050 (mp10) cc_final: 0.7842 (mp10) REVERT: j 136 GLN cc_start: 0.8645 (mt0) cc_final: 0.8310 (mp10) REVERT: k 20 MET cc_start: 0.7894 (ttm) cc_final: 0.7519 (ttm) REVERT: k 87 LEU cc_start: 0.7457 (mt) cc_final: 0.7007 (mt) REVERT: l 59 ARG cc_start: 0.8675 (mtp180) cc_final: 0.8083 (tpp80) REVERT: m 44 ARG cc_start: 0.8543 (ttm110) cc_final: 0.8273 (tpm170) REVERT: m 45 GLN cc_start: 0.7673 (mt0) cc_final: 0.7415 (tt0) REVERT: m 65 ILE cc_start: 0.8313 (mt) cc_final: 0.7818 (pt) REVERT: n 8 ARG cc_start: 0.8104 (ttm-80) cc_final: 0.7535 (ttm-80) REVERT: n 17 ARG cc_start: 0.9009 (ttp-170) cc_final: 0.8511 (ptt90) REVERT: n 35 LYS cc_start: 0.9163 (tttm) cc_final: 0.8590 (tttm) REVERT: n 62 ASN cc_start: 0.8468 (m-40) cc_final: 0.8078 (m-40) REVERT: n 106 ASP cc_start: 0.7181 (p0) cc_final: 0.6641 (t0) REVERT: o 18 LEU cc_start: 0.8878 (mm) cc_final: 0.8499 (mm) REVERT: o 38 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8209 (mp10) REVERT: o 43 ASN cc_start: 0.8576 (p0) cc_final: 0.8293 (p0) REVERT: o 67 ASN cc_start: 0.8840 (p0) cc_final: 0.7988 (m-40) REVERT: o 98 GLN cc_start: 0.8140 (tp-100) cc_final: 0.7886 (tp40) REVERT: o 102 ARG cc_start: 0.7470 (mtm180) cc_final: 0.6312 (ttm170) REVERT: p 23 ASP cc_start: 0.6822 (m-30) cc_final: 0.6618 (m-30) REVERT: p 67 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7134 (mm-30) REVERT: p 93 LYS cc_start: 0.8034 (mppt) cc_final: 0.7813 (mptt) REVERT: p 97 TYR cc_start: 0.6949 (m-80) cc_final: 0.6359 (m-80) REVERT: p 102 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.7284 (mtt180) REVERT: q 27 ARG cc_start: 0.6923 (mtt180) cc_final: 0.6572 (ttm110) REVERT: q 52 ARG cc_start: 0.7546 (ptt-90) cc_final: 0.7308 (ptt-90) REVERT: q 55 GLN cc_start: 0.8807 (mt0) cc_final: 0.7981 (mm-40) REVERT: q 88 GLU cc_start: 0.3356 (OUTLIER) cc_final: 0.3152 (mm-30) REVERT: r 6 GLN cc_start: 0.7019 (mp10) cc_final: 0.6589 (mp10) REVERT: r 10 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7220 (mtmm) REVERT: r 24 LYS cc_start: 0.7318 (ttpt) cc_final: 0.5975 (tptt) REVERT: r 45 GLU cc_start: 0.7475 (tp30) cc_final: 0.6990 (tm-30) REVERT: r 53 PHE cc_start: 0.7177 (OUTLIER) cc_final: 0.6951 (m-80) REVERT: r 82 HIS cc_start: 0.7639 (t-90) cc_final: 0.7404 (t-90) REVERT: r 90 ARG cc_start: 0.7039 (ttt-90) cc_final: 0.6773 (ttt-90) REVERT: s 28 LYS cc_start: 0.7127 (mmtt) cc_final: 0.6442 (mmtt) REVERT: s 40 ASN cc_start: 0.8152 (OUTLIER) cc_final: 0.7790 (p0) REVERT: s 41 LYS cc_start: 0.7621 (mmtt) cc_final: 0.7316 (tppt) REVERT: s 77 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.7872 (p0) REVERT: s 99 ARG cc_start: 0.7621 (mtt-85) cc_final: 0.7348 (mtt-85) REVERT: t 1 MET cc_start: 0.2899 (mmt) cc_final: 0.1844 (mmt) REVERT: t 6 ARG cc_start: 0.8499 (tpm170) cc_final: 0.7607 (tpm170) REVERT: t 19 LYS cc_start: 0.8531 (tttt) cc_final: 0.8087 (tptt) REVERT: t 24 MET cc_start: 0.5623 (tpp) cc_final: 0.5318 (ttt) REVERT: u 85 ARG cc_start: 0.6805 (ptp-170) cc_final: 0.6424 (ptp90) REVERT: u 100 GLU cc_start: 0.8434 (tp30) cc_final: 0.8141 (tp30) REVERT: v 7 GLU cc_start: 0.7053 (tm-30) cc_final: 0.6588 (tm-30) REVERT: v 48 MET cc_start: 0.8372 (mmt) cc_final: 0.8079 (mmt) REVERT: v 55 GLU cc_start: 0.9354 (mp0) cc_final: 0.8997 (mp0) REVERT: v 56 PHE cc_start: 0.8881 (t80) cc_final: 0.8632 (t80) REVERT: v 76 ASP cc_start: 0.7473 (t70) cc_final: 0.6828 (t70) REVERT: v 87 GLN cc_start: 0.7463 (mt0) cc_final: 0.6916 (mt0) REVERT: w 15 LYS cc_start: 0.8038 (tppt) cc_final: 0.7523 (ptpp) REVERT: w 63 VAL cc_start: 0.8884 (t) cc_final: 0.8603 (t) REVERT: w 65 PHE cc_start: 0.6619 (m-80) cc_final: 0.6409 (m-80) REVERT: w 74 LYS cc_start: 0.8489 (mmmt) cc_final: 0.8186 (mmmt) REVERT: x 40 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8578 (mm-30) REVERT: y 41 HIS cc_start: 0.8032 (p-80) cc_final: 0.7622 (p-80) REVERT: z 30 ARG cc_start: 0.8471 (pmt170) cc_final: 0.8035 (pmt170) REVERT: z 36 GLU cc_start: 0.8609 (pm20) cc_final: 0.8109 (mp0) REVERT: C 9 LYS cc_start: 0.7092 (OUTLIER) cc_final: 0.6684 (pttt) REVERT: E 4 LYS cc_start: 0.7076 (tppt) cc_final: 0.4304 (tppt) REVERT: E 25 HIS cc_start: 0.8368 (m-70) cc_final: 0.8019 (m90) REVERT: F 24 ARG cc_start: 0.7348 (mmt90) cc_final: 0.6511 (tmt-80) REVERT: G 34 ARG cc_start: 0.8428 (mmt-90) cc_final: 0.8107 (mmt180) REVERT: G 55 GLU cc_start: 0.9064 (tp30) cc_final: 0.8667 (pp20) REVERT: G 67 LEU cc_start: 0.7668 (tp) cc_final: 0.6838 (mm) REVERT: G 93 HIS cc_start: 0.8111 (OUTLIER) cc_final: 0.7093 (t-90) REVERT: G 138 ARG cc_start: 0.8257 (mtm110) cc_final: 0.7170 (mtp85) REVERT: G 142 LYS cc_start: 0.8997 (ttpt) cc_final: 0.8463 (mttt) REVERT: G 153 MET cc_start: 0.5942 (mtp) cc_final: 0.5596 (mtm) REVERT: H 5 HIS cc_start: 0.8586 (t-90) cc_final: 0.8204 (t70) REVERT: H 161 ILE cc_start: 0.6601 (mm) cc_final: 0.6269 (mm) REVERT: H 163 ARG cc_start: 0.6914 (pmt170) cc_final: 0.6706 (pmt170) REVERT: I 74 TYR cc_start: 0.8605 (m-80) cc_final: 0.8139 (m-80) REVERT: I 102 TYR cc_start: 0.6732 (t80) cc_final: 0.5975 (t80) REVERT: I 127 ARG cc_start: 0.7665 (ttt180) cc_final: 0.6864 (ttt180) REVERT: I 162 GLU cc_start: 0.8915 (tp30) cc_final: 0.8693 (pp20) REVERT: J 42 ASN cc_start: 0.8200 (t0) cc_final: 0.7394 (p0) REVERT: J 70 MET cc_start: 0.6970 (tpp) cc_final: 0.5142 (ptt) REVERT: J 80 LEU cc_start: 0.8626 (mp) cc_final: 0.8410 (tp) REVERT: J 115 GLU cc_start: 0.9083 (pt0) cc_final: 0.8800 (pt0) REVERT: J 131 ASN cc_start: 0.8269 (m110) cc_final: 0.7933 (m110) REVERT: K 5 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6173 (tp30) REVERT: K 36 ILE cc_start: 0.6792 (OUTLIER) cc_final: 0.6078 (mp) REVERT: K 90 MET cc_start: 0.8266 (mmm) cc_final: 0.7805 (mmm) REVERT: L 4 ARG cc_start: 0.6576 (OUTLIER) cc_final: 0.5408 (mmp-170) REVERT: L 84 TYR cc_start: 0.5732 (p90) cc_final: 0.4947 (p90) REVERT: L 94 ARG cc_start: 0.7911 (ttt180) cc_final: 0.6653 (ttt90) REVERT: M 32 LYS cc_start: 0.8046 (mttm) cc_final: 0.7771 (mttp) REVERT: M 72 GLU cc_start: 0.8479 (mm-30) cc_final: 0.7898 (mm-30) REVERT: M 113 ARG cc_start: 0.6624 (OUTLIER) cc_final: 0.5965 (ttp-110) REVERT: N 45 MET cc_start: 0.7326 (ptm) cc_final: 0.7051 (ptt) REVERT: N 109 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7760 (mt0) REVERT: N 112 ARG cc_start: 0.6516 (OUTLIER) cc_final: 0.6082 (ttt90) REVERT: P 58 THR cc_start: 0.5182 (p) cc_final: 0.4861 (p) REVERT: P 63 GLN cc_start: 0.8865 (tt0) cc_final: 0.8576 (pt0) REVERT: P 93 GLU cc_start: 0.6609 (mm-30) cc_final: 0.6136 (mm-30) REVERT: Q 9 LYS cc_start: 0.8925 (ttpp) cc_final: 0.8680 (tttp) REVERT: Q 28 GLN cc_start: 0.8430 (mm-40) cc_final: 0.7750 (mm-40) REVERT: Q 80 LEU cc_start: 0.8007 (tp) cc_final: 0.7561 (mt) REVERT: Q 95 HIS cc_start: 0.8327 (OUTLIER) cc_final: 0.7935 (t-90) REVERT: R 2 ARG cc_start: 0.9048 (ttt180) cc_final: 0.8323 (tpt170) REVERT: R 51 GLN cc_start: 0.8852 (mt0) cc_final: 0.8626 (mp10) REVERT: S 11 LYS cc_start: 0.7643 (mmtt) cc_final: 0.7239 (mmtt) REVERT: S 45 LEU cc_start: 0.9086 (mp) cc_final: 0.8715 (mt) REVERT: U 60 TRP cc_start: 0.8787 (m100) cc_final: 0.7755 (t-100) REVERT: V 27 PHE cc_start: 0.3654 (OUTLIER) cc_final: 0.2515 (t80) REVERT: V 30 HIS cc_start: 0.7557 (t-90) cc_final: 0.7282 (t-90) REVERT: V 70 LYS cc_start: 0.6436 (OUTLIER) cc_final: 0.6192 (ttpp) REVERT: X 80 ARG cc_start: 0.2350 (mtt-85) cc_final: 0.0306 (mmt180) REVERT: Y 12 GLN cc_start: 0.8831 (mt0) cc_final: 0.8526 (mp10) REVERT: Y 27 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8479 (mmm) REVERT: Y 39 GLU cc_start: 0.8334 (pp20) cc_final: 0.8093 (pp20) REVERT: a 8 MET cc_start: 0.1183 (mpp) cc_final: 0.0731 (mpp) outliers start: 392 outliers final: 261 residues processed: 1430 average time/residue: 1.3563 time to fit residues: 3298.0511 Evaluate side-chains 1402 residues out of total 4852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 1119 time to evaluate : 6.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LYS Chi-restraints excluded: chain b residue 42 ARG Chi-restraints excluded: chain b residue 78 GLU Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 97 ASP Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 145 MET Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 176 ARG Chi-restraints excluded: chain b residue 181 ARG Chi-restraints excluded: chain b residue 231 HIS Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain c residue 27 ILE Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 36 GLN Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 101 PHE Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 178 VAL Chi-restraints excluded: chain c residue 193 VAL Chi-restraints excluded: chain c residue 203 VAL Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 57 LYS Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 178 VAL Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 16 MET Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 49 LEU Chi-restraints excluded: chain e residue 80 GLN Chi-restraints excluded: chain e residue 96 TRP Chi-restraints excluded: chain e residue 120 SER Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain f residue 18 ILE Chi-restraints excluded: chain f residue 46 ASP Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 113 ASP Chi-restraints excluded: chain f residue 148 ARG Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 19 VAL Chi-restraints excluded: chain g residue 20 ASN Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain h residue 86 MET Chi-restraints excluded: chain j residue 3 THR Chi-restraints excluded: chain j residue 7 LYS Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 36 LEU Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 70 THR Chi-restraints excluded: chain j residue 78 THR Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 130 HIS Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 52 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 61 LEU Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 100 ILE Chi-restraints excluded: chain l residue 110 VAL Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 72 ASP Chi-restraints excluded: chain o residue 21 LEU Chi-restraints excluded: chain o residue 26 LEU Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 38 GLN Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 68 LYS Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 55 HIS Chi-restraints excluded: chain p residue 69 VAL Chi-restraints excluded: chain p residue 83 ILE Chi-restraints excluded: chain p residue 102 ARG Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 43 GLN Chi-restraints excluded: chain q residue 88 GLU Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain r residue 10 LYS Chi-restraints excluded: chain r residue 11 GLN Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain r residue 79 ARG Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 24 ILE Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 52 GLU Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 53 VAL Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain u residue 7 ASP Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 40 LEU Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 49 ASN Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 7 ARG Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 47 VAL Chi-restraints excluded: chain w residue 52 ASP Chi-restraints excluded: chain x residue 29 LEU Chi-restraints excluded: chain x residue 33 HIS Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 70 LEU Chi-restraints excluded: chain y residue 14 LEU Chi-restraints excluded: chain y residue 16 THR Chi-restraints excluded: chain y residue 17 GLU Chi-restraints excluded: chain y residue 18 LEU Chi-restraints excluded: chain y residue 26 PHE Chi-restraints excluded: chain y residue 56 LEU Chi-restraints excluded: chain z residue 24 LEU Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 93 HIS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 136 ARG Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 173 ASP Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain K residue 33 GLU Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 58 HIS Chi-restraints excluded: chain K residue 59 TYR Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 4 ARG Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 61 PHE Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 113 ARG Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 108 ARG Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 112 ARG Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain P residue 76 TYR Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 95 HIS Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain R residue 22 TYR Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 40 GLU Chi-restraints excluded: chain R residue 54 THR Chi-restraints excluded: chain S residue 2 LYS Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 39 GLN Chi-restraints excluded: chain T residue 55 LEU Chi-restraints excluded: chain T residue 59 VAL Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 59 HIS Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 70 LYS Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain W residue 12 PHE Chi-restraints excluded: chain W residue 71 ASP Chi-restraints excluded: chain X residue 6 LYS Chi-restraints excluded: chain X residue 13 HIS Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 65 MET Chi-restraints excluded: chain X residue 72 GLU Chi-restraints excluded: chain Y residue 27 MET Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain a residue 16 ASP Chi-restraints excluded: chain a residue 202 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 845 optimal weight: 10.0000 chunk 576 optimal weight: 20.0000 chunk 14 optimal weight: 0.9980 chunk 755 optimal weight: 20.0000 chunk 418 optimal weight: 0.0050 chunk 866 optimal weight: 10.0000 chunk 701 optimal weight: 20.0000 chunk 1 optimal weight: 4.9990 chunk 518 optimal weight: 8.9990 chunk 910 optimal weight: 9.9990 chunk 256 optimal weight: 1.9990 overall best weight: 3.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 36 GLN ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 164 GLN d 94 GLN ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 3 GLN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 3 HIS n 18 GLN ** o 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 40 GLN ** q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 9 HIS ** s 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 49 ASN ** v 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 HIS ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 145 ASN ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 70 GLN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 HIS L 27 ASN ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 GLN ** P 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 19 ASN ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 63 GLN V 8 GLN Y 69 ASN ** a 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 162606 Z= 0.192 Angle : 0.656 13.980 243356 Z= 0.337 Chirality : 0.037 0.457 31135 Planarity : 0.005 0.111 12986 Dihedral : 23.664 177.164 81655 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 22.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.19 % Favored : 89.69 % Rotamer: Outliers : 5.89 % Allowed : 25.82 % Favored : 68.28 % 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: -3.01 (0.10), residues: 5849 helix: -1.08 (0.11), residues: 1759 sheet: -2.07 (0.17), residues: 799 loop : -2.58 (0.10), residues: 3291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP G 103 HIS 0.008 0.001 HIS T 45 PHE 0.038 0.002 PHE e 99 TYR 0.021 0.002 TYR o 99 ARG 0.013 0.001 ARG M 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1521 residues out of total 4852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 1235 time to evaluate : 6.713 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: b 35 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8310 (pttm) REVERT: b 81 GLU cc_start: 0.7175 (tp30) cc_final: 0.6906 (tp30) REVERT: b 83 ASP cc_start: 0.8679 (t0) cc_final: 0.8226 (t0) REVERT: b 200 MET cc_start: 0.7798 (ptt) cc_final: 0.7454 (ptp) REVERT: b 250 GLN cc_start: 0.8924 (mm-40) cc_final: 0.8290 (mt0) REVERT: b 269 ARG cc_start: 0.4557 (tpt170) cc_final: 0.3631 (mmm160) REVERT: c 33 ARG cc_start: 0.8126 (mpp80) cc_final: 0.7339 (mpp80) REVERT: c 82 PHE cc_start: 0.8193 (m-80) cc_final: 0.7894 (m-80) REVERT: c 157 LYS cc_start: 0.6641 (mttt) cc_final: 0.6178 (tttt) REVERT: c 167 ASN cc_start: 0.8931 (t0) cc_final: 0.8452 (t0) REVERT: d 187 VAL cc_start: 0.8631 (t) cc_final: 0.8346 (p) REVERT: e 3 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.7967 (pp) REVERT: e 97 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8218 (pp20) REVERT: e 129 MET cc_start: 0.7599 (tmm) cc_final: 0.7219 (tmm) REVERT: e 140 ILE cc_start: 0.6198 (mm) cc_final: 0.5967 (mm) REVERT: f 74 MET cc_start: 0.7055 (ttt) cc_final: 0.5236 (tpt) REVERT: f 137 LYS cc_start: 0.6077 (ttpt) cc_final: 0.5822 (ttpt) REVERT: f 142 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8592 (tt0) REVERT: g 25 TYR cc_start: 0.7369 (t80) cc_final: 0.6809 (t80) REVERT: g 33 GLN cc_start: 0.8373 (mp10) cc_final: 0.7927 (mp10) REVERT: i 116 MET cc_start: 0.5331 (mmp) cc_final: 0.4289 (mmm) REVERT: j 12 LYS cc_start: 0.8872 (tttm) cc_final: 0.8559 (tmtt) REVERT: j 57 LEU cc_start: 0.8972 (pp) cc_final: 0.8673 (pp) REVERT: j 78 THR cc_start: 0.9123 (OUTLIER) cc_final: 0.8894 (t) REVERT: j 86 GLN cc_start: 0.7811 (pt0) cc_final: 0.7400 (pp30) REVERT: j 91 GLU cc_start: 0.7384 (mp0) cc_final: 0.6870 (pm20) REVERT: j 109 LEU cc_start: 0.8974 (mt) cc_final: 0.8609 (mt) REVERT: j 136 GLN cc_start: 0.8718 (mt0) cc_final: 0.8410 (mp10) REVERT: k 20 MET cc_start: 0.7710 (ttm) cc_final: 0.7208 (ttt) REVERT: k 41 ILE cc_start: 0.8774 (mm) cc_final: 0.8285 (mm) REVERT: k 56 ASP cc_start: 0.6072 (m-30) cc_final: 0.5829 (m-30) REVERT: l 59 ARG cc_start: 0.8551 (mtp180) cc_final: 0.8040 (tpp80) REVERT: m 44 ARG cc_start: 0.8574 (ttm110) cc_final: 0.8330 (tpm170) REVERT: m 65 ILE cc_start: 0.8155 (mt) cc_final: 0.7634 (pt) REVERT: m 111 GLU cc_start: 0.8375 (tm-30) cc_final: 0.7519 (tm-30) REVERT: m 115 GLU cc_start: 0.8335 (pt0) cc_final: 0.8121 (pt0) REVERT: m 127 LYS cc_start: 0.8239 (tppt) cc_final: 0.7776 (mmmt) REVERT: n 8 ARG cc_start: 0.7893 (ttm-80) cc_final: 0.7283 (ttm-80) REVERT: n 17 ARG cc_start: 0.9047 (ttp-170) cc_final: 0.8616 (ptt90) REVERT: n 35 LYS cc_start: 0.8946 (tttm) cc_final: 0.8561 (tttm) REVERT: n 40 LYS cc_start: 0.8254 (mttt) cc_final: 0.8011 (mtmt) REVERT: n 62 ASN cc_start: 0.8246 (m-40) cc_final: 0.7833 (m-40) REVERT: n 106 ASP cc_start: 0.6810 (p0) cc_final: 0.6087 (t0) REVERT: o 16 ARG cc_start: 0.8051 (mmm160) cc_final: 0.7275 (mmm160) REVERT: o 38 GLN cc_start: 0.8005 (pm20) cc_final: 0.7762 (pm20) REVERT: o 43 ASN cc_start: 0.8641 (p0) cc_final: 0.8333 (p0) REVERT: o 67 ASN cc_start: 0.8873 (p0) cc_final: 0.8109 (m-40) REVERT: o 76 LYS cc_start: 0.9107 (tttt) cc_final: 0.8702 (mttp) REVERT: o 98 GLN cc_start: 0.8320 (tp-100) cc_final: 0.7996 (tp40) REVERT: o 99 TYR cc_start: 0.6955 (t80) cc_final: 0.6526 (t80) REVERT: o 102 ARG cc_start: 0.7474 (mtm180) cc_final: 0.6402 (ttm170) REVERT: p 67 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6075 (mm-30) REVERT: p 97 TYR cc_start: 0.6882 (m-80) cc_final: 0.6338 (m-80) REVERT: p 102 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7158 (mtt180) REVERT: r 6 GLN cc_start: 0.7054 (mt0) cc_final: 0.6128 (mp10) REVERT: r 24 LYS cc_start: 0.7198 (ttpt) cc_final: 0.5888 (tptt) REVERT: r 45 GLU cc_start: 0.7415 (tp30) cc_final: 0.6948 (tm-30) REVERT: s 28 LYS cc_start: 0.6905 (mmtt) cc_final: 0.6101 (mmtt) REVERT: s 40 ASN cc_start: 0.8257 (m-40) cc_final: 0.7857 (p0) REVERT: s 75 PHE cc_start: 0.9084 (p90) cc_final: 0.8697 (p90) REVERT: s 77 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7892 (p0) REVERT: t 6 ARG cc_start: 0.8542 (tpm170) cc_final: 0.8085 (tpm170) REVERT: t 19 LYS cc_start: 0.8257 (tttt) cc_final: 0.7883 (tptt) REVERT: u 85 ARG cc_start: 0.6630 (ptp-170) cc_final: 0.6242 (ptp90) REVERT: u 95 PHE cc_start: 0.6505 (m-10) cc_final: 0.6234 (m-10) REVERT: v 7 GLU cc_start: 0.7008 (tm-30) cc_final: 0.6808 (tm-30) REVERT: v 48 MET cc_start: 0.8152 (mmt) cc_final: 0.7751 (mmt) REVERT: v 55 GLU cc_start: 0.9269 (mp0) cc_final: 0.8874 (mp0) REVERT: v 56 PHE cc_start: 0.8812 (t80) cc_final: 0.8606 (t80) REVERT: w 15 LYS cc_start: 0.7869 (tppt) cc_final: 0.7485 (ptpp) REVERT: w 56 PHE cc_start: 0.7634 (p90) cc_final: 0.6673 (p90) REVERT: w 63 VAL cc_start: 0.8858 (t) cc_final: 0.8553 (t) REVERT: y 39 GLN cc_start: 0.7919 (mt0) cc_final: 0.7535 (tt0) REVERT: z 36 GLU cc_start: 0.8537 (pm20) cc_final: 0.8195 (mp0) REVERT: B 9 ARG cc_start: 0.6187 (OUTLIER) cc_final: 0.5754 (mtt90) REVERT: E 4 LYS cc_start: 0.6821 (tppt) cc_final: 0.4051 (tppt) REVERT: E 25 HIS cc_start: 0.8183 (m-70) cc_final: 0.7948 (m-70) REVERT: F 24 ARG cc_start: 0.7409 (mmt90) cc_final: 0.6507 (tmt-80) REVERT: G 26 MET cc_start: 0.6128 (tpp) cc_final: 0.5429 (mmt) REVERT: G 67 LEU cc_start: 0.7838 (tp) cc_final: 0.7158 (mm) REVERT: G 93 HIS cc_start: 0.8041 (OUTLIER) cc_final: 0.7089 (t-90) REVERT: G 138 ARG cc_start: 0.8237 (mtm110) cc_final: 0.7373 (mtp85) REVERT: G 142 LYS cc_start: 0.9000 (ttpt) cc_final: 0.8517 (mttt) REVERT: G 153 MET cc_start: 0.5181 (mtp) cc_final: 0.4905 (mtm) REVERT: G 180 ILE cc_start: 0.8674 (mt) cc_final: 0.8274 (tt) REVERT: H 5 HIS cc_start: 0.8446 (t-90) cc_final: 0.8167 (t70) REVERT: H 139 ASN cc_start: 0.8744 (m-40) cc_final: 0.8501 (m-40) REVERT: H 161 ILE cc_start: 0.6492 (mm) cc_final: 0.6220 (mm) REVERT: H 163 ARG cc_start: 0.7100 (pmt170) cc_final: 0.6791 (pmt170) REVERT: I 70 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8526 (mt0) REVERT: I 74 TYR cc_start: 0.8636 (m-80) cc_final: 0.8378 (m-80) REVERT: I 127 ARG cc_start: 0.7528 (ttt180) cc_final: 0.6664 (ttt180) REVERT: J 42 ASN cc_start: 0.8150 (t0) cc_final: 0.7304 (p0) REVERT: J 67 ARG cc_start: 0.8226 (tpp80) cc_final: 0.7522 (tpm170) REVERT: J 70 MET cc_start: 0.7435 (tpp) cc_final: 0.6107 (tpp) REVERT: J 96 GLN cc_start: 0.8789 (tp-100) cc_final: 0.7711 (tm-30) REVERT: J 131 ASN cc_start: 0.8467 (m110) cc_final: 0.8047 (m110) REVERT: J 146 MET cc_start: 0.2188 (ttp) cc_final: 0.1887 (tmm) REVERT: L 84 TYR cc_start: 0.5876 (p90) cc_final: 0.5088 (p90) REVERT: L 94 ARG cc_start: 0.7860 (ttt180) cc_final: 0.7317 (ttt180) REVERT: L 141 HIS cc_start: 0.6564 (m-70) cc_final: 0.6239 (m-70) REVERT: M 32 LYS cc_start: 0.7963 (mttm) cc_final: 0.7737 (mttt) REVERT: M 113 ARG cc_start: 0.6943 (OUTLIER) cc_final: 0.5896 (ttp-110) REVERT: N 11 ARG cc_start: 0.8491 (tpt-90) cc_final: 0.7963 (tpt170) REVERT: N 56 MET cc_start: 0.6777 (mmm) cc_final: 0.6512 (mmm) REVERT: N 108 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7881 (mtp85) REVERT: N 109 GLN cc_start: 0.8235 (mm-40) cc_final: 0.7967 (mt0) REVERT: O 71 LEU cc_start: 0.6235 (OUTLIER) cc_final: 0.5616 (pp) REVERT: P 58 THR cc_start: 0.5080 (p) cc_final: 0.4822 (p) REVERT: P 63 GLN cc_start: 0.8821 (tt0) cc_final: 0.8506 (pm20) REVERT: P 93 GLU cc_start: 0.6793 (mm-30) cc_final: 0.6591 (mm-30) REVERT: Q 9 LYS cc_start: 0.8873 (ttpp) cc_final: 0.8555 (tptt) REVERT: Q 28 GLN cc_start: 0.8438 (mm-40) cc_final: 0.7725 (mm-40) REVERT: Q 80 LEU cc_start: 0.7906 (tp) cc_final: 0.7390 (mt) REVERT: Q 95 HIS cc_start: 0.8169 (OUTLIER) cc_final: 0.7919 (t-90) REVERT: R 2 ARG cc_start: 0.8865 (ttt180) cc_final: 0.8191 (tpt170) REVERT: R 51 GLN cc_start: 0.8829 (mt0) cc_final: 0.8585 (mp10) REVERT: R 99 GLN cc_start: 0.7301 (mp10) cc_final: 0.6840 (mp10) REVERT: S 11 LYS cc_start: 0.7628 (mmtt) cc_final: 0.7175 (mmtt) REVERT: S 89 ARG cc_start: 0.8170 (tpm170) cc_final: 0.7651 (tpm170) REVERT: S 100 TRP cc_start: 0.6308 (OUTLIER) cc_final: 0.5743 (p90) REVERT: T 47 LYS cc_start: 0.6515 (mttt) cc_final: 0.6246 (mttm) REVERT: T 48 ASP cc_start: 0.8364 (t0) cc_final: 0.8069 (t0) REVERT: U 14 ARG cc_start: 0.8288 (tpp80) cc_final: 0.7553 (mmm-85) REVERT: V 17 GLU cc_start: 0.6069 (pt0) cc_final: 0.5841 (pt0) REVERT: V 27 PHE cc_start: 0.3169 (OUTLIER) cc_final: 0.2095 (t80) REVERT: V 30 HIS cc_start: 0.7491 (t-90) cc_final: 0.7228 (t-90) REVERT: X 80 ARG cc_start: 0.2465 (mtt-85) cc_final: 0.0329 (mmt180) REVERT: Y 7 LYS cc_start: 0.8992 (ptpt) cc_final: 0.8765 (ptmm) REVERT: Y 12 GLN cc_start: 0.8732 (mt0) cc_final: 0.8399 (mp10) REVERT: Y 60 GLN cc_start: 0.7398 (OUTLIER) cc_final: 0.7175 (mp10) REVERT: a 8 MET cc_start: 0.1254 (mpp) cc_final: 0.0857 (mpp) outliers start: 286 outliers final: 206 residues processed: 1401 average time/residue: 1.4588 time to fit residues: 3501.7173 Evaluate side-chains 1348 residues out of total 4852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1126 time to evaluate : 6.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LYS Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 78 GLU Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 109 LEU Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 145 MET Chi-restraints excluded: chain b residue 179 GLU Chi-restraints excluded: chain b residue 231 HIS Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain c residue 27 ILE Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 58 ASN Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 67 HIS Chi-restraints excluded: chain c residue 101 PHE Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 203 VAL Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 176 ASP Chi-restraints excluded: chain d residue 178 VAL Chi-restraints excluded: chain d residue 191 ASP Chi-restraints excluded: chain d residue 200 LEU Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 49 LEU Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 120 SER Chi-restraints excluded: chain e residue 152 ASP Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 46 ASP Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain f residue 142 GLN Chi-restraints excluded: chain f residue 148 ARG Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 19 VAL Chi-restraints excluded: chain g residue 20 ASN Chi-restraints excluded: chain g residue 108 VAL Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain h residue 86 MET Chi-restraints excluded: chain j residue 3 THR Chi-restraints excluded: chain j residue 7 LYS Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 13 ARG Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 78 THR Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain k residue 13 ASN Chi-restraints excluded: chain k residue 52 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 55 MET Chi-restraints excluded: chain l residue 100 ILE Chi-restraints excluded: chain l residue 110 VAL Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 69 VAL Chi-restraints excluded: chain p residue 83 ILE Chi-restraints excluded: chain p residue 102 ARG Chi-restraints excluded: chain p residue 114 ASN Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 43 GLN Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 98 ILE Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 52 GLU Chi-restraints excluded: chain s residue 61 ASN Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 53 VAL Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 40 LEU Chi-restraints excluded: chain u residue 51 LEU Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain w residue 7 ARG Chi-restraints excluded: chain w residue 47 VAL Chi-restraints excluded: chain w residue 52 ASP Chi-restraints excluded: chain x residue 29 LEU Chi-restraints excluded: chain x residue 33 HIS Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain y residue 14 LEU Chi-restraints excluded: chain y residue 16 THR Chi-restraints excluded: chain y residue 26 PHE Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 9 ARG Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 93 HIS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 136 ARG Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain I residue 70 GLN Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 120 LYS Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 58 HIS Chi-restraints excluded: chain K residue 59 TYR Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 61 PHE Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 113 ARG Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 108 ARG Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 76 TYR Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 95 HIS Chi-restraints excluded: chain R residue 22 TYR Chi-restraints excluded: chain R residue 40 GLU Chi-restraints excluded: chain R residue 53 ASP Chi-restraints excluded: chain R residue 54 THR Chi-restraints excluded: chain S residue 2 LYS Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain S residue 100 TRP Chi-restraints excluded: chain T residue 55 LEU Chi-restraints excluded: chain T residue 59 VAL Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 59 HIS 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 56 ASP Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain W residue 71 ASP Chi-restraints excluded: chain X residue 13 HIS Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 65 MET Chi-restraints excluded: chain X residue 72 GLU Chi-restraints excluded: chain Y residue 35 TYR Chi-restraints excluded: chain Y residue 60 GLN Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain a residue 16 ASP Chi-restraints excluded: chain a residue 63 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 341 optimal weight: 4.9990 chunk 913 optimal weight: 20.0000 chunk 200 optimal weight: 9.9990 chunk 595 optimal weight: 30.0000 chunk 250 optimal weight: 0.7980 chunk 1015 optimal weight: 20.0000 chunk 843 optimal weight: 20.0000 chunk 470 optimal weight: 20.0000 chunk 84 optimal weight: 30.0000 chunk 336 optimal weight: 8.9990 chunk 533 optimal weight: 0.6980 overall best weight: 5.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 134 HIS ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 3 GLN ** l 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN ** o 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 42 HIS ** y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 ASN ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 70 GLN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN ** P 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 76 HIS ** a 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 188 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.5417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 162606 Z= 0.249 Angle : 0.705 12.979 243356 Z= 0.360 Chirality : 0.039 0.390 31135 Planarity : 0.005 0.088 12986 Dihedral : 23.713 177.925 81653 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 27.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.68 % Favored : 88.22 % Rotamer: Outliers : 6.86 % Allowed : 26.28 % Favored : 66.86 % 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: -3.00 (0.10), residues: 5849 helix: -1.03 (0.12), residues: 1741 sheet: -2.07 (0.17), residues: 807 loop : -2.60 (0.10), residues: 3301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP G 103 HIS 0.035 0.002 HIS K 55 PHE 0.042 0.002 PHE Z 36 TYR 0.018 0.002 TYR L 84 ARG 0.011 0.001 ARG b 213 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1500 residues out of total 4852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 333 poor density : 1167 time to evaluate : 6.735 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: b 35 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8498 (pttm) REVERT: b 83 ASP cc_start: 0.8486 (t0) cc_final: 0.7816 (t0) REVERT: b 269 ARG cc_start: 0.4731 (tpt170) cc_final: 0.3722 (mmm160) REVERT: c 33 ARG cc_start: 0.8182 (mpp80) cc_final: 0.7346 (mpp80) REVERT: c 82 PHE cc_start: 0.8208 (m-80) cc_final: 0.7980 (m-80) REVERT: c 157 LYS cc_start: 0.6645 (mttt) cc_final: 0.6163 (tttt) REVERT: c 167 ASN cc_start: 0.8939 (t0) cc_final: 0.8421 (t0) REVERT: d 1 MET cc_start: 0.7178 (tpp) cc_final: 0.6978 (tpp) REVERT: d 187 VAL cc_start: 0.8691 (t) cc_final: 0.8396 (p) REVERT: d 200 LEU cc_start: 0.6342 (OUTLIER) cc_final: 0.6137 (tp) REVERT: e 129 MET cc_start: 0.7629 (tmm) cc_final: 0.7211 (tmm) REVERT: f 68 ARG cc_start: 0.8532 (tmt170) cc_final: 0.8162 (ttp80) REVERT: f 74 MET cc_start: 0.7303 (ttt) cc_final: 0.5755 (tpt) REVERT: f 137 LYS cc_start: 0.6183 (ttpt) cc_final: 0.5935 (ttpt) REVERT: g 25 TYR cc_start: 0.7414 (t80) cc_final: 0.6846 (t80) REVERT: g 33 GLN cc_start: 0.8430 (mp10) cc_final: 0.7870 (mp10) REVERT: i 116 MET cc_start: 0.5595 (mmp) cc_final: 0.3888 (mmm) REVERT: i 135 MET cc_start: 0.4826 (mmt) cc_final: 0.4581 (mmt) REVERT: j 34 ARG cc_start: 0.8409 (ttm170) cc_final: 0.8135 (mtp85) REVERT: j 86 GLN cc_start: 0.7962 (pt0) cc_final: 0.7560 (pp30) REVERT: j 91 GLU cc_start: 0.7457 (mp0) cc_final: 0.6946 (pm20) REVERT: j 136 GLN cc_start: 0.8767 (mt0) cc_final: 0.8453 (mp10) REVERT: k 41 ILE cc_start: 0.8767 (mm) cc_final: 0.8207 (mm) REVERT: l 59 ARG cc_start: 0.8582 (mtp180) cc_final: 0.8028 (tpp80) REVERT: m 18 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7783 (ppt90) REVERT: m 44 ARG cc_start: 0.8500 (ttm110) cc_final: 0.8123 (tpm170) REVERT: m 45 GLN cc_start: 0.7870 (tt0) cc_final: 0.7540 (tt0) REVERT: m 65 ILE cc_start: 0.8085 (mt) cc_final: 0.7595 (pt) REVERT: m 82 MET cc_start: 0.7564 (tpp) cc_final: 0.6634 (tpt) REVERT: m 104 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8204 (mt-10) REVERT: m 119 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7693 (tt) REVERT: m 127 LYS cc_start: 0.7903 (tppt) cc_final: 0.7360 (mmmt) REVERT: n 8 ARG cc_start: 0.7980 (ttm-80) cc_final: 0.7332 (ttm-80) REVERT: n 17 ARG cc_start: 0.8982 (ttp-170) cc_final: 0.8479 (ptt90) REVERT: n 35 LYS cc_start: 0.9011 (tttm) cc_final: 0.8544 (tttm) REVERT: n 62 ASN cc_start: 0.8307 (m-40) cc_final: 0.7914 (m-40) REVERT: n 120 GLU cc_start: 0.5947 (OUTLIER) cc_final: 0.4410 (mt-10) REVERT: o 38 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7850 (pm20) REVERT: o 43 ASN cc_start: 0.8639 (p0) cc_final: 0.8134 (p0) REVERT: o 67 ASN cc_start: 0.8836 (p0) cc_final: 0.8057 (m-40) REVERT: o 76 LYS cc_start: 0.9118 (tttt) cc_final: 0.8698 (mttp) REVERT: o 98 GLN cc_start: 0.8336 (tp-100) cc_final: 0.8005 (tp40) REVERT: o 99 TYR cc_start: 0.7143 (t80) cc_final: 0.6667 (t80) REVERT: o 102 ARG cc_start: 0.7374 (mtm180) cc_final: 0.6138 (ttm170) REVERT: p 67 GLU cc_start: 0.7329 (mm-30) cc_final: 0.6163 (mm-30) REVERT: p 97 TYR cc_start: 0.6932 (m-80) cc_final: 0.6389 (m-80) REVERT: p 102 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.7191 (mtp180) REVERT: q 50 ARG cc_start: 0.8462 (mtm-85) cc_final: 0.8259 (mtm-85) REVERT: q 55 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8259 (mm-40) REVERT: q 58 GLN cc_start: 0.8419 (tt0) cc_final: 0.8191 (tp40) REVERT: q 92 LYS cc_start: 0.8162 (tttt) cc_final: 0.7359 (tttm) REVERT: r 45 GLU cc_start: 0.7548 (tp30) cc_final: 0.7086 (tm-30) REVERT: s 28 LYS cc_start: 0.6972 (mmtt) cc_final: 0.6089 (mmtt) REVERT: s 40 ASN cc_start: 0.8172 (m-40) cc_final: 0.7922 (p0) REVERT: s 75 PHE cc_start: 0.9014 (p90) cc_final: 0.8812 (p90) REVERT: s 77 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7978 (p0) REVERT: s 83 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.6863 (ttpp) REVERT: t 6 ARG cc_start: 0.8568 (tpm170) cc_final: 0.7827 (tpm170) REVERT: t 7 LEU cc_start: 0.8761 (mp) cc_final: 0.8361 (mp) REVERT: t 9 LYS cc_start: 0.8322 (mtpt) cc_final: 0.7966 (ttpp) REVERT: t 19 LYS cc_start: 0.8437 (tttt) cc_final: 0.8020 (tptt) REVERT: u 95 PHE cc_start: 0.6563 (m-10) cc_final: 0.6255 (m-10) REVERT: v 7 GLU cc_start: 0.7015 (tm-30) cc_final: 0.6694 (tm-30) REVERT: v 55 GLU cc_start: 0.9293 (mp0) cc_final: 0.8902 (mp0) REVERT: v 56 PHE cc_start: 0.8811 (t80) cc_final: 0.8603 (t80) REVERT: w 15 LYS cc_start: 0.7953 (tppt) cc_final: 0.7530 (ptpp) REVERT: w 40 LYS cc_start: 0.7150 (pttt) cc_final: 0.6609 (pttt) REVERT: w 56 PHE cc_start: 0.7633 (p90) cc_final: 0.7321 (p90) REVERT: w 74 LYS cc_start: 0.8466 (mmmt) cc_final: 0.8173 (mmmt) REVERT: E 4 LYS cc_start: 0.6789 (tppt) cc_final: 0.3909 (tppt) REVERT: E 25 HIS cc_start: 0.8352 (m-70) cc_final: 0.8070 (m-70) REVERT: F 24 ARG cc_start: 0.7234 (mmt90) cc_final: 0.6465 (tmt-80) REVERT: G 26 MET cc_start: 0.6480 (tpp) cc_final: 0.5691 (mmm) REVERT: G 67 LEU cc_start: 0.7822 (tp) cc_final: 0.7114 (mm) REVERT: G 138 ARG cc_start: 0.8081 (mtm110) cc_final: 0.7103 (mtp85) REVERT: G 142 LYS cc_start: 0.8995 (ttpt) cc_final: 0.8431 (mttt) REVERT: G 153 MET cc_start: 0.4891 (mtp) cc_final: 0.4570 (mtm) REVERT: H 5 HIS cc_start: 0.8716 (t-90) cc_final: 0.8184 (t70) REVERT: H 139 ASN cc_start: 0.8769 (m-40) cc_final: 0.8538 (m-40) REVERT: H 163 ARG cc_start: 0.7110 (pmt170) cc_final: 0.6836 (pmt170) REVERT: I 69 ARG cc_start: 0.6549 (ptt180) cc_final: 0.6126 (mmp80) REVERT: I 74 TYR cc_start: 0.8653 (m-80) cc_final: 0.7860 (m-80) REVERT: I 127 ARG cc_start: 0.7367 (ttt180) cc_final: 0.6649 (ttt180) REVERT: J 42 ASN cc_start: 0.7857 (t0) cc_final: 0.7118 (p0) REVERT: J 70 MET cc_start: 0.6976 (tpp) cc_final: 0.5641 (tpp) REVERT: J 115 GLU cc_start: 0.8978 (pt0) cc_final: 0.8703 (pt0) REVERT: J 131 ASN cc_start: 0.8475 (m110) cc_final: 0.7881 (m110) REVERT: J 150 GLU cc_start: 0.8698 (mp0) cc_final: 0.8492 (mp0) REVERT: L 84 TYR cc_start: 0.5859 (p90) cc_final: 0.4975 (p90) REVERT: L 94 ARG cc_start: 0.7783 (ttt180) cc_final: 0.7494 (ttt180) REVERT: L 139 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.7843 (m-30) REVERT: L 141 HIS cc_start: 0.6393 (m-70) cc_final: 0.5893 (m-70) REVERT: M 72 GLU cc_start: 0.8449 (mm-30) cc_final: 0.7886 (mm-30) REVERT: M 113 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6136 (ttp-110) REVERT: M 123 GLU cc_start: 0.6660 (tt0) cc_final: 0.6451 (tt0) REVERT: N 21 LYS cc_start: 0.9368 (ttmm) cc_final: 0.9131 (mmtp) REVERT: N 109 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7800 (mt0) REVERT: O 71 LEU cc_start: 0.6394 (OUTLIER) cc_final: 0.5495 (pp) REVERT: P 58 THR cc_start: 0.5169 (p) cc_final: 0.4898 (p) REVERT: P 63 GLN cc_start: 0.8676 (tt0) cc_final: 0.8422 (pm20) REVERT: P 93 GLU cc_start: 0.6619 (mm-30) cc_final: 0.6236 (mm-30) REVERT: P 121 ARG cc_start: 0.7194 (ttp80) cc_final: 0.6876 (ttp80) REVERT: Q 9 LYS cc_start: 0.8884 (ttpp) cc_final: 0.8578 (tptt) REVERT: Q 28 GLN cc_start: 0.8483 (mm-40) cc_final: 0.7790 (mm-40) REVERT: Q 80 LEU cc_start: 0.8014 (tp) cc_final: 0.7520 (mt) REVERT: Q 95 HIS cc_start: 0.8131 (OUTLIER) cc_final: 0.7840 (t-90) REVERT: R 2 ARG cc_start: 0.8965 (ttt180) cc_final: 0.8273 (tpt170) REVERT: R 80 MET cc_start: 0.9210 (ptp) cc_final: 0.8894 (tmm) REVERT: R 99 GLN cc_start: 0.7337 (mp10) cc_final: 0.6862 (mp10) REVERT: S 11 LYS cc_start: 0.8008 (mmtt) cc_final: 0.7592 (mmtp) REVERT: S 80 ARG cc_start: 0.7428 (ptt90) cc_final: 0.6966 (ptt-90) REVERT: S 88 MET cc_start: 0.7136 (mmt) cc_final: 0.6752 (mmt) REVERT: S 89 ARG cc_start: 0.8317 (tpm170) cc_final: 0.7902 (tpm170) REVERT: T 48 ASP cc_start: 0.8627 (t0) cc_final: 0.8257 (t0) REVERT: V 27 PHE cc_start: 0.3274 (OUTLIER) cc_final: 0.2154 (t80) REVERT: V 30 HIS cc_start: 0.7572 (t-90) cc_final: 0.7301 (t-90) REVERT: V 64 ARG cc_start: 0.9321 (mmm-85) cc_final: 0.8858 (tpp80) REVERT: X 80 ARG cc_start: 0.2621 (mtt-85) cc_final: 0.0596 (mmt180) REVERT: Y 7 LYS cc_start: 0.8995 (ptpt) cc_final: 0.8744 (ptmm) REVERT: Y 12 GLN cc_start: 0.8854 (mt0) cc_final: 0.8526 (mp10) REVERT: a 8 MET cc_start: 0.1080 (mpp) cc_final: 0.0694 (mpp) outliers start: 333 outliers final: 253 residues processed: 1360 average time/residue: 1.3690 time to fit residues: 3173.3922 Evaluate side-chains 1386 residues out of total 4852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 1117 time to evaluate : 6.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LYS Chi-restraints excluded: chain b residue 78 GLU Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 145 MET Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 179 GLU Chi-restraints excluded: chain b residue 213 ARG Chi-restraints excluded: chain b residue 231 HIS Chi-restraints excluded: chain b residue 249 VAL Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain c residue 27 ILE Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 58 ASN Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 101 PHE Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 178 VAL Chi-restraints excluded: chain c residue 203 VAL Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 178 VAL Chi-restraints excluded: chain d residue 191 ASP Chi-restraints excluded: chain d residue 200 LEU Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 49 LEU Chi-restraints excluded: chain e residue 80 GLN Chi-restraints excluded: chain e residue 120 SER Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 18 ILE Chi-restraints excluded: chain f residue 46 ASP Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 113 ASP Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain f residue 148 ARG Chi-restraints excluded: chain g residue 19 VAL Chi-restraints excluded: chain g residue 20 ASN Chi-restraints excluded: chain g residue 108 VAL Chi-restraints excluded: chain h residue 86 MET Chi-restraints excluded: chain j residue 3 THR Chi-restraints excluded: chain j residue 7 LYS Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 13 ARG Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 36 LEU Chi-restraints excluded: chain j residue 70 THR Chi-restraints excluded: chain j residue 78 THR Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 130 HIS Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 13 ASN Chi-restraints excluded: chain k residue 29 HIS Chi-restraints excluded: chain k residue 52 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 110 VAL Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 18 ARG Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 62 LYS Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain m residue 119 LEU Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 72 ASP Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain n residue 120 GLU Chi-restraints excluded: chain o residue 21 LEU Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 38 GLN Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 55 HIS Chi-restraints excluded: chain p residue 69 VAL Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 83 ILE Chi-restraints excluded: chain p residue 102 ARG Chi-restraints excluded: chain p residue 114 ASN Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 43 GLN Chi-restraints excluded: chain q residue 55 GLN Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain q residue 93 ILE Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 98 ILE Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 52 GLU Chi-restraints excluded: chain s residue 61 ASN Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 83 LYS Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 53 VAL Chi-restraints excluded: chain u residue 7 ASP Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 40 LEU Chi-restraints excluded: chain u residue 51 LEU Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain u residue 101 THR Chi-restraints excluded: chain v residue 19 ARG Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain w residue 7 ARG Chi-restraints excluded: chain w residue 8 ASN Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 47 VAL Chi-restraints excluded: chain w residue 52 ASP Chi-restraints excluded: chain x residue 29 LEU Chi-restraints excluded: chain x residue 33 HIS Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain y residue 17 GLU Chi-restraints excluded: chain y residue 26 PHE Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain y residue 56 LEU Chi-restraints excluded: chain z residue 22 THR Chi-restraints excluded: chain z residue 24 LEU Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 136 ARG Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain I residue 70 GLN Chi-restraints excluded: chain I residue 71 PHE Chi-restraints excluded: chain I residue 120 LYS Chi-restraints excluded: chain I residue 197 HIS Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 58 HIS Chi-restraints excluded: chain K residue 59 TYR Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 61 PHE Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 139 ASP Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 113 ARG Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 108 ARG Chi-restraints excluded: chain N residue 109 GLN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 112 ARG Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 76 TYR Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 95 HIS Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain R residue 22 TYR Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 54 THR Chi-restraints excluded: chain S residue 2 LYS Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 55 LEU Chi-restraints excluded: chain T residue 59 VAL Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 59 HIS 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 56 ASP Chi-restraints excluded: chain V residue 63 CYS Chi-restraints excluded: chain W residue 12 PHE Chi-restraints excluded: chain W residue 71 ASP Chi-restraints excluded: chain X residue 13 HIS Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 65 MET Chi-restraints excluded: chain X residue 72 GLU Chi-restraints excluded: chain Y residue 35 TYR Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain a residue 16 ASP Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 202 THR Chi-restraints excluded: chain a residue 207 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 979 optimal weight: 10.0000 chunk 114 optimal weight: 0.9990 chunk 578 optimal weight: 20.0000 chunk 741 optimal weight: 20.0000 chunk 574 optimal weight: 10.0000 chunk 855 optimal weight: 10.0000 chunk 567 optimal weight: 0.5980 chunk 1012 optimal weight: 10.0000 chunk 633 optimal weight: 20.0000 chunk 616 optimal weight: 30.0000 chunk 467 optimal weight: 0.5980 overall best weight: 4.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 75 GLN ** y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 145 ASN ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 70 GLN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 135 GLN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN ** P 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 188 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.5602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 162606 Z= 0.220 Angle : 0.673 14.944 243356 Z= 0.343 Chirality : 0.037 0.402 31135 Planarity : 0.005 0.087 12986 Dihedral : 23.731 179.161 81653 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 25.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.94 % Favored : 88.96 % Rotamer: Outliers : 6.57 % Allowed : 27.49 % Favored : 65.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.89 (0.10), residues: 5849 helix: -0.91 (0.12), residues: 1749 sheet: -2.02 (0.17), residues: 836 loop : -2.54 (0.10), residues: 3264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.003 TRP G 103 HIS 0.013 0.002 HIS j 77 PHE 0.028 0.002 PHE e 99 TYR 0.022 0.002 TYR b 160 ARG 0.012 0.001 ARG M 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1477 residues out of total 4852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 319 poor density : 1158 time to evaluate : 6.676 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: b 35 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8515 (pttm) REVERT: b 83 ASP cc_start: 0.8687 (t0) cc_final: 0.8031 (t0) REVERT: b 160 TYR cc_start: 0.8083 (p90) cc_final: 0.7798 (p90) REVERT: b 176 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.6868 (mmm160) REVERT: b 250 GLN cc_start: 0.8924 (mm-40) cc_final: 0.8310 (mt0) REVERT: b 269 ARG cc_start: 0.4704 (tpt170) cc_final: 0.3760 (mmm160) REVERT: c 33 ARG cc_start: 0.8242 (mpp80) cc_final: 0.7549 (mpp80) REVERT: c 82 PHE cc_start: 0.8180 (m-80) cc_final: 0.7932 (m-80) REVERT: c 124 ARG cc_start: 0.8047 (mmm160) cc_final: 0.7778 (mmm160) REVERT: c 157 LYS cc_start: 0.6619 (mttt) cc_final: 0.6145 (tttt) REVERT: c 167 ASN cc_start: 0.8896 (t0) cc_final: 0.8330 (t0) REVERT: d 1 MET cc_start: 0.7217 (tpp) cc_final: 0.6919 (tpp) REVERT: e 97 GLU cc_start: 0.8931 (tp30) cc_final: 0.8053 (pp20) REVERT: e 129 MET cc_start: 0.7632 (tmm) cc_final: 0.7201 (tmm) REVERT: e 154 THR cc_start: 0.7145 (m) cc_final: 0.6889 (p) REVERT: f 68 ARG cc_start: 0.8522 (tmt170) cc_final: 0.8099 (ttp80) REVERT: f 93 TYR cc_start: 0.5587 (m-80) cc_final: 0.4309 (m-80) REVERT: f 137 LYS cc_start: 0.6128 (ttpt) cc_final: 0.5814 (ttpt) REVERT: f 140 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8895 (tp) REVERT: f 151 ARG cc_start: 0.7644 (tpt-90) cc_final: 0.7333 (ttt180) REVERT: g 25 TYR cc_start: 0.7282 (t80) cc_final: 0.6689 (t80) REVERT: g 33 GLN cc_start: 0.8408 (mp10) cc_final: 0.7845 (mp10) REVERT: g 55 GLU cc_start: 0.1031 (OUTLIER) cc_final: 0.0301 (pp20) REVERT: i 116 MET cc_start: 0.5718 (mmp) cc_final: 0.3444 (mtm) REVERT: j 57 LEU cc_start: 0.8964 (pp) cc_final: 0.8683 (pp) REVERT: j 78 THR cc_start: 0.9211 (OUTLIER) cc_final: 0.8901 (t) REVERT: j 86 GLN cc_start: 0.7940 (pt0) cc_final: 0.7581 (pp30) REVERT: j 91 GLU cc_start: 0.7504 (mp0) cc_final: 0.6983 (pm20) REVERT: j 136 GLN cc_start: 0.8746 (mt0) cc_final: 0.8426 (mp10) REVERT: k 3 GLN cc_start: 0.8057 (pm20) cc_final: 0.7840 (pm20) REVERT: k 20 MET cc_start: 0.7743 (ttm) cc_final: 0.7509 (ttt) REVERT: k 41 ILE cc_start: 0.8765 (mm) cc_final: 0.8202 (mm) REVERT: l 59 ARG cc_start: 0.8513 (mtp180) cc_final: 0.7964 (tpp80) REVERT: m 44 ARG cc_start: 0.8456 (ttm110) cc_final: 0.8078 (tpm170) REVERT: m 45 GLN cc_start: 0.7819 (tt0) cc_final: 0.7507 (tt0) REVERT: m 65 ILE cc_start: 0.8010 (mt) cc_final: 0.7541 (pt) REVERT: m 104 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8097 (mt-10) REVERT: m 127 LYS cc_start: 0.8200 (tppt) cc_final: 0.7697 (mmmt) REVERT: n 8 ARG cc_start: 0.7886 (ttm-80) cc_final: 0.7509 (ttm-80) REVERT: n 17 ARG cc_start: 0.8970 (ttp-170) cc_final: 0.8525 (ptt90) REVERT: n 35 LYS cc_start: 0.8972 (tttm) cc_final: 0.8636 (tttm) REVERT: n 62 ASN cc_start: 0.8247 (m-40) cc_final: 0.7850 (m-40) REVERT: o 67 ASN cc_start: 0.8829 (p0) cc_final: 0.7953 (m-40) REVERT: o 76 LYS cc_start: 0.9102 (tttt) cc_final: 0.8682 (mttp) REVERT: o 98 GLN cc_start: 0.8362 (tp-100) cc_final: 0.8000 (tp40) REVERT: o 99 TYR cc_start: 0.7132 (t80) cc_final: 0.6677 (t80) REVERT: o 102 ARG cc_start: 0.7591 (mtm180) cc_final: 0.6514 (ttm170) REVERT: p 67 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6037 (mm-30) REVERT: p 97 TYR cc_start: 0.6885 (m-80) cc_final: 0.6384 (m-80) REVERT: p 102 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.7182 (mtp180) REVERT: q 50 ARG cc_start: 0.8468 (mtm-85) cc_final: 0.8218 (mtm-85) REVERT: q 92 LYS cc_start: 0.8138 (tttt) cc_final: 0.7348 (tttm) REVERT: r 19 THR cc_start: 0.7419 (OUTLIER) cc_final: 0.7193 (p) REVERT: r 24 LYS cc_start: 0.7213 (OUTLIER) cc_final: 0.6047 (tptt) REVERT: r 45 GLU cc_start: 0.7505 (tp30) cc_final: 0.7042 (tm-30) REVERT: r 78 ARG cc_start: 0.8390 (tpp80) cc_final: 0.8071 (tpp80) REVERT: s 28 LYS cc_start: 0.6957 (mmtt) cc_final: 0.6062 (mmtt) REVERT: s 40 ASN cc_start: 0.8155 (m-40) cc_final: 0.7862 (p0) REVERT: s 77 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7807 (p0) REVERT: s 83 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.6930 (ttpp) REVERT: t 6 ARG cc_start: 0.8555 (tpm170) cc_final: 0.7867 (tpm170) REVERT: t 7 LEU cc_start: 0.8767 (mp) cc_final: 0.8528 (mp) REVERT: t 19 LYS cc_start: 0.8438 (tttt) cc_final: 0.7961 (tptt) REVERT: u 100 GLU cc_start: 0.8407 (tp30) cc_final: 0.8164 (tp30) REVERT: v 55 GLU cc_start: 0.9267 (mp0) cc_final: 0.8877 (mp0) REVERT: w 15 LYS cc_start: 0.7932 (tppt) cc_final: 0.7508 (ptpp) REVERT: w 40 LYS cc_start: 0.7208 (pttt) cc_final: 0.6684 (pttt) REVERT: w 74 LYS cc_start: 0.8506 (mmmt) cc_final: 0.8215 (mmmt) REVERT: y 27 ASN cc_start: 0.8024 (m110) cc_final: 0.7557 (m-40) REVERT: z 36 GLU cc_start: 0.8446 (mp0) cc_final: 0.7346 (tm-30) REVERT: E 4 LYS cc_start: 0.6682 (tppt) cc_final: 0.3679 (tppt) REVERT: E 25 HIS cc_start: 0.8306 (m-70) cc_final: 0.7991 (m-70) REVERT: F 24 ARG cc_start: 0.7413 (mmt90) cc_final: 0.6568 (tmt-80) REVERT: G 57 ASN cc_start: 0.7538 (m-40) cc_final: 0.7164 (m-40) REVERT: G 67 LEU cc_start: 0.7824 (tp) cc_final: 0.7136 (mm) REVERT: G 93 HIS cc_start: 0.8087 (OUTLIER) cc_final: 0.7066 (t-90) REVERT: G 103 TRP cc_start: 0.7088 (t60) cc_final: 0.6696 (t60) REVERT: G 107 ARG cc_start: 0.7110 (ptt90) cc_final: 0.6322 (ptt90) REVERT: G 138 ARG cc_start: 0.8237 (mtm110) cc_final: 0.7297 (mtp85) REVERT: G 142 LYS cc_start: 0.9002 (ttpt) cc_final: 0.8438 (mttt) REVERT: G 153 MET cc_start: 0.4362 (mtp) cc_final: 0.3883 (mtm) REVERT: G 183 PHE cc_start: 0.7008 (m-80) cc_final: 0.6530 (m-80) REVERT: H 5 HIS cc_start: 0.8731 (t-90) cc_final: 0.8140 (t70) REVERT: H 139 ASN cc_start: 0.8743 (m-40) cc_final: 0.8543 (m-40) REVERT: H 163 ARG cc_start: 0.7053 (pmt170) cc_final: 0.6769 (pmt170) REVERT: I 71 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7993 (m-10) REVERT: I 102 TYR cc_start: 0.6738 (t80) cc_final: 0.6201 (t80) REVERT: J 63 MET cc_start: 0.8499 (tmm) cc_final: 0.8117 (tmm) REVERT: J 67 ARG cc_start: 0.8040 (mmm160) cc_final: 0.7317 (tpm170) REVERT: J 70 MET cc_start: 0.7239 (tpp) cc_final: 0.6490 (tpp) REVERT: J 95 MET cc_start: 0.6122 (ptp) cc_final: 0.5826 (ptt) REVERT: J 96 GLN cc_start: 0.8938 (tp-100) cc_final: 0.8053 (tm-30) REVERT: J 115 GLU cc_start: 0.8985 (pt0) cc_final: 0.8724 (pt0) REVERT: J 120 HIS cc_start: 0.6884 (p-80) cc_final: 0.6567 (p-80) REVERT: J 131 ASN cc_start: 0.8408 (m110) cc_final: 0.7737 (m110) REVERT: J 150 GLU cc_start: 0.8723 (mp0) cc_final: 0.8453 (mp0) REVERT: K 5 GLU cc_start: 0.7307 (tt0) cc_final: 0.6913 (pt0) REVERT: L 84 TYR cc_start: 0.5813 (p90) cc_final: 0.4944 (p90) REVERT: L 94 ARG cc_start: 0.7658 (ttt180) cc_final: 0.6814 (ttt90) REVERT: L 139 ASP cc_start: 0.8567 (m-30) cc_final: 0.7955 (m-30) REVERT: L 141 HIS cc_start: 0.6557 (m-70) cc_final: 0.6249 (m-70) REVERT: M 32 LYS cc_start: 0.7950 (mttm) cc_final: 0.7720 (mttp) REVERT: M 72 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7756 (mm-30) REVERT: M 86 LYS cc_start: 0.8452 (mmtm) cc_final: 0.7800 (mmtm) REVERT: M 113 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6040 (ttp-110) REVERT: N 11 ARG cc_start: 0.8353 (tpt-90) cc_final: 0.8077 (tpt-90) REVERT: N 21 LYS cc_start: 0.9389 (ttmm) cc_final: 0.9141 (mmtp) REVERT: N 45 MET cc_start: 0.6370 (ptt) cc_final: 0.5660 (ptt) REVERT: N 109 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7759 (mt0) REVERT: O 11 LYS cc_start: 0.8233 (ptpt) cc_final: 0.7926 (mttt) REVERT: P 58 THR cc_start: 0.5135 (p) cc_final: 0.4857 (p) REVERT: P 93 GLU cc_start: 0.7024 (mm-30) cc_final: 0.6565 (mm-30) REVERT: Q 8 ARG cc_start: 0.6854 (ttt180) cc_final: 0.6625 (ttt180) REVERT: Q 9 LYS cc_start: 0.8863 (ttpp) cc_final: 0.8565 (tptt) REVERT: Q 28 GLN cc_start: 0.8456 (mm-40) cc_final: 0.7729 (mm-40) REVERT: Q 95 HIS cc_start: 0.8298 (OUTLIER) cc_final: 0.8030 (t-90) REVERT: R 2 ARG cc_start: 0.8911 (ttt180) cc_final: 0.8313 (tpp80) REVERT: R 99 GLN cc_start: 0.7323 (mp10) cc_final: 0.6934 (mp10) REVERT: S 11 LYS cc_start: 0.8260 (mmtt) cc_final: 0.7984 (mmtp) REVERT: S 45 LEU cc_start: 0.9066 (mt) cc_final: 0.8490 (mt) REVERT: S 84 ARG cc_start: 0.4795 (ttp-170) cc_final: 0.4423 (ttp-170) REVERT: S 89 ARG cc_start: 0.8332 (tpm170) cc_final: 0.7860 (tpm170) REVERT: S 100 TRP cc_start: 0.6371 (OUTLIER) cc_final: 0.5534 (p90) REVERT: T 48 ASP cc_start: 0.8526 (t0) cc_final: 0.8245 (t0) REVERT: V 27 PHE cc_start: 0.3137 (OUTLIER) cc_final: 0.2070 (t80) REVERT: V 30 HIS cc_start: 0.7554 (t-90) cc_final: 0.7267 (t-90) REVERT: V 64 ARG cc_start: 0.9308 (mmm-85) cc_final: 0.8804 (tpp80) REVERT: X 80 ARG cc_start: 0.2241 (mtt-85) cc_final: 0.1942 (ttm-80) REVERT: Y 7 LYS cc_start: 0.9021 (ptpt) cc_final: 0.8756 (ptmm) REVERT: Y 82 ILE cc_start: 0.8961 (pt) cc_final: 0.8640 (pt) REVERT: a 8 MET cc_start: 0.1108 (mpp) cc_final: 0.0707 (mpp) REVERT: a 225 ASP cc_start: 0.4427 (OUTLIER) cc_final: 0.4015 (m-30) outliers start: 319 outliers final: 252 residues processed: 1351 average time/residue: 1.3549 time to fit residues: 3120.4578 Evaluate side-chains 1376 residues out of total 4852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 1106 time to evaluate : 8.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LYS Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 78 GLU Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 145 MET Chi-restraints excluded: chain b residue 176 ARG Chi-restraints excluded: chain b residue 179 GLU Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 231 HIS Chi-restraints excluded: chain b residue 249 VAL Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain c residue 27 ILE Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 58 ASN Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 101 PHE Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 203 VAL Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 178 VAL Chi-restraints excluded: chain d residue 191 ASP Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 49 LEU Chi-restraints excluded: chain e residue 80 GLN Chi-restraints excluded: chain e residue 120 SER Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 18 ILE Chi-restraints excluded: chain f residue 46 ASP Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 113 ASP Chi-restraints excluded: chain f residue 120 ILE Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain f residue 148 ARG Chi-restraints excluded: chain g residue 19 VAL Chi-restraints excluded: chain g residue 20 ASN Chi-restraints excluded: chain g residue 55 GLU Chi-restraints excluded: chain g residue 108 VAL Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain h residue 86 MET Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain i residue 117 THR Chi-restraints excluded: chain i residue 137 LEU Chi-restraints excluded: chain j residue 3 THR Chi-restraints excluded: chain j residue 7 LYS Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 70 THR Chi-restraints excluded: chain j residue 78 THR Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 130 HIS Chi-restraints excluded: chain k residue 13 ASN Chi-restraints excluded: chain k residue 29 HIS Chi-restraints excluded: chain k residue 52 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 110 VAL Chi-restraints excluded: chain l residue 111 ILE Chi-restraints excluded: chain l residue 112 LEU Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 62 LYS Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 131 VAL Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 69 VAL Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 102 ARG Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 43 GLN Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain r residue 11 GLN Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 24 LYS Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 98 ILE Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 52 GLU Chi-restraints excluded: chain s residue 61 ASN Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 83 LYS Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 53 VAL Chi-restraints excluded: chain u residue 7 ASP Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 40 LEU Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain u residue 101 THR Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 19 ARG Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain v residue 75 GLN Chi-restraints excluded: chain w residue 7 ARG Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 47 VAL Chi-restraints excluded: chain w residue 52 ASP Chi-restraints excluded: chain x residue 29 LEU Chi-restraints excluded: chain x residue 33 HIS Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain y residue 14 LEU Chi-restraints excluded: chain y residue 16 THR Chi-restraints excluded: chain y residue 26 PHE Chi-restraints excluded: chain y residue 53 VAL Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 22 THR Chi-restraints excluded: chain z residue 29 ARG Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 93 HIS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 136 ARG Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain I residue 70 GLN Chi-restraints excluded: chain I residue 71 PHE Chi-restraints excluded: chain I residue 120 LYS Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 197 HIS Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 19 ARG Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 58 HIS Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 61 PHE Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 113 ARG Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 108 ARG Chi-restraints excluded: chain N residue 109 GLN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 76 TYR Chi-restraints excluded: chain P residue 113 THR Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 95 HIS Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain R residue 22 TYR Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 40 GLU Chi-restraints excluded: chain R residue 53 ASP Chi-restraints excluded: chain R residue 54 THR Chi-restraints excluded: chain S residue 2 LYS Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain S residue 100 TRP Chi-restraints excluded: chain T residue 55 LEU Chi-restraints excluded: chain T residue 59 VAL Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 59 HIS 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 56 ASP Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain W residue 12 PHE Chi-restraints excluded: chain W residue 71 ASP Chi-restraints excluded: chain X residue 13 HIS Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 65 MET Chi-restraints excluded: chain X residue 72 GLU Chi-restraints excluded: chain Y residue 35 TYR Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain a residue 16 ASP Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 202 THR Chi-restraints excluded: chain a residue 211 LYS Chi-restraints excluded: chain a residue 225 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 626 optimal weight: 20.0000 chunk 404 optimal weight: 6.9990 chunk 604 optimal weight: 20.0000 chunk 304 optimal weight: 0.9990 chunk 198 optimal weight: 9.9990 chunk 196 optimal weight: 6.9990 chunk 643 optimal weight: 20.0000 chunk 689 optimal weight: 30.0000 chunk 500 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 795 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 229 HIS ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 126 ASN ** f 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 75 GLN ** y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 ASN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 145 ASN H 189 HIS I 53 GLN I 70 GLN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN ** N 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 188 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.5999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 162606 Z= 0.293 Angle : 0.757 12.862 243356 Z= 0.384 Chirality : 0.041 0.486 31135 Planarity : 0.006 0.083 12986 Dihedral : 23.906 179.251 81653 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 31.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.48 % Favored : 87.42 % Rotamer: Outliers : 7.01 % Allowed : 27.91 % Favored : 65.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.02 (0.10), residues: 5849 helix: -1.04 (0.12), residues: 1742 sheet: -2.08 (0.17), residues: 827 loop : -2.61 (0.10), residues: 3280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP G 103 HIS 0.014 0.002 HIS p 76 PHE 0.033 0.003 PHE n 67 TYR 0.024 0.002 TYR b 160 ARG 0.017 0.001 ARG P 121 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1475 residues out of total 4852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 340 poor density : 1135 time to evaluate : 6.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 83 ASP cc_start: 0.8712 (t0) cc_final: 0.7980 (t0) REVERT: b 160 TYR cc_start: 0.8085 (p90) cc_final: 0.7811 (p90) REVERT: b 269 ARG cc_start: 0.4783 (tpt170) cc_final: 0.3800 (mmm160) REVERT: c 33 ARG cc_start: 0.8408 (mpp80) cc_final: 0.7523 (mpp80) REVERT: c 82 PHE cc_start: 0.8248 (m-80) cc_final: 0.8018 (m-80) REVERT: c 157 LYS cc_start: 0.6727 (mttt) cc_final: 0.6177 (tttt) REVERT: c 167 ASN cc_start: 0.8955 (t0) cc_final: 0.8369 (t0) REVERT: e 121 PHE cc_start: 0.4827 (m-80) cc_final: 0.4100 (t80) REVERT: e 129 MET cc_start: 0.7628 (tmm) cc_final: 0.7137 (tmm) REVERT: e 140 ILE cc_start: 0.5764 (mm) cc_final: 0.5380 (mt) REVERT: e 154 THR cc_start: 0.7151 (m) cc_final: 0.6897 (p) REVERT: f 68 ARG cc_start: 0.8515 (tmt170) cc_final: 0.8116 (ttp80) REVERT: f 142 GLN cc_start: 0.9030 (tt0) cc_final: 0.8538 (tt0) REVERT: g 33 GLN cc_start: 0.8464 (mp10) cc_final: 0.7953 (mp10) REVERT: g 55 GLU cc_start: 0.1146 (OUTLIER) cc_final: 0.0416 (pp20) REVERT: i 116 MET cc_start: 0.5106 (mmp) cc_final: 0.3451 (mmm) REVERT: j 13 ARG cc_start: 0.7114 (OUTLIER) cc_final: 0.6642 (mmt-90) REVERT: j 78 THR cc_start: 0.9285 (OUTLIER) cc_final: 0.9013 (t) REVERT: j 86 GLN cc_start: 0.7928 (pt0) cc_final: 0.7527 (pp30) REVERT: j 91 GLU cc_start: 0.7484 (mp0) cc_final: 0.6931 (pm20) REVERT: j 136 GLN cc_start: 0.8713 (mt0) cc_final: 0.8350 (mp10) REVERT: k 3 GLN cc_start: 0.8129 (pm20) cc_final: 0.7902 (pm20) REVERT: k 41 ILE cc_start: 0.8911 (mm) cc_final: 0.8376 (mm) REVERT: l 59 ARG cc_start: 0.8567 (mtp180) cc_final: 0.7950 (tpp80) REVERT: m 44 ARG cc_start: 0.8446 (ttm110) cc_final: 0.8196 (tpm170) REVERT: m 45 GLN cc_start: 0.7766 (tt0) cc_final: 0.7408 (tt0) REVERT: m 65 ILE cc_start: 0.8145 (mt) cc_final: 0.7715 (pt) REVERT: m 104 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7902 (mt-10) REVERT: m 119 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7562 (tt) REVERT: n 8 ARG cc_start: 0.7849 (ttm-80) cc_final: 0.7445 (ttm-80) REVERT: n 17 ARG cc_start: 0.9151 (ttp-170) cc_final: 0.8673 (ptt90) REVERT: n 35 LYS cc_start: 0.9047 (tttm) cc_final: 0.8730 (tttm) REVERT: n 62 ASN cc_start: 0.8413 (m-40) cc_final: 0.8018 (m-40) REVERT: n 120 GLU cc_start: 0.6171 (OUTLIER) cc_final: 0.4703 (mt-10) REVERT: o 48 LEU cc_start: 0.6623 (OUTLIER) cc_final: 0.6358 (mm) REVERT: o 67 ASN cc_start: 0.8776 (p0) cc_final: 0.7796 (m-40) REVERT: o 76 LYS cc_start: 0.9137 (tttt) cc_final: 0.8714 (mttp) REVERT: o 98 GLN cc_start: 0.8345 (tp-100) cc_final: 0.7990 (tp40) REVERT: o 102 ARG cc_start: 0.7460 (mtm180) cc_final: 0.6081 (ttm170) REVERT: p 23 ASP cc_start: 0.7470 (m-30) cc_final: 0.7226 (m-30) REVERT: p 67 GLU cc_start: 0.7381 (mm-30) cc_final: 0.6215 (mm-30) REVERT: p 97 TYR cc_start: 0.6973 (m-80) cc_final: 0.6464 (m-80) REVERT: p 102 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.7110 (mtp180) REVERT: q 50 ARG cc_start: 0.8559 (mtm-85) cc_final: 0.8231 (mtm-85) REVERT: r 6 GLN cc_start: 0.6292 (mp10) cc_final: 0.6041 (mp10) REVERT: r 19 THR cc_start: 0.7370 (OUTLIER) cc_final: 0.7065 (p) REVERT: r 24 LYS cc_start: 0.7705 (ptpt) cc_final: 0.6336 (tptp) REVERT: r 45 GLU cc_start: 0.7525 (tp30) cc_final: 0.6946 (tm-30) REVERT: r 78 ARG cc_start: 0.8376 (tpp80) cc_final: 0.8036 (tpp80) REVERT: r 80 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.6237 (ptp90) REVERT: s 28 LYS cc_start: 0.7018 (mmtt) cc_final: 0.6136 (mmtt) REVERT: s 75 PHE cc_start: 0.9061 (p90) cc_final: 0.8832 (p90) REVERT: s 77 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7771 (p0) REVERT: s 83 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.7169 (ttpp) REVERT: s 99 ARG cc_start: 0.7601 (mtt-85) cc_final: 0.7373 (mtt-85) REVERT: t 6 ARG cc_start: 0.8529 (tpm170) cc_final: 0.7777 (tpm170) REVERT: t 9 LYS cc_start: 0.8409 (mtpt) cc_final: 0.7845 (mttm) REVERT: t 19 LYS cc_start: 0.8474 (tttt) cc_final: 0.8000 (tptt) REVERT: v 55 GLU cc_start: 0.9308 (mp0) cc_final: 0.8919 (mp0) REVERT: w 15 LYS cc_start: 0.8021 (tppt) cc_final: 0.7531 (ptpp) REVERT: w 40 LYS cc_start: 0.7165 (pttt) cc_final: 0.6665 (pttt) REVERT: w 65 PHE cc_start: 0.6303 (m-80) cc_final: 0.5913 (m-80) REVERT: w 74 LYS cc_start: 0.8492 (mmmt) cc_final: 0.8193 (mmmt) REVERT: x 59 ASP cc_start: 0.8275 (t0) cc_final: 0.7839 (m-30) REVERT: y 27 ASN cc_start: 0.8204 (m110) cc_final: 0.7766 (m110) REVERT: z 36 GLU cc_start: 0.8581 (mp0) cc_final: 0.7720 (tm-30) REVERT: B 14 MET cc_start: 0.7420 (OUTLIER) cc_final: 0.7060 (mmt) REVERT: E 4 LYS cc_start: 0.6815 (tppt) cc_final: 0.3851 (tppt) REVERT: E 25 HIS cc_start: 0.8221 (m-70) cc_final: 0.7946 (m-70) REVERT: G 26 MET cc_start: 0.6128 (tpp) cc_final: 0.5816 (tpp) REVERT: G 67 LEU cc_start: 0.7875 (tp) cc_final: 0.7164 (mm) REVERT: G 138 ARG cc_start: 0.8192 (mtm110) cc_final: 0.7316 (mtp85) REVERT: G 142 LYS cc_start: 0.9001 (ttpt) cc_final: 0.8437 (mttt) REVERT: G 153 MET cc_start: 0.4535 (mtp) cc_final: 0.4225 (mtm) REVERT: H 5 HIS cc_start: 0.8602 (t-90) cc_final: 0.8019 (t70) REVERT: H 163 ARG cc_start: 0.7017 (pmt170) cc_final: 0.6754 (pmt170) REVERT: I 71 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7957 (m-10) REVERT: I 102 TYR cc_start: 0.6799 (t80) cc_final: 0.6061 (t80) REVERT: J 63 MET cc_start: 0.8478 (tmm) cc_final: 0.8110 (tmm) REVERT: J 67 ARG cc_start: 0.8150 (mmm160) cc_final: 0.7335 (tpm170) REVERT: J 70 MET cc_start: 0.6810 (tpp) cc_final: 0.5650 (tpp) REVERT: J 95 MET cc_start: 0.6604 (ptp) cc_final: 0.6395 (ptt) REVERT: J 115 GLU cc_start: 0.9262 (pt0) cc_final: 0.8858 (pt0) REVERT: J 120 HIS cc_start: 0.6995 (p-80) cc_final: 0.6725 (p-80) REVERT: J 131 ASN cc_start: 0.8433 (m110) cc_final: 0.7857 (m110) REVERT: J 150 GLU cc_start: 0.8703 (mp0) cc_final: 0.8402 (mp0) REVERT: L 4 ARG cc_start: 0.6742 (OUTLIER) cc_final: 0.5090 (mmp-170) REVERT: L 84 TYR cc_start: 0.5615 (p90) cc_final: 0.4711 (p90) REVERT: L 94 ARG cc_start: 0.7674 (ttt180) cc_final: 0.7440 (ttt180) REVERT: L 139 ASP cc_start: 0.8482 (m-30) cc_final: 0.7873 (m-30) REVERT: M 32 LYS cc_start: 0.7896 (mttm) cc_final: 0.7664 (mttp) REVERT: M 72 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7792 (mm-30) REVERT: M 86 LYS cc_start: 0.8482 (mmtm) cc_final: 0.7825 (mmtm) REVERT: M 87 ARG cc_start: 0.7678 (tmm-80) cc_final: 0.7212 (tmm-80) REVERT: M 113 ARG cc_start: 0.6906 (OUTLIER) cc_final: 0.6227 (ttp-110) REVERT: M 123 GLU cc_start: 0.6643 (tt0) cc_final: 0.6418 (tt0) REVERT: N 11 ARG cc_start: 0.8359 (tpt-90) cc_final: 0.8080 (tpt-90) REVERT: N 21 LYS cc_start: 0.9375 (ttmm) cc_final: 0.9124 (mmtp) REVERT: N 45 MET cc_start: 0.6561 (ptt) cc_final: 0.5940 (ptt) REVERT: N 109 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7715 (mt0) REVERT: P 19 VAL cc_start: 0.8783 (m) cc_final: 0.7796 (m) REVERT: P 58 THR cc_start: 0.5422 (p) cc_final: 0.5155 (p) REVERT: P 63 GLN cc_start: 0.8295 (pt0) cc_final: 0.6916 (pp30) REVERT: P 93 GLU cc_start: 0.6800 (mm-30) cc_final: 0.6369 (mm-30) REVERT: Q 9 LYS cc_start: 0.8858 (ttpp) cc_final: 0.8585 (tptt) REVERT: Q 28 GLN cc_start: 0.8462 (mm-40) cc_final: 0.7765 (mm-40) REVERT: Q 95 HIS cc_start: 0.8279 (OUTLIER) cc_final: 0.7976 (t-90) REVERT: R 2 ARG cc_start: 0.8893 (ttt180) cc_final: 0.8201 (tpt170) REVERT: R 99 GLN cc_start: 0.7492 (mp10) cc_final: 0.7086 (mp10) REVERT: S 11 LYS cc_start: 0.8268 (mmtt) cc_final: 0.7992 (mmtp) REVERT: S 88 MET cc_start: 0.7081 (mmt) cc_final: 0.6867 (mmt) REVERT: S 89 ARG cc_start: 0.8470 (tpm170) cc_final: 0.8045 (tpm170) REVERT: S 100 TRP cc_start: 0.6354 (OUTLIER) cc_final: 0.5522 (p90) REVERT: V 27 PHE cc_start: 0.3684 (OUTLIER) cc_final: 0.2815 (t80) REVERT: V 30 HIS cc_start: 0.7616 (t-90) cc_final: 0.7345 (t-90) REVERT: V 64 ARG cc_start: 0.9276 (mmm-85) cc_final: 0.8935 (mmm-85) REVERT: X 80 ARG cc_start: 0.2453 (mtt-85) cc_final: 0.0497 (mmt180) REVERT: Y 7 LYS cc_start: 0.8990 (ptpt) cc_final: 0.8755 (ptmm) REVERT: Y 82 ILE cc_start: 0.9177 (pt) cc_final: 0.8971 (pt) REVERT: a 8 MET cc_start: 0.1314 (mpp) cc_final: 0.1048 (mpp) REVERT: a 225 ASP cc_start: 0.4586 (OUTLIER) cc_final: 0.4184 (m-30) outliers start: 340 outliers final: 282 residues processed: 1338 average time/residue: 1.3849 time to fit residues: 3166.0747 Evaluate side-chains 1403 residues out of total 4852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 302 poor density : 1101 time to evaluate : 6.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LYS Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 78 GLU Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 179 GLU Chi-restraints excluded: chain b residue 229 HIS Chi-restraints excluded: chain b residue 231 HIS Chi-restraints excluded: chain b residue 249 VAL Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain c residue 27 ILE Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 58 ASN Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 101 PHE Chi-restraints excluded: chain c residue 110 THR Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 178 VAL Chi-restraints excluded: chain c residue 203 VAL Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain d residue 29 HIS Chi-restraints excluded: chain d residue 57 LYS Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 97 ASN Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 125 SER Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 176 ASP Chi-restraints excluded: chain d residue 178 VAL Chi-restraints excluded: chain d residue 191 ASP Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 49 LEU Chi-restraints excluded: chain e residue 80 GLN Chi-restraints excluded: chain e residue 120 SER Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain e residue 152 ASP Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 18 ILE Chi-restraints excluded: chain f residue 46 ASP Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 113 ASP Chi-restraints excluded: chain f residue 148 ARG Chi-restraints excluded: chain g residue 19 VAL Chi-restraints excluded: chain g residue 55 GLU Chi-restraints excluded: chain g residue 108 VAL Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain h residue 86 MET Chi-restraints excluded: chain h residue 123 ILE Chi-restraints excluded: chain i residue 117 THR Chi-restraints excluded: chain i residue 137 LEU Chi-restraints excluded: chain j residue 3 THR Chi-restraints excluded: chain j residue 7 LYS Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 13 ARG Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 36 LEU Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 70 THR Chi-restraints excluded: chain j residue 78 THR Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 118 MET Chi-restraints excluded: chain j residue 130 HIS Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 13 ASN Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 29 HIS Chi-restraints excluded: chain k residue 52 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 110 VAL Chi-restraints excluded: chain l residue 111 ILE Chi-restraints excluded: chain l residue 112 LEU Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 62 LYS Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain m residue 119 LEU Chi-restraints excluded: chain m residue 131 VAL Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 72 ASP Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain n residue 120 GLU Chi-restraints excluded: chain o residue 21 LEU Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 68 LYS Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain p residue 19 PHE Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 69 VAL Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 83 ILE Chi-restraints excluded: chain p residue 102 ARG Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 43 GLN Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain q residue 93 ILE Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain r residue 11 GLN Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 80 ARG Chi-restraints excluded: chain r residue 98 ILE Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 52 GLU Chi-restraints excluded: chain s residue 61 ASN Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 83 LYS Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 53 VAL Chi-restraints excluded: chain u residue 7 ASP Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 40 LEU Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain u residue 101 THR Chi-restraints excluded: chain v residue 19 ARG Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 41 GLU Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 44 HIS Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain v residue 82 TYR Chi-restraints excluded: chain w residue 7 ARG Chi-restraints excluded: chain w residue 8 ASN Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 47 VAL Chi-restraints excluded: chain w residue 52 ASP Chi-restraints excluded: chain x residue 29 LEU Chi-restraints excluded: chain x residue 33 HIS Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain y residue 14 LEU Chi-restraints excluded: chain y residue 16 THR Chi-restraints excluded: chain y residue 26 PHE Chi-restraints excluded: chain y residue 53 VAL Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 22 THR Chi-restraints excluded: chain z residue 24 LEU Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 136 ARG Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 71 PHE Chi-restraints excluded: chain I residue 120 LYS Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 197 HIS Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 58 HIS Chi-restraints excluded: chain K residue 59 TYR Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 4 ARG Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 47 GLU Chi-restraints excluded: chain L residue 61 PHE Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 95 MET Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 113 ARG Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 108 ARG Chi-restraints excluded: chain N residue 109 GLN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 76 TYR Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 95 HIS Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain R residue 22 TYR Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 40 GLU Chi-restraints excluded: chain R residue 54 THR Chi-restraints excluded: chain S residue 2 LYS Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain S residue 100 TRP Chi-restraints excluded: chain T residue 55 LEU Chi-restraints excluded: chain T residue 59 VAL Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 59 HIS 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 56 ASP Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain W residue 12 PHE Chi-restraints excluded: chain W residue 71 ASP Chi-restraints excluded: chain X residue 13 HIS Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 65 MET Chi-restraints excluded: chain X residue 72 GLU Chi-restraints excluded: chain Y residue 35 TYR Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 15 LEU Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain a residue 16 ASP Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 202 THR Chi-restraints excluded: chain a residue 211 LYS Chi-restraints excluded: chain a residue 225 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 920 optimal weight: 10.0000 chunk 969 optimal weight: 10.0000 chunk 884 optimal weight: 20.0000 chunk 943 optimal weight: 50.0000 chunk 567 optimal weight: 30.0000 chunk 410 optimal weight: 0.0470 chunk 740 optimal weight: 20.0000 chunk 289 optimal weight: 1.9990 chunk 852 optimal weight: 10.0000 chunk 891 optimal weight: 10.0000 chunk 939 optimal weight: 50.0000 overall best weight: 6.4092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 229 HIS ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 94 GLN ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 62 GLN ** f 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 103 ASN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 71 ASN ** s 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 51 GLN ** y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 GLN ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 70 GLN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN ** P 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 188 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.6296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 162606 Z= 0.289 Angle : 0.755 14.770 243356 Z= 0.383 Chirality : 0.041 0.470 31135 Planarity : 0.006 0.151 12986 Dihedral : 24.024 179.985 81653 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 30.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.76 % Favored : 88.13 % Rotamer: Outliers : 7.01 % Allowed : 28.15 % Favored : 64.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.98 (0.10), residues: 5849 helix: -1.03 (0.12), residues: 1738 sheet: -2.07 (0.17), residues: 820 loop : -2.56 (0.10), residues: 3291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP G 103 HIS 0.042 0.002 HIS b 229 PHE 0.033 0.002 PHE s 75 TYR 0.022 0.002 TYR b 160 ARG 0.020 0.001 ARG u 85 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1478 residues out of total 4852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 340 poor density : 1138 time to evaluate : 6.676 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: b 83 ASP cc_start: 0.8713 (t0) cc_final: 0.8015 (t0) REVERT: b 160 TYR cc_start: 0.8030 (p90) cc_final: 0.7793 (p90) REVERT: b 200 MET cc_start: 0.7360 (ptt) cc_final: 0.7110 (ptp) REVERT: b 269 ARG cc_start: 0.4753 (tpt170) cc_final: 0.3786 (mmm160) REVERT: c 33 ARG cc_start: 0.8474 (mpp80) cc_final: 0.7572 (mpp80) REVERT: c 82 PHE cc_start: 0.8276 (m-80) cc_final: 0.8034 (m-80) REVERT: c 123 LYS cc_start: 0.8313 (tmtt) cc_final: 0.8101 (tmtt) REVERT: c 128 ARG cc_start: 0.6819 (mtt180) cc_final: 0.6022 (mtt-85) REVERT: c 157 LYS cc_start: 0.6657 (mttt) cc_final: 0.6161 (tttt) REVERT: c 167 ASN cc_start: 0.8931 (t0) cc_final: 0.8341 (t0) REVERT: d 1 MET cc_start: 0.6890 (tpp) cc_final: 0.6682 (tpp) REVERT: e 62 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8111 (tt0) REVERT: e 100 GLU cc_start: 0.9054 (pm20) cc_final: 0.8742 (tp30) REVERT: e 129 MET cc_start: 0.7650 (tmm) cc_final: 0.7129 (tmm) REVERT: e 140 ILE cc_start: 0.5776 (mm) cc_final: 0.5554 (mt) REVERT: e 154 THR cc_start: 0.6972 (m) cc_final: 0.6769 (p) REVERT: f 21 GLN cc_start: 0.8475 (pm20) cc_final: 0.7991 (pp30) REVERT: f 74 MET cc_start: 0.7125 (ttt) cc_final: 0.5486 (tpt) REVERT: f 142 GLN cc_start: 0.9015 (tt0) cc_final: 0.8668 (tt0) REVERT: g 33 GLN cc_start: 0.8500 (mp10) cc_final: 0.7981 (mp10) REVERT: g 55 GLU cc_start: 0.1102 (OUTLIER) cc_final: 0.0431 (pp20) REVERT: i 116 MET cc_start: 0.6011 (mmp) cc_final: 0.4660 (mmm) REVERT: j 57 LEU cc_start: 0.8937 (pp) cc_final: 0.8692 (pp) REVERT: j 78 THR cc_start: 0.9284 (OUTLIER) cc_final: 0.9014 (t) REVERT: j 86 GLN cc_start: 0.7932 (pt0) cc_final: 0.7531 (pp30) REVERT: j 91 GLU cc_start: 0.7501 (mp0) cc_final: 0.6845 (pm20) REVERT: j 136 GLN cc_start: 0.8707 (mt0) cc_final: 0.8314 (mp10) REVERT: k 3 GLN cc_start: 0.8140 (pm20) cc_final: 0.7891 (pm20) REVERT: k 20 MET cc_start: 0.7925 (ttm) cc_final: 0.7643 (ttt) REVERT: k 41 ILE cc_start: 0.8935 (mm) cc_final: 0.8390 (mm) REVERT: l 33 ARG cc_start: 0.8256 (ttm-80) cc_final: 0.7424 (ttm-80) REVERT: l 59 ARG cc_start: 0.8518 (mtp180) cc_final: 0.7860 (tpp80) REVERT: m 44 ARG cc_start: 0.8508 (ttm110) cc_final: 0.8249 (tpm170) REVERT: m 45 GLN cc_start: 0.7650 (tt0) cc_final: 0.7270 (tt0) REVERT: m 65 ILE cc_start: 0.8199 (mt) cc_final: 0.7802 (pt) REVERT: m 104 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7998 (mt-10) REVERT: n 8 ARG cc_start: 0.7765 (ttm-80) cc_final: 0.7362 (ttm-80) REVERT: n 17 ARG cc_start: 0.9031 (ttp-170) cc_final: 0.8599 (ptt90) REVERT: n 35 LYS cc_start: 0.9006 (tttm) cc_final: 0.8654 (tttm) REVERT: n 62 ASN cc_start: 0.8347 (m-40) cc_final: 0.7905 (m-40) REVERT: n 120 GLU cc_start: 0.6126 (OUTLIER) cc_final: 0.4772 (mt-10) REVERT: o 48 LEU cc_start: 0.6749 (OUTLIER) cc_final: 0.6500 (mm) REVERT: o 67 ASN cc_start: 0.8698 (p0) cc_final: 0.7689 (m-40) REVERT: o 76 LYS cc_start: 0.9078 (tttt) cc_final: 0.8643 (mttp) REVERT: o 98 GLN cc_start: 0.8360 (tp-100) cc_final: 0.7998 (tp40) REVERT: o 102 ARG cc_start: 0.7467 (mtm180) cc_final: 0.6071 (ttm170) REVERT: p 23 ASP cc_start: 0.7596 (m-30) cc_final: 0.7294 (m-30) REVERT: p 67 GLU cc_start: 0.7326 (mm-30) cc_final: 0.6129 (mm-30) REVERT: p 97 TYR cc_start: 0.6780 (m-80) cc_final: 0.6321 (m-80) REVERT: r 6 GLN cc_start: 0.6627 (mp10) cc_final: 0.6323 (mp10) REVERT: r 19 THR cc_start: 0.7381 (OUTLIER) cc_final: 0.7011 (p) REVERT: r 24 LYS cc_start: 0.7356 (OUTLIER) cc_final: 0.6147 (tptt) REVERT: r 45 GLU cc_start: 0.7202 (tp30) cc_final: 0.6632 (tm-30) REVERT: r 78 ARG cc_start: 0.8384 (tpp80) cc_final: 0.8049 (tpp80) REVERT: r 80 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.6307 (ptp90) REVERT: s 28 LYS cc_start: 0.7047 (mmtt) cc_final: 0.6175 (mmtt) REVERT: s 77 ASP cc_start: 0.8194 (OUTLIER) cc_final: 0.7808 (p0) REVERT: s 99 ARG cc_start: 0.7606 (mtt-85) cc_final: 0.7365 (mtt-85) REVERT: t 9 LYS cc_start: 0.8505 (mtpt) cc_final: 0.8140 (mttm) REVERT: t 19 LYS cc_start: 0.8458 (tttt) cc_final: 0.7960 (tptt) REVERT: t 33 LYS cc_start: 0.7672 (tptp) cc_final: 0.7433 (mmmt) REVERT: v 46 LYS cc_start: 0.8582 (mmtp) cc_final: 0.7899 (tptm) REVERT: v 55 GLU cc_start: 0.9283 (mp0) cc_final: 0.8877 (mp0) REVERT: w 15 LYS cc_start: 0.8093 (tppt) cc_final: 0.7488 (pttm) REVERT: w 56 PHE cc_start: 0.8405 (p90) cc_final: 0.8187 (p90) REVERT: w 62 LYS cc_start: 0.8205 (mttt) cc_final: 0.7793 (mtpp) REVERT: w 65 PHE cc_start: 0.6464 (m-80) cc_final: 0.6164 (m-80) REVERT: w 74 LYS cc_start: 0.8508 (mmmt) cc_final: 0.8221 (mmmt) REVERT: x 59 ASP cc_start: 0.8281 (t0) cc_final: 0.7794 (m-30) REVERT: y 27 ASN cc_start: 0.8180 (m110) cc_final: 0.7863 (m-40) REVERT: y 41 HIS cc_start: 0.7995 (p-80) cc_final: 0.7663 (p-80) REVERT: z 44 ARG cc_start: 0.7907 (mtm180) cc_final: 0.7540 (mtm180) REVERT: E 4 LYS cc_start: 0.6521 (tppt) cc_final: 0.5895 (pttt) REVERT: E 25 HIS cc_start: 0.8260 (m-70) cc_final: 0.8009 (m-70) REVERT: G 26 MET cc_start: 0.6329 (tpp) cc_final: 0.5916 (tpp) REVERT: G 55 GLU cc_start: 0.8973 (tp30) cc_final: 0.8376 (pp20) REVERT: G 67 LEU cc_start: 0.7907 (tp) cc_final: 0.7236 (mm) REVERT: G 107 ARG cc_start: 0.7212 (ptt90) cc_final: 0.6598 (ptt90) REVERT: G 138 ARG cc_start: 0.8175 (mtm110) cc_final: 0.7554 (mtp85) REVERT: G 142 LYS cc_start: 0.8993 (ttpt) cc_final: 0.8474 (mttt) REVERT: G 153 MET cc_start: 0.4525 (mtp) cc_final: 0.3581 (mmm) REVERT: G 180 ILE cc_start: 0.8672 (mt) cc_final: 0.8367 (tt) REVERT: H 5 HIS cc_start: 0.8587 (t-90) cc_final: 0.7952 (t70) REVERT: H 163 ARG cc_start: 0.7050 (pmt170) cc_final: 0.6712 (pmt170) REVERT: I 71 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.8036 (m-10) REVERT: I 102 TYR cc_start: 0.6767 (t80) cc_final: 0.6191 (t80) REVERT: J 63 MET cc_start: 0.8479 (tmm) cc_final: 0.8109 (tmm) REVERT: J 67 ARG cc_start: 0.8188 (mmm160) cc_final: 0.7324 (tpm170) REVERT: J 70 MET cc_start: 0.6842 (tpp) cc_final: 0.5709 (tpp) REVERT: J 80 LEU cc_start: 0.7750 (tp) cc_final: 0.7391 (tp) REVERT: J 115 GLU cc_start: 0.9262 (pt0) cc_final: 0.8846 (pt0) REVERT: J 120 HIS cc_start: 0.6983 (p-80) cc_final: 0.6727 (p-80) REVERT: J 131 ASN cc_start: 0.8506 (m110) cc_final: 0.7917 (m110) REVERT: J 156 ARG cc_start: 0.7177 (tmm-80) cc_final: 0.6779 (tmm-80) REVERT: K 5 GLU cc_start: 0.7646 (tt0) cc_final: 0.7298 (tm-30) REVERT: K 90 MET cc_start: 0.7467 (mmm) cc_final: 0.6989 (mmm) REVERT: L 4 ARG cc_start: 0.6465 (OUTLIER) cc_final: 0.4913 (mmp-170) REVERT: L 84 TYR cc_start: 0.5504 (p90) cc_final: 0.4640 (p90) REVERT: L 94 ARG cc_start: 0.7805 (ttt180) cc_final: 0.6826 (ttt90) REVERT: L 139 ASP cc_start: 0.8489 (m-30) cc_final: 0.7732 (m-30) REVERT: M 32 LYS cc_start: 0.7954 (mttm) cc_final: 0.7708 (mttp) REVERT: M 72 GLU cc_start: 0.8381 (mm-30) cc_final: 0.7883 (mm-30) REVERT: M 86 LYS cc_start: 0.8461 (mmtm) cc_final: 0.7865 (mmtm) REVERT: M 87 ARG cc_start: 0.7703 (tmm-80) cc_final: 0.7189 (tmm-80) REVERT: M 113 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.6069 (ttp-110) REVERT: M 123 GLU cc_start: 0.6619 (tt0) cc_final: 0.6382 (tt0) REVERT: N 10 ARG cc_start: 0.7262 (mtm-85) cc_final: 0.6829 (mtm-85) REVERT: N 11 ARG cc_start: 0.8336 (tpt-90) cc_final: 0.7917 (tpt170) REVERT: N 21 LYS cc_start: 0.9367 (ttmm) cc_final: 0.9116 (mmtp) REVERT: N 45 MET cc_start: 0.6833 (ptt) cc_final: 0.6171 (ptt) REVERT: N 109 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7684 (mt0) REVERT: P 58 THR cc_start: 0.5484 (p) cc_final: 0.5188 (p) REVERT: P 63 GLN cc_start: 0.7885 (pt0) cc_final: 0.7529 (pm20) REVERT: Q 9 LYS cc_start: 0.8852 (ttpp) cc_final: 0.8584 (tptt) REVERT: Q 13 ARG cc_start: 0.8435 (ptm-80) cc_final: 0.8196 (tmt170) REVERT: Q 28 GLN cc_start: 0.8426 (mm-40) cc_final: 0.7719 (mm-40) REVERT: Q 95 HIS cc_start: 0.8157 (OUTLIER) cc_final: 0.7930 (t-90) REVERT: R 2 ARG cc_start: 0.8930 (ttt180) cc_final: 0.8325 (tpp80) REVERT: R 77 LYS cc_start: 0.9662 (mmmt) cc_final: 0.9440 (mmmt) REVERT: R 99 GLN cc_start: 0.7583 (mp10) cc_final: 0.7189 (mp10) REVERT: S 11 LYS cc_start: 0.8359 (mmtt) cc_final: 0.8138 (mmtp) REVERT: S 84 ARG cc_start: 0.4627 (ttp-170) cc_final: 0.4259 (ttp-170) REVERT: S 89 ARG cc_start: 0.8521 (tpm170) cc_final: 0.8039 (tpm170) REVERT: S 100 TRP cc_start: 0.6400 (OUTLIER) cc_final: 0.5602 (p90) REVERT: V 27 PHE cc_start: 0.3723 (OUTLIER) cc_final: 0.2937 (t80) REVERT: V 30 HIS cc_start: 0.7583 (t-90) cc_final: 0.7311 (t-90) REVERT: V 64 ARG cc_start: 0.9265 (mmm-85) cc_final: 0.8960 (mmm-85) REVERT: X 80 ARG cc_start: 0.2472 (mtt-85) cc_final: 0.0537 (mmt180) REVERT: Y 7 LYS cc_start: 0.9037 (ptpt) cc_final: 0.8796 (ptmm) REVERT: Y 18 LYS cc_start: 0.9295 (tppt) cc_final: 0.9040 (mtmm) REVERT: a 8 MET cc_start: 0.1323 (mpp) cc_final: 0.1112 (mpp) REVERT: a 225 ASP cc_start: 0.4927 (OUTLIER) cc_final: 0.4532 (m-30) outliers start: 340 outliers final: 282 residues processed: 1347 average time/residue: 1.3606 time to fit residues: 3121.7049 Evaluate side-chains 1394 residues out of total 4852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 299 poor density : 1095 time to evaluate : 6.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LYS Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 78 GLU Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 179 GLU Chi-restraints excluded: chain b residue 231 HIS Chi-restraints excluded: chain b residue 249 VAL Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain c residue 27 ILE Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 58 ASN Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 101 PHE Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 178 VAL Chi-restraints excluded: chain c residue 203 VAL Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 29 HIS Chi-restraints excluded: chain d residue 57 LYS Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 125 SER Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 176 ASP Chi-restraints excluded: chain d residue 178 VAL Chi-restraints excluded: chain d residue 191 ASP Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 49 LEU Chi-restraints excluded: chain e residue 62 GLN Chi-restraints excluded: chain e residue 80 GLN Chi-restraints excluded: chain e residue 120 SER Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain e residue 152 ASP Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 18 ILE Chi-restraints excluded: chain f residue 46 ASP Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 113 ASP Chi-restraints excluded: chain f residue 148 ARG Chi-restraints excluded: chain f residue 150 TYR Chi-restraints excluded: chain g residue 19 VAL Chi-restraints excluded: chain g residue 55 GLU Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain h residue 86 MET Chi-restraints excluded: chain h residue 103 ASN Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain i residue 117 THR Chi-restraints excluded: chain i residue 137 LEU Chi-restraints excluded: chain j residue 3 THR Chi-restraints excluded: chain j residue 7 LYS Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 13 ARG Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 36 LEU Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 70 THR Chi-restraints excluded: chain j residue 78 THR Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 130 HIS Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 13 ASN Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 29 HIS Chi-restraints excluded: chain k residue 52 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 84 LYS Chi-restraints excluded: chain l residue 110 VAL Chi-restraints excluded: chain l residue 111 ILE Chi-restraints excluded: chain l residue 112 LEU Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 62 LYS Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 131 VAL Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain n residue 99 LYS Chi-restraints excluded: chain n residue 120 GLU Chi-restraints excluded: chain o residue 21 LEU Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain p residue 19 PHE Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 69 VAL Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 83 ILE Chi-restraints excluded: chain p residue 102 ARG Chi-restraints excluded: chain p residue 114 ASN Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 43 GLN Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain q residue 93 ILE Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain r residue 11 GLN Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 24 LYS Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 80 ARG Chi-restraints excluded: chain r residue 98 ILE Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 52 GLU Chi-restraints excluded: chain s residue 61 ASN Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 53 VAL Chi-restraints excluded: chain u residue 7 ASP Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 40 LEU Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain u residue 86 PHE Chi-restraints excluded: chain u residue 101 THR Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain w residue 7 ARG Chi-restraints excluded: chain w residue 8 ASN Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 47 VAL Chi-restraints excluded: chain w residue 52 ASP Chi-restraints excluded: chain x residue 29 LEU Chi-restraints excluded: chain x residue 33 HIS Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain y residue 14 LEU Chi-restraints excluded: chain y residue 16 THR Chi-restraints excluded: chain y residue 17 GLU Chi-restraints excluded: chain y residue 26 PHE Chi-restraints excluded: chain y residue 53 VAL Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 22 THR Chi-restraints excluded: chain z residue 24 LEU Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain I residue 71 PHE Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 120 LYS Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 197 HIS Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 19 ARG Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 58 HIS Chi-restraints excluded: chain K residue 59 TYR Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 4 ARG Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 47 GLU Chi-restraints excluded: chain L residue 61 PHE Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 95 MET Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 113 ARG Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 108 ARG Chi-restraints excluded: chain N residue 109 GLN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 76 TYR Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 95 HIS Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain R residue 22 TYR Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 54 THR Chi-restraints excluded: chain S residue 2 LYS Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain S residue 100 TRP Chi-restraints excluded: chain T residue 55 LEU Chi-restraints excluded: chain T residue 59 VAL Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 59 HIS Chi-restraints excluded: chain V residue 7 LEU Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain W residue 12 PHE Chi-restraints excluded: chain W residue 71 ASP Chi-restraints excluded: chain X residue 13 HIS Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 65 MET Chi-restraints excluded: chain X residue 72 GLU Chi-restraints excluded: chain Y residue 35 TYR Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 15 LEU Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain a residue 11 ILE Chi-restraints excluded: chain a residue 16 ASP Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 202 THR Chi-restraints excluded: chain a residue 211 LYS Chi-restraints excluded: chain a residue 225 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 619 optimal weight: 50.0000 chunk 997 optimal weight: 10.0000 chunk 608 optimal weight: 20.0000 chunk 473 optimal weight: 10.0000 chunk 693 optimal weight: 30.0000 chunk 1046 optimal weight: 30.0000 chunk 962 optimal weight: 10.0000 chunk 832 optimal weight: 50.0000 chunk 86 optimal weight: 7.9990 chunk 643 optimal weight: 20.0000 chunk 510 optimal weight: 20.0000 overall best weight: 11.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 138 GLN ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 23 ASN ** o 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 145 ASN ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 70 GLN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 ASN ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 36 ASN ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.7076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.116 162606 Z= 0.497 Angle : 1.053 14.869 243356 Z= 0.524 Chirality : 0.052 0.621 31135 Planarity : 0.008 0.128 12986 Dihedral : 24.670 179.595 81653 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 49.18 Ramachandran Plot: Outliers : 0.21 % Allowed : 15.27 % Favored : 84.53 % Rotamer: Outliers : 6.92 % Allowed : 28.63 % Favored : 64.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.10), residues: 5849 helix: -1.58 (0.11), residues: 1718 sheet: -2.52 (0.16), residues: 780 loop : -2.90 (0.09), residues: 3351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.090 0.005 TRP t 80 HIS 0.021 0.003 HIS p 76 PHE 0.048 0.004 PHE s 75 TYR 0.040 0.003 TYR q 44 ARG 0.020 0.001 ARG u 85 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1454 residues out of total 4852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 336 poor density : 1118 time to evaluate : 6.707 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: b 160 TYR cc_start: 0.8218 (p90) cc_final: 0.7944 (p90) REVERT: b 269 ARG cc_start: 0.4920 (tpt170) cc_final: 0.3792 (mmm160) REVERT: c 33 ARG cc_start: 0.8615 (mpp80) cc_final: 0.7923 (mpp80) REVERT: c 82 PHE cc_start: 0.8444 (m-80) cc_final: 0.8184 (m-80) REVERT: c 157 LYS cc_start: 0.7019 (mttt) cc_final: 0.6192 (ptmt) REVERT: c 167 ASN cc_start: 0.9020 (t0) cc_final: 0.8468 (t0) REVERT: e 9 ASP cc_start: 0.7169 (OUTLIER) cc_final: 0.6403 (m-30) REVERT: e 97 GLU cc_start: 0.8847 (tp30) cc_final: 0.7968 (pp20) REVERT: e 121 PHE cc_start: 0.5496 (m-80) cc_final: 0.4913 (t80) REVERT: e 129 MET cc_start: 0.7611 (tmm) cc_final: 0.6959 (tmm) REVERT: f 68 ARG cc_start: 0.8426 (tmt170) cc_final: 0.8074 (tmm160) REVERT: f 93 TYR cc_start: 0.5580 (m-80) cc_final: 0.3887 (m-80) REVERT: f 94 ARG cc_start: 0.8314 (mmm160) cc_final: 0.7529 (ttp80) REVERT: f 136 ASP cc_start: 0.8591 (t0) cc_final: 0.8117 (t0) REVERT: f 142 GLN cc_start: 0.9063 (tt0) cc_final: 0.8756 (tt0) REVERT: f 151 ARG cc_start: 0.7635 (ttt180) cc_final: 0.6913 (ttt180) REVERT: g 33 GLN cc_start: 0.8597 (mp10) cc_final: 0.8119 (mp10) REVERT: g 55 GLU cc_start: 0.1574 (OUTLIER) cc_final: 0.0713 (pp20) REVERT: i 116 MET cc_start: 0.5810 (mmp) cc_final: 0.4266 (mmm) REVERT: j 13 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6731 (mmt-90) REVERT: j 86 GLN cc_start: 0.8109 (pt0) cc_final: 0.7510 (pp30) REVERT: j 91 GLU cc_start: 0.7549 (mp0) cc_final: 0.6888 (pm20) REVERT: j 136 GLN cc_start: 0.8801 (mt0) cc_final: 0.8375 (mp10) REVERT: k 3 GLN cc_start: 0.8298 (pm20) cc_final: 0.7937 (pm20) REVERT: l 60 ARG cc_start: 0.7676 (mtm180) cc_final: 0.6663 (mtm180) REVERT: m 44 ARG cc_start: 0.8368 (ttm110) cc_final: 0.7910 (tpm170) REVERT: m 45 GLN cc_start: 0.7784 (tt0) cc_final: 0.7387 (tt0) REVERT: n 8 ARG cc_start: 0.7941 (ttm-80) cc_final: 0.7298 (ttm-80) REVERT: n 17 ARG cc_start: 0.9277 (ttp-170) cc_final: 0.9037 (ttp-170) REVERT: n 35 LYS cc_start: 0.9053 (tttm) cc_final: 0.8668 (tttm) REVERT: n 62 ASN cc_start: 0.8612 (m-40) cc_final: 0.8208 (m-40) REVERT: n 120 GLU cc_start: 0.6143 (OUTLIER) cc_final: 0.4996 (mt-10) REVERT: o 18 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8573 (mm) REVERT: o 48 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6584 (mm) REVERT: o 67 ASN cc_start: 0.8792 (p0) cc_final: 0.7705 (m-40) REVERT: o 76 LYS cc_start: 0.9055 (tttt) cc_final: 0.8589 (mttp) REVERT: o 98 GLN cc_start: 0.8333 (tp-100) cc_final: 0.8015 (tp40) REVERT: o 99 TYR cc_start: 0.7393 (t80) cc_final: 0.6812 (t80) REVERT: o 102 ARG cc_start: 0.7281 (mtm180) cc_final: 0.5675 (ttm170) REVERT: p 23 ASP cc_start: 0.7484 (m-30) cc_final: 0.7204 (m-30) REVERT: p 26 GLU cc_start: 0.8057 (tp30) cc_final: 0.7823 (tp30) REVERT: p 67 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7454 (mm-30) REVERT: p 97 TYR cc_start: 0.7083 (m-80) cc_final: 0.6585 (m-80) REVERT: r 6 GLN cc_start: 0.6661 (mp10) cc_final: 0.6340 (mp10) REVERT: r 80 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.6515 (ptp90) REVERT: s 28 LYS cc_start: 0.7201 (mmtt) cc_final: 0.6374 (mmtt) REVERT: s 68 ASP cc_start: 0.7733 (m-30) cc_final: 0.7439 (t0) REVERT: s 77 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.7913 (p0) REVERT: s 99 ARG cc_start: 0.7564 (mtt-85) cc_final: 0.7329 (mtt-85) REVERT: t 19 LYS cc_start: 0.8546 (tttt) cc_final: 0.8039 (tptt) REVERT: v 46 LYS cc_start: 0.8685 (mmtp) cc_final: 0.8026 (tptm) REVERT: v 55 GLU cc_start: 0.9387 (mp0) cc_final: 0.9028 (mp0) REVERT: v 87 GLN cc_start: 0.7172 (mt0) cc_final: 0.6671 (mt0) REVERT: w 15 LYS cc_start: 0.8191 (tppt) cc_final: 0.7699 (pttm) REVERT: w 74 LYS cc_start: 0.8297 (mmmt) cc_final: 0.7824 (mmmt) REVERT: x 56 ARG cc_start: 0.8790 (mtp-110) cc_final: 0.7958 (mtp-110) REVERT: x 59 ASP cc_start: 0.8205 (t0) cc_final: 0.7716 (m-30) REVERT: y 27 ASN cc_start: 0.8497 (m110) cc_final: 0.8192 (m110) REVERT: y 41 HIS cc_start: 0.8340 (p-80) cc_final: 0.8028 (p90) REVERT: z 36 GLU cc_start: 0.8694 (mp0) cc_final: 0.7587 (tm-30) REVERT: z 40 THR cc_start: 0.7860 (OUTLIER) cc_final: 0.7626 (p) REVERT: C 12 SER cc_start: 0.6878 (t) cc_final: 0.6186 (p) REVERT: E 4 LYS cc_start: 0.7024 (tppt) cc_final: 0.6094 (pttt) REVERT: G 5 MET cc_start: 0.6473 (mmm) cc_final: 0.6239 (mmm) REVERT: G 26 MET cc_start: 0.6897 (tpp) cc_final: 0.6661 (tpp) REVERT: G 55 GLU cc_start: 0.9079 (tp30) cc_final: 0.8328 (pp20) REVERT: G 138 ARG cc_start: 0.8435 (mtm110) cc_final: 0.7738 (mtp85) REVERT: G 142 LYS cc_start: 0.9075 (ttpt) cc_final: 0.8451 (mttt) REVERT: H 5 HIS cc_start: 0.8753 (t-90) cc_final: 0.8228 (t70) REVERT: H 163 ARG cc_start: 0.7005 (pmt170) cc_final: 0.6596 (pmt170) REVERT: H 202 PHE cc_start: 0.7201 (t80) cc_final: 0.6952 (t80) REVERT: I 71 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.8072 (m-10) REVERT: I 102 TYR cc_start: 0.6887 (t80) cc_final: 0.6037 (t80) REVERT: J 63 MET cc_start: 0.8497 (tmm) cc_final: 0.8135 (tmm) REVERT: J 67 ARG cc_start: 0.8250 (mmm160) cc_final: 0.7352 (tpm170) REVERT: J 70 MET cc_start: 0.7104 (tpp) cc_final: 0.6196 (tpp) REVERT: J 115 GLU cc_start: 0.9300 (pt0) cc_final: 0.8835 (pt0) REVERT: J 150 GLU cc_start: 0.8865 (mp0) cc_final: 0.8578 (mp0) REVERT: J 156 ARG cc_start: 0.7550 (tmm-80) cc_final: 0.7121 (tmm-80) REVERT: K 90 MET cc_start: 0.7492 (mmm) cc_final: 0.7271 (mmm) REVERT: L 4 ARG cc_start: 0.6330 (OUTLIER) cc_final: 0.4643 (mmp-170) REVERT: L 94 ARG cc_start: 0.8014 (ttt180) cc_final: 0.7072 (ttt90) REVERT: M 72 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7842 (mm-30) REVERT: M 86 LYS cc_start: 0.8456 (mmtm) cc_final: 0.7814 (mmtm) REVERT: M 87 ARG cc_start: 0.8078 (tmm-80) cc_final: 0.7786 (tmm-80) REVERT: M 113 ARG cc_start: 0.6921 (OUTLIER) cc_final: 0.6176 (ttp-110) REVERT: N 10 ARG cc_start: 0.7783 (mtm-85) cc_final: 0.7283 (mtm-85) REVERT: N 21 LYS cc_start: 0.9398 (ttmm) cc_final: 0.9138 (mmtp) REVERT: N 45 MET cc_start: 0.6962 (ptt) cc_final: 0.6339 (ptt) REVERT: N 108 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.6875 (mtp180) REVERT: P 63 GLN cc_start: 0.8053 (pt0) cc_final: 0.7736 (pp30) REVERT: Q 9 LYS cc_start: 0.8901 (ttpp) cc_final: 0.8337 (tptp) REVERT: Q 28 GLN cc_start: 0.8526 (mm-40) cc_final: 0.7761 (mm-40) REVERT: Q 93 ARG cc_start: 0.7500 (mmt-90) cc_final: 0.7016 (mmt180) REVERT: Q 95 HIS cc_start: 0.8321 (OUTLIER) cc_final: 0.7935 (t-90) REVERT: R 77 LYS cc_start: 0.9672 (mmmt) cc_final: 0.9424 (mmmt) REVERT: R 90 HIS cc_start: 0.8397 (m170) cc_final: 0.8035 (m90) REVERT: S 11 LYS cc_start: 0.8287 (mmtt) cc_final: 0.7889 (mmtt) REVERT: S 41 TRP cc_start: 0.8082 (m100) cc_final: 0.7319 (m100) REVERT: S 58 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7671 (ttp-110) REVERT: S 100 TRP cc_start: 0.6630 (OUTLIER) cc_final: 0.5815 (p90) REVERT: V 27 PHE cc_start: 0.4161 (OUTLIER) cc_final: 0.3551 (t80) REVERT: V 30 HIS cc_start: 0.7748 (t-90) cc_final: 0.7515 (t-90) REVERT: V 39 ARG cc_start: 0.8296 (tpp80) cc_final: 0.7887 (tpp80) REVERT: W 66 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6996 (mm) REVERT: X 51 HIS cc_start: 0.7064 (t-90) cc_final: 0.6127 (t70) REVERT: Y 18 LYS cc_start: 0.9498 (tppt) cc_final: 0.9169 (mtmm) REVERT: Y 27 MET cc_start: 0.8984 (mtp) cc_final: 0.8778 (mmm) REVERT: Z 38 GLU cc_start: 0.7073 (tp30) cc_final: 0.6599 (tp30) REVERT: a 225 ASP cc_start: 0.4875 (OUTLIER) cc_final: 0.4581 (m-30) outliers start: 336 outliers final: 281 residues processed: 1336 average time/residue: 1.3804 time to fit residues: 3154.4148 Evaluate side-chains 1386 residues out of total 4852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 1086 time to evaluate : 6.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LYS Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 78 GLU Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 172 THR Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 179 GLU Chi-restraints excluded: chain b residue 231 HIS Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 58 ASN Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 101 PHE Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 178 VAL Chi-restraints excluded: chain c residue 203 VAL Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 29 HIS Chi-restraints excluded: chain d residue 57 LYS Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 125 SER Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 176 ASP Chi-restraints excluded: chain d residue 178 VAL Chi-restraints excluded: chain d residue 191 ASP Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 9 ASP Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 49 LEU Chi-restraints excluded: chain e residue 78 ILE Chi-restraints excluded: chain e residue 80 GLN Chi-restraints excluded: chain e residue 120 SER Chi-restraints excluded: chain e residue 137 PHE Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain e residue 152 ASP Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 18 ILE Chi-restraints excluded: chain f residue 46 ASP Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 113 ASP Chi-restraints excluded: chain f residue 120 ILE Chi-restraints excluded: chain f residue 148 ARG Chi-restraints excluded: chain g residue 19 VAL Chi-restraints excluded: chain g residue 20 ASN Chi-restraints excluded: chain g residue 42 LYS Chi-restraints excluded: chain g residue 55 GLU Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain h residue 86 MET Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain i residue 117 THR Chi-restraints excluded: chain i residue 137 LEU Chi-restraints excluded: chain j residue 7 LYS Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 13 ARG Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 36 LEU Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 70 THR Chi-restraints excluded: chain j residue 78 THR Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 118 MET Chi-restraints excluded: chain j residue 130 HIS Chi-restraints excluded: chain j residue 138 GLN Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 13 ASN Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 29 HIS Chi-restraints excluded: chain k residue 52 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 55 MET Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 84 LYS Chi-restraints excluded: chain l residue 110 VAL Chi-restraints excluded: chain l residue 111 ILE Chi-restraints excluded: chain l residue 112 LEU Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 62 LYS Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain m residue 131 VAL Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain n residue 120 GLU Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 21 LEU Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 68 LYS Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain p residue 2 ASN Chi-restraints excluded: chain p residue 3 ILE Chi-restraints excluded: chain p residue 9 GLN Chi-restraints excluded: chain p residue 19 PHE Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 69 VAL Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 83 ILE Chi-restraints excluded: chain p residue 102 ARG Chi-restraints excluded: chain p residue 114 ASN Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 43 GLN Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain q residue 93 ILE Chi-restraints excluded: chain r residue 11 GLN Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 80 ARG Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 52 GLU Chi-restraints excluded: chain s residue 61 ASN Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 53 VAL Chi-restraints excluded: chain u residue 7 ASP Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 40 LEU Chi-restraints excluded: chain u residue 86 PHE Chi-restraints excluded: chain u residue 101 THR Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 19 ARG Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 41 GLU Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 44 HIS Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain w residue 7 ARG Chi-restraints excluded: chain w residue 8 ASN Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 47 VAL Chi-restraints excluded: chain w residue 52 ASP Chi-restraints excluded: chain x residue 29 LEU Chi-restraints excluded: chain x residue 33 HIS Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 70 LEU Chi-restraints excluded: chain y residue 16 THR Chi-restraints excluded: chain y residue 26 PHE Chi-restraints excluded: chain y residue 53 VAL Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 22 THR Chi-restraints excluded: chain z residue 24 LEU Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 93 HIS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 68 HIS Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain I residue 71 PHE Chi-restraints excluded: chain I residue 120 LYS Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 58 HIS Chi-restraints excluded: chain K residue 59 TYR Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 4 ARG Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 47 GLU Chi-restraints excluded: chain L residue 61 PHE Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 113 ARG Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 108 ARG Chi-restraints excluded: chain N residue 109 GLN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 76 TYR Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain Q residue 95 HIS Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain R residue 22 TYR Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 53 ASP Chi-restraints excluded: chain S residue 2 LYS Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 58 ARG Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain S residue 100 TRP Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 55 LEU Chi-restraints excluded: chain T residue 59 VAL Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 59 HIS Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain W residue 12 PHE Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 71 ASP Chi-restraints excluded: chain X residue 13 HIS Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 65 MET Chi-restraints excluded: chain X residue 72 GLU Chi-restraints excluded: chain Y residue 35 TYR Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 15 LEU Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 202 THR Chi-restraints excluded: chain a residue 211 LYS Chi-restraints excluded: chain a residue 225 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 661 optimal weight: 10.0000 chunk 887 optimal weight: 10.0000 chunk 255 optimal weight: 8.9990 chunk 768 optimal weight: 10.0000 chunk 122 optimal weight: 0.2980 chunk 231 optimal weight: 0.8980 chunk 834 optimal weight: 50.0000 chunk 349 optimal weight: 1.9990 chunk 856 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 138 GLN ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 145 ASN ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.130728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.108589 restraints weight = 532110.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.111359 restraints weight = 207139.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.112973 restraints weight = 110083.398| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3822 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3822 r_free = 0.3822 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3821 r_free = 0.3821 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.7082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.534 162606 Z= 0.432 Angle : 1.044 59.200 243356 Z= 0.525 Chirality : 0.051 0.906 31135 Planarity : 0.008 0.163 12986 Dihedral : 24.669 179.309 81653 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 49.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 15.27 % Favored : 84.61 % Rotamer: Outliers : 6.82 % Allowed : 29.14 % Favored : 64.04 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.63 (0.10), residues: 5849 helix: -1.62 (0.11), residues: 1719 sheet: -2.52 (0.16), residues: 785 loop : -2.91 (0.09), residues: 3345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.005 TRP t 80 HIS 0.021 0.003 HIS p 76 PHE 0.099 0.004 PHE y 26 TYR 0.037 0.003 TYR q 44 ARG 0.030 0.001 ARG G 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 44083.17 seconds wall clock time: 771 minutes 2.04 seconds (46262.04 seconds total)