Starting phenix.real_space_refine on Mon Mar 25 12:01:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wnw_21858/03_2024/6wnw_21858.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wnw_21858/03_2024/6wnw_21858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wnw_21858/03_2024/6wnw_21858.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wnw_21858/03_2024/6wnw_21858.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wnw_21858/03_2024/6wnw_21858.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wnw_21858/03_2024/6wnw_21858.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.802 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4729 5.49 5 S 159 5.16 5 C 75058 2.51 5 N 27750 2.21 5 O 41384 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b ASP 65": "OD1" <-> "OD2" Residue "b ASP 83": "OD1" <-> "OD2" Residue "b ASP 113": "OD1" <-> "OD2" Residue "b TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 13": "NH1" <-> "NH2" Residue "c GLU 17": "OE1" <-> "OE2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c ARG 59": "NH1" <-> "NH2" Residue "c ARG 77": "NH1" <-> "NH2" Residue "c ARG 83": "NH1" <-> "NH2" Residue "c GLU 88": "OE1" <-> "OE2" Residue "c PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 103": "OD1" <-> "OD2" Residue "c GLU 168": "OE1" <-> "OE2" Residue "c ARG 169": "NH1" <-> "NH2" Residue "c ASP 181": "OD1" <-> "OD2" Residue "c GLU 183": "OE1" <-> "OE2" Residue "c ARG 184": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 49": "NH1" <-> "NH2" Residue "d ARG 61": "NH1" <-> "NH2" Residue "d ARG 88": "NH1" <-> "NH2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "d GLU 152": "OE1" <-> "OE2" Residue "d ARG 162": "NH1" <-> "NH2" Residue "d ASP 168": "OD1" <-> "OD2" Residue "d ARG 170": "NH1" <-> "NH2" Residue "e ASP 5": "OD1" <-> "OD2" Residue "e ARG 70": "NH1" <-> "NH2" Residue "e ARG 79": "NH1" <-> "NH2" Residue "e ARG 91": "NH1" <-> "NH2" Residue "e GLU 93": "OE1" <-> "OE2" Residue "e ARG 101": "NH1" <-> "NH2" Residue "e ARG 109": "NH1" <-> "NH2" Residue "e ARG 111": "NH1" <-> "NH2" Residue "e ASP 112": "OD1" <-> "OD2" Residue "e ARG 114": "NH1" <-> "NH2" Residue "e ASP 122": "OD1" <-> "OD2" Residue "e ARG 132": "NH1" <-> "NH2" Residue "e GLU 139": "OE1" <-> "OE2" Residue "e ASP 141": "OD1" <-> "OD2" Residue "e ASP 173": "OD1" <-> "OD2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "f ASP 136": "OD1" <-> "OD2" Residue "f ASP 146": "OD1" <-> "OD2" Residue "f ARG 152": "NH1" <-> "NH2" Residue "f ARG 162": "NH1" <-> "NH2" Residue "f ARG 169": "NH1" <-> "NH2" Residue "g GLU 53": "OE1" <-> "OE2" Residue "g GLU 60": "OE1" <-> "OE2" Residue "g PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 101": "OD1" <-> "OD2" Residue "g PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 74": "OD1" <-> "OD2" Residue "h GLU 98": "OE1" <-> "OE2" Residue "i GLU 36": "OE1" <-> "OE2" Residue "i ASP 95": "OD1" <-> "OD2" Residue "i ASP 120": "OD1" <-> "OD2" Residue "i GLU 140": "OE1" <-> "OE2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j ASP 71": "OD1" <-> "OD2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j GLU 102": "OE1" <-> "OE2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "j GLU 129": "OE1" <-> "OE2" Residue "j ASP 141": "OD1" <-> "OD2" Residue "k ASP 12": "OD1" <-> "OD2" Residue "k GLU 45": "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 ARG 60": "NH1" <-> "NH2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l ASP 81": "OD1" <-> "OD2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 18": "NH1" <-> "NH2" Residue "m ARG 40": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m ARG 50": "NH1" <-> "NH2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m ARG 59": "NH1" <-> "NH2" Residue "m ARG 114": "NH1" <-> "NH2" Residue "m PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 8": "NH1" <-> "NH2" Residue "n ARG 12": "NH1" <-> "NH2" Residue "n ARG 17": "NH1" <-> "NH2" Residue "n ARG 22": "NH1" <-> "NH2" Residue "n ARG 46": "NH1" <-> "NH2" Residue "n ARG 63": "NH1" <-> "NH2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n ARG 69": "NH1" <-> "NH2" Residue "n ARG 71": "NH1" <-> "NH2" Residue "n ARG 96": "NH1" <-> "NH2" Residue "n ASP 117": "OD1" <-> "OD2" 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 TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 81": "NH1" <-> "NH2" Residue "o ASP 93": "OD1" <-> "OD2" Residue "o ARG 94": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "o PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 20": "NH1" <-> "NH2" Residue "p GLU 33": "OE1" <-> "OE2" Residue "p ARG 38": "NH1" <-> "NH2" Residue "p ARG 61": "NH1" <-> "NH2" Residue "p ARG 88": "NH1" <-> "NH2" Residue "p ARG 100": "NH1" <-> "NH2" Residue "p ARG 108": "NH1" <-> "NH2" Residue "q ARG 2": "NH1" <-> "NH2" Residue "q ARG 5": "NH1" <-> "NH2" Residue "q ARG 12": "NH1" <-> "NH2" Residue "q ARG 32": "NH1" <-> "NH2" Residue "q ARG 47": "NH1" <-> "NH2" Residue "q ARG 69": "NH1" <-> "NH2" Residue "q GLU 88": "OE1" <-> "OE2" Residue "q ASP 90": "OD1" <-> "OD2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r GLU 37": "OE1" <-> "OE2" Residue "r ARG 68": "NH1" <-> "NH2" Residue "r GLU 70": "OE1" <-> "OE2" 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 GLU 2": "OE1" <-> "OE2" Residue "s ASP 22": "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 5": "OE1" <-> "OE2" Residue "t PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 54": "OE1" <-> "OE2" Residue "t GLU 56": "OE1" <-> "OE2" Residue "t ARG 73": "NH1" <-> "NH2" Residue "t ASP 79": "OD1" <-> "OD2" Residue "t TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 89": "OE1" <-> "OE2" Residue "u ARG 5": "NH1" <-> "NH2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u ASP 7": "OD1" <-> "OD2" Residue "u ASP 8": "OD1" <-> "OD2" Residue "u ARG 81": "NH1" <-> "NH2" Residue "u ARG 85": "NH1" <-> "NH2" Residue "u ASP 88": "OD1" <-> "OD2" Residue "u ARG 93": "NH1" <-> "NH2" Residue "v GLU 11": "OE1" <-> "OE2" Residue "v GLU 35": "OE1" <-> "OE2" Residue "v GLU 59": "OE1" <-> "OE2" Residue "x ASP 64": "OD1" <-> "OD2" 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 PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A ARG 56": "NH1" <-> "NH2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ASP 45": "OD1" <-> "OD2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 3": "NH1" <-> "NH2" Residue "D ARG 12": "NH1" <-> "NH2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D ARG 19": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 41": "NH1" <-> "NH2" Residue "E ARG 12": "NH1" <-> "NH2" Residue "E PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 43": "OE1" <-> "OE2" Residue "G GLU 117": "OE1" <-> "OE2" Residue "G GLU 174": "OE1" <-> "OE2" Residue "G PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 191": "OD1" <-> "OD2" Residue "G ASP 193": "OD1" <-> "OD2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "H ASP 30": "OD1" <-> "OD2" Residue "H GLU 45": "OE1" <-> "OE2" Residue "H ASP 82": "OD1" <-> "OD2" Residue "H GLU 84": "OE1" <-> "OE2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H ASP 111": "OD1" <-> "OD2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "I ASP 28": "OD1" <-> "OD2" Residue "I GLU 94": "OE1" <-> "OE2" Residue "I TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 146": "OE1" <-> "OE2" Residue "I PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 201": "OE1" <-> "OE2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "K PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 16": "OE1" <-> "OE2" Residue "K ASP 72": "OD1" <-> "OD2" Residue "L GLU 20": "OE1" <-> "OE2" Residue "L TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 122": "OE1" <-> "OE2" Residue "M GLU 41": "OE1" <-> "OE2" Residue "M GLU 42": "OE1" <-> "OE2" Residue "M GLU 46": "OE1" <-> "OE2" Residue "M ASP 47": "OD1" <-> "OD2" Residue "M GLU 57": "OE1" <-> "OE2" Residue "M GLU 123": "OE1" <-> "OE2" Residue "N GLU 52": "OE1" <-> "OE2" Residue "N ASP 55": "OD1" <-> "OD2" Residue "N GLU 91": "OE1" <-> "OE2" Residue "N GLU 111": "OE1" <-> "OE2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "O GLU 24": "OE1" <-> "OE2" Residue "O ASP 60": "OD1" <-> "OD2" Residue "O ASP 63": "OD1" <-> "OD2" Residue "O ASP 97": "OD1" <-> "OD2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 69": "OE1" <-> "OE2" Residue "R TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 40": "OE1" <-> "OE2" Residue "S GLU 91": "OE1" <-> "OE2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 45": "OE1" <-> "OE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "W GLU 19": "OE1" <-> "OE2" Residue "W ASP 21": "OD1" <-> "OD2" Residue "W GLU 34": "OE1" <-> "OE2" Residue "X GLU 23": "OE1" <-> "OE2" Residue "X PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 64": "OE1" <-> "OE2" Residue "Y ASP 42": "OD1" <-> "OD2" Residue "Y GLU 52": "OE1" <-> "OE2" Residue "Z GLU 62": "OE1" <-> "OE2" Residue "Z ARG 66": "NH1" <-> "NH2" Residue "a ARG 7": "NH1" <-> "NH2" Residue "a ARG 12": "NH1" <-> "NH2" Residue "a GLU 40": "OE1" <-> "OE2" Residue "a ARG 162": "NH1" <-> "NH2" Residue "a TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 149080 Number of models: 1 Model: "" Number of chains: 57 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: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "j" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "k" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "l" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "m" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "n" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 961 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "o" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "p" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "r" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "s" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "t" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 739 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "u" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "v" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "w" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "x" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "A" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} 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: "4" Number of atoms: 65057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3031, 65057 Classifications: {'RNA': 3031} Modifications used: {'5*END': 1, 'rna2p_pur': 222, 'rna2p_pyr': 106, 'rna3p_pur': 1520, 'rna3p_pyr': 1183} Link IDs: {'rna2p': 328, 'rna3p': 2702} 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: "1" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 213 Classifications: {'RNA': 10} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "7" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1619 Classifications: {'RNA': 76} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 33, 'rna3p_pyr': 31} Link IDs: {'rna2p': 12, 'rna3p': 63} Time building chain proxies: 60.13, per 1000 atoms: 0.40 Number of scatterers: 149080 At special positions: 0 Unit cell: (276.66, 265.35, 241.86, 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 159 16.00 P 4729 15.00 O 41384 8.00 N 27750 7.00 C 75058 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 64.16 Conformation dependent library (CDL) restraints added in 7.1 seconds 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11194 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 78 sheets defined 34.6% alpha, 16.7% beta 1418 base pairs and 2770 stacking pairs defined. Time for finding SS restraints: 56.63 Creating SS restraints... Processing helix chain 'b' and resid 29 through 31 No H-bonds generated for 'chain 'b' and resid 29 through 31' Processing helix chain 'b' and resid 198 through 202 Processing helix chain 'b' and resid 206 through 212 removed outlier: 3.953A pdb=" N ALA b 210 " --> pdb=" O LYS b 206 " (cutoff:3.500A) Processing helix chain 'b' and resid 220 through 224 Processing helix chain 'b' and resid 262 through 264 No H-bonds generated for 'chain 'b' and resid 262 through 264' Processing helix chain 'c' and resid 61 through 72 Processing helix chain 'c' and resid 97 through 102 removed outlier: 3.545A pdb=" N LEU c 100 " --> pdb=" O SER c 97 " (cutoff:3.500A) Processing helix chain 'c' and resid 120 through 126 Processing helix chain 'd' and resid 15 through 20 Processing helix chain 'd' and resid 24 through 40 removed outlier: 3.669A pdb=" N ARG d 40 " --> pdb=" O ALA d 36 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 115 removed outlier: 3.669A pdb=" N ARG d 114 " --> pdb=" O SER d 110 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 140 removed outlier: 3.669A pdb=" N LEU d 134 " --> pdb=" O LYS d 130 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 161 Processing helix chain 'd' and resid 173 through 175 No H-bonds generated for 'chain 'd' and resid 173 through 175' Processing helix chain 'd' and resid 176 through 183 removed outlier: 3.681A pdb=" N PHE d 183 " --> pdb=" O SER d 179 " (cutoff:3.500A) Processing helix chain 'd' and resid 190 through 200 Processing helix chain 'e' and resid 2 through 8 Processing helix chain 'e' and resid 9 through 17 removed outlier: 3.651A pdb=" N LYS e 13 " --> pdb=" O ASP e 9 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR e 17 " --> pdb=" O LYS e 13 " (cutoff:3.500A) Processing helix chain 'e' and resid 23 through 27 removed outlier: 3.797A pdb=" N VAL e 27 " --> pdb=" O VAL e 24 " (cutoff:3.500A) Processing helix chain 'e' and resid 40 through 44 removed outlier: 3.957A pdb=" N ILE e 43 " --> pdb=" O GLY e 40 " (cutoff:3.500A) Processing helix chain 'e' and resid 45 through 60 removed outlier: 3.676A pdb=" N LEU e 49 " --> pdb=" O ASP e 45 " (cutoff:3.500A) Processing helix chain 'e' and resid 92 through 104 Processing helix chain 'e' and resid 106 through 110 Processing helix chain 'e' and resid 133 through 137 removed outlier: 4.165A pdb=" N ILE e 136 " --> pdb=" O GLU e 133 " (cutoff:3.500A) Processing helix chain 'e' and resid 161 through 172 removed outlier: 3.790A pdb=" N PHE e 172 " --> pdb=" O LEU e 168 " (cutoff:3.500A) Processing helix chain 'f' and resid 2 through 6 removed outlier: 3.582A pdb=" N ALA f 6 " --> pdb=" O ARG f 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 2 through 6' Processing helix chain 'f' and resid 59 through 80 Processing helix chain 'f' and resid 136 through 151 removed outlier: 4.245A pdb=" N ARG f 151 " --> pdb=" O LEU f 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 29 Processing helix chain 'g' and resid 40 through 49 removed outlier: 3.534A pdb=" N PHE g 46 " --> pdb=" O LYS g 42 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA g 49 " --> pdb=" O GLU g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 55 through 71 removed outlier: 3.802A pdb=" N ALA g 59 " --> pdb=" O GLU g 55 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU g 60 " --> pdb=" O ALA g 56 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU g 70 " --> pdb=" O ASN g 66 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS g 71 " --> pdb=" O ALA g 67 " (cutoff:3.500A) Processing helix chain 'g' and resid 95 through 104 removed outlier: 4.144A pdb=" N ILE g 99 " --> pdb=" O GLY g 95 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP g 101 " --> pdb=" O ARG g 97 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA g 102 " --> pdb=" O ASP g 98 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR g 104 " --> pdb=" O ALA g 100 " (cutoff:3.500A) Processing helix chain 'g' and resid 111 through 113 No H-bonds generated for 'chain 'g' and resid 111 through 113' Processing helix chain 'h' and resid 3 through 20 removed outlier: 3.642A pdb=" N GLN h 9 " --> pdb=" O LEU h 5 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU h 17 " --> pdb=" O ALA h 13 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS h 20 " --> pdb=" O SER h 16 " (cutoff:3.500A) Processing helix chain 'h' and resid 33 through 48 removed outlier: 3.868A pdb=" N THR h 39 " --> pdb=" O VAL h 35 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG h 42 " --> pdb=" O MET h 38 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA h 44 " --> pdb=" O GLU h 40 " (cutoff:3.500A) Processing helix chain 'h' and resid 62 through 67 removed outlier: 3.777A pdb=" N THR h 67 " --> pdb=" O ALA h 63 " (cutoff:3.500A) Processing helix chain 'h' and resid 73 through 78 removed outlier: 4.089A pdb=" N PHE h 76 " --> pdb=" O LYS h 73 " (cutoff:3.500A) Processing helix chain 'h' and resid 97 through 105 removed outlier: 4.143A pdb=" N LYS h 101 " --> pdb=" O LYS h 97 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA h 102 " --> pdb=" O GLU h 98 " (cutoff:3.500A) Processing helix chain 'i' and resid 26 through 30 Processing helix chain 'i' and resid 34 through 42 removed outlier: 3.847A pdb=" N LYS i 39 " --> pdb=" O MET i 35 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA i 40 " --> pdb=" O GLU i 36 " (cutoff:3.500A) Processing helix chain 'i' and resid 74 through 84 removed outlier: 3.543A pdb=" N ALA i 83 " --> pdb=" O LEU i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 101 through 114 removed outlier: 3.608A pdb=" N ILE i 108 " --> pdb=" O GLN i 104 " (cutoff:3.500A) Processing helix chain 'i' and resid 120 through 136 removed outlier: 3.659A pdb=" N MET i 124 " --> pdb=" O ASP i 120 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR i 125 " --> pdb=" O ILE i 121 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG i 126 " --> pdb=" O GLU i 122 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER i 127 " --> pdb=" O ALA i 123 " (cutoff:3.500A) Processing helix chain 'j' and resid 7 through 11 removed outlier: 3.767A pdb=" N VAL j 11 " --> pdb=" O PRO j 8 " (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 98 through 107 Processing helix chain 'j' and resid 112 through 118 Processing helix chain 'j' and resid 132 through 136 Processing helix chain 'k' and resid 104 through 108 Processing helix chain 'k' and resid 112 through 119 Processing helix chain 'l' and resid 56 through 60 Processing helix chain 'l' and resid 80 through 83 removed outlier: 3.913A pdb=" N ALA l 83 " --> pdb=" O SER l 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 80 through 83' Processing helix chain 'l' and resid 91 through 96 removed outlier: 4.152A pdb=" N LEU l 95 " --> pdb=" O ASP l 91 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS l 96 " --> pdb=" O LEU l 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 91 through 96' Processing helix chain 'l' and resid 128 through 138 removed outlier: 3.523A pdb=" N ALA l 138 " --> pdb=" O ALA l 134 " (cutoff:3.500A) Processing helix chain 'm' and resid 43 through 57 removed outlier: 3.636A pdb=" N ALA m 56 " --> pdb=" O ALA m 52 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 122 removed outlier: 3.621A pdb=" N LYS m 118 " --> pdb=" O ARG m 114 " (cutoff:3.500A) Processing helix chain 'n' and resid 13 through 32 Processing helix chain 'n' and resid 38 through 55 removed outlier: 3.522A pdb=" N ARG n 45 " --> pdb=" O ALA n 41 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Proline residue: n 50 - end of helix Processing helix chain 'n' and resid 59 through 69 removed outlier: 3.756A pdb=" N ARG n 63 " --> pdb=" O SER n 59 " (cutoff:3.500A) Processing helix chain 'n' and resid 72 through 79 Processing helix chain 'n' and resid 82 through 87 Processing helix chain 'o' and resid 3 through 19 removed outlier: 4.666A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 60 Processing helix chain 'o' and resid 67 through 83 Processing helix chain 'o' and resid 101 through 112 Processing helix chain 'p' and resid 2 through 10 Processing helix chain 'p' and resid 52 through 55 Processing helix chain 'p' and resid 96 through 101 removed outlier: 3.896A pdb=" N GLU p 101 " --> pdb=" O TYR p 98 " (cutoff:3.500A) Processing helix chain 'p' and resid 103 through 108 removed outlier: 3.501A pdb=" N ARG p 108 " --> pdb=" O LYS p 105 " (cutoff:3.500A) Processing helix chain 'q' and resid 6 through 18 Processing helix chain 'q' and resid 24 through 29 removed outlier: 3.777A pdb=" N SER q 28 " --> pdb=" O GLY q 25 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG q 29 " --> pdb=" O ALA q 26 " (cutoff:3.500A) Processing helix chain 'q' and resid 30 through 71 removed outlier: 3.623A pdb=" N GLN q 36 " --> pdb=" O ARG q 32 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ARG q 50 " --> pdb=" O TYR q 46 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LYS q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG q 57 " --> pdb=" O LYS q 53 " (cutoff:3.500A) Processing helix chain 'q' and resid 75 through 85 Processing helix chain 'q' and resid 90 through 101 Processing helix chain 'q' and resid 101 through 117 Processing helix chain 's' and resid 13 through 22 removed outlier: 3.549A pdb=" N VAL s 17 " --> pdb=" O SER s 13 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 37 removed outlier: 3.573A pdb=" N ASP s 34 " --> pdb=" O SER s 30 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 62 Processing helix chain 's' and resid 89 through 91 No H-bonds generated for 'chain 's' and resid 89 through 91' Processing helix chain 't' and resid 2 through 10 removed outlier: 3.566A pdb=" N LEU t 8 " --> pdb=" O GLU t 4 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS t 9 " --> pdb=" O GLU t 5 " (cutoff:3.500A) Processing helix chain 't' and resid 17 through 28 Processing helix chain 't' and resid 39 through 51 Processing helix chain 'v' and resid 13 through 22 removed outlier: 3.565A pdb=" N ALA v 22 " --> pdb=" O ARG v 18 " (cutoff:3.500A) Processing helix chain 'v' and resid 44 through 51 Processing helix chain 'v' and resid 53 through 58 removed outlier: 3.540A pdb=" N TYR v 57 " --> pdb=" O ALA v 54 " (cutoff:3.500A) Processing helix chain 'x' and resid 51 through 62 Processing helix chain 'x' and resid 62 through 74 Processing helix chain 'y' and resid 2 through 6 removed outlier: 3.502A pdb=" N LEU y 6 " --> pdb=" O LYS y 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 2 through 6' Processing helix chain 'y' and resid 9 through 23 removed outlier: 3.613A pdb=" N THR y 16 " --> pdb=" O GLU y 12 " (cutoff:3.500A) Processing helix chain 'y' and resid 24 through 34 removed outlier: 3.742A pdb=" N ARG y 29 " --> pdb=" O GLN y 25 " (cutoff:3.500A) Processing helix chain 'y' and resid 40 through 61 removed outlier: 4.038A pdb=" N LYS y 44 " --> pdb=" O SER y 40 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 27 Processing helix chain 'z' and resid 40 through 50 Processing helix chain 'A' and resid 56 through 65 removed outlier: 4.250A pdb=" N ARG A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 16 Processing helix chain 'B' and resid 17 through 19 No H-bonds generated for 'chain 'B' and resid 17 through 19' Processing helix chain 'D' and resid 8 through 17 Processing helix chain 'D' and resid 17 through 23 Processing helix chain 'D' and resid 24 through 38 Processing helix chain 'E' and resid 6 through 11 Processing helix chain 'E' and resid 36 through 43 Processing helix chain 'E' and resid 53 through 61 Processing helix chain 'F' and resid 18 through 22 removed outlier: 3.644A pdb=" N GLY F 21 " --> pdb=" O LYS F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 34 Processing helix chain 'G' and resid 7 through 12 removed outlier: 4.017A pdb=" N GLY G 12 " --> pdb=" O MET G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 27 removed outlier: 3.700A pdb=" N LYS G 27 " --> pdb=" O PRO G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 44 removed outlier: 3.743A pdb=" N LYS G 44 " --> pdb=" O ASN G 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 41 through 44' Processing helix chain 'G' and resid 45 through 62 Processing helix chain 'G' and resid 72 through 74 No H-bonds generated for 'chain 'G' and resid 72 through 74' Processing helix chain 'G' and resid 75 through 85 removed outlier: 3.507A pdb=" N SER G 85 " --> pdb=" O ASP G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 123 removed outlier: 4.586A pdb=" N GLN G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN G 119 " --> pdb=" O ASP G 115 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP G 122 " --> pdb=" O THR G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 147 Processing helix chain 'G' and resid 148 through 151 Processing helix chain 'G' and resid 168 through 178 removed outlier: 3.656A pdb=" N ILE G 172 " --> pdb=" O GLU G 168 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN G 177 " --> pdb=" O LYS G 173 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU G 178 " --> pdb=" O GLU G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 224 removed outlier: 3.550A pdb=" N THR G 210 " --> pdb=" O ILE G 206 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 12 removed outlier: 4.364A pdb=" N GLY H 12 " --> pdb=" O ILE H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 45 removed outlier: 4.212A pdb=" N ALA H 29 " --> pdb=" O THR H 25 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ASP H 30 " --> pdb=" O LYS H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 77 removed outlier: 3.551A pdb=" N VAL H 75 " --> pdb=" O ARG H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 95 removed outlier: 3.595A pdb=" N ALA H 91 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP H 92 " --> pdb=" O LYS H 88 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE H 93 " --> pdb=" O VAL H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 110 Processing helix chain 'H' and resid 111 through 124 removed outlier: 3.592A pdb=" N GLN H 122 " --> pdb=" O SER H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 143 Processing helix chain 'I' and resid 8 through 15 Processing helix chain 'I' and resid 48 through 65 Processing helix chain 'I' and resid 67 through 80 Processing helix chain 'I' and resid 84 through 95 removed outlier: 3.833A pdb=" N LEU I 90 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU I 94 " --> pdb=" O LEU I 90 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY I 95 " --> pdb=" O ALA I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 103 removed outlier: 3.525A pdb=" N TYR I 102 " --> pdb=" O ASP I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 118 Processing helix chain 'I' and resid 146 through 149 Processing helix chain 'I' and resid 152 through 163 removed outlier: 4.046A pdb=" N ALA I 156 " --> pdb=" O SER I 152 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU I 159 " --> pdb=" O LYS I 155 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA I 161 " --> pdb=" O ALA I 157 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 190 Processing helix chain 'I' and resid 195 through 205 removed outlier: 4.234A pdb=" N ILE I 199 " --> pdb=" O ASN I 195 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR I 203 " --> pdb=" O ILE I 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 69 removed outlier: 3.544A pdb=" N GLN J 60 " --> pdb=" O PRO J 56 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS J 65 " --> pdb=" O LYS J 61 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG J 68 " --> pdb=" O GLU J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 118 Processing helix chain 'J' and resid 131 through 146 removed outlier: 3.502A pdb=" N MET J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 156 removed outlier: 4.230A pdb=" N ALA J 154 " --> pdb=" O GLU J 150 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS J 155 " --> pdb=" O MET J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 165 Processing helix chain 'K' and resid 12 through 16 Processing helix chain 'K' and resid 17 through 31 Processing helix chain 'K' and resid 50 through 54 removed outlier: 3.798A pdb=" N LYS K 53 " --> pdb=" O PRO K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 81 removed outlier: 3.683A pdb=" N ILE K 71 " --> pdb=" O PRO K 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 30 Processing helix chain 'L' and resid 34 through 54 Processing helix chain 'L' and resid 57 through 63 Processing helix chain 'L' and resid 91 through 108 removed outlier: 3.616A pdb=" N ASN L 96 " --> pdb=" O PRO L 92 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA L 97 " --> pdb=" O VAL L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 127 Processing helix chain 'L' and resid 131 through 145 Processing helix chain 'M' and resid 4 through 19 Processing helix chain 'M' and resid 29 through 42 Processing helix chain 'M' and resid 112 through 119 removed outlier: 3.929A pdb=" N GLN M 117 " --> pdb=" O ARG M 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 38 Processing helix chain 'N' and resid 48 through 53 removed outlier: 4.018A pdb=" N LEU N 53 " --> pdb=" O GLN N 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 86 Processing helix chain 'O' and resid 14 through 32 removed outlier: 4.954A pdb=" N GLN O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA O 21 " --> pdb=" O LEU O 17 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA O 23 " --> pdb=" O ASP O 19 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU O 24 " --> pdb=" O GLN O 20 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA O 29 " --> pdb=" O ILE O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 86 removed outlier: 3.848A pdb=" N ASP O 85 " --> pdb=" O LYS O 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 57 Processing helix chain 'P' and resid 58 through 69 Processing helix chain 'P' and resid 91 through 101 removed outlier: 3.670A pdb=" N ILE P 96 " --> pdb=" O ARG P 92 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ARG P 97 " --> pdb=" O GLU P 93 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA P 98 " --> pdb=" O SER P 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 9 Processing helix chain 'R' and resid 13 through 19 Processing helix chain 'R' and resid 26 through 37 Processing helix chain 'R' and resid 48 through 60 removed outlier: 4.365A pdb=" N THR R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA R 60 " --> pdb=" O ARG R 56 " (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 Processing helix chain 'S' and resid 2 through 15 removed outlier: 3.658A pdb=" N LYS S 6 " --> pdb=" O LYS S 2 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 18 No H-bonds generated for 'chain 'S' and resid 16 through 18' Processing helix chain 'S' and resid 24 through 29 Processing helix chain 'S' and resid 37 through 48 removed outlier: 3.716A pdb=" N GLN S 48 " --> pdb=" O VAL S 44 " (cutoff:3.500A) Processing helix chain 'S' and resid 55 through 59 Processing helix chain 'S' and resid 79 through 90 removed outlier: 3.549A pdb=" N GLU S 85 " --> pdb=" O ILE S 81 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG S 89 " --> pdb=" O GLU S 85 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 15 Processing helix chain 'T' and resid 23 through 39 Processing helix chain 'T' and resid 48 through 73 removed outlier: 3.574A pdb=" N GLY T 54 " --> pdb=" O HIS T 50 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 85 removed outlier: 3.600A pdb=" N GLU T 82 " --> pdb=" O THR T 78 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 62 Processing helix chain 'U' and resid 68 through 78 removed outlier: 3.564A pdb=" N ALA U 72 " --> pdb=" O SER U 68 " (cutoff:3.500A) Processing helix chain 'W' and resid 24 through 29 Processing helix chain 'W' and resid 30 through 32 No H-bonds generated for 'chain 'W' and resid 30 through 32' Processing helix chain 'W' and resid 47 through 64 Processing helix chain 'X' and resid 11 through 23 Processing helix chain 'X' and resid 40 through 44 Processing helix chain 'X' and resid 69 through 74 Processing helix chain 'Y' and resid 4 through 6 No H-bonds generated for 'chain 'Y' and resid 4 through 6' Processing helix chain 'Y' and resid 7 through 41 removed outlier: 3.705A pdb=" N ILE Y 11 " --> pdb=" O LYS Y 7 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 63 Proline residue: Y 55 - end of helix Processing helix chain 'Y' and resid 68 through 83 Processing helix chain 'Z' and resid 18 through 23 removed outlier: 3.516A pdb=" N CYS Z 22 " --> pdb=" O PHE Z 18 " (cutoff:3.500A) Processing helix chain 'Z' and resid 23 through 29 Processing helix chain 'Z' and resid 38 through 60 removed outlier: 3.562A pdb=" N THR Z 42 " --> pdb=" O GLU Z 38 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS Z 58 " --> pdb=" O ARG Z 54 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU Z 59 " --> pdb=" O HIS Z 55 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 15 removed outlier: 3.853A pdb=" N ILE a 11 " --> pdb=" O ARG a 7 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG a 12 " --> pdb=" O MET a 8 " (cutoff:3.500A) Processing helix chain 'a' and resid 22 through 34 removed outlier: 3.690A pdb=" N ALA a 26 " --> pdb=" O ASP a 22 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE a 27 " --> pdb=" O ILE a 23 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ALA a 28 " --> pdb=" O ASN a 24 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LYS a 31 " --> pdb=" O ILE a 27 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU a 32 " --> pdb=" O ALA a 28 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA a 34 " --> pdb=" O LEU a 30 " (cutoff:3.500A) Processing helix chain 'a' and resid 54 through 58 removed outlier: 3.588A pdb=" N GLN a 57 " --> pdb=" O LYS a 54 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN a 58 " --> pdb=" O SER a 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 54 through 58' Processing helix chain 'a' and resid 181 through 199 removed outlier: 3.540A pdb=" N LEU a 192 " --> pdb=" O ASN a 188 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA a 195 " --> pdb=" O ALA a 191 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'b' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'b' and resid 33 through 36 removed outlier: 4.159A pdb=" N ASN b 36 " --> pdb=" O GLN b 59 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLN b 59 " --> pdb=" O ASN b 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'b' and resid 100 through 104 removed outlier: 6.283A pdb=" N LEU b 94 " --> pdb=" O VAL b 77 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N VAL b 77 " --> pdb=" O LEU b 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'b' and resid 128 through 130 removed outlier: 6.135A pdb=" N ILE b 163 " --> pdb=" O ARG b 174 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG b 174 " --> pdb=" O ILE b 163 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA b 165 " --> pdb=" O THR b 172 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS b 182 " --> pdb=" O ILE b 266 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE b 266 " --> pdb=" O LYS b 182 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'c' and resid 4 through 15 removed outlier: 5.849A pdb=" N LYS c 8 " --> pdb=" O GLU c 28 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLU c 28 " --> pdb=" O LYS c 8 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY c 10 " --> pdb=" O VAL c 26 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU c 186 " --> pdb=" O VAL c 180 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL c 180 " --> pdb=" O LEU c 186 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU c 188 " --> pdb=" O VAL c 178 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASP c 176 " --> pdb=" O LYS c 190 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N THR c 171 " --> pdb=" O GLY c 111 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N GLY c 111 " --> pdb=" O THR c 171 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N GLN c 173 " --> pdb=" O VAL c 109 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL c 109 " --> pdb=" O GLN c 173 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N THR c 112 " --> pdb=" O ASP c 200 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASP c 200 " --> pdb=" O THR c 112 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'c' and resid 80 through 83 removed outlier: 6.472A pdb=" N THR c 51 " --> pdb=" O VAL c 34 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N VAL c 34 " --> pdb=" O THR c 51 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'c' and resid 117 through 119 Processing sheet with id=AA8, first strand: chain 'd' and resid 2 through 4 Processing sheet with id=AA9, first strand: chain 'd' and resid 118 through 121 removed outlier: 6.199A pdb=" N ILE d 119 " --> pdb=" O MET d 188 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'd' and resid 147 through 150 Processing sheet with id=AB2, first strand: chain 'e' and resid 65 through 68 removed outlier: 3.546A pdb=" N GLY e 85 " --> pdb=" O THR e 67 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'e' and resid 65 through 68 removed outlier: 3.546A pdb=" N GLY e 85 " --> pdb=" O THR e 67 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU e 151 " --> pdb=" O VAL e 131 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'f' and resid 8 through 9 Processing sheet with id=AB5, first strand: chain 'f' and resid 15 through 19 Processing sheet with id=AB6, first strand: chain 'f' and resid 122 through 126 removed outlier: 7.156A pdb=" N GLU f 129 " --> pdb=" O PRO f 125 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'f' and resid 94 through 98 Processing sheet with id=AB8, first strand: chain 'g' and resid 19 through 20 removed outlier: 3.678A pdb=" N VAL g 19 " --> pdb=" O VAL g 3 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'g' and resid 77 through 80 removed outlier: 6.706A pdb=" N VAL g 78 " --> pdb=" O ASN g 145 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL g 144 " --> pdb=" O HIS g 128 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N HIS g 128 " --> pdb=" O VAL g 144 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER g 131 " --> pdb=" O ARG g 116 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG g 116 " --> pdb=" O SER g 131 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'h' and resid 23 through 24 removed outlier: 4.080A pdb=" N LEU h 23 " --> pdb=" O GLU h 87 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'i' and resid 8 through 10 Processing sheet with id=AC3, first strand: chain 'i' and resid 99 through 100 Processing sheet with id=AC4, first strand: chain 'j' and resid 122 through 124 removed outlier: 6.686A pdb=" N ILE j 54 " --> pdb=" O LYS j 123 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N TYR j 16 " --> pdb=" O ILE j 55 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU j 57 " --> pdb=" O TYR j 16 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL j 18 " --> pdb=" O LEU j 57 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN j 138 " --> pdb=" O TRP j 15 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'j' and resid 74 through 77 Processing sheet with id=AC6, first strand: chain 'k' and resid 7 through 10 removed outlier: 3.769A pdb=" N VAL k 10 " --> pdb=" O ARG k 17 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ARG k 17 " --> pdb=" O VAL k 10 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA k 16 " --> pdb=" O ALA k 46 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ALA k 46 " --> pdb=" O ALA k 16 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG k 18 " --> pdb=" O LYS k 44 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LYS k 40 " --> pdb=" O ILE k 22 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL k 24 " --> pdb=" O ILE k 38 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ILE k 38 " --> pdb=" O VAL k 24 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS k 59 " --> pdb=" O LEU k 87 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA k 83 " --> pdb=" O VAL k 63 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N CYS k 84 " --> pdb=" O MET k 7 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASN k 9 " --> pdb=" O CYS k 84 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N LEU k 86 " --> pdb=" O ASN k 9 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'k' and resid 69 through 70 removed outlier: 4.052A pdb=" N VAL k 76 " --> pdb=" O VAL p 72 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA p 48 " --> pdb=" O THR p 59 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARG p 61 " --> pdb=" O VAL p 46 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL p 46 " --> pdb=" O ARG p 61 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N ILE p 63 " --> pdb=" O GLY p 44 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N GLY p 44 " --> pdb=" O ILE p 63 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N THR p 24 " --> pdb=" O LYS p 86 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER p 84 " --> pdb=" O GLU p 26 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N TRP p 30 " --> pdb=" O VAL p 80 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL p 80 " --> pdb=" O TRP p 30 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'l' and resid 74 through 78 Processing sheet with id=AC9, first strand: chain 'l' and resid 89 through 90 Processing sheet with id=AD1, first strand: chain 'm' and resid 62 through 65 removed outlier: 6.253A pdb=" N VAL m 101 " --> pdb=" O ALA m 35 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA m 35 " --> pdb=" O VAL m 101 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR m 103 " --> pdb=" O LEU m 33 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'm' and resid 39 through 42 removed outlier: 5.286A pdb=" N VAL m 89 " --> pdb=" O GLU m 75 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLU m 75 " --> pdb=" O VAL m 89 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'n' and resid 33 through 37 removed outlier: 6.899A pdb=" N MET n 110 " --> pdb=" O CYS n 100 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'o' and resid 47 through 52 removed outlier: 3.577A pdb=" N VAL o 49 " --> pdb=" O VAL o 39 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS o 34 " --> pdb=" O THR o 31 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'r' and resid 11 through 15 removed outlier: 6.937A pdb=" N TYR r 2 " --> pdb=" O ILE r 41 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ILE r 41 " --> pdb=" O TYR r 2 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL r 4 " --> pdb=" O LEU r 39 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'r' and resid 19 through 22 removed outlier: 6.139A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'r' and resid 72 through 78 removed outlier: 4.196A pdb=" N TYR r 83 " --> pdb=" O ARG r 78 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 's' and resid 4 through 10 removed outlier: 5.860A pdb=" N ILE s 4 " --> pdb=" O VAL s 107 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL s 107 " --> pdb=" O ILE s 4 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LYS s 6 " --> pdb=" O VAL s 105 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL s 105 " --> pdb=" O LYS s 6 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ARG s 8 " --> pdb=" O ILE s 103 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE s 103 " --> pdb=" O ARG s 8 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LYS s 98 " --> pdb=" O PRO s 80 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N THR s 100 " --> pdb=" O GLU s 78 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N GLU s 78 " --> pdb=" O THR s 100 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N HIS s 102 " --> pdb=" O VAL s 76 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL s 76 " --> pdb=" O HIS s 102 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR s 104 " --> pdb=" O ILE s 74 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILE s 74 " --> pdb=" O THR s 104 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL s 106 " --> pdb=" O THR s 72 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 's' and resid 86 through 87 Processing sheet with id=AE1, first strand: chain 't' and resid 11 through 14 removed outlier: 4.350A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 't' and resid 69 through 70 Processing sheet with id=AE3, first strand: chain 'u' and resid 64 through 65 removed outlier: 3.776A pdb=" N ASN u 26 " --> pdb=" O ILE u 34 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'u' and resid 40 through 44 Processing sheet with id=AE5, first strand: chain 'u' and resid 82 through 86 Processing sheet with id=AE6, first strand: chain 'v' and resid 3 through 5 removed outlier: 5.660A pdb=" N ALA v 74 " --> pdb=" O VAL v 92 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL v 92 " --> pdb=" O ALA v 74 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS v 88 " --> pdb=" O GLN v 78 " (cutoff:3.500A) removed outlier: 8.903A pdb=" N LYS v 25 " --> pdb=" O GLN v 87 " (cutoff:3.500A) removed outlier: 9.826A pdb=" N ILE v 89 " --> pdb=" O LYS v 25 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N PHE v 91 " --> pdb=" O PRO v 27 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ILE v 29 " --> pdb=" O PHE v 91 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ARG v 93 " --> pdb=" O ILE v 29 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR v 31 " --> pdb=" O ARG v 93 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLY v 32 " --> pdb=" O ALA v 36 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ALA v 36 " --> pdb=" O GLY v 32 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'w' and resid 18 through 19 removed outlier: 7.023A pdb=" N LEU w 55 " --> pdb=" O ILE w 33 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'w' and resid 26 through 27 Processing sheet with id=AE9, first strand: chain 'x' and resid 12 through 15 Processing sheet with id=AF1, first strand: chain 'x' and resid 33 through 39 Processing sheet with id=AF2, first strand: chain 'z' and resid 34 through 38 Processing sheet with id=AF3, first strand: chain 'A' and resid 22 through 26 removed outlier: 8.899A pdb=" N LEU A 32 " --> pdb=" O GLU A 11 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N THR A 13 " --> pdb=" O LEU A 32 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 27 through 29 Processing sheet with id=AF5, first strand: chain 'C' and resid 19 through 24 removed outlier: 3.680A pdb=" N LEU C 35 " --> pdb=" O TYR C 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 14 through 15 Processing sheet with id=AF7, first strand: chain 'F' and resid 15 through 17 Processing sheet with id=AF8, first strand: chain 'G' and resid 66 through 69 removed outlier: 6.914A pdb=" N VAL G 182 " --> pdb=" O PHE G 197 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE G 199 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA G 184 " --> pdb=" O ILE G 199 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 19 through 20 removed outlier: 6.759A pdb=" N HIS H 68 " --> pdb=" O SER H 52 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ILE H 54 " --> pdb=" O THR H 66 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N THR H 66 " --> pdb=" O ILE H 54 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ILE H 56 " --> pdb=" O ARG H 64 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ARG H 64 " --> pdb=" O ILE H 56 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE H 63 " --> pdb=" O GLN H 99 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ASN H 101 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N VAL H 65 " --> pdb=" O ASN H 101 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA H 103 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE H 67 " --> pdb=" O ALA H 103 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 166 through 170 removed outlier: 6.821A pdb=" N ASP H 180 " --> pdb=" O LYS H 203 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 127 through 128 removed outlier: 3.654A pdb=" N MET I 123 " --> pdb=" O SER I 143 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 12 through 14 Processing sheet with id=AG4, first strand: chain 'J' and resid 18 through 21 Processing sheet with id=AG5, first strand: chain 'J' and resid 84 through 85 Processing sheet with id=AG6, first strand: chain 'K' and resid 2 through 3 Processing sheet with id=AG7, first strand: chain 'K' and resid 43 through 45 removed outlier: 6.782A pdb=" N VAL K 7 " --> pdb=" O SER K 87 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N SER K 87 " --> pdb=" O VAL K 7 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 72 through 73 removed outlier: 3.524A pdb=" N GLU L 73 " --> pdb=" O VAL L 88 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 76 through 77 removed outlier: 3.942A pdb=" N ARG L 77 " --> pdb=" O TYR L 84 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR L 84 " --> pdb=" O ARG L 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'M' and resid 23 through 27 Processing sheet with id=AH2, first strand: chain 'M' and resid 73 through 76 Processing sheet with id=AH3, first strand: chain 'M' and resid 73 through 76 removed outlier: 6.793A pdb=" N VAL M 102 " --> pdb=" O ILE M 125 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N TYR M 127 " --> pdb=" O ILE M 100 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE M 100 " --> pdb=" O TYR M 127 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'N' and resid 5 through 7 Processing sheet with id=AH5, first strand: chain 'O' and resid 9 through 12 Processing sheet with id=AH6, first strand: chain 'O' and resid 49 through 52 Processing sheet with id=AH7, first strand: chain 'P' and resid 40 through 44 removed outlier: 3.751A pdb=" N GLY P 42 " --> pdb=" O ILE P 33 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU P 81 " --> pdb=" O ASN P 108 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N THR P 110 " --> pdb=" O LEU P 81 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL P 83 " --> pdb=" O THR P 110 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'Q' and resid 29 through 30 Processing sheet with id=AH9, first strand: chain 'Q' and resid 34 through 39 removed outlier: 4.824A pdb=" N ARG Q 35 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'U' and resid 2 through 11 removed outlier: 3.719A pdb=" N ALA U 7 " --> pdb=" O GLN U 18 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN U 18 " --> pdb=" O ALA U 7 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ASP U 23 " --> pdb=" O PHE U 32 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE U 32 " --> pdb=" O ASP U 23 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'V' and resid 10 through 13 removed outlier: 6.977A pdb=" N VAL V 21 " --> pdb=" O VAL V 12 " (cutoff:3.500A) removed outlier: 13.237A pdb=" N LYS V 42 " --> pdb=" O LYS V 70 " (cutoff:3.500A) removed outlier: 9.119A pdb=" N TRP V 72 " --> pdb=" O LYS V 42 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N HIS V 44 " --> pdb=" O TRP V 72 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU V 74 " --> pdb=" O HIS V 44 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N HIS V 46 " --> pdb=" O LEU V 74 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N ARG V 76 " --> pdb=" O HIS V 46 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLU V 59 " --> pdb=" O VAL V 75 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'V' and resid 26 through 29 Processing sheet with id=AI4, first strand: chain 'X' and resid 31 through 32 removed outlier: 7.730A pdb=" N THR X 32 " --> pdb=" O HIS X 51 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'a' and resid 170 through 177 removed outlier: 6.805A pdb=" N ILE a 170 " --> pdb=" O LEU a 48 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LEU a 48 " --> pdb=" O ILE a 170 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N HIS a 172 " --> pdb=" O VAL a 46 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N VAL a 46 " --> pdb=" O HIS a 172 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N THR a 174 " --> pdb=" O VAL a 44 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL a 44 " --> pdb=" O THR a 174 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLY a 176 " --> pdb=" O VAL a 42 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS a 211 " --> pdb=" O ASN a 47 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL a 212 " --> pdb=" O VAL a 224 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'a' and resid 60 through 62 removed outlier: 3.928A pdb=" N GLY a 61 " --> pdb=" O TYR a 163 " (cutoff:3.500A) 1771 hydrogen bonds defined for protein. 4887 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3543 hydrogen bonds 5750 hydrogen bond angles 0 basepair planarities 1418 basepair parallelities 2770 stacking parallelities Total time for adding SS restraints: 302.09 Time building geometry restraints manager: 69.24 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: 33333 1.34 - 1.47: 66314 1.47 - 1.59: 53204 1.59 - 1.72: 8757 1.72 - 1.84: 284 Bond restraints: 161892 Sorted by residual: bond pdb=" CA VAL J 55 " pdb=" CB VAL J 55 " ideal model delta sigma weight residual 1.534 1.571 -0.037 6.80e-03 2.16e+04 2.94e+01 bond pdb=" CA VAL h 54 " pdb=" CB VAL h 54 " ideal model delta sigma weight residual 1.540 1.582 -0.041 1.36e-02 5.41e+03 9.29e+00 bond pdb=" CA VAL K 18 " pdb=" CB VAL K 18 " ideal model delta sigma weight residual 1.534 1.555 -0.021 6.80e-03 2.16e+04 9.12e+00 bond pdb=" CA PRO i 21 " pdb=" C PRO i 21 " ideal model delta sigma weight residual 1.517 1.545 -0.028 9.30e-03 1.16e+04 8.90e+00 bond pdb=" CA ILE h 118 " pdb=" CB ILE h 118 " ideal model delta sigma weight residual 1.537 1.575 -0.038 1.29e-02 6.01e+03 8.57e+00 ... (remaining 161887 not shown) Histogram of bond angle deviations from ideal: 98.40 - 105.51: 23822 105.51 - 112.62: 89809 112.62 - 119.73: 57559 119.73 - 126.85: 58477 126.85 - 133.96: 12357 Bond angle restraints: 242024 Sorted by residual: angle pdb=" CA GLU Z 23 " pdb=" C GLU Z 23 " pdb=" N LYS Z 24 " ideal model delta sigma weight residual 119.56 113.43 6.13 5.80e-01 2.97e+00 1.12e+02 angle pdb=" N ILE t 2 " pdb=" CA ILE t 2 " pdb=" C ILE t 2 " ideal model delta sigma weight residual 111.88 102.30 9.58 1.06e+00 8.90e-01 8.16e+01 angle pdb=" N ALA S 21 " pdb=" CA ALA S 21 " pdb=" C ALA S 21 " ideal model delta sigma weight residual 114.31 102.84 11.47 1.29e+00 6.01e-01 7.91e+01 angle pdb=" N ARG b 213 " pdb=" CA ARG b 213 " pdb=" C ARG b 213 " ideal model delta sigma weight residual 112.45 100.20 12.25 1.39e+00 5.18e-01 7.77e+01 angle pdb=" N LYS I 30 " pdb=" CA LYS I 30 " pdb=" C LYS I 30 " ideal model delta sigma weight residual 113.61 100.46 13.15 1.50e+00 4.44e-01 7.69e+01 ... (remaining 242019 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 92417 35.88 - 71.76: 10072 71.76 - 107.64: 1245 107.64 - 143.52: 7 143.52 - 179.40: 21 Dihedral angle restraints: 103762 sinusoidal: 86416 harmonic: 17346 Sorted by residual: dihedral pdb=" C4' U 42424 " pdb=" C3' U 42424 " pdb=" C2' U 42424 " pdb=" C1' U 42424 " ideal model delta sinusoidal sigma weight residual -35.00 32.74 -67.74 1 8.00e+00 1.56e-02 9.32e+01 dihedral pdb=" O4' U 4 162 " pdb=" C1' U 4 162 " pdb=" N1 U 4 162 " pdb=" C2 U 4 162 " ideal model delta sinusoidal sigma weight residual 200.00 21.60 178.40 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 42043 " pdb=" C1' U 42043 " pdb=" N1 U 42043 " pdb=" C2 U 42043 " ideal model delta sinusoidal sigma weight residual -160.00 15.28 -175.28 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 103759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 26360 0.110 - 0.221: 4217 0.221 - 0.331: 323 0.331 - 0.442: 26 0.442 - 0.552: 2 Chirality restraints: 30928 Sorted by residual: chirality pdb=" P A 1 13 " pdb=" OP1 A 1 13 " pdb=" OP2 A 1 13 " pdb=" O5' A 1 13 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.62e+00 chirality pdb=" C3' G 41025 " pdb=" C4' G 41025 " pdb=" O3' G 41025 " pdb=" C2' G 41025 " both_signs ideal model delta sigma weight residual False -2.74 -2.23 -0.52 2.00e-01 2.50e+01 6.71e+00 chirality pdb=" C3' A 41020 " pdb=" C4' A 41020 " pdb=" O3' A 41020 " pdb=" C2' A 41020 " both_signs ideal model delta sigma weight residual False -2.74 -2.33 -0.42 2.00e-01 2.50e+01 4.32e+00 ... (remaining 30925 not shown) Planarity restraints: 13097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U 42237 " 0.103 2.00e-02 2.50e+03 5.63e-02 7.13e+01 pdb=" N1 U 42237 " -0.004 2.00e-02 2.50e+03 pdb=" C2 U 42237 " -0.020 2.00e-02 2.50e+03 pdb=" O2 U 42237 " -0.039 2.00e-02 2.50e+03 pdb=" N3 U 42237 " -0.017 2.00e-02 2.50e+03 pdb=" C4 U 42237 " -0.019 2.00e-02 2.50e+03 pdb=" O4 U 42237 " 0.100 2.00e-02 2.50e+03 pdb=" C5 U 42237 " -0.055 2.00e-02 2.50e+03 pdb=" C6 U 42237 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 4 775 " 0.099 2.00e-02 2.50e+03 4.28e-02 5.50e+01 pdb=" N9 G 4 775 " -0.004 2.00e-02 2.50e+03 pdb=" C8 G 4 775 " -0.047 2.00e-02 2.50e+03 pdb=" N7 G 4 775 " -0.047 2.00e-02 2.50e+03 pdb=" C5 G 4 775 " -0.021 2.00e-02 2.50e+03 pdb=" C6 G 4 775 " 0.019 2.00e-02 2.50e+03 pdb=" O6 G 4 775 " 0.069 2.00e-02 2.50e+03 pdb=" N1 G 4 775 " 0.014 2.00e-02 2.50e+03 pdb=" C2 G 4 775 " -0.009 2.00e-02 2.50e+03 pdb=" N2 G 4 775 " -0.029 2.00e-02 2.50e+03 pdb=" N3 G 4 775 " -0.018 2.00e-02 2.50e+03 pdb=" C4 G 4 775 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 41456 " -0.099 2.00e-02 2.50e+03 4.42e-02 5.38e+01 pdb=" N9 A 41456 " 0.004 2.00e-02 2.50e+03 pdb=" C8 A 41456 " 0.041 2.00e-02 2.50e+03 pdb=" N7 A 41456 " 0.040 2.00e-02 2.50e+03 pdb=" C5 A 41456 " 0.020 2.00e-02 2.50e+03 pdb=" C6 A 41456 " -0.014 2.00e-02 2.50e+03 pdb=" N6 A 41456 " -0.075 2.00e-02 2.50e+03 pdb=" N1 A 41456 " 0.000 2.00e-02 2.50e+03 pdb=" C2 A 41456 " 0.023 2.00e-02 2.50e+03 pdb=" N3 A 41456 " 0.030 2.00e-02 2.50e+03 pdb=" C4 A 41456 " 0.028 2.00e-02 2.50e+03 ... (remaining 13094 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 432 2.56 - 3.15: 109279 3.15 - 3.73: 275913 3.73 - 4.32: 404853 4.32 - 4.90: 551014 Nonbonded interactions: 1341491 Sorted by model distance: nonbonded pdb=" O2' A 41154 " pdb=" OP1 A 41155 " model vdw 1.975 2.440 nonbonded pdb=" OP1 A 41155 " pdb=" O3' A 41155 " model vdw 2.006 3.040 nonbonded pdb=" O HIS G 14 " pdb=" O PHE G 15 " model vdw 2.019 3.040 nonbonded pdb=" O ALA o 105 " pdb=" OD1 ASP o 108 " model vdw 2.215 3.040 nonbonded pdb=" O GLU y 12 " pdb=" OD1 ASN y 15 " model vdw 2.247 3.040 ... (remaining 1341486 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 19.050 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: 0.180 Extract box with map and model: 50.440 Check model and map are aligned: 1.690 Set scattering table: 1.100 Process input model: 593.460 Find NCS groups from input model: 3.210 Set up NCS constraints: 0.430 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 672.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 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 : 0.007 0.053 161892 Z= 0.421 Angle : 0.961 13.727 242024 Z= 0.639 Chirality : 0.081 0.552 30928 Planarity : 0.008 0.069 13097 Dihedral : 22.327 179.395 92568 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 1.96 % Allowed : 11.48 % Favored : 86.56 % Rotamer: Outliers : 0.77 % Allowed : 6.85 % Favored : 92.39 % 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: -4.63 (0.09), residues: 5983 helix: -2.90 (0.09), residues: 1819 sheet: -2.98 (0.14), residues: 1064 loop : -3.23 (0.09), residues: 3100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.006 TRP b 247 HIS 0.002 0.000 HIS b 242 PHE 0.028 0.005 PHE e 176 TYR 0.060 0.007 TYR W 31 ARG 0.007 0.001 ARG U 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1813 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 1775 time to evaluate : 6.785 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: c 108 ASP cc_start: 0.7329 (m-30) cc_final: 0.7004 (m-30) REVERT: c 173 GLN cc_start: 0.8131 (tp-100) cc_final: 0.7913 (tp40) REVERT: d 1 MET cc_start: 0.5557 (tpt) cc_final: 0.5049 (mmm) REVERT: d 35 TYR cc_start: 0.8420 (t80) cc_final: 0.8068 (t80) REVERT: d 195 GLN cc_start: 0.8579 (mt0) cc_final: 0.8345 (mt0) REVERT: f 86 LEU cc_start: 0.8636 (mp) cc_final: 0.7923 (mm) REVERT: f 142 GLN cc_start: 0.8594 (tp40) cc_final: 0.8321 (tp-100) REVERT: h 38 MET cc_start: 0.1852 (mtp) cc_final: 0.1498 (mtp) REVERT: h 52 MET cc_start: -0.3997 (tpp) cc_final: -0.4363 (tpt) REVERT: i 94 LYS cc_start: 0.6755 (mmmt) cc_final: 0.6552 (mptt) REVERT: j 16 TYR cc_start: 0.8462 (m-80) cc_final: 0.8117 (m-80) REVERT: m 63 ILE cc_start: 0.9180 (mt) cc_final: 0.8963 (tt) REVERT: p 4 ILE cc_start: 0.8793 (pt) cc_final: 0.8210 (mt) REVERT: p 26 GLU cc_start: 0.7399 (tt0) cc_final: 0.7114 (tt0) REVERT: p 70 GLU cc_start: 0.7120 (tt0) cc_final: 0.6854 (tt0) REVERT: q 19 GLN cc_start: 0.7800 (mt0) cc_final: 0.7070 (mt0) REVERT: r 59 ILE cc_start: 0.9033 (mt) cc_final: 0.8759 (mm) REVERT: s 31 GLN cc_start: 0.8247 (mt0) cc_final: 0.8026 (mt0) REVERT: s 55 ILE cc_start: 0.9226 (mt) cc_final: 0.8616 (mm) REVERT: t 1 MET cc_start: 0.1307 (mmt) cc_final: 0.0523 (mpp) REVERT: y 13 GLU cc_start: 0.8497 (pt0) cc_final: 0.8246 (pt0) REVERT: y 45 GLN cc_start: 0.8438 (tp40) cc_final: 0.8148 (tp40) REVERT: z 5 LYS cc_start: 0.8560 (mttm) cc_final: 0.8123 (mtpp) REVERT: A 35 ASP cc_start: 0.7739 (p0) cc_final: 0.7378 (p0) REVERT: B 35 GLU cc_start: 0.6152 (mt-10) cc_final: 0.5562 (mt-10) REVERT: C 9 LYS cc_start: 0.8888 (ttpt) cc_final: 0.8483 (mmtp) REVERT: C 35 LEU cc_start: 0.8587 (mt) cc_final: 0.8210 (mt) REVERT: G 119 GLN cc_start: 0.8924 (mp10) cc_final: 0.8625 (mp10) REVERT: H 52 SER cc_start: 0.8793 (t) cc_final: 0.8394 (p) REVERT: J 13 LYS cc_start: 0.8722 (tttp) cc_final: 0.8398 (tppp) REVERT: K 21 MET cc_start: 0.8300 (mtp) cc_final: 0.8015 (mtt) REVERT: K 24 ARG cc_start: 0.8638 (ptp-170) cc_final: 0.8367 (ptp-170) REVERT: K 47 LEU cc_start: 0.8428 (mt) cc_final: 0.7889 (mt) REVERT: K 64 VAL cc_start: 0.8654 (m) cc_final: 0.8418 (p) REVERT: K 71 ILE cc_start: 0.9387 (mm) cc_final: 0.9168 (mm) REVERT: L 14 ASP cc_start: 0.8494 (t70) cc_final: 0.8218 (t0) REVERT: L 67 ASN cc_start: 0.8863 (m-40) cc_final: 0.8610 (m-40) REVERT: L 100 MET cc_start: 0.8468 (mtm) cc_final: 0.8185 (mtm) REVERT: M 60 LEU cc_start: 0.8955 (mt) cc_final: 0.8523 (mt) REVERT: M 66 GLN cc_start: 0.8328 (mm110) cc_final: 0.8126 (mm110) REVERT: M 89 ASP cc_start: 0.8563 (p0) cc_final: 0.8028 (p0) REVERT: O 19 ASP cc_start: 0.9011 (p0) cc_final: 0.8803 (p0) REVERT: P 93 GLU cc_start: 0.8246 (tp30) cc_final: 0.7557 (tp30) REVERT: P 104 PHE cc_start: 0.8092 (m-80) cc_final: 0.7819 (m-80) REVERT: Q 28 GLN cc_start: 0.8590 (mp10) cc_final: 0.8276 (mp10) REVERT: Q 76 HIS cc_start: 0.8525 (m-70) cc_final: 0.7775 (m-70) REVERT: S 9 GLU cc_start: 0.8506 (tp30) cc_final: 0.7838 (mm-30) REVERT: T 17 ASP cc_start: 0.8213 (p0) cc_final: 0.7793 (p0) REVERT: U 23 ASP cc_start: 0.7116 (t0) cc_final: 0.6590 (m-30) REVERT: U 24 SER cc_start: 0.7378 (m) cc_final: 0.7140 (m) REVERT: U 36 VAL cc_start: 0.8889 (m) cc_final: 0.8660 (m) REVERT: U 52 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8136 (pp) REVERT: V 47 ASP cc_start: 0.6752 (p0) cc_final: 0.6525 (p0) REVERT: W 20 ILE cc_start: 0.8915 (mm) cc_final: 0.8580 (mp) REVERT: W 53 GLN cc_start: 0.8617 (tt0) cc_final: 0.8348 (tt0) REVERT: W 56 ARG cc_start: 0.8306 (mtm-85) cc_final: 0.7845 (mtt90) REVERT: W 69 TYR cc_start: 0.8290 (m-80) cc_final: 0.7975 (m-10) REVERT: X 40 PHE cc_start: 0.8392 (m-80) cc_final: 0.7666 (m-80) REVERT: Y 31 ILE cc_start: 0.9344 (mt) cc_final: 0.8579 (mt) REVERT: Y 47 GLN cc_start: 0.8905 (tp40) cc_final: 0.8531 (tp-100) REVERT: Y 51 ASN cc_start: 0.8661 (m-40) cc_final: 0.8368 (m110) REVERT: Y 56 ILE cc_start: 0.9037 (mm) cc_final: 0.8206 (mm) outliers start: 38 outliers final: 17 residues processed: 1803 average time/residue: 1.3326 time to fit residues: 4113.6152 Evaluate side-chains 1381 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1363 time to evaluate : 8.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 86 ASP Chi-restraints excluded: chain g residue 110 VAL Chi-restraints excluded: chain h residue 118 ILE Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain y residue 17 GLU Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain U residue 55 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 892 optimal weight: 10.0000 chunk 801 optimal weight: 10.0000 chunk 444 optimal weight: 20.0000 chunk 273 optimal weight: 6.9990 chunk 540 optimal weight: 7.9990 chunk 428 optimal weight: 6.9990 chunk 828 optimal weight: 20.0000 chunk 320 optimal weight: 8.9990 chunk 503 optimal weight: 3.9990 chunk 616 optimal weight: 10.0000 chunk 959 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 20 ASN b 36 ASN b 85 ASN b 89 ASN b 127 ASN b 133 ASN c 32 ASN c 49 GLN d 41 GLN d 97 ASN e 20 ASN e 62 GLN f 44 HIS g 18 GLN h 4 ASN i 33 ASN i 104 GLN j 58 ASN j 135 GLN k 29 HIS ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 93 ASN m 13 HIS n 3 HIS n 81 ASN o 19 GLN o 38 GLN o 100 HIS ** p 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 89 HIS r 91 GLN s 61 ASN t 48 GLN u 39 ASN u 44 HIS ** u 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 5 ASN v 78 GLN w 8 ASN x 22 ASN y 20 ASN y 27 ASN z 19 HIS ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 HIS G 23 ASN H 184 ASN ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 ASN ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 163 GLN ** K 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 HIS ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 GLN M 117 GLN N 3 ASN N 4 GLN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 74 GLN O 56 HIS P 27 ASN P 63 GLN Q 72 ASN ** Q 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 7 ASN R 13 HIS R 104 ASN S 65 GLN T 27 GLN ** U 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 30 HIS X 51 HIS Y 60 GLN Y 81 GLN ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 161892 Z= 0.387 Angle : 0.733 13.019 242024 Z= 0.381 Chirality : 0.042 0.302 30928 Planarity : 0.006 0.090 13097 Dihedral : 23.020 179.917 80660 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.96 % Favored : 90.76 % Rotamer: Outliers : 4.71 % Allowed : 17.13 % Favored : 78.16 % 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: -3.19 (0.10), residues: 5983 helix: -1.11 (0.11), residues: 1880 sheet: -2.34 (0.14), residues: 1040 loop : -2.73 (0.10), residues: 3063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 22 HIS 0.009 0.002 HIS d 165 PHE 0.028 0.002 PHE H 36 TYR 0.021 0.002 TYR e 142 ARG 0.008 0.001 ARG M 12 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1679 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1445 time to evaluate : 6.811 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: b 65 ASP cc_start: 0.7881 (t0) cc_final: 0.7186 (t0) REVERT: b 113 ASP cc_start: 0.6896 (m-30) cc_final: 0.6674 (m-30) REVERT: d 35 TYR cc_start: 0.8566 (t80) cc_final: 0.8244 (t80) REVERT: e 51 ASN cc_start: 0.8846 (m-40) cc_final: 0.8472 (m110) REVERT: e 65 LEU cc_start: 0.9058 (tp) cc_final: 0.8761 (tt) REVERT: e 95 MET cc_start: 0.7924 (ttt) cc_final: 0.7700 (ttt) REVERT: g 45 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8227 (mm-30) REVERT: h 1 MET cc_start: 0.5059 (ptt) cc_final: 0.3784 (ttp) REVERT: h 52 MET cc_start: -0.4072 (tpp) cc_final: -0.4650 (tpp) REVERT: h 86 MET cc_start: 0.2417 (ttt) cc_final: 0.2137 (tpp) REVERT: i 116 MET cc_start: -0.2117 (mmt) cc_final: -0.2530 (mmt) REVERT: j 16 TYR cc_start: 0.8490 (m-80) cc_final: 0.8180 (m-80) REVERT: p 4 ILE cc_start: 0.8691 (pt) cc_final: 0.8169 (mt) REVERT: p 5 LYS cc_start: 0.9006 (tppt) cc_final: 0.8747 (mmtt) REVERT: p 8 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7624 (mt-10) REVERT: p 81 ASP cc_start: 0.7817 (t0) cc_final: 0.7564 (t0) REVERT: r 11 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8004 (mp-120) REVERT: s 33 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8865 (mm) REVERT: u 9 GLU cc_start: 0.7438 (tp30) cc_final: 0.6919 (tm-30) REVERT: v 24 ASN cc_start: 0.6119 (t0) cc_final: 0.5904 (t0) REVERT: A 35 ASP cc_start: 0.7831 (p0) cc_final: 0.7236 (p0) REVERT: A 63 ARG cc_start: 0.8273 (mtm180) cc_final: 0.7910 (mtt90) REVERT: C 9 LYS cc_start: 0.8617 (ttpt) cc_final: 0.8410 (mmtp) REVERT: I 39 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7469 (tt0) REVERT: I 47 LEU cc_start: 0.8652 (tp) cc_final: 0.8452 (tp) REVERT: I 125 ASN cc_start: 0.7673 (t0) cc_final: 0.7207 (t0) REVERT: K 47 LEU cc_start: 0.8371 (mt) cc_final: 0.8131 (mt) REVERT: L 100 MET cc_start: 0.8364 (mtm) cc_final: 0.8059 (mtm) REVERT: L 125 ASP cc_start: 0.8769 (t0) cc_final: 0.8448 (t0) REVERT: M 65 PHE cc_start: 0.8599 (t80) cc_final: 0.8384 (t80) REVERT: M 79 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8370 (mtp-110) REVERT: M 87 ARG cc_start: 0.8814 (mtm-85) cc_final: 0.8010 (ttm-80) REVERT: M 90 GLU cc_start: 0.8163 (pm20) cc_final: 0.7623 (pm20) REVERT: P 82 GLU cc_start: 0.6962 (mp0) cc_final: 0.6570 (mp0) REVERT: P 104 PHE cc_start: 0.8005 (m-80) cc_final: 0.7744 (m-80) REVERT: R 52 ILE cc_start: 0.9370 (OUTLIER) cc_final: 0.9166 (mp) REVERT: R 62 PHE cc_start: 0.6623 (t80) cc_final: 0.6283 (t80) REVERT: R 65 GLU cc_start: 0.8212 (tp30) cc_final: 0.7945 (tm-30) REVERT: S 9 GLU cc_start: 0.8661 (tp30) cc_final: 0.8145 (mm-30) REVERT: T 17 ASP cc_start: 0.7921 (p0) cc_final: 0.7456 (p0) REVERT: T 77 TYR cc_start: 0.8520 (t80) cc_final: 0.8246 (t80) REVERT: U 14 ARG cc_start: 0.7589 (tpt170) cc_final: 0.7077 (mtp-110) REVERT: U 23 ASP cc_start: 0.7166 (t0) cc_final: 0.6307 (m-30) REVERT: V 10 ARG cc_start: 0.8341 (ttp80) cc_final: 0.7861 (tmm-80) REVERT: V 47 ASP cc_start: 0.6900 (p0) cc_final: 0.6590 (p0) REVERT: W 56 ARG cc_start: 0.8346 (mtm-85) cc_final: 0.7935 (mtt90) REVERT: X 16 LYS cc_start: 0.8944 (mtpt) cc_final: 0.8567 (tttm) REVERT: Y 20 ASN cc_start: 0.9231 (m-40) cc_final: 0.9015 (m-40) REVERT: Y 47 GLN cc_start: 0.9000 (tp40) cc_final: 0.8514 (tp-100) REVERT: Y 51 ASN cc_start: 0.8728 (m-40) cc_final: 0.8305 (m-40) REVERT: Y 54 GLN cc_start: 0.8422 (tt0) cc_final: 0.7724 (tm-30) REVERT: Y 58 ASP cc_start: 0.8605 (m-30) cc_final: 0.8175 (m-30) outliers start: 234 outliers final: 158 residues processed: 1541 average time/residue: 1.2664 time to fit residues: 3405.7276 Evaluate side-chains 1454 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1291 time to evaluate : 8.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain c residue 21 SER Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 157 LEU Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 163 GLU Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 146 ASP Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 2 GLN Chi-restraints excluded: chain g residue 86 ASP Chi-restraints excluded: chain g residue 110 VAL Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain h residue 118 ILE Chi-restraints excluded: chain i residue 78 LEU Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 102 GLU Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 80 ASP Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 75 GLU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 48 VAL Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain o residue 26 LEU Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 88 ARG Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain r residue 11 GLN Chi-restraints excluded: chain r residue 40 MET Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 68 ASP Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 78 GLU Chi-restraints excluded: chain s residue 81 SER Chi-restraints excluded: chain t residue 49 LYS Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 41 VAL Chi-restraints excluded: chain v residue 3 THR Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 66 GLU Chi-restraints excluded: chain w residue 68 LYS Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 20 LYS Chi-restraints excluded: chain z residue 36 GLU Chi-restraints excluded: chain B residue 9 ARG Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain I residue 3 TYR Chi-restraints excluded: chain I residue 39 GLN Chi-restraints excluded: chain I residue 69 ARG Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 163 ILE 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 70 VAL Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 75 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 94 HIS Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 130 LYS Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 20 ASN Chi-restraints excluded: chain M residue 79 ARG Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 126 PHE Chi-restraints excluded: chain O residue 14 ASP Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 17 LYS Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 54 THR Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain W residue 10 CYS Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 81 GLN Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 222 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 533 optimal weight: 20.0000 chunk 297 optimal weight: 6.9990 chunk 798 optimal weight: 10.0000 chunk 653 optimal weight: 10.0000 chunk 264 optimal weight: 7.9990 chunk 961 optimal weight: 10.0000 chunk 1038 optimal weight: 10.0000 chunk 856 optimal weight: 20.0000 chunk 953 optimal weight: 7.9990 chunk 327 optimal weight: 8.9990 chunk 771 optimal weight: 10.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 152 GLN c 173 GLN c 185 ASN e 4 HIS ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 72 ASN ** f 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 54 GLN n 16 HIS o 43 ASN q 43 GLN q 51 GLN r 6 GLN r 11 GLN r 87 GLN t 15 HIS ** t 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 39 ASN ** u 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 5 ASN v 75 GLN y 20 ASN ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 GLN ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 GLN ** H 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN H 175 HIS ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 HIS ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 ASN ** Q 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 ASN ** U 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 51 GLN ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 57 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.113 161892 Z= 0.449 Angle : 0.730 14.697 242024 Z= 0.378 Chirality : 0.042 0.322 30928 Planarity : 0.006 0.083 13097 Dihedral : 23.299 178.993 80651 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.33 % Favored : 88.42 % Rotamer: Outliers : 6.85 % Allowed : 18.66 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.10), residues: 5983 helix: -0.66 (0.12), residues: 1896 sheet: -2.15 (0.15), residues: 1045 loop : -2.52 (0.10), residues: 3042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP U 60 HIS 0.009 0.002 HIS r 12 PHE 0.048 0.002 PHE W 12 TYR 0.024 0.002 TYR K 59 ARG 0.017 0.001 ARG b 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1704 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 340 poor density : 1364 time to evaluate : 6.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 108 ASP cc_start: 0.6958 (m-30) cc_final: 0.6618 (m-30) REVERT: d 35 TYR cc_start: 0.8695 (t80) cc_final: 0.8292 (t80) REVERT: e 51 ASN cc_start: 0.8836 (m-40) cc_final: 0.8429 (m110) REVERT: e 95 MET cc_start: 0.8153 (ttt) cc_final: 0.7833 (ttt) REVERT: g 4 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.8008 (tp) REVERT: h 52 MET cc_start: -0.3701 (tpp) cc_final: -0.4315 (tpp) REVERT: h 86 MET cc_start: 0.2523 (ttt) cc_final: 0.2293 (tpp) REVERT: i 116 MET cc_start: -0.1810 (mmt) cc_final: -0.2137 (tpt) REVERT: j 16 TYR cc_start: 0.8575 (m-80) cc_final: 0.8305 (m-80) REVERT: j 98 GLU cc_start: 0.8346 (pm20) cc_final: 0.7958 (pm20) REVERT: o 63 LYS cc_start: 0.8628 (ptmt) cc_final: 0.8345 (ptmm) REVERT: o 108 ASP cc_start: 0.8761 (p0) cc_final: 0.8456 (p0) REVERT: p 5 LYS cc_start: 0.8992 (tppt) cc_final: 0.8728 (mmtt) REVERT: u 5 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7772 (mtt90) REVERT: u 25 LYS cc_start: 0.8273 (mtpt) cc_final: 0.8056 (ttmt) REVERT: x 70 LEU cc_start: 0.9078 (mt) cc_final: 0.8829 (mt) REVERT: z 20 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8838 (mttm) REVERT: A 35 ASP cc_start: 0.7699 (p0) cc_final: 0.7200 (p0) REVERT: A 63 ARG cc_start: 0.8336 (mtm180) cc_final: 0.7943 (mtt90) REVERT: C 9 LYS cc_start: 0.8721 (ttpt) cc_final: 0.8423 (mmtm) REVERT: C 20 TYR cc_start: 0.8625 (m-80) cc_final: 0.8413 (m-80) REVERT: G 22 TRP cc_start: 0.8529 (p-90) cc_final: 0.8217 (p-90) REVERT: G 53 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8993 (mm) REVERT: H 52 SER cc_start: 0.8844 (OUTLIER) cc_final: 0.8513 (p) REVERT: H 183 TYR cc_start: 0.9110 (t80) cc_final: 0.8560 (t80) REVERT: I 39 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7599 (tt0) REVERT: J 44 ARG cc_start: 0.8612 (mtp-110) cc_final: 0.8113 (mtp-110) REVERT: J 115 GLU cc_start: 0.8348 (pp20) cc_final: 0.8049 (pp20) REVERT: K 47 LEU cc_start: 0.8259 (mt) cc_final: 0.8022 (mm) REVERT: M 42 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7204 (mm-30) REVERT: M 87 ARG cc_start: 0.8834 (mtm-85) cc_final: 0.8109 (ttm-80) REVERT: O 76 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8211 (mp) REVERT: P 104 PHE cc_start: 0.7978 (m-80) cc_final: 0.7606 (m-80) REVERT: Q 95 HIS cc_start: 0.7833 (OUTLIER) cc_final: 0.7571 (m-70) REVERT: R 52 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.9152 (mp) REVERT: S 9 GLU cc_start: 0.8703 (tp30) cc_final: 0.8230 (mm-30) REVERT: T 77 TYR cc_start: 0.8464 (t80) cc_final: 0.8161 (t80) REVERT: U 1 MET cc_start: 0.6493 (tpp) cc_final: 0.6273 (tpp) REVERT: U 14 ARG cc_start: 0.7459 (tpt170) cc_final: 0.6778 (mtp-110) REVERT: U 23 ASP cc_start: 0.7339 (t0) cc_final: 0.5837 (m-30) REVERT: U 36 VAL cc_start: 0.9322 (m) cc_final: 0.9016 (m) REVERT: U 76 LYS cc_start: 0.7585 (mttt) cc_final: 0.7106 (pttt) REVERT: V 47 ASP cc_start: 0.6984 (p0) cc_final: 0.6706 (p0) REVERT: W 56 ARG cc_start: 0.8374 (mtm-85) cc_final: 0.7909 (mtt90) REVERT: W 69 TYR cc_start: 0.8474 (m-10) cc_final: 0.8272 (m-10) REVERT: X 16 LYS cc_start: 0.8935 (mtpt) cc_final: 0.8604 (tttm) REVERT: X 40 PHE cc_start: 0.8547 (m-80) cc_final: 0.8261 (m-80) REVERT: Y 47 GLN cc_start: 0.8990 (tp40) cc_final: 0.8593 (tp-100) REVERT: Y 53 MET cc_start: 0.9018 (ppp) cc_final: 0.8769 (ppp) REVERT: Y 54 GLN cc_start: 0.8751 (tt0) cc_final: 0.7896 (tm-30) REVERT: Y 58 ASP cc_start: 0.8596 (m-30) cc_final: 0.8009 (m-30) REVERT: Z 35 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7155 (pm20) REVERT: a 8 MET cc_start: 0.2692 (mpp) cc_final: 0.2440 (mpp) outliers start: 340 outliers final: 225 residues processed: 1529 average time/residue: 1.2645 time to fit residues: 3386.3906 Evaluate side-chains 1490 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1255 time to evaluate : 6.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 167 ASP Chi-restraints excluded: chain b residue 186 ASP Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain c residue 21 SER Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 157 LEU Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 163 GLU Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 71 LEU Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 146 ASP Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 2 GLN Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 94 ILE Chi-restraints excluded: chain g residue 110 VAL Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain h residue 81 LEU Chi-restraints excluded: chain h residue 118 ILE Chi-restraints excluded: chain i residue 78 LEU Chi-restraints excluded: chain i residue 94 LYS Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 100 VAL Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 80 ASP Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 103 ILE Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 75 GLU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 48 VAL Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 68 LYS Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 19 PHE Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain p residue 101 GLU Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain r residue 11 GLN Chi-restraints excluded: chain r residue 39 LEU Chi-restraints excluded: chain r residue 40 MET Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 68 ASP Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 78 GLU Chi-restraints excluded: chain s residue 81 SER Chi-restraints excluded: chain t residue 49 LYS Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain u residue 5 ARG Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 41 VAL Chi-restraints excluded: chain v residue 3 THR Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 41 GLU Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 66 GLU Chi-restraints excluded: chain w residue 68 LYS Chi-restraints excluded: chain w residue 71 LYS Chi-restraints excluded: chain x residue 6 VAL Chi-restraints excluded: chain x residue 34 SER Chi-restraints excluded: chain x residue 57 VAL Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 20 LYS Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain B residue 9 ARG Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain I residue 39 GLN Chi-restraints excluded: chain I residue 69 ARG Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 75 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 14 ASP Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 130 LYS Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 147 ASN Chi-restraints excluded: chain M residue 20 ASN Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 75 GLN Chi-restraints excluded: chain M residue 79 ARG Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 126 PHE Chi-restraints excluded: chain O residue 14 ASP Chi-restraints excluded: chain O residue 20 GLN Chi-restraints excluded: chain O residue 49 PHE Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 76 TYR Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 17 LYS Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 95 HIS Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 54 THR Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 26 ASN Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 70 ARG Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain W residue 10 CYS Chi-restraints excluded: chain W residue 18 GLN Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 71 ASP Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain Z residue 62 GLU Chi-restraints excluded: chain a residue 46 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 950 optimal weight: 6.9990 chunk 722 optimal weight: 10.0000 chunk 499 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 458 optimal weight: 10.0000 chunk 645 optimal weight: 10.0000 chunk 965 optimal weight: 50.0000 chunk 1021 optimal weight: 7.9990 chunk 504 optimal weight: 6.9990 chunk 914 optimal weight: 10.0000 chunk 275 optimal weight: 20.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 62 GLN d 195 GLN ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 66 ASN h 6 GLN ** k 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 93 GLN l 4 ASN o 38 GLN ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 GLN r 6 GLN s 9 HIS ** s 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 39 ASN ** u 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 75 GLN y 20 ASN y 58 ASN z 8 GLN A 20 ASN B 4 GLN ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 GLN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 GLN ** K 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 ASN ** L 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 HIS ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 56 HIS ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 13 HIS T 61 GLN ** Y 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 161892 Z= 0.319 Angle : 0.644 11.900 242024 Z= 0.335 Chirality : 0.038 0.286 30928 Planarity : 0.005 0.081 13097 Dihedral : 23.356 179.911 80648 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.04 % Favored : 90.72 % Rotamer: Outliers : 5.78 % Allowed : 21.22 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.10), residues: 5983 helix: -0.28 (0.12), residues: 1890 sheet: -1.90 (0.15), residues: 1037 loop : -2.33 (0.10), residues: 3056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP U 60 HIS 0.010 0.001 HIS r 12 PHE 0.031 0.002 PHE Z 36 TYR 0.021 0.002 TYR e 142 ARG 0.011 0.001 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1648 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 287 poor density : 1361 time to evaluate : 6.751 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: b 144 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6860 (mt-10) REVERT: c 167 ASN cc_start: 0.8564 (t0) cc_final: 0.8281 (t0) REVERT: d 7 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7502 (p0) REVERT: d 35 TYR cc_start: 0.8648 (t80) cc_final: 0.8264 (t80) REVERT: e 51 ASN cc_start: 0.8827 (m-40) cc_final: 0.8385 (m110) REVERT: e 95 MET cc_start: 0.8127 (ttt) cc_final: 0.7857 (ttt) REVERT: g 45 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8160 (mm-30) REVERT: h 52 MET cc_start: -0.3586 (tpp) cc_final: -0.4215 (tpp) REVERT: h 86 MET cc_start: 0.2552 (ttt) cc_final: 0.2312 (tpp) REVERT: i 94 LYS cc_start: 0.6660 (OUTLIER) cc_final: 0.6122 (mptt) REVERT: i 116 MET cc_start: -0.1815 (mmt) cc_final: -0.2149 (tpt) REVERT: j 16 TYR cc_start: 0.8545 (m-80) cc_final: 0.8322 (m-80) REVERT: j 98 GLU cc_start: 0.8300 (pm20) cc_final: 0.7961 (pm20) REVERT: m 31 PHE cc_start: 0.8796 (m-80) cc_final: 0.7262 (m-80) REVERT: o 63 LYS cc_start: 0.8582 (ptmt) cc_final: 0.8347 (ptmm) REVERT: p 4 ILE cc_start: 0.8660 (pt) cc_final: 0.8271 (mt) REVERT: q 90 ASP cc_start: 0.6661 (p0) cc_final: 0.6341 (p0) REVERT: r 11 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8209 (mp10) REVERT: t 1 MET cc_start: 0.4333 (pmm) cc_final: 0.1433 (mmt) REVERT: t 89 GLU cc_start: 0.7939 (mp0) cc_final: 0.7703 (mp0) REVERT: t 91 GLN cc_start: 0.7912 (pm20) cc_final: 0.7647 (tm-30) REVERT: u 5 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7831 (mtt90) REVERT: A 35 ASP cc_start: 0.7597 (p0) cc_final: 0.7161 (p0) REVERT: A 63 ARG cc_start: 0.8261 (mtm180) cc_final: 0.7911 (mtt90) REVERT: C 9 LYS cc_start: 0.8725 (ttpt) cc_final: 0.8414 (mptt) REVERT: C 20 TYR cc_start: 0.8600 (m-80) cc_final: 0.8160 (m-10) REVERT: D 26 ASN cc_start: 0.7511 (m110) cc_final: 0.7294 (m-40) REVERT: G 22 TRP cc_start: 0.8568 (p-90) cc_final: 0.8161 (p-90) REVERT: G 53 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8955 (mm) REVERT: H 52 SER cc_start: 0.8821 (OUTLIER) cc_final: 0.8492 (p) REVERT: H 128 MET cc_start: 0.8271 (tpp) cc_final: 0.7845 (mtt) REVERT: H 183 TYR cc_start: 0.9087 (t80) cc_final: 0.8830 (t80) REVERT: I 125 ASN cc_start: 0.7694 (t0) cc_final: 0.7235 (t0) REVERT: I 195 ASN cc_start: 0.7154 (OUTLIER) cc_final: 0.6895 (p0) REVERT: J 115 GLU cc_start: 0.8429 (pp20) cc_final: 0.8189 (pp20) REVERT: K 21 MET cc_start: 0.8554 (mtt) cc_final: 0.8180 (mtt) REVERT: L 125 ASP cc_start: 0.8775 (t0) cc_final: 0.8392 (t0) REVERT: M 87 ARG cc_start: 0.8756 (mtm-85) cc_final: 0.8132 (ttm-80) REVERT: O 11 LYS cc_start: 0.9121 (pttt) cc_final: 0.8875 (pttp) REVERT: O 76 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.7989 (mp) REVERT: P 104 PHE cc_start: 0.7931 (m-80) cc_final: 0.7650 (m-80) REVERT: Q 76 HIS cc_start: 0.8462 (m-70) cc_final: 0.7976 (m-70) REVERT: Q 95 HIS cc_start: 0.7568 (OUTLIER) cc_final: 0.7356 (m-70) REVERT: U 1 MET cc_start: 0.6553 (tpp) cc_final: 0.6231 (tpp) REVERT: U 14 ARG cc_start: 0.7482 (tpt170) cc_final: 0.7083 (mtp-110) REVERT: U 23 ASP cc_start: 0.7355 (t0) cc_final: 0.5827 (m-30) REVERT: U 76 LYS cc_start: 0.7475 (mttt) cc_final: 0.7125 (pttt) REVERT: W 56 ARG cc_start: 0.8367 (mtm-85) cc_final: 0.8074 (mtt180) REVERT: W 69 TYR cc_start: 0.8416 (m-80) cc_final: 0.8164 (m-10) REVERT: X 16 LYS cc_start: 0.8971 (mtpt) cc_final: 0.8614 (tttm) REVERT: Y 54 GLN cc_start: 0.8695 (tt0) cc_final: 0.7727 (tm-30) REVERT: Y 58 ASP cc_start: 0.8512 (m-30) cc_final: 0.7904 (m-30) REVERT: Z 35 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6986 (pm20) REVERT: Z 44 ARG cc_start: 0.8189 (mmt180) cc_final: 0.7583 (mmt180) REVERT: a 8 MET cc_start: 0.2724 (mpp) cc_final: 0.2499 (mpp) outliers start: 287 outliers final: 201 residues processed: 1501 average time/residue: 1.2719 time to fit residues: 3359.8799 Evaluate side-chains 1478 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 1267 time to evaluate : 6.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 167 ASP Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain c residue 21 SER Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain e residue 163 GLU Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 71 LEU Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 146 ASP Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 2 GLN Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 110 VAL Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain h residue 118 ILE Chi-restraints excluded: chain i residue 94 LYS Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 81 ILE Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 100 VAL Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 80 ASP Chi-restraints excluded: chain l residue 51 GLU Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 103 ILE Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 75 GLU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain o residue 38 GLN Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 101 GLU Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain r residue 11 GLN Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 39 LEU Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 68 ASP Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 78 GLU Chi-restraints excluded: chain u residue 5 ARG Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 41 VAL Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain v residue 3 THR Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 68 LYS Chi-restraints excluded: chain w residue 71 LYS Chi-restraints excluded: chain x residue 6 VAL Chi-restraints excluded: chain x residue 34 SER Chi-restraints excluded: chain x residue 57 VAL Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain z residue 51 SER Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 9 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain I residue 39 GLN Chi-restraints excluded: chain I residue 69 ARG Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 195 ASN Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 75 GLU Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 14 ASP Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 130 LYS Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 147 ASN Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 126 PHE Chi-restraints excluded: chain O residue 14 ASP Chi-restraints excluded: chain O residue 20 GLN Chi-restraints excluded: chain O residue 49 PHE Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 76 TYR Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 17 LYS Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 95 HIS Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain R residue 54 THR Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain W residue 10 CYS Chi-restraints excluded: chain W residue 18 GLN Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 71 ASP Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Y residue 81 GLN Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain Z residue 62 GLU Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 222 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 850 optimal weight: 10.0000 chunk 579 optimal weight: 40.0000 chunk 14 optimal weight: 1.9990 chunk 760 optimal weight: 10.0000 chunk 421 optimal weight: 0.8980 chunk 871 optimal weight: 10.0000 chunk 706 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 521 optimal weight: 6.9990 chunk 917 optimal weight: 10.0000 chunk 257 optimal weight: 9.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 116 GLN b 152 GLN c 94 GLN d 41 GLN d 62 GLN ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 ASN ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 40 GLN q 36 GLN q 51 GLN r 6 GLN r 11 GLN u 39 ASN ** u 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 20 ASN ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 GLN ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 GLN ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 HIS ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 56 HIS ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 ASN Y 60 GLN ** Y 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 161892 Z= 0.301 Angle : 0.631 11.343 242024 Z= 0.328 Chirality : 0.037 0.339 30928 Planarity : 0.005 0.080 13097 Dihedral : 23.375 179.839 80644 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.05 % Favored : 89.70 % Rotamer: Outliers : 6.18 % Allowed : 22.15 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.10), residues: 5983 helix: -0.09 (0.12), residues: 1873 sheet: -1.82 (0.15), residues: 1054 loop : -2.23 (0.11), residues: 3056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP U 60 HIS 0.009 0.001 HIS I 40 PHE 0.035 0.002 PHE H 36 TYR 0.024 0.002 TYR K 59 ARG 0.010 0.001 ARG F 4 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1654 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 1347 time to evaluate : 6.807 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: b 144 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6815 (mt-10) REVERT: c 108 ASP cc_start: 0.7062 (m-30) cc_final: 0.6684 (m-30) REVERT: c 167 ASN cc_start: 0.8511 (t0) cc_final: 0.8229 (t0) REVERT: d 7 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7523 (p0) REVERT: d 35 TYR cc_start: 0.8639 (t80) cc_final: 0.8227 (t80) REVERT: e 51 ASN cc_start: 0.8806 (m-40) cc_final: 0.8319 (m110) REVERT: e 95 MET cc_start: 0.8102 (ttt) cc_final: 0.7816 (ttt) REVERT: f 154 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7415 (tm-30) REVERT: g 4 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7997 (tp) REVERT: g 45 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8141 (mm-30) REVERT: i 116 MET cc_start: -0.1640 (mmt) cc_final: -0.1940 (tpt) REVERT: j 16 TYR cc_start: 0.8541 (m-80) cc_final: 0.8319 (m-80) REVERT: j 74 TYR cc_start: 0.8551 (m-80) cc_final: 0.8271 (m-80) REVERT: m 111 GLU cc_start: 0.8150 (pm20) cc_final: 0.7874 (pm20) REVERT: o 63 LYS cc_start: 0.8549 (ptmt) cc_final: 0.8228 (ptmm) REVERT: p 4 ILE cc_start: 0.8658 (pt) cc_final: 0.8304 (mt) REVERT: u 5 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7636 (mtt90) REVERT: v 24 ASN cc_start: 0.6602 (t0) cc_final: 0.6384 (t0) REVERT: A 35 ASP cc_start: 0.7549 (p0) cc_final: 0.7073 (p0) REVERT: A 63 ARG cc_start: 0.8209 (mtm180) cc_final: 0.7871 (mpt-90) REVERT: F 11 CYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8065 (p) REVERT: G 22 TRP cc_start: 0.8607 (p-90) cc_final: 0.8150 (p-90) REVERT: G 53 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8940 (mm) REVERT: H 52 SER cc_start: 0.8770 (OUTLIER) cc_final: 0.8438 (p) REVERT: I 39 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7750 (tt0) REVERT: I 125 ASN cc_start: 0.7720 (t0) cc_final: 0.7261 (t0) REVERT: L 67 ASN cc_start: 0.8446 (m-40) cc_final: 0.8225 (m-40) REVERT: L 125 ASP cc_start: 0.8762 (t0) cc_final: 0.8341 (t0) REVERT: M 79 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8423 (mtp-110) REVERT: M 87 ARG cc_start: 0.8773 (mtm-85) cc_final: 0.8115 (ttm-80) REVERT: O 76 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.7979 (mp) REVERT: Q 76 HIS cc_start: 0.8425 (m-70) cc_final: 0.8022 (m-70) REVERT: R 18 LEU cc_start: 0.9270 (tp) cc_final: 0.9032 (tt) REVERT: R 43 LYS cc_start: 0.8627 (mppt) cc_final: 0.8394 (mmmt) REVERT: U 1 MET cc_start: 0.6753 (tpp) cc_final: 0.6542 (tpp) REVERT: U 14 ARG cc_start: 0.7453 (tpt170) cc_final: 0.6964 (mtp-110) REVERT: U 23 ASP cc_start: 0.7446 (t0) cc_final: 0.5795 (m-30) REVERT: U 60 TRP cc_start: 0.8220 (m100) cc_final: 0.7813 (m-10) REVERT: U 76 LYS cc_start: 0.7574 (mttt) cc_final: 0.6949 (pttp) REVERT: W 18 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.7272 (pp30) REVERT: W 69 TYR cc_start: 0.8437 (m-80) cc_final: 0.8215 (m-10) REVERT: Y 54 GLN cc_start: 0.8711 (tt0) cc_final: 0.7693 (tm-30) REVERT: Y 58 ASP cc_start: 0.8523 (m-30) cc_final: 0.7812 (m-30) REVERT: Z 35 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6923 (pm20) REVERT: Z 44 ARG cc_start: 0.8191 (mmt180) cc_final: 0.7589 (mmt180) REVERT: a 8 MET cc_start: 0.2808 (mpp) cc_final: 0.2601 (mpp) outliers start: 307 outliers final: 234 residues processed: 1505 average time/residue: 1.2697 time to fit residues: 3360.4675 Evaluate side-chains 1531 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 1286 time to evaluate : 6.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 116 GLN Chi-restraints excluded: chain b residue 167 ASP Chi-restraints excluded: chain b residue 186 ASP Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain c residue 21 SER Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 28 VAL Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 71 LEU Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 146 ASP Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 2 GLN Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 94 ILE Chi-restraints excluded: chain g residue 110 VAL Chi-restraints excluded: chain g residue 122 LEU Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain h residue 118 ILE Chi-restraints excluded: chain i residue 16 MET Chi-restraints excluded: chain i residue 78 LEU Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 81 ILE Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 100 VAL Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 80 ASP Chi-restraints excluded: chain k residue 88 ASN Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 51 GLU Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 103 ILE Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 66 ARG Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 75 GLU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 48 VAL Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain o residue 26 LEU Chi-restraints excluded: chain o residue 45 SER Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain p residue 101 GLU Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 39 LEU Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 68 ASP Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 78 GLU Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain u residue 5 ARG Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 41 VAL Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain v residue 3 THR Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 68 LYS Chi-restraints excluded: chain w residue 71 LYS Chi-restraints excluded: chain x residue 6 VAL Chi-restraints excluded: chain x residue 34 SER Chi-restraints excluded: chain x residue 57 VAL Chi-restraints excluded: chain y residue 15 ASN Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain z residue 51 SER Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 9 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain I residue 39 GLN Chi-restraints excluded: chain I residue 69 ARG Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 75 GLU Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 14 ASP Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 130 LYS Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 147 ASN Chi-restraints excluded: chain M residue 20 ASN Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 79 ARG Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain N residue 126 PHE Chi-restraints excluded: chain O residue 14 ASP Chi-restraints excluded: chain O residue 20 GLN Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 76 TYR Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 17 LYS Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain W residue 10 CYS Chi-restraints excluded: chain W residue 18 GLN Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain W residue 71 ASP Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 60 GLN Chi-restraints excluded: chain Y residue 81 GLN Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain Z residue 62 GLU Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 222 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 343 optimal weight: 20.0000 chunk 920 optimal weight: 10.0000 chunk 201 optimal weight: 2.9990 chunk 599 optimal weight: 20.0000 chunk 252 optimal weight: 0.9990 chunk 1022 optimal weight: 10.0000 chunk 848 optimal weight: 10.0000 chunk 473 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 338 optimal weight: 1.9990 chunk 536 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 152 GLN d 62 GLN ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 29 HIS l 4 ASN l 38 GLN n 13 ASN o 38 GLN o 61 GLN o 116 GLN ** p 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 40 GLN q 51 GLN r 6 GLN u 39 ASN ** u 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 20 ASN C 18 HIS ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 HIS M 15 ASN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 4 ASN Q 72 ASN ** Q 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 GLN ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 161892 Z= 0.181 Angle : 0.580 11.887 242024 Z= 0.300 Chirality : 0.034 0.273 30928 Planarity : 0.004 0.076 13097 Dihedral : 23.339 179.333 80644 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.29 % Favored : 91.51 % Rotamer: Outliers : 5.34 % Allowed : 23.94 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.11), residues: 5983 helix: 0.12 (0.12), residues: 1860 sheet: -1.66 (0.16), residues: 1054 loop : -2.05 (0.11), residues: 3069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP G 95 HIS 0.008 0.001 HIS r 12 PHE 0.030 0.001 PHE q 105 TYR 0.024 0.001 TYR e 142 ARG 0.011 0.001 ARG F 4 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1656 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 1391 time to evaluate : 6.692 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: b 144 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6831 (mt-10) REVERT: c 108 ASP cc_start: 0.7072 (m-30) cc_final: 0.6473 (m-30) REVERT: d 7 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7528 (p0) REVERT: d 35 TYR cc_start: 0.8531 (t80) cc_final: 0.8173 (t80) REVERT: e 51 ASN cc_start: 0.8778 (m-40) cc_final: 0.8215 (m110) REVERT: e 95 MET cc_start: 0.8063 (ttt) cc_final: 0.7773 (ttt) REVERT: f 154 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7317 (pp20) REVERT: g 4 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.7972 (tp) REVERT: g 41 LYS cc_start: 0.8363 (pptt) cc_final: 0.8132 (pptt) REVERT: g 45 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8117 (mm-30) REVERT: i 39 LYS cc_start: 0.7672 (mmmt) cc_final: 0.7276 (ptpt) REVERT: i 116 MET cc_start: -0.1815 (OUTLIER) cc_final: -0.2201 (tpt) REVERT: n 94 TYR cc_start: 0.8172 (m-10) cc_final: 0.7953 (m-80) REVERT: p 4 ILE cc_start: 0.8605 (pt) cc_final: 0.8265 (mt) REVERT: u 5 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7881 (mtt90) REVERT: v 24 ASN cc_start: 0.6594 (t0) cc_final: 0.6371 (t0) REVERT: w 51 ARG cc_start: 0.8707 (ptm-80) cc_final: 0.8439 (ptm-80) REVERT: A 8 LYS cc_start: 0.8055 (mtmm) cc_final: 0.7778 (ptpp) REVERT: A 35 ASP cc_start: 0.7326 (p0) cc_final: 0.6989 (p0) REVERT: G 22 TRP cc_start: 0.8572 (p-90) cc_final: 0.8053 (p-90) REVERT: G 53 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8908 (mm) REVERT: H 52 SER cc_start: 0.8704 (OUTLIER) cc_final: 0.8346 (p) REVERT: H 128 MET cc_start: 0.8201 (tpp) cc_final: 0.7705 (mtt) REVERT: H 183 TYR cc_start: 0.9096 (t80) cc_final: 0.8809 (t80) REVERT: I 125 ASN cc_start: 0.7738 (t0) cc_final: 0.7240 (t0) REVERT: J 13 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7458 (ttpp) REVERT: J 67 ARG cc_start: 0.8189 (tpp80) cc_final: 0.7518 (mtm-85) REVERT: K 21 MET cc_start: 0.8323 (mtt) cc_final: 0.7918 (mmt) REVERT: L 67 ASN cc_start: 0.8399 (m-40) cc_final: 0.8194 (m-40) REVERT: L 96 ASN cc_start: 0.8729 (p0) cc_final: 0.7934 (p0) REVERT: L 100 MET cc_start: 0.8181 (mtp) cc_final: 0.7563 (mpp) REVERT: L 125 ASP cc_start: 0.8717 (t0) cc_final: 0.8290 (t0) REVERT: M 87 ARG cc_start: 0.8724 (mtm-85) cc_final: 0.8089 (ttm-80) REVERT: N 103 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.8092 (t) REVERT: N 119 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8766 (ptpp) REVERT: O 11 LYS cc_start: 0.8942 (pttp) cc_final: 0.8714 (ptpp) REVERT: O 18 ILE cc_start: 0.9327 (tp) cc_final: 0.9013 (tp) REVERT: O 76 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7792 (mp) REVERT: O 99 GLN cc_start: 0.7480 (mm-40) cc_final: 0.7206 (mm-40) REVERT: P 35 ASP cc_start: 0.8454 (p0) cc_final: 0.8218 (p0) REVERT: Q 76 HIS cc_start: 0.8411 (OUTLIER) cc_final: 0.8123 (m-70) REVERT: R 71 GLU cc_start: 0.8661 (tp30) cc_final: 0.8377 (tp30) REVERT: R 77 LYS cc_start: 0.9272 (tptt) cc_final: 0.9033 (tptt) REVERT: U 14 ARG cc_start: 0.7369 (tpt170) cc_final: 0.7049 (mtp-110) REVERT: U 23 ASP cc_start: 0.7434 (t0) cc_final: 0.5943 (m-30) REVERT: W 69 TYR cc_start: 0.8370 (m-80) cc_final: 0.8133 (m-10) REVERT: X 16 LYS cc_start: 0.9083 (mttt) cc_final: 0.8666 (tttm) REVERT: Y 54 GLN cc_start: 0.8625 (tt0) cc_final: 0.7550 (tm-30) REVERT: Y 58 ASP cc_start: 0.8507 (m-30) cc_final: 0.7869 (m-30) REVERT: Z 11 PHE cc_start: 0.2894 (OUTLIER) cc_final: 0.1085 (p90) REVERT: Z 35 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6684 (pm20) REVERT: Z 44 ARG cc_start: 0.8169 (mmt180) cc_final: 0.7605 (mmt180) REVERT: a 8 MET cc_start: 0.3112 (mpp) cc_final: 0.1964 (mmt) outliers start: 265 outliers final: 175 residues processed: 1520 average time/residue: 1.2563 time to fit residues: 3351.8751 Evaluate side-chains 1491 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1303 time to evaluate : 6.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 167 ASP Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain c residue 21 SER Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 28 VAL Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 71 LEU Chi-restraints excluded: chain f residue 127 GLN Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 62 LEU Chi-restraints excluded: chain g residue 94 ILE Chi-restraints excluded: chain g residue 110 VAL Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain h residue 118 ILE Chi-restraints excluded: chain i residue 16 MET Chi-restraints excluded: chain i residue 35 MET Chi-restraints excluded: chain i residue 78 LEU Chi-restraints excluded: chain i residue 116 MET Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 81 ILE Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 80 ASP Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 51 GLU Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 75 GLU Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain o residue 38 GLN Chi-restraints excluded: chain o residue 45 SER Chi-restraints excluded: chain o residue 67 ASN Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 39 LEU Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 68 ASP Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 81 SER Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain u residue 5 ARG Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 68 LYS Chi-restraints excluded: chain w residue 71 LYS Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain y residue 59 GLU Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain z residue 51 SER Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 9 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain I residue 39 GLN Chi-restraints excluded: chain I residue 69 ARG Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 75 GLU Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 130 LYS Chi-restraints excluded: chain L residue 147 ASN Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain O residue 14 ASP Chi-restraints excluded: chain O residue 20 GLN Chi-restraints excluded: chain O residue 49 PHE Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 76 TYR Chi-restraints excluded: chain Q residue 17 LYS Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 76 HIS Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 70 ARG Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain W residue 71 ASP Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Y residue 81 GLN Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain Z residue 62 GLU Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 222 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 986 optimal weight: 10.0000 chunk 115 optimal weight: 20.0000 chunk 582 optimal weight: 20.0000 chunk 746 optimal weight: 10.0000 chunk 578 optimal weight: 40.0000 chunk 860 optimal weight: 40.0000 chunk 571 optimal weight: 9.9990 chunk 1018 optimal weight: 10.0000 chunk 637 optimal weight: 20.0000 chunk 621 optimal weight: 20.0000 chunk 470 optimal weight: 20.0000 overall best weight: 11.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 24 HIS b 152 GLN c 94 GLN ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 41 GLN d 46 GLN d 62 GLN d 195 GLN ** e 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 44 HIS ** g 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 136 GLN ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 ASN n 18 GLN ** n 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN ** o 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 40 GLN q 51 GLN r 6 GLN ** r 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 87 GLN s 15 GLN t 59 ASN ** t 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 39 ASN ** u 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 75 GLN y 20 ASN z 8 GLN B 4 GLN C 18 HIS ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 GLN ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 HIS M 15 ASN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 109 GLN ** O 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 23 HIS ** Q 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 67 HIS a 172 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.120 161892 Z= 0.627 Angle : 0.845 13.189 242024 Z= 0.427 Chirality : 0.046 0.308 30928 Planarity : 0.006 0.061 13097 Dihedral : 23.496 179.391 80644 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 23.62 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.55 % Favored : 88.22 % Rotamer: Outliers : 6.99 % Allowed : 23.84 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.10), residues: 5983 helix: -0.39 (0.12), residues: 1897 sheet: -1.84 (0.15), residues: 1067 loop : -2.26 (0.11), residues: 3019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP I 169 HIS 0.011 0.002 HIS r 12 PHE 0.035 0.003 PHE g 46 TYR 0.039 0.003 TYR j 16 ARG 0.013 0.001 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1599 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 347 poor density : 1252 time to evaluate : 6.838 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: c 108 ASP cc_start: 0.6900 (m-30) cc_final: 0.6657 (m-30) REVERT: d 7 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.7325 (p0) REVERT: d 35 TYR cc_start: 0.8829 (t80) cc_final: 0.8406 (t80) REVERT: d 62 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7213 (mm-40) REVERT: d 164 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8805 (mm) REVERT: e 51 ASN cc_start: 0.8858 (m-40) cc_final: 0.8476 (m110) REVERT: e 95 MET cc_start: 0.8271 (ttt) cc_final: 0.7956 (ttt) REVERT: g 45 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8185 (mm-30) REVERT: i 39 LYS cc_start: 0.7661 (mmmt) cc_final: 0.7253 (ptpt) REVERT: i 44 LYS cc_start: 0.5623 (mttt) cc_final: 0.5240 (ptpt) REVERT: i 116 MET cc_start: -0.1883 (OUTLIER) cc_final: -0.2140 (tpt) REVERT: j 74 TYR cc_start: 0.8487 (m-80) cc_final: 0.8240 (m-80) REVERT: k 20 MET cc_start: 0.7413 (tmm) cc_final: 0.6874 (ttt) REVERT: n 58 ASP cc_start: 0.8460 (t0) cc_final: 0.8066 (t0) REVERT: p 4 ILE cc_start: 0.8697 (pt) cc_final: 0.8180 (mt) REVERT: p 8 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7723 (mt-10) REVERT: u 5 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7653 (mtt90) REVERT: u 8 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.6592 (p0) REVERT: A 25 ARG cc_start: 0.8506 (mtp-110) cc_final: 0.7856 (mtp-110) REVERT: B 47 TYR cc_start: 0.8509 (m-10) cc_final: 0.8228 (m-10) REVERT: C 9 LYS cc_start: 0.8800 (ttpt) cc_final: 0.8430 (mmtm) REVERT: F 11 CYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8443 (p) REVERT: G 153 MET cc_start: 0.7506 (tpt) cc_final: 0.7082 (tpp) REVERT: H 52 SER cc_start: 0.8893 (OUTLIER) cc_final: 0.8592 (p) REVERT: H 167 TYR cc_start: 0.8067 (m-10) cc_final: 0.7820 (m-10) REVERT: I 160 LEU cc_start: 0.4120 (OUTLIER) cc_final: 0.3899 (mp) REVERT: J 13 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7809 (ttpp) REVERT: L 30 MET cc_start: 0.8689 (tpp) cc_final: 0.8077 (tpp) REVERT: L 67 ASN cc_start: 0.8519 (m-40) cc_final: 0.8300 (m-40) REVERT: L 96 ASN cc_start: 0.8891 (p0) cc_final: 0.8069 (p0) REVERT: L 100 MET cc_start: 0.8240 (mtp) cc_final: 0.7609 (mpp) REVERT: M 87 ARG cc_start: 0.8796 (mtm-85) cc_final: 0.8137 (ttm-80) REVERT: N 49 GLN cc_start: 0.8878 (mt0) cc_final: 0.8667 (pt0) REVERT: N 99 LYS cc_start: 0.8748 (mmtt) cc_final: 0.8286 (mppt) REVERT: O 76 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8325 (mp) REVERT: Q 76 HIS cc_start: 0.8553 (OUTLIER) cc_final: 0.8052 (m-70) REVERT: Q 95 HIS cc_start: 0.7845 (OUTLIER) cc_final: 0.7486 (m-70) REVERT: U 1 MET cc_start: 0.7269 (tpp) cc_final: 0.6644 (tpt) REVERT: U 14 ARG cc_start: 0.7490 (tpt170) cc_final: 0.6974 (mtp-110) REVERT: W 24 ASP cc_start: 0.8541 (t0) cc_final: 0.8276 (t0) REVERT: W 50 TYR cc_start: 0.7899 (m-80) cc_final: 0.7640 (m-80) REVERT: W 69 TYR cc_start: 0.8581 (m-80) cc_final: 0.8350 (m-10) REVERT: X 16 LYS cc_start: 0.9118 (mttt) cc_final: 0.8708 (tttm) REVERT: Y 54 GLN cc_start: 0.8865 (tt0) cc_final: 0.7894 (tm-30) REVERT: Y 58 ASP cc_start: 0.8644 (m-30) cc_final: 0.8111 (m-30) REVERT: Z 35 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7236 (pm20) REVERT: a 172 HIS cc_start: -0.0362 (OUTLIER) cc_final: -0.1745 (t-170) outliers start: 347 outliers final: 273 residues processed: 1432 average time/residue: 1.3585 time to fit residues: 3444.8992 Evaluate side-chains 1497 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 1209 time to evaluate : 6.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 128 THR Chi-restraints excluded: chain b residue 167 ASP Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain c residue 21 SER Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 42 ASN Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 28 VAL Chi-restraints excluded: chain d residue 62 GLN Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 71 LEU Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain f residue 127 GLN Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 146 ASP Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 2 GLN Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 62 LEU Chi-restraints excluded: chain g residue 94 ILE Chi-restraints excluded: chain g residue 110 VAL Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain h residue 118 ILE Chi-restraints excluded: chain i residue 16 MET Chi-restraints excluded: chain i residue 49 GLU Chi-restraints excluded: chain i residue 78 LEU Chi-restraints excluded: chain i residue 108 ILE Chi-restraints excluded: chain i residue 116 MET Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 81 ILE Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain j residue 100 VAL Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain j residue 140 LEU Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 80 ASP Chi-restraints excluded: chain k residue 88 ASN Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 51 GLU Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 103 ILE Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 44 ARG Chi-restraints excluded: chain m residue 75 GLU Chi-restraints excluded: chain m residue 119 LEU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 48 VAL Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain o residue 26 LEU Chi-restraints excluded: chain o residue 38 GLN Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 67 ASN Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain p residue 101 GLU Chi-restraints excluded: chain p residue 111 GLU Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 39 LEU Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 68 ASP Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 78 GLU Chi-restraints excluded: chain s residue 81 SER Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain u residue 5 ARG Chi-restraints excluded: chain u residue 8 ASP Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain v residue 3 THR Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 68 LYS Chi-restraints excluded: chain w residue 71 LYS Chi-restraints excluded: chain x residue 34 SER Chi-restraints excluded: chain x residue 51 SER Chi-restraints excluded: chain x residue 57 VAL Chi-restraints excluded: chain y residue 15 ASN Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain z residue 51 SER Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 9 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain I residue 69 ARG Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 160 LEU Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 98 GLU Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 14 ASP Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 130 LYS Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 147 ASN Chi-restraints excluded: chain M residue 20 ASN Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 29 SER Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 79 ARG Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain N residue 126 PHE Chi-restraints excluded: chain O residue 14 ASP Chi-restraints excluded: chain O residue 20 GLN Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 76 TYR Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain Q residue 17 LYS Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 76 HIS Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 95 HIS Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 54 THR Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 58 MET Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 70 ARG Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain W residue 71 ASP Chi-restraints excluded: chain X residue 10 ILE Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Y residue 81 GLN Chi-restraints excluded: chain Z residue 11 PHE 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 Z residue 35 GLU Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain Z residue 62 GLU Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 172 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 630 optimal weight: 20.0000 chunk 406 optimal weight: 4.9990 chunk 608 optimal weight: 20.0000 chunk 306 optimal weight: 6.9990 chunk 200 optimal weight: 8.9990 chunk 197 optimal weight: 3.9990 chunk 647 optimal weight: 20.0000 chunk 694 optimal weight: 10.0000 chunk 503 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 chunk 800 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 94 GLN c 167 ASN d 41 GLN d 62 GLN d 195 GLN ** e 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 103 ASN ** g 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 128 HIS ** h 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 136 GLN ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 ASN ** n 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 GLN r 6 GLN t 48 GLN u 39 ASN ** u 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 20 ASN z 8 GLN B 3 GLN B 4 GLN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 GLN ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 HIS ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 GLN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 109 GLN ** O 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 4 ASN ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 172 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 161892 Z= 0.357 Angle : 0.679 12.848 242024 Z= 0.350 Chirality : 0.039 0.290 30928 Planarity : 0.005 0.083 13097 Dihedral : 23.550 179.572 80644 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.18 % Favored : 90.61 % Rotamer: Outliers : 5.88 % Allowed : 25.99 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.10), residues: 5983 helix: -0.20 (0.12), residues: 1888 sheet: -1.74 (0.15), residues: 1086 loop : -2.18 (0.11), residues: 3009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP I 169 HIS 0.007 0.001 HIS r 12 PHE 0.036 0.002 PHE H 36 TYR 0.032 0.002 TYR K 59 ARG 0.012 0.001 ARG F 4 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1580 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 1288 time to evaluate : 6.784 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: b 144 GLU cc_start: 0.7451 (mt-10) cc_final: 0.6968 (mt-10) REVERT: c 108 ASP cc_start: 0.6861 (m-30) cc_final: 0.6659 (m-30) REVERT: d 7 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7439 (p0) REVERT: d 35 TYR cc_start: 0.8665 (t80) cc_final: 0.8276 (t80) REVERT: d 62 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.7087 (mm-40) REVERT: d 164 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8738 (mm) REVERT: e 51 ASN cc_start: 0.8806 (m-40) cc_final: 0.8381 (m110) REVERT: e 95 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7837 (ttt) REVERT: f 154 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7262 (pp20) REVERT: g 4 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.8026 (tp) REVERT: g 45 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8133 (mm-30) REVERT: i 44 LYS cc_start: 0.5549 (mttt) cc_final: 0.5170 (ptpt) REVERT: i 116 MET cc_start: -0.1850 (OUTLIER) cc_final: -0.2165 (tpt) REVERT: k 20 MET cc_start: 0.7325 (tmm) cc_final: 0.6875 (ttt) REVERT: n 58 ASP cc_start: 0.8410 (t0) cc_final: 0.8008 (t0) REVERT: r 11 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8278 (mp10) REVERT: u 5 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7700 (mtt90) REVERT: y 13 GLU cc_start: 0.8547 (pt0) cc_final: 0.8331 (pt0) REVERT: A 34 LEU cc_start: 0.9056 (mm) cc_final: 0.8692 (mm) REVERT: A 35 ASP cc_start: 0.7549 (p0) cc_final: 0.7081 (p0) REVERT: C 9 LYS cc_start: 0.8739 (ttpt) cc_final: 0.8380 (mmtm) REVERT: F 11 CYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8112 (p) REVERT: H 52 SER cc_start: 0.8741 (OUTLIER) cc_final: 0.8507 (p) REVERT: H 128 MET cc_start: 0.8221 (tpp) cc_final: 0.7743 (mtt) REVERT: I 160 LEU cc_start: 0.4088 (OUTLIER) cc_final: 0.3843 (mp) REVERT: J 13 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7753 (ttpp) REVERT: L 30 MET cc_start: 0.8615 (tpp) cc_final: 0.8023 (tpp) REVERT: L 67 ASN cc_start: 0.8486 (m-40) cc_final: 0.8251 (m-40) REVERT: L 96 ASN cc_start: 0.8837 (p0) cc_final: 0.7970 (p0) REVERT: L 100 MET cc_start: 0.8214 (mtp) cc_final: 0.7533 (mpp) REVERT: L 125 ASP cc_start: 0.8689 (t0) cc_final: 0.8298 (t0) REVERT: M 87 ARG cc_start: 0.8739 (mtm-85) cc_final: 0.8182 (ttm-80) REVERT: O 11 LYS cc_start: 0.9111 (pttt) cc_final: 0.8890 (ptpp) REVERT: O 43 PRO cc_start: 0.8426 (Cg_endo) cc_final: 0.8225 (Cg_exo) REVERT: Q 76 HIS cc_start: 0.8387 (OUTLIER) cc_final: 0.8040 (m-70) REVERT: Q 95 HIS cc_start: 0.7472 (OUTLIER) cc_final: 0.7155 (m-70) REVERT: R 43 LYS cc_start: 0.8728 (mppt) cc_final: 0.8315 (mmtm) REVERT: U 1 MET cc_start: 0.7019 (tpp) cc_final: 0.6574 (tpp) REVERT: U 14 ARG cc_start: 0.7475 (tpt170) cc_final: 0.7032 (mtp-110) REVERT: U 23 ASP cc_start: 0.7625 (t0) cc_final: 0.5385 (m-30) REVERT: V 5 ARG cc_start: 0.7514 (mtp85) cc_final: 0.7279 (mtp85) REVERT: W 50 TYR cc_start: 0.7764 (m-80) cc_final: 0.7527 (m-80) REVERT: W 56 ARG cc_start: 0.8244 (mtt90) cc_final: 0.7889 (mtt90) REVERT: X 16 LYS cc_start: 0.9095 (mttt) cc_final: 0.8690 (tttm) REVERT: Y 54 GLN cc_start: 0.8743 (tt0) cc_final: 0.7724 (tm-30) REVERT: Y 58 ASP cc_start: 0.8556 (m-30) cc_final: 0.7925 (m-30) REVERT: Z 35 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6999 (pm20) REVERT: Z 44 ARG cc_start: 0.8295 (mmt180) cc_final: 0.7673 (mmt180) REVERT: a 172 HIS cc_start: 0.0507 (OUTLIER) cc_final: -0.1512 (t-170) outliers start: 292 outliers final: 241 residues processed: 1439 average time/residue: 1.3201 time to fit residues: 3358.9142 Evaluate side-chains 1507 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 1250 time to evaluate : 6.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 167 ASP Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 224 MET Chi-restraints excluded: chain c residue 21 SER Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 42 ASN Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 28 VAL Chi-restraints excluded: chain d residue 62 GLN Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 71 LEU Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain f residue 127 GLN Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 146 ASP Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 2 GLN Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 62 LEU Chi-restraints excluded: chain g residue 94 ILE Chi-restraints excluded: chain g residue 110 VAL Chi-restraints excluded: chain g residue 122 LEU Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain h residue 118 ILE Chi-restraints excluded: chain i residue 16 MET Chi-restraints excluded: chain i residue 78 LEU Chi-restraints excluded: chain i residue 116 MET Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 81 ILE Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain j residue 100 VAL Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain j residue 140 LEU Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 80 ASP Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 51 GLU Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 44 ARG Chi-restraints excluded: chain m residue 75 GLU Chi-restraints excluded: chain m residue 119 LEU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain m residue 136 MET Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain o residue 26 LEU Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 67 ASN Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain r residue 11 GLN Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 39 LEU Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 68 ASP Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 81 SER Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain u residue 5 ARG Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 68 LYS Chi-restraints excluded: chain w residue 71 LYS Chi-restraints excluded: chain x residue 34 SER Chi-restraints excluded: chain x residue 57 VAL Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 6 LEU Chi-restraints excluded: chain y residue 15 ASN Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain z residue 51 SER Chi-restraints excluded: chain A residue 16 CYS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 9 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain I residue 69 ARG Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 160 LEU Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 98 GLU Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 14 ASP Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 130 LYS Chi-restraints excluded: chain L residue 147 ASN Chi-restraints excluded: chain M residue 20 ASN Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain N residue 126 PHE Chi-restraints excluded: chain O residue 14 ASP Chi-restraints excluded: chain O residue 20 GLN Chi-restraints excluded: chain O residue 49 PHE Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 76 TYR Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain Q residue 17 LYS Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 76 HIS Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 95 HIS Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 58 MET Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 70 ARG Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain W residue 71 ASP Chi-restraints excluded: chain W residue 72 ARG Chi-restraints excluded: chain X residue 10 ILE Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 81 GLN Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain Z residue 62 GLU Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 172 HIS Chi-restraints excluded: chain a residue 222 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 926 optimal weight: 10.0000 chunk 976 optimal weight: 10.0000 chunk 890 optimal weight: 10.0000 chunk 949 optimal weight: 8.9990 chunk 975 optimal weight: 8.9990 chunk 571 optimal weight: 7.9990 chunk 413 optimal weight: 7.9990 chunk 745 optimal weight: 10.0000 chunk 291 optimal weight: 6.9990 chunk 857 optimal weight: 30.0000 chunk 897 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 167 ASN d 41 GLN d 62 GLN d 195 GLN ** e 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 136 GLN ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 ASN ** n 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 GLN r 6 GLN r 87 GLN u 39 ASN ** u 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN B 4 GLN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN ** L 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 HIS ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 4 ASN ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 172 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 161892 Z= 0.442 Angle : 0.730 12.102 242024 Z= 0.375 Chirality : 0.041 0.340 30928 Planarity : 0.005 0.085 13097 Dihedral : 23.574 179.138 80644 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 21.58 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.40 % Favored : 88.37 % Rotamer: Outliers : 6.28 % Allowed : 26.05 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.10), residues: 5983 helix: -0.28 (0.12), residues: 1899 sheet: -1.77 (0.15), residues: 1071 loop : -2.24 (0.11), residues: 3013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP I 169 HIS 0.008 0.001 HIS r 12 PHE 0.036 0.002 PHE H 36 TYR 0.029 0.002 TYR M 127 ARG 0.012 0.001 ARG q 10 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1578 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 312 poor density : 1266 time to evaluate : 6.050 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: d 7 ASP cc_start: 0.7693 (OUTLIER) cc_final: 0.7415 (p0) REVERT: d 35 TYR cc_start: 0.8701 (t80) cc_final: 0.8299 (t80) REVERT: e 51 ASN cc_start: 0.8817 (m-40) cc_final: 0.8394 (m110) REVERT: e 95 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7868 (ttt) REVERT: f 154 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7237 (pp20) REVERT: g 4 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.8012 (tp) REVERT: g 45 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8154 (mm-30) REVERT: i 39 LYS cc_start: 0.7676 (mmmt) cc_final: 0.7187 (ptpt) REVERT: i 44 LYS cc_start: 0.5701 (mttt) cc_final: 0.5323 (ptpt) REVERT: i 116 MET cc_start: -0.1858 (OUTLIER) cc_final: -0.2221 (tpt) REVERT: k 20 MET cc_start: 0.7346 (tmm) cc_final: 0.6924 (ttt) REVERT: p 8 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7695 (mt-10) REVERT: r 11 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8330 (mp10) REVERT: u 5 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7670 (mtt90) REVERT: y 13 GLU cc_start: 0.8631 (pt0) cc_final: 0.8371 (pt0) REVERT: A 25 ARG cc_start: 0.8475 (mtp-110) cc_final: 0.8204 (mtp85) REVERT: A 35 ASP cc_start: 0.7737 (p0) cc_final: 0.7382 (p0) REVERT: C 9 LYS cc_start: 0.8738 (ttpt) cc_final: 0.8377 (mmtm) REVERT: F 11 CYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8233 (p) REVERT: H 52 SER cc_start: 0.8789 (OUTLIER) cc_final: 0.8556 (p) REVERT: H 128 MET cc_start: 0.8243 (tpp) cc_final: 0.7715 (mtt) REVERT: I 160 LEU cc_start: 0.4133 (OUTLIER) cc_final: 0.3884 (mp) REVERT: J 13 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7787 (ttpp) REVERT: K 44 ARG cc_start: 0.8302 (ttm110) cc_final: 0.7913 (ttm110) REVERT: K 56 LYS cc_start: 0.7664 (tptt) cc_final: 0.7383 (tptt) REVERT: L 30 MET cc_start: 0.8599 (tpp) cc_final: 0.8012 (tpp) REVERT: L 67 ASN cc_start: 0.8496 (m-40) cc_final: 0.8259 (m-40) REVERT: L 96 ASN cc_start: 0.8855 (p0) cc_final: 0.7980 (p0) REVERT: L 100 MET cc_start: 0.8215 (mtp) cc_final: 0.7541 (mpp) REVERT: L 125 ASP cc_start: 0.8704 (t0) cc_final: 0.8317 (t0) REVERT: M 87 ARG cc_start: 0.8789 (mtm-85) cc_final: 0.8196 (ttm-80) REVERT: O 11 LYS cc_start: 0.9110 (pttt) cc_final: 0.8891 (ptpp) REVERT: O 43 PRO cc_start: 0.8430 (Cg_endo) cc_final: 0.8210 (Cg_exo) REVERT: Q 75 GLU cc_start: 0.8300 (tm-30) cc_final: 0.8096 (tm-30) REVERT: Q 76 HIS cc_start: 0.8477 (OUTLIER) cc_final: 0.7917 (m-70) REVERT: Q 77 SER cc_start: 0.6231 (OUTLIER) cc_final: 0.5475 (p) REVERT: Q 95 HIS cc_start: 0.7621 (OUTLIER) cc_final: 0.7278 (m-70) REVERT: R 43 LYS cc_start: 0.8696 (mppt) cc_final: 0.8281 (mmtm) REVERT: U 1 MET cc_start: 0.7295 (tpp) cc_final: 0.7018 (tpp) REVERT: U 14 ARG cc_start: 0.7517 (tpt170) cc_final: 0.7033 (mtp-110) REVERT: V 39 ARG cc_start: 0.7878 (mmm-85) cc_final: 0.7536 (mmp80) REVERT: W 50 TYR cc_start: 0.7835 (m-80) cc_final: 0.7585 (m-80) REVERT: W 56 ARG cc_start: 0.8272 (mtt90) cc_final: 0.7862 (mtt90) REVERT: X 16 LYS cc_start: 0.9095 (mttt) cc_final: 0.8699 (tttm) REVERT: Y 54 GLN cc_start: 0.8787 (tt0) cc_final: 0.7773 (tm-30) REVERT: Y 58 ASP cc_start: 0.8566 (m-30) cc_final: 0.7976 (m-30) REVERT: Z 35 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7156 (pm20) REVERT: Z 44 ARG cc_start: 0.8272 (mmt180) cc_final: 0.7846 (mmt180) outliers start: 312 outliers final: 258 residues processed: 1436 average time/residue: 1.2556 time to fit residues: 3167.9573 Evaluate side-chains 1517 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 1245 time to evaluate : 6.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 167 ASP Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain c residue 21 SER Chi-restraints excluded: chain c residue 42 ASN Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 28 VAL Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 71 LEU Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain f residue 127 GLN Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 146 ASP Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 2 GLN Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 62 LEU Chi-restraints excluded: chain g residue 94 ILE Chi-restraints excluded: chain g residue 110 VAL Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain h residue 118 ILE Chi-restraints excluded: chain i residue 16 MET Chi-restraints excluded: chain i residue 49 GLU Chi-restraints excluded: chain i residue 78 LEU Chi-restraints excluded: chain i residue 116 MET Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 81 ILE Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain j residue 100 VAL Chi-restraints excluded: chain j residue 102 GLU Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain j residue 140 LEU Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 80 ASP Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 14 LYS Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 51 GLU Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 103 ILE Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 75 GLU Chi-restraints excluded: chain m residue 119 LEU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain m residue 136 MET Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain o residue 38 GLN Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 67 ASN Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 19 PHE Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain r residue 11 GLN Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 39 LEU Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 68 ASP Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 81 SER Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain u residue 5 ARG Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 68 LYS Chi-restraints excluded: chain w residue 71 LYS Chi-restraints excluded: chain x residue 34 SER Chi-restraints excluded: chain x residue 51 SER Chi-restraints excluded: chain x residue 57 VAL Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 6 LEU Chi-restraints excluded: chain y residue 15 ASN Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain z residue 51 SER Chi-restraints excluded: chain A residue 16 CYS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 9 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 133 MET Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain I residue 69 ARG Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 160 LEU Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 98 GLU Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 14 ASP Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 130 LYS Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 147 ASN Chi-restraints excluded: chain M residue 20 ASN Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 29 SER Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain N residue 56 MET Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain N residue 126 PHE Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 14 ASP Chi-restraints excluded: chain O residue 20 GLN Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 76 TYR Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain Q residue 17 LYS Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 76 HIS Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 95 HIS Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain R residue 54 THR Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 58 MET Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 70 ARG Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 10 CYS Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain W residue 71 ASP Chi-restraints excluded: chain W residue 72 ARG Chi-restraints excluded: chain X residue 10 ILE Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 81 GLN Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain Z residue 62 GLU Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 222 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 946 optimal weight: 7.9990 chunk 623 optimal weight: 20.0000 chunk 1003 optimal weight: 6.9990 chunk 612 optimal weight: 10.0000 chunk 476 optimal weight: 10.0000 chunk 697 optimal weight: 20.0000 chunk 1053 optimal weight: 20.0000 chunk 969 optimal weight: 50.0000 chunk 838 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 647 optimal weight: 20.0000 overall best weight: 8.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 94 GLN ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 41 GLN d 62 GLN d 195 GLN ** e 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 136 GLN ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 ASN ** n 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 GLN r 6 GLN r 87 GLN ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 39 ASN ** u 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 GLN ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 GLN ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 HIS ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 4 GLN ** O 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 4 ASN ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 172 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 161892 Z= 0.437 Angle : 0.733 15.280 242024 Z= 0.376 Chirality : 0.042 0.521 30928 Planarity : 0.005 0.083 13097 Dihedral : 23.639 178.781 80644 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 21.67 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.28 % Favored : 89.49 % Rotamer: Outliers : 5.96 % Allowed : 26.90 % Favored : 67.14 % 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: -2.30 (0.10), residues: 5983 helix: -0.28 (0.12), residues: 1888 sheet: -1.75 (0.15), residues: 1064 loop : -2.28 (0.11), residues: 3031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP I 169 HIS 0.007 0.001 HIS r 12 PHE 0.036 0.002 PHE q 105 TYR 0.030 0.002 TYR M 127 ARG 0.013 0.001 ARG F 4 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1554 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 1258 time to evaluate : 6.788 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: d 7 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7434 (p0) REVERT: d 35 TYR cc_start: 0.8698 (t80) cc_final: 0.8299 (t80) REVERT: e 51 ASN cc_start: 0.8817 (m-40) cc_final: 0.8427 (m110) REVERT: e 95 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7869 (ttt) REVERT: f 154 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7359 (tm-30) REVERT: g 45 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8119 (mm-30) REVERT: i 39 LYS cc_start: 0.7681 (mmmt) cc_final: 0.7173 (ptpt) REVERT: i 116 MET cc_start: -0.2062 (OUTLIER) cc_final: -0.2406 (tpt) REVERT: k 20 MET cc_start: 0.7338 (tmm) cc_final: 0.6931 (ttt) REVERT: p 8 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7704 (mt-10) REVERT: r 6 GLN cc_start: 0.7678 (tm130) cc_final: 0.7450 (tm-30) REVERT: r 11 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8308 (mp10) REVERT: u 5 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7807 (mtt90) REVERT: x 55 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7346 (mtp) REVERT: y 13 GLU cc_start: 0.8618 (pt0) cc_final: 0.8309 (pt0) REVERT: A 25 ARG cc_start: 0.8471 (mtp-110) cc_final: 0.8200 (mtp85) REVERT: A 35 ASP cc_start: 0.7751 (p0) cc_final: 0.7430 (p0) REVERT: C 9 LYS cc_start: 0.8696 (ttpt) cc_final: 0.8368 (mmtm) REVERT: F 11 CYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8156 (p) REVERT: G 153 MET cc_start: 0.7407 (tpt) cc_final: 0.7046 (tpp) REVERT: H 52 SER cc_start: 0.8790 (OUTLIER) cc_final: 0.8563 (p) REVERT: H 128 MET cc_start: 0.8276 (tpp) cc_final: 0.7743 (mtt) REVERT: I 160 LEU cc_start: 0.4148 (OUTLIER) cc_final: 0.3889 (mp) REVERT: J 13 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7788 (ttpp) REVERT: K 17 GLN cc_start: 0.8205 (pm20) cc_final: 0.7907 (pm20) REVERT: L 30 MET cc_start: 0.8598 (tpp) cc_final: 0.8005 (tpp) REVERT: L 67 ASN cc_start: 0.8516 (m-40) cc_final: 0.8281 (m-40) REVERT: L 96 ASN cc_start: 0.8874 (p0) cc_final: 0.8000 (p0) REVERT: L 100 MET cc_start: 0.8214 (mtp) cc_final: 0.7537 (mpp) REVERT: L 125 ASP cc_start: 0.8702 (t0) cc_final: 0.8324 (t0) REVERT: M 79 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8464 (mtp-110) REVERT: M 87 ARG cc_start: 0.8845 (mtm-85) cc_final: 0.8213 (ttm-80) REVERT: O 11 LYS cc_start: 0.9094 (pttt) cc_final: 0.8892 (ptpp) REVERT: O 43 PRO cc_start: 0.8383 (Cg_endo) cc_final: 0.8169 (Cg_exo) REVERT: Q 76 HIS cc_start: 0.8468 (OUTLIER) cc_final: 0.7989 (m-70) REVERT: Q 77 SER cc_start: 0.6283 (OUTLIER) cc_final: 0.5555 (p) REVERT: R 43 LYS cc_start: 0.8730 (mppt) cc_final: 0.8337 (mmtm) REVERT: U 1 MET cc_start: 0.7107 (tpp) cc_final: 0.6773 (tpp) REVERT: U 14 ARG cc_start: 0.7492 (tpt170) cc_final: 0.7042 (mtp-110) REVERT: V 39 ARG cc_start: 0.7893 (mmm-85) cc_final: 0.7612 (mmp80) REVERT: W 50 TYR cc_start: 0.7825 (m-80) cc_final: 0.7596 (m-80) REVERT: W 56 ARG cc_start: 0.8274 (mtt90) cc_final: 0.7860 (mtt90) REVERT: W 69 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.8207 (m-10) REVERT: W 72 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7356 (mmt180) REVERT: X 12 LEU cc_start: 0.8453 (mp) cc_final: 0.8047 (mt) REVERT: X 16 LYS cc_start: 0.9092 (mttt) cc_final: 0.8692 (tttm) REVERT: Y 54 GLN cc_start: 0.8786 (tt0) cc_final: 0.8254 (tm-30) REVERT: Z 35 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7133 (pm20) REVERT: Z 44 ARG cc_start: 0.8392 (mmt180) cc_final: 0.7859 (mmt180) outliers start: 296 outliers final: 251 residues processed: 1419 average time/residue: 1.2572 time to fit residues: 3140.2493 Evaluate side-chains 1503 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 1236 time to evaluate : 6.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 167 ASP Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 194 VAL Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain c residue 21 SER Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 28 VAL Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 71 LEU Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 146 ASP Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 2 GLN Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 62 LEU Chi-restraints excluded: chain g residue 94 ILE Chi-restraints excluded: chain g residue 110 VAL Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 118 ILE Chi-restraints excluded: chain i residue 16 MET Chi-restraints excluded: chain i residue 49 GLU Chi-restraints excluded: chain i residue 78 LEU Chi-restraints excluded: chain i residue 116 MET Chi-restraints excluded: chain j residue 81 ILE Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 102 GLU Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain j residue 140 LEU Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 80 ASP Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 14 LYS Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 51 GLU Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 103 ILE Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 44 ARG Chi-restraints excluded: chain m residue 119 LEU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain m residue 136 MET Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain o residue 38 GLN Chi-restraints excluded: chain o residue 67 ASN Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 19 PHE Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain r residue 11 GLN Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 39 LEU Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 68 ASP Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 81 SER Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain u residue 5 ARG Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 68 LYS Chi-restraints excluded: chain w residue 71 LYS Chi-restraints excluded: chain x residue 34 SER Chi-restraints excluded: chain x residue 51 SER Chi-restraints excluded: chain x residue 55 MET Chi-restraints excluded: chain x residue 57 VAL Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 6 LEU Chi-restraints excluded: chain y residue 8 GLU Chi-restraints excluded: chain y residue 15 ASN Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain z residue 51 SER Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 9 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 133 MET Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain I residue 69 ARG Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 160 LEU Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 98 GLU Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 14 ASP Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 130 LYS Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 147 ASN Chi-restraints excluded: chain M residue 20 ASN Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 29 SER Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 79 ARG Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 99 LYS Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain N residue 126 PHE Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 14 ASP Chi-restraints excluded: chain O residue 20 GLN Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 76 TYR Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain Q residue 17 LYS Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 76 HIS Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain R residue 54 THR Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 58 MET Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 70 ARG Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain W residue 10 CYS Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain W residue 69 TYR Chi-restraints excluded: chain W residue 71 ASP Chi-restraints excluded: chain W residue 72 ARG Chi-restraints excluded: chain X residue 10 ILE Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 81 GLN Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain Z residue 62 GLU Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 222 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 514 optimal weight: 0.0470 chunk 666 optimal weight: 8.9990 chunk 893 optimal weight: 10.0000 chunk 256 optimal weight: 7.9990 chunk 773 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 chunk 233 optimal weight: 0.7980 chunk 839 optimal weight: 8.9990 chunk 351 optimal weight: 8.9990 chunk 862 optimal weight: 30.0000 chunk 106 optimal weight: 8.9990 overall best weight: 4.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 41 GLN d 62 GLN d 195 GLN ** e 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 136 GLN ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 ASN l 38 GLN ** n 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 GLN t 48 GLN u 39 ASN ** u 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 HIS ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 4 GLN ** N 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 4 ASN Q 72 ASN ** Q 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.052909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.038152 restraints weight = 828045.938| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.31 r_work: 0.2806 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 161892 Z= 0.253 Angle : 0.640 14.797 242024 Z= 0.329 Chirality : 0.037 0.379 30928 Planarity : 0.005 0.079 13097 Dihedral : 23.587 179.530 80644 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.54 % Favored : 90.26 % Rotamer: Outliers : 4.81 % Allowed : 28.05 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.11), residues: 5983 helix: 0.01 (0.12), residues: 1882 sheet: -1.57 (0.16), residues: 1061 loop : -2.09 (0.11), residues: 3040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP I 169 HIS 0.008 0.001 HIS P 117 PHE 0.037 0.002 PHE H 36 TYR 0.035 0.002 TYR K 25 ARG 0.014 0.001 ARG F 4 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 47081.47 seconds wall clock time: 818 minutes 48.60 seconds (49128.60 seconds total)