Starting phenix.real_space_refine on Mon Feb 26 05:49:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6og7_20052/02_2024/6og7_20052.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6og7_20052/02_2024/6og7_20052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6og7_20052/02_2024/6og7_20052.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6og7_20052/02_2024/6og7_20052.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6og7_20052/02_2024/6og7_20052.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6og7_20052/02_2024/6og7_20052.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.480 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 4652 5.49 5 S 152 5.16 5 C 74506 2.51 5 N 27528 2.21 5 O 40956 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b GLU 22": "OE1" <-> "OE2" Residue "b ASP 120": "OD1" <-> "OD2" Residue "c ARG 13": "NH1" <-> "NH2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c ARG 59": "NH1" <-> "NH2" Residue "c ARG 77": "NH1" <-> "NH2" Residue "c ARG 83": "NH1" <-> "NH2" Residue "c GLU 88": "OE1" <-> "OE2" Residue "c ASP 103": "OD1" <-> "OD2" Residue "c PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 169": "NH1" <-> "NH2" Residue "c ARG 184": "NH1" <-> "NH2" Residue "d ASP 7": "OD1" <-> "OD2" Residue "d PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 49": "NH1" <-> "NH2" Residue "d ARG 61": "NH1" <-> "NH2" Residue "d ARG 88": "NH1" <-> "NH2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "d ARG 162": "NH1" <-> "NH2" Residue "d ARG 170": "NH1" <-> "NH2" Residue "e ASP 45": "OD1" <-> "OD2" Residue "e ARG 70": "NH1" <-> "NH2" Residue "e ARG 79": "NH1" <-> "NH2" Residue "e ARG 91": "NH1" <-> "NH2" Residue "e ARG 101": "NH1" <-> "NH2" Residue "e ARG 109": "NH1" <-> "NH2" Residue "e ARG 111": "NH1" <-> "NH2" Residue "e ARG 114": "NH1" <-> "NH2" Residue "e ARG 132": "NH1" <-> "NH2" Residue "e ASP 146": "OD1" <-> "OD2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "f GLU 123": "OE1" <-> "OE2" Residue "f GLU 129": "OE1" <-> "OE2" Residue "f ARG 152": "NH1" <-> "NH2" Residue "f ARG 162": "NH1" <-> "NH2" Residue "f ASP 165": "OD1" <-> "OD2" Residue "f GLU 166": "OE1" <-> "OE2" Residue "f ARG 169": "NH1" <-> "NH2" Residue "g GLU 48": "OE1" <-> "OE2" Residue "g GLU 53": "OE1" <-> "OE2" Residue "g ASP 86": "OD1" <-> "OD2" Residue "g ASP 101": "OD1" <-> "OD2" Residue "g GLU 114": "OE1" <-> "OE2" Residue "g GLU 127": "OE1" <-> "OE2" Residue "g GLU 129": "OE1" <-> "OE2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j GLU 90": "OE1" <-> "OE2" Residue "j GLU 91": "OE1" <-> "OE2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "j GLU 129": "OE1" <-> "OE2" Residue "j ASP 141": "OD1" <-> "OD2" Residue "k GLU 92": "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 91": "OD1" <-> "OD2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "l GLU 136": "OE1" <-> "OE2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 18": "NH1" <-> "NH2" Residue "m ASP 25": "OD1" <-> "OD2" Residue "m PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 40": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m ARG 50": "NH1" <-> "NH2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m ARG 59": "NH1" <-> "NH2" Residue "m TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 114": "NH1" <-> "NH2" Residue "n ARG 8": "NH1" <-> "NH2" Residue "n ARG 12": "NH1" <-> "NH2" Residue "n ARG 17": "NH1" <-> "NH2" Residue "n ARG 22": "NH1" <-> "NH2" Residue "n ARG 46": "NH1" <-> "NH2" Residue "n ARG 63": "NH1" <-> "NH2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n ARG 69": "NH1" <-> "NH2" Residue "n ARG 71": "NH1" <-> "NH2" Residue "n ARG 96": "NH1" <-> "NH2" Residue "n ASP 106": "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 GLU 46": "OE1" <-> "OE2" Residue "o ARG 81": "NH1" <-> "NH2" Residue "o ASP 89": "OD1" <-> "OD2" Residue "o ARG 94": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ASP 108": "OD1" <-> "OD2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "p ARG 20": "NH1" <-> "NH2" Residue "p GLU 33": "OE1" <-> "OE2" Residue "p ARG 38": "NH1" <-> "NH2" Residue "p ARG 61": "NH1" <-> "NH2" Residue "p GLU 70": "OE1" <-> "OE2" Residue "p ARG 88": "NH1" <-> "NH2" Residue "p ARG 100": "NH1" <-> "NH2" Residue "p 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 ASP 96": "OD1" <-> "OD2" Residue "q PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 101": "OD1" <-> "OD2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r GLU 23": "OE1" <-> "OE2" Residue "r GLU 34": "OE1" <-> "OE2" Residue "r GLU 37": "OE1" <-> "OE2" Residue "r ARG 68": "NH1" <-> "NH2" Residue "r ARG 78": "NH1" <-> "NH2" Residue "r ARG 79": "NH1" <-> "NH2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "s ASP 68": "OD1" <-> "OD2" Residue "s GLU 78": "OE1" <-> "OE2" 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 ASP 37": "OD1" <-> "OD2" Residue "t ARG 73": "NH1" <-> "NH2" Residue "u ARG 5": "NH1" <-> "NH2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u ARG 81": "NH1" <-> "NH2" Residue "u ARG 85": "NH1" <-> "NH2" Residue "u ARG 93": "NH1" <-> "NH2" Residue "v ASP 45": "OD1" <-> "OD2" Residue "v ASP 90": "OD1" <-> "OD2" Residue "w GLU 13": "OE1" <-> "OE2" Residue "y ARG 29": "NH1" <-> "NH2" Residue "y ARG 47": "NH1" <-> "NH2" Residue "y ARG 52": "NH1" <-> "NH2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 29": "NH1" <-> "NH2" Residue "z ARG 44": "NH1" <-> "NH2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ASP 45": "OD1" <-> "OD2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "C GLU 34": "OE1" <-> "OE2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "D ARG 3": "NH1" <-> "NH2" Residue "D ARG 12": "NH1" <-> "NH2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D ARG 19": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 41": "NH1" <-> "NH2" Residue "E ARG 12": "NH1" <-> "NH2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "E ARG 41": "NH1" <-> "NH2" Residue "F ARG 12": "NH1" <-> "NH2" Residue "F ARG 24": "NH1" <-> "NH2" Residue "G ASP 122": "OD1" <-> "OD2" Residue "G ASP 126": "OD1" <-> "OD2" Residue "G GLU 141": "OE1" <-> "OE2" Residue "G GLU 144": "OE1" <-> "OE2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "H ASP 30": "OD1" <-> "OD2" Residue "H GLU 81": "OE1" <-> "OE2" Residue "H GLU 84": "OE1" <-> "OE2" Residue "H ASP 92": "OD1" <-> "OD2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H GLU 109": "OE1" <-> "OE2" Residue "H ASP 117": "OD1" <-> "OD2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "H GLU 151": "OE1" <-> "OE2" Residue "H GLU 165": "OE1" <-> "OE2" Residue "I ASP 17": "OD1" <-> "OD2" Residue "I GLU 94": "OE1" <-> "OE2" Residue "I GLU 196": "OE1" <-> "OE2" Residue "J GLU 54": "OE1" <-> "OE2" Residue "J GLU 144": "OE1" <-> "OE2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "K GLU 5": "OE1" <-> "OE2" Residue "K GLU 69": "OE1" <-> "OE2" Residue "K GLU 98": "OE1" <-> "OE2" Residue "L PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 20": "OE1" <-> "OE2" Residue "L GLU 39": "OE1" <-> "OE2" Residue "L GLU 73": "OE1" <-> "OE2" Residue "L GLU 128": "OE1" <-> "OE2" Residue "L ASP 139": "OD1" <-> "OD2" Residue "M GLU 72": "OE1" <-> "OE2" Residue "N GLU 35": "OE1" <-> "OE2" Residue "N GLU 96": "OE1" <-> "OE2" Residue "N ASP 106": "OD1" <-> "OD2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "O ASP 63": "OD1" <-> "OD2" Residue "P ASP 71": "OD1" <-> "OD2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q ASP 102": "OD1" <-> "OD2" Residue "R ASP 41": "OD1" <-> "OD2" Residue "S ASP 17": "OD1" <-> "OD2" Residue "S PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 53": "OD1" <-> "OD2" Residue "T GLU 5": "OE1" <-> "OE2" Residue "T GLU 25": "OE1" <-> "OE2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 55": "OD1" <-> "OD2" Residue "V GLU 25": "OE1" <-> "OE2" Residue "V ASP 56": "OD1" <-> "OD2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "W ASP 71": "OD1" <-> "OD2" Residue "X ASP 63": "OD1" <-> "OD2" Residue "X GLU 64": "OE1" <-> "OE2" Residue "Z GLU 38": "OE1" <-> "OE2" Residue "Z ARG 66": "NH1" <-> "NH2" Residue "a ARG 7": "NH1" <-> "NH2" Residue "a ARG 12": "NH1" <-> "NH2" Residue "a ASP 22": "OD1" <-> "OD2" Residue "a GLU 25": "OE1" <-> "OE2" Residue "a ASP 43": "OD1" <-> "OD2" Residue "a ARG 162": "NH1" <-> "NH2" Residue "8 ASP 28": "OD1" <-> "OD2" Residue "8 GLU 40": "OE1" <-> "OE2" Residue "8 GLU 49": "OE1" <-> "OE2" Residue "8 GLU 64": "OE1" <-> "OE2" Residue "8 ASP 79": "OD1" <-> "OD2" Residue "8 GLU 89": "OE1" <-> "OE2" Residue "8 ASP 91": "OD1" <-> "OD2" Residue "8 GLU 114": "OE1" <-> "OE2" Residue "8 ASP 143": "OD1" <-> "OD2" Residue "8 GLU 149": "OE1" <-> "OE2" Residue "8 GLU 170": "OE1" <-> "OE2" Residue "8 GLU 172": "OE1" <-> "OE2" Residue "8 ARG 213": "NH1" <-> "NH2" Residue "8 ASP 229": "OD1" <-> "OD2" Residue "8 GLU 233": "OE1" <-> "OE2" Residue "8 TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 285": "OD1" <-> "OD2" Residue "8 GLU 299": "OE1" <-> "OE2" Residue "8 ASP 329": "OD1" <-> "OD2" Residue "8 GLU 358": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 147794 Number of models: 1 Model: "" Number of chains: 55 Chain: "b" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "c" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "d" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "e" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "f" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "g" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "j" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "k" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "l" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "m" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "n" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 961 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "o" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "p" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "r" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "s" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "t" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 739 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "u" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "v" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "w" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "x" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "B" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "C" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 410 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "D" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "E" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "F" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "G" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1757 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "H" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1625 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "I" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "J" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1157 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "K" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 824 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "L" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1182 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "M" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "N" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "O" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 787 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "P" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 870 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "Q" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "R" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 884 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "S" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "T" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "U" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "V" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "W" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 536 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "X" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "Y" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "Z" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 545 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "a" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1027 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 1 Chain: "3" Number of atoms: 33012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33012 Classifications: {'RNA': 1539} Modifications used: {'5*END': 1, 'rna2p_pur': 92, 'rna2p_pyr': 49, 'rna3p_pur': 782, 'rna3p_pyr': 616} Link IDs: {'rna2p': 141, 'rna3p': 1397} Chain: "1" Number of atoms: 62317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62317 Classifications: {'RNA': 2903} Modifications used: {'5*END': 1, 'rna2p_pur': 219, 'rna2p_pyr': 98, 'rna3p_pur': 1455, 'rna3p_pyr': 1131} Link IDs: {'rna2p': 317, 'rna3p': 2585} Chain: "2" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2568 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 61, 'rna3p_pyr': 53} Link IDs: {'rna2p': 6, 'rna3p': 113} Chain: "5" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1598 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 33, 'rna3p_pyr': 32} Link IDs: {'rna2p': 10, 'rna3p': 64} Chain: "4" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 437 Classifications: {'RNA': 20} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 14, 'rna3p_pyr': 3} Link IDs: {'rna2p': 3, 'rna3p': 16} Chain: "8" Number of atoms: 2860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2860 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 7, 'TRANS': 353} Time building chain proxies: 57.55, per 1000 atoms: 0.39 Number of scatterers: 147794 At special positions: 0 Unit cell: (232.116, 260.13, 270.802, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 152 16.00 P 4652 15.00 O 40956 8.00 N 27528 7.00 C 74506 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: 64.45 Conformation dependent library (CDL) restraints added in 7.3 seconds 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11242 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 75 sheets defined 35.2% alpha, 17.0% beta 1271 base pairs and 2343 stacking pairs defined. Time for finding SS restraints: 51.59 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: 3.753A 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: 3.902A pdb=" N LEU c 100 " --> pdb=" O SER c 97 " (cutoff:3.500A) Processing helix chain 'c' and resid 120 through 125 Processing helix chain 'd' and resid 15 through 20 Processing helix chain 'd' and resid 24 through 38 Processing helix chain 'd' and resid 97 through 113 Processing helix chain 'd' and resid 130 through 142 Processing helix chain 'd' and resid 154 through 161 removed outlier: 3.603A pdb=" N ALA d 160 " --> pdb=" O ASN d 156 " (cutoff:3.500A) Processing helix chain 'd' and resid 176 through 183 Processing helix chain 'd' and resid 190 through 200 removed outlier: 3.731A pdb=" N LYS d 194 " --> pdb=" O ALA d 190 " (cutoff:3.500A) Processing helix chain 'e' and resid 2 through 17 removed outlier: 5.609A pdb=" N VAL e 12 " --> pdb=" O LYS e 8 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS e 13 " --> pdb=" O ASP e 9 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS e 14 " --> pdb=" O GLU e 10 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU e 15 " --> pdb=" O VAL e 11 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR e 17 " --> pdb=" O LYS e 13 " (cutoff:3.500A) Processing helix chain 'e' and resid 23 through 27 removed outlier: 3.571A pdb=" N VAL e 27 " --> pdb=" O VAL e 24 " (cutoff:3.500A) Processing helix chain 'e' and resid 47 through 59 removed outlier: 3.580A pdb=" N ALA e 54 " --> pdb=" O ASP e 50 " (cutoff:3.500A) Processing helix chain 'e' and resid 93 through 104 Processing helix chain 'e' and resid 133 through 137 removed outlier: 3.721A pdb=" N ILE e 136 " --> pdb=" O GLU e 133 " (cutoff:3.500A) Processing helix chain 'e' and resid 161 through 170 removed outlier: 4.565A pdb=" N ALA e 167 " --> pdb=" O GLU e 163 " (cutoff:3.500A) Processing helix chain 'f' and resid 59 through 80 removed outlier: 3.554A pdb=" N THR f 79 " --> pdb=" O VAL f 75 " (cutoff:3.500A) Processing helix chain 'f' and resid 136 through 149 Processing helix chain 'g' and resid 22 through 28 Processing helix chain 'g' and resid 40 through 48 removed outlier: 3.583A pdb=" N GLU g 45 " --> pdb=" O LYS g 41 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU g 48 " --> pdb=" O ILE g 44 " (cutoff:3.500A) Processing helix chain 'g' and resid 54 through 70 removed outlier: 3.586A pdb=" N ALA g 67 " --> pdb=" O ALA g 63 " (cutoff:3.500A) Processing helix chain 'g' and resid 71 through 74 removed outlier: 3.889A pdb=" N ALA g 74 " --> pdb=" O LYS g 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 71 through 74' Processing helix chain 'g' and resid 96 through 107 removed outlier: 3.986A pdb=" N ALA g 100 " --> pdb=" O THR g 96 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA g 105 " --> pdb=" O ASP g 101 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 37 Processing helix chain 'j' and resid 67 through 72 Processing helix chain 'j' and resid 88 through 96 Processing helix chain 'j' and resid 98 through 107 removed outlier: 3.639A pdb=" N GLU j 102 " --> pdb=" O GLU j 98 " (cutoff:3.500A) 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 removed outlier: 3.542A pdb=" N LEU k 107 " --> pdb=" O THR k 104 " (cutoff:3.500A) Processing helix chain 'k' and resid 112 through 118 Processing helix chain 'l' and resid 2 through 6 removed outlier: 3.962A pdb=" N LEU l 6 " --> pdb=" O LEU l 3 " (cutoff:3.500A) Processing helix chain 'l' and resid 37 through 41 removed outlier: 3.751A pdb=" N SER l 40 " --> pdb=" O GLY l 37 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 61 Processing helix chain 'l' and resid 68 through 72 Processing helix chain 'l' and resid 80 through 85 removed outlier: 4.597A pdb=" N ALA l 83 " --> pdb=" O SER l 80 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL l 85 " --> pdb=" O LEU l 82 " (cutoff:3.500A) Processing helix chain 'l' and resid 128 through 138 Processing helix chain 'm' and resid 43 through 57 removed outlier: 3.742A pdb=" N ALA m 56 " --> pdb=" O ALA m 52 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 122 Processing helix chain 'n' and resid 13 through 32 Processing helix chain 'n' and resid 38 through 56 removed outlier: 4.649A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) removed outlier: 3.549A 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 60 through 69 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 22 removed outlier: 4.673A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 60 Processing helix chain 'o' and resid 67 through 86 removed outlier: 3.781A pdb=" N LEU o 83 " --> pdb=" O ALA o 79 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU o 84 " --> pdb=" O GLU o 80 " (cutoff:3.500A) Processing helix chain 'o' and resid 101 through 114 Processing helix chain 'p' and resid 2 through 10 removed outlier: 3.609A pdb=" N GLU p 10 " --> pdb=" O GLN p 6 " (cutoff:3.500A) Processing helix chain 'p' and resid 52 through 55 Processing helix chain 'p' and resid 96 through 100 Processing helix chain 'p' and resid 103 through 108 Processing helix chain 'q' and resid 8 through 20 removed outlier: 3.841A pdb=" N GLN q 19 " --> pdb=" O LYS q 15 " (cutoff:3.500A) Processing helix chain 'q' and resid 24 through 28 Processing helix chain 'q' and resid 30 through 71 removed outlier: 4.335A pdb=" N GLN q 36 " --> pdb=" O ARG q 32 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG q 50 " --> pdb=" O TYR q 46 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LYS q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) Processing helix chain 'q' and resid 74 through 85 Processing helix chain 'q' and resid 90 through 100 Processing helix chain 'q' and resid 101 through 116 Processing helix chain 's' and resid 13 through 22 removed outlier: 3.723A pdb=" N VAL s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 37 Processing helix chain 's' and resid 41 through 61 removed outlier: 3.546A pdb=" N VAL s 45 " --> pdb=" O LYS s 41 " (cutoff:3.500A) Processing helix chain 's' and resid 89 through 91 No H-bonds generated for 'chain 's' and resid 89 through 91' Processing helix chain 't' and resid 2 through 10 removed outlier: 3.734A pdb=" N LEU t 7 " --> pdb=" O ARG t 3 " (cutoff:3.500A) removed outlier: 3.867A 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 'u' and resid 14 through 18 removed outlier: 3.997A pdb=" N ASP u 17 " --> pdb=" O THR u 14 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS u 18 " --> pdb=" O GLY u 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 14 through 18' Processing helix chain 'v' and resid 13 through 22 Processing helix chain 'v' and resid 43 through 51 removed outlier: 4.068A pdb=" N VAL v 47 " --> pdb=" O ASP v 43 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN v 49 " --> pdb=" O ASP v 45 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET v 50 " --> pdb=" O LYS v 46 " (cutoff:3.500A) Processing helix chain 'v' and resid 54 through 59 removed outlier: 4.024A pdb=" N SER v 58 " --> pdb=" O ALA v 54 " (cutoff:3.500A) Processing helix chain 'x' and resid 52 through 61 removed outlier: 3.674A pdb=" N ARG x 56 " --> pdb=" O ALA x 52 " (cutoff:3.500A) Processing helix chain 'x' and resid 62 through 74 Processing helix chain 'y' and resid 9 through 22 removed outlier: 3.529A pdb=" N LEU y 18 " --> pdb=" O LEU y 14 " (cutoff:3.500A) Processing helix chain 'y' and resid 24 through 34 Processing helix chain 'y' and resid 40 through 61 removed outlier: 4.045A pdb=" N LYS y 44 " --> pdb=" O SER y 40 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 26 Processing helix chain 'z' and resid 40 through 50 Processing helix chain 'B' and resid 8 through 16 Processing helix chain 'B' and resid 17 through 20 removed outlier: 4.134A pdb=" N ALA B 20 " --> pdb=" O SER B 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 17 through 20' Processing helix chain 'D' and resid 8 through 17 Processing helix chain 'D' and resid 17 through 22 Processing helix chain 'D' and resid 24 through 38 Processing helix chain 'E' and resid 6 through 11 removed outlier: 3.687A pdb=" N LYS E 11 " --> pdb=" O ARG E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 43 removed outlier: 3.515A pdb=" N LEU E 43 " --> pdb=" O ARG E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 61 removed outlier: 3.724A pdb=" N VAL E 57 " --> pdb=" O ASP E 53 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA E 59 " --> pdb=" O GLY E 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 12 removed outlier: 4.044A pdb=" N LYS G 10 " --> pdb=" O ARG G 6 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA G 11 " --> pdb=" O ASP G 7 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY G 12 " --> pdb=" O MET G 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 6 through 12' Processing helix chain 'G' and resid 23 through 30 Proline residue: G 28 - end of helix Processing helix chain 'G' and resid 33 through 37 removed outlier: 3.729A pdb=" N LYS G 36 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 43 No H-bonds generated for 'chain 'G' and resid 41 through 43' Processing helix chain 'G' and resid 44 through 62 removed outlier: 4.204A pdb=" N MET G 48 " --> pdb=" O LYS G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 85 Processing helix chain 'G' and resid 102 through 120 removed outlier: 4.885A pdb=" N GLN G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 128 Processing helix chain 'G' and resid 129 through 146 removed outlier: 4.019A pdb=" N SER G 146 " --> pdb=" O LYS G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 177 removed outlier: 3.685A pdb=" N ILE G 172 " --> pdb=" O GLU G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 222 removed outlier: 3.865A pdb=" N VAL G 209 " --> pdb=" O ALA G 205 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 225 No H-bonds generated for 'chain 'G' and resid 223 through 225' Processing helix chain 'H' and resid 7 through 11 Processing helix chain 'H' and resid 27 through 47 removed outlier: 3.637A pdb=" N ASN H 31 " --> pdb=" O GLU H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 77 Processing helix chain 'H' and resid 80 through 95 removed outlier: 3.695A pdb=" N ALA H 91 " --> pdb=" O ARG H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 124 removed outlier: 3.626A pdb=" N GLN H 122 " --> pdb=" O SER H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 144 Processing helix chain 'I' and resid 6 through 15 removed outlier: 4.448A pdb=" N LEU I 10 " --> pdb=" O PRO I 6 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER I 11 " --> pdb=" O LYS I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 65 removed outlier: 3.772A pdb=" N TYR I 64 " --> pdb=" O VAL I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 79 Processing helix chain 'I' and resid 84 through 95 removed outlier: 4.289A pdb=" N LEU I 90 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA I 91 " --> pdb=" O GLU I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 104 Processing helix chain 'I' and resid 109 through 119 Processing helix chain 'I' and resid 146 through 149 Processing helix chain 'I' and resid 153 through 160 Processing helix chain 'I' and resid 161 through 164 Processing helix chain 'I' and resid 195 through 204 removed outlier: 3.950A pdb=" N ILE I 199 " --> pdb=" O ASN I 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 68 Processing helix chain 'J' and resid 109 through 116 Processing helix chain 'J' and resid 131 through 146 removed outlier: 3.827A pdb=" N ARG J 137 " --> pdb=" O ILE J 133 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE J 140 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP J 141 " --> pdb=" O ARG J 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 153 removed outlier: 3.587A pdb=" N VAL J 152 " --> pdb=" O SER J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 164 Processing helix chain 'K' and resid 13 through 16 removed outlier: 3.577A pdb=" N GLU K 16 " --> pdb=" O ASP K 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 13 through 16' Processing helix chain 'K' and resid 17 through 31 Processing helix chain 'K' and resid 67 through 80 removed outlier: 3.547A pdb=" N ILE K 71 " --> pdb=" O PRO K 67 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP K 72 " --> pdb=" O GLN K 68 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR K 76 " --> pdb=" O ASP K 72 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE K 78 " --> pdb=" O LEU K 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 30 Processing helix chain 'L' and resid 36 through 52 Processing helix chain 'L' and resid 56 through 66 removed outlier: 3.947A pdb=" N GLU L 62 " --> pdb=" O LEU L 58 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA L 64 " --> pdb=" O ALA L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 108 removed outlier: 3.961A pdb=" N ALA L 97 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE L 103 " --> pdb=" O ALA L 99 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA L 106 " --> pdb=" O TRP L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 128 removed outlier: 3.550A pdb=" N ASP L 125 " --> pdb=" O ASN L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 146 removed outlier: 3.560A pdb=" N ARG L 137 " --> pdb=" O ALA L 133 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA L 146 " --> pdb=" O ARG L 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 19 removed outlier: 3.590A pdb=" N ARG M 12 " --> pdb=" O ASP M 8 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 43 Processing helix chain 'M' and resid 93 through 98 removed outlier: 3.859A pdb=" N ALA M 96 " --> pdb=" O LYS M 93 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU M 98 " --> pdb=" O MET M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 119 Processing helix chain 'N' and resid 34 through 38 removed outlier: 3.934A pdb=" N PHE N 38 " --> pdb=" O LEU N 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 34 through 38' Processing helix chain 'N' and resid 49 through 53 removed outlier: 3.513A pdb=" N LEU N 53 " --> pdb=" O PRO N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 86 removed outlier: 3.509A pdb=" N ILE N 78 " --> pdb=" O GLN N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 90 through 95 Processing helix chain 'N' and resid 96 through 99 Processing helix chain 'O' and resid 14 through 31 removed outlier: 3.639A pdb=" N ILE O 18 " --> pdb=" O ASP O 14 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N GLN O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA O 29 " --> pdb=" O ILE O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 88 Processing helix chain 'P' and resid 58 through 71 removed outlier: 3.601A pdb=" N GLU P 67 " --> pdb=" O GLN P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 93 through 101 removed outlier: 4.159A pdb=" N ARG P 97 " --> pdb=" O GLU P 93 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 9 Processing helix chain 'Q' and resid 114 through 118 removed outlier: 4.385A pdb=" N VAL Q 118 " --> pdb=" O LYS Q 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 20 removed outlier: 3.611A pdb=" N SER R 20 " --> pdb=" O ILE R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 37 Processing helix chain 'R' and resid 43 through 47 Processing helix chain 'R' and resid 48 through 60 removed outlier: 4.640A pdb=" N THR R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP R 57 " --> pdb=" O ASP R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 81 removed outlier: 3.579A pdb=" N ARG R 69 " --> pdb=" O GLU R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 91 removed outlier: 3.640A pdb=" N LEU R 88 " --> pdb=" O CYS R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 110 Processing helix chain 'S' and resid 2 through 19 removed outlier: 3.512A pdb=" N VAL S 10 " --> pdb=" O LYS S 6 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR S 19 " --> pdb=" O LEU S 15 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 29 removed outlier: 3.523A pdb=" N ILE S 29 " --> pdb=" O GLU S 25 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 47 removed outlier: 3.652A pdb=" N TRP S 41 " --> pdb=" O ASP S 37 " (cutoff:3.500A) Processing helix chain 'S' and resid 48 through 50 No H-bonds generated for 'chain 'S' and resid 48 through 50' Processing helix chain 'S' and resid 55 through 59 Processing helix chain 'S' and resid 79 through 88 removed outlier: 3.891A pdb=" N ARG S 84 " --> pdb=" O ARG S 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 15 removed outlier: 3.614A pdb=" N GLU T 13 " --> pdb=" O LYS T 9 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY T 15 " --> pdb=" O VAL T 11 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 44 removed outlier: 3.842A pdb=" N GLY T 40 " --> pdb=" O ASN T 36 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N HIS T 41 " --> pdb=" O HIS T 37 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU T 44 " --> pdb=" O GLY T 40 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 73 Processing helix chain 'T' and resid 73 through 85 removed outlier: 3.507A pdb=" N ARG T 83 " --> pdb=" O GLN T 79 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 62 Processing helix chain 'U' and resid 68 through 78 Processing helix chain 'W' and resid 24 through 30 removed outlier: 3.670A pdb=" N ASN W 30 " --> pdb=" O ALA W 26 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 45 Processing helix chain 'W' and resid 47 through 64 Processing helix chain 'X' and resid 11 through 25 removed outlier: 3.631A pdb=" N LYS X 17 " --> pdb=" O HIS X 13 " (cutoff:3.500A) Processing helix chain 'X' and resid 40 through 44 Processing helix chain 'X' and resid 69 through 74 Processing helix chain 'Y' and resid 7 through 41 removed outlier: 3.889A pdb=" N ILE Y 11 " --> pdb=" O LYS Y 7 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU Y 39 " --> pdb=" O TYR Y 35 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 63 Proline residue: Y 55 - end of helix removed outlier: 3.554A pdb=" N ARG Y 59 " --> pdb=" O PRO Y 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 67 through 86 removed outlier: 3.526A pdb=" N LYS Y 84 " --> pdb=" O ALA Y 80 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 22 removed outlier: 3.559A pdb=" N CYS Z 22 " --> pdb=" O PHE Z 18 " (cutoff:3.500A) Processing helix chain 'Z' and resid 27 through 32 removed outlier: 3.572A pdb=" N ARG Z 32 " --> pdb=" O LEU Z 28 " (cutoff:3.500A) Processing helix chain 'Z' and resid 38 through 60 removed outlier: 3.542A pdb=" N LYS Z 58 " --> pdb=" O ARG Z 54 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA Z 60 " --> pdb=" O ALA Z 56 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 13 removed outlier: 3.866A pdb=" N ILE a 11 " --> pdb=" O ARG a 7 " (cutoff:3.500A) Processing helix chain 'a' and resid 22 through 30 removed outlier: 3.536A pdb=" N ILE a 27 " --> pdb=" O ILE a 23 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA a 28 " --> pdb=" O ASN a 24 " (cutoff:3.500A) Processing helix chain 'a' and resid 31 through 33 No H-bonds generated for 'chain 'a' and resid 31 through 33' Processing helix chain 'a' and resid 54 through 58 removed outlier: 3.609A pdb=" N ASN a 58 " --> pdb=" O SER a 55 " (cutoff:3.500A) Processing helix chain 'a' and resid 181 through 198 removed outlier: 3.537A pdb=" N LYS a 197 " --> pdb=" O LEU a 193 " (cutoff:3.500A) Processing helix chain '8' and resid 5 through 25 removed outlier: 4.041A pdb=" N ILE 8 11 " --> pdb=" O VAL 8 7 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN 8 12 " --> pdb=" O ASN 8 8 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU 8 25 " --> pdb=" O LEU 8 21 " (cutoff:3.500A) Processing helix chain '8' and resid 26 through 40 Processing helix chain '8' and resid 45 through 48 removed outlier: 3.649A pdb=" N ASN 8 48 " --> pdb=" O ASP 8 45 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 45 through 48' Processing helix chain '8' and resid 49 through 91 removed outlier: 3.520A pdb=" N ALA 8 53 " --> pdb=" O GLU 8 49 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER 8 61 " --> pdb=" O GLY 8 57 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER 8 62 " --> pdb=" O LYS 8 58 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU 8 63 " --> pdb=" O GLU 8 59 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL 8 66 " --> pdb=" O SER 8 62 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR 8 69 " --> pdb=" O ALA 8 65 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER 8 81 " --> pdb=" O LEU 8 77 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU 8 86 " --> pdb=" O GLY 8 82 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA 8 87 " --> pdb=" O LEU 8 83 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL 8 88 " --> pdb=" O LEU 8 84 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU 8 89 " --> pdb=" O GLU 8 85 " (cutoff:3.500A) Processing helix chain '8' and resid 92 through 118 removed outlier: 3.822A pdb=" N VAL 8 100 " --> pdb=" O PHE 8 96 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA 8 101 " --> pdb=" O ASN 8 97 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU 8 102 " --> pdb=" O GLU 8 98 " (cutoff:3.500A) Processing helix chain '8' and resid 138 through 159 Processing helix chain '8' and resid 279 through 314 Processing helix chain '8' and resid 344 through 349 removed outlier: 3.546A pdb=" N VAL 8 348 " --> pdb=" O ASN 8 344 " (cutoff:3.500A) Processing helix chain '8' and resid 353 through 358 Processing helix chain '8' and resid 358 through 364 Processing sheet with id=AA1, first strand: chain 'b' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'b' and resid 33 through 35 Processing sheet with id=AA3, first strand: chain 'b' and resid 99 through 104 removed outlier: 3.782A pdb=" N GLU b 99 " --> pdb=" O TYR b 95 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU b 94 " --> pdb=" O VAL b 77 " (cutoff:3.500A) removed outlier: 5.529A 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: 7.280A pdb=" N ARG b 188 " --> pdb=" O VAL b 143 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N VAL b 143 " --> pdb=" O ARG b 188 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N THR b 172 " --> pdb=" O VAL b 164 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU b 179 " --> pdb=" O LEU b 175 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LYS b 182 " --> pdb=" O ILE b 266 " (cutoff:3.500A) removed outlier: 6.063A 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: 5.292A pdb=" N LYS c 8 " --> pdb=" O GLU c 28 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N GLU c 28 " --> pdb=" O LYS c 8 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLY c 10 " --> pdb=" O VAL c 26 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU c 188 " --> pdb=" O VAL c 178 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ASP c 176 " --> pdb=" O LYS c 190 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N THR c 171 " --> pdb=" O GLY c 111 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N GLY c 111 " --> pdb=" O THR c 171 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N GLN c 173 " --> pdb=" O VAL c 109 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL c 109 " --> pdb=" O GLN c 173 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N THR c 112 " --> pdb=" O ASP c 200 " (cutoff:3.500A) removed outlier: 6.849A 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: 6.242A pdb=" N ALA c 47 " --> pdb=" O VAL c 37 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N VAL c 37 " --> pdb=" O ALA c 47 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLN c 49 " --> pdb=" O THR c 35 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'c' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'd' and resid 2 through 3 Processing sheet with id=AA9, first strand: chain 'd' and resid 118 through 121 Processing sheet with id=AB1, first strand: chain 'd' and resid 148 through 150 Processing sheet with id=AB2, first strand: chain 'e' and resid 88 through 90 removed outlier: 3.746A pdb=" N LYS e 32 " --> pdb=" O THR e 156 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN e 36 " --> pdb=" O ASP e 152 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'f' and resid 8 through 9 Processing sheet with id=AB4, first strand: chain 'f' and resid 15 through 19 removed outlier: 3.599A pdb=" N LEU f 32 " --> pdb=" O ILE f 25 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'f' and resid 121 through 126 removed outlier: 6.971A pdb=" N GLU f 129 " --> pdb=" O PRO f 125 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'f' and resid 94 through 98 removed outlier: 3.690A pdb=" N SER f 105 " --> pdb=" O ARG f 94 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'g' and resid 18 through 19 Processing sheet with id=AB8, first strand: chain 'g' and resid 77 through 82 removed outlier: 5.982A pdb=" N VAL g 78 " --> pdb=" O ASN g 145 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL g 147 " --> pdb=" O VAL g 78 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ILE g 80 " --> pdb=" O VAL g 147 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL g 142 " --> pdb=" O VAL g 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'j' and resid 122 through 124 removed outlier: 6.424A pdb=" N TYR j 16 " --> pdb=" O ILE j 55 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU j 57 " --> pdb=" O TYR j 16 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL j 18 " --> pdb=" O LEU j 57 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN j 138 " --> pdb=" O TRP j 15 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'j' and resid 74 through 77 Processing sheet with id=AC2, first strand: chain 'k' and resid 6 through 10 removed outlier: 3.728A pdb=" N THR k 6 " --> pdb=" O CYS k 21 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ARG k 17 " --> pdb=" O VAL k 10 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLU k 45 " --> pdb=" O ARG k 17 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL k 19 " --> pdb=" O ILE k 43 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE k 43 " --> pdb=" O VAL k 19 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N CYS k 21 " --> pdb=" O ILE k 41 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE k 41 " --> pdb=" O CYS k 21 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS k 23 " --> pdb=" O ILE k 39 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ILE k 39 " --> pdb=" O LYS k 23 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA k 83 " --> pdb=" O VAL k 63 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N CYS k 84 " --> pdb=" O MET k 7 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASN k 9 " --> pdb=" O CYS k 84 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N LEU k 86 " --> pdb=" O ASN k 9 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'k' and resid 77 through 78 removed outlier: 3.851A pdb=" N ALA p 48 " --> pdb=" O THR p 59 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG p 61 " --> pdb=" O VAL p 46 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N VAL p 46 " --> pdb=" O ARG p 61 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER p 82 " --> pdb=" O LYS p 28 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TRP p 30 " --> pdb=" O VAL p 80 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL p 80 " --> pdb=" O TRP p 30 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'l' and resid 74 through 78 Processing sheet with id=AC5, first strand: chain 'l' and resid 89 through 90 removed outlier: 5.608A pdb=" N VAL l 90 " --> pdb=" O ARG l 123 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL l 122 " --> pdb=" O GLU l 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'm' and resid 62 through 65 removed outlier: 6.131A pdb=" N VAL m 101 " --> pdb=" O ALA m 35 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA m 35 " --> pdb=" O VAL m 101 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR m 103 " --> pdb=" O LEU m 33 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'm' and resid 39 through 42 removed outlier: 5.930A pdb=" N VAL m 89 " --> pdb=" O GLU m 75 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLU m 75 " --> pdb=" O VAL m 89 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR m 91 " --> pdb=" O ILE m 73 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'n' and resid 33 through 37 removed outlier: 6.847A pdb=" N MET n 110 " --> pdb=" O CYS n 100 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'o' and resid 47 through 52 removed outlier: 6.632A pdb=" N VAL o 39 " --> pdb=" O LEU o 48 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ALA o 50 " --> pdb=" O ALA o 37 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ALA o 37 " --> pdb=" O ALA o 50 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N SER o 52 " --> pdb=" O ILE o 35 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE o 35 " --> pdb=" O SER o 52 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'p' and resid 89 through 90 removed outlier: 4.469A pdb=" N LYS p 110 " --> pdb=" O ALA p 90 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'r' and resid 11 through 15 removed outlier: 3.765A pdb=" N PHE r 5 " --> pdb=" O HIS r 12 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TYR r 2 " --> pdb=" O ILE r 41 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ILE r 41 " --> pdb=" O TYR r 2 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL r 4 " --> pdb=" O LEU r 39 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'r' and resid 19 through 23 removed outlier: 6.999A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'r' and resid 72 through 78 removed outlier: 4.318A pdb=" N TYR r 83 " --> pdb=" O ARG r 78 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 's' and resid 4 through 10 removed outlier: 5.489A pdb=" N SER s 101 " --> pdb=" O HIS s 9 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASP s 94 " --> pdb=" O ARG s 84 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ARG s 84 " --> pdb=" O ASP s 94 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE s 96 " --> pdb=" O MET s 82 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N MET s 82 " --> pdb=" O ILE s 96 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LYS s 98 " --> pdb=" O PRO s 80 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N THR s 100 " --> pdb=" O GLU s 78 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLU s 78 " --> pdb=" O THR s 100 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N HIS s 102 " --> pdb=" O VAL s 76 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL s 76 " --> pdb=" O HIS s 102 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N THR s 104 " --> pdb=" O ILE s 74 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE s 74 " --> pdb=" O THR s 104 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL s 106 " --> pdb=" O THR s 72 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 't' and resid 11 through 14 removed outlier: 3.529A pdb=" N ALA t 13 " --> pdb=" O LYS t 33 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP t 80 " --> pdb=" O VAL t 62 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N VAL t 62 " --> pdb=" O TRP t 80 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LYS t 82 " --> pdb=" O THR t 60 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N THR t 60 " --> pdb=" O LYS t 82 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N TYR t 84 " --> pdb=" O VAL t 58 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL t 58 " --> pdb=" O TYR t 84 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N THR t 86 " --> pdb=" O GLU t 56 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 't' and resid 67 through 70 Processing sheet with id=AD8, first strand: chain 'u' and resid 64 through 65 removed outlier: 3.971A pdb=" N ASN u 26 " --> pdb=" O ILE u 34 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'u' and resid 40 through 44 Processing sheet with id=AE1, first strand: chain 'u' and resid 82 through 86 Processing sheet with id=AE2, first strand: chain 'v' and resid 2 through 5 removed outlier: 6.132A pdb=" N PHE v 2 " --> pdb=" O THR v 62 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL v 64 " --> pdb=" O PHE v 2 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE v 4 " --> pdb=" O VAL v 64 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'v' and resid 78 through 79 removed outlier: 3.553A pdb=" N HIS v 88 " --> pdb=" O GLN v 78 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'w' and resid 18 through 19 removed outlier: 7.091A pdb=" N LEU w 55 " --> pdb=" O ILE w 33 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'w' and resid 26 through 27 Processing sheet with id=AE6, first strand: chain 'x' and resid 12 through 14 removed outlier: 3.529A pdb=" N VAL x 12 " --> pdb=" O PHE x 28 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'x' and resid 32 through 39 Processing sheet with id=AE8, first strand: chain 'z' and resid 34 through 38 removed outlier: 3.923A pdb=" N LYS z 5 " --> pdb=" O GLU z 57 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 27 through 29 Processing sheet with id=AF1, first strand: chain 'C' and resid 19 through 25 Processing sheet with id=AF2, first strand: chain 'E' and resid 14 through 15 Processing sheet with id=AF3, first strand: chain 'F' and resid 2 through 3 removed outlier: 7.045A pdb=" N LYS F 2 " --> pdb=" O ARG F 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'F' and resid 16 through 19 Processing sheet with id=AF5, first strand: chain 'G' and resid 89 through 91 removed outlier: 6.309A pdb=" N ILE G 66 " --> pdb=" O PHE G 89 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL G 91 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE G 68 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL G 182 " --> pdb=" O PHE G 197 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE G 199 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ALA G 184 " --> pdb=" O ILE G 199 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 19 through 20 removed outlier: 7.141A pdb=" N ILE H 63 " --> pdb=" O GLN H 99 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ASN H 101 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL H 65 " --> pdb=" O ASN H 101 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 163 through 170 removed outlier: 6.589A pdb=" N ASP H 180 " --> pdb=" O LYS H 203 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 127 through 128 removed outlier: 3.664A pdb=" N SER I 143 " --> pdb=" O MET I 123 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 12 through 21 removed outlier: 5.284A pdb=" N GLU J 12 " --> pdb=" O GLY J 39 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLY J 39 " --> pdb=" O GLU J 12 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N LEU J 14 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL J 37 " --> pdb=" O LEU J 14 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA J 16 " --> pdb=" O LEU J 35 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 84 through 85 removed outlier: 3.503A pdb=" N VAL J 84 " --> pdb=" O MET J 95 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 2 through 3 Processing sheet with id=AG3, first strand: chain 'K' and resid 43 through 46 removed outlier: 3.570A pdb=" N GLY K 43 " --> pdb=" O TYR K 59 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL K 7 " --> pdb=" O SER K 87 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER K 87 " --> pdb=" O VAL K 7 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 72 through 76 Processing sheet with id=AG5, first strand: chain 'M' and resid 74 through 76 Processing sheet with id=AG6, first strand: chain 'M' and resid 74 through 76 removed outlier: 6.782A pdb=" N VAL M 102 " --> pdb=" O ILE M 125 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N TYR M 127 " --> pdb=" O ILE M 100 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE M 100 " --> pdb=" O TYR M 127 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 5 through 9 removed outlier: 3.784A pdb=" N GLY N 9 " --> pdb=" O ALA N 16 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS N 21 " --> pdb=" O ASP N 61 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'O' and resid 45 through 52 removed outlier: 3.600A pdb=" N GLU O 47 " --> pdb=" O ILE O 67 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'O' and resid 45 through 52 removed outlier: 3.600A pdb=" N GLU O 47 " --> pdb=" O ILE O 67 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS S 96 " --> pdb=" O GLU O 66 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'P' and resid 43 through 45 removed outlier: 3.726A pdb=" N GLY P 18 " --> pdb=" O ASN P 80 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU P 81 " --> pdb=" O ILE P 106 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASN P 108 " --> pdb=" O LEU P 81 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Q' and resid 29 through 30 Processing sheet with id=AH3, first strand: chain 'Q' and resid 34 through 39 removed outlier: 4.459A pdb=" N ARG Q 35 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'U' and resid 34 through 35 Processing sheet with id=AH5, first strand: chain 'U' and resid 9 through 11 Processing sheet with id=AH6, first strand: chain 'U' and resid 37 through 39 Processing sheet with id=AH7, first strand: chain 'V' and resid 10 through 13 removed outlier: 6.907A pdb=" N VAL V 21 " --> pdb=" O VAL V 12 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TRP V 72 " --> pdb=" O HIS V 44 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLU V 59 " --> pdb=" O VAL V 75 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'X' and resid 31 through 32 removed outlier: 7.959A pdb=" N THR X 32 " --> pdb=" O HIS X 51 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'a' and resid 170 through 177 removed outlier: 4.011A pdb=" N ILE a 175 " --> pdb=" O VAL a 42 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N VAL a 42 " --> pdb=" O ILE a 175 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS a 211 " --> pdb=" O ASN a 47 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL a 212 " --> pdb=" O VAL a 224 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N THR a 216 " --> pdb=" O ALA a 220 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ALA a 220 " --> pdb=" O THR a 216 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'a' and resid 62 through 64 Processing sheet with id=AI2, first strand: chain '8' and resid 162 through 170 removed outlier: 6.820A pdb=" N THR 8 180 " --> pdb=" O ILE 8 166 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N GLU 8 168 " --> pdb=" O SER 8 178 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER 8 178 " --> pdb=" O GLU 8 168 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLU 8 170 " --> pdb=" O ILE 8 176 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ILE 8 176 " --> pdb=" O GLU 8 170 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LYS 8 177 " --> pdb=" O ALA 8 134 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG 8 203 " --> pdb=" O HIS 8 214 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL 8 198 " --> pdb=" O ARG 8 324 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N TYR 8 326 " --> pdb=" O VAL 8 198 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ARG 8 200 " --> pdb=" O TYR 8 326 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain '8' and resid 240 through 246 removed outlier: 4.024A pdb=" N VAL 8 261 " --> pdb=" O CYS 8 274 " (cutoff:3.500A) 1842 hydrogen bonds defined for protein. 5151 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3122 hydrogen bonds 5176 hydrogen bond angles 0 basepair planarities 1271 basepair parallelities 2343 stacking parallelities Total time for adding SS restraints: 246.00 Time building geometry restraints manager: 69.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 25859 1.33 - 1.45: 61838 1.45 - 1.57: 63152 1.57 - 1.69: 9304 1.69 - 1.81: 274 Bond restraints: 160427 Sorted by residual: bond pdb=" CA VAL G 46 " pdb=" CB VAL G 46 " ideal model delta sigma weight residual 1.539 1.556 -0.017 5.40e-03 3.43e+04 1.00e+01 bond pdb=" N GLY H 1 " pdb=" CA GLY H 1 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.24e+00 bond pdb=" N GLY C 3 " pdb=" CA GLY C 3 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 5.82e+00 bond pdb=" CA ILE 8 266 " pdb=" CB ILE 8 266 " ideal model delta sigma weight residual 1.534 1.551 -0.016 6.80e-03 2.16e+04 5.55e+00 bond pdb=" O5' A 12333 " pdb=" C5' A 12333 " ideal model delta sigma weight residual 1.420 1.452 -0.032 1.50e-02 4.44e+03 4.50e+00 ... (remaining 160422 not shown) Histogram of bond angle deviations from ideal: 100.05 - 106.83: 28540 106.83 - 113.61: 95518 113.61 - 120.39: 58541 120.39 - 127.17: 46470 127.17 - 133.95: 10608 Bond angle restraints: 239677 Sorted by residual: angle pdb=" N VAL N 57 " pdb=" CA VAL N 57 " pdb=" C VAL N 57 " ideal model delta sigma weight residual 110.62 120.26 -9.64 1.02e+00 9.61e-01 8.93e+01 angle pdb=" N SER Q 114 " pdb=" CA SER Q 114 " pdb=" C SER Q 114 " ideal model delta sigma weight residual 111.14 101.73 9.41 1.08e+00 8.57e-01 7.60e+01 angle pdb=" N LYS P 74 " pdb=" CA LYS P 74 " pdb=" C LYS P 74 " ideal model delta sigma weight residual 112.54 103.94 8.60 1.22e+00 6.72e-01 4.97e+01 angle pdb=" N LYS Q 115 " pdb=" CA LYS Q 115 " pdb=" C LYS Q 115 " ideal model delta sigma weight residual 110.48 100.11 10.37 1.48e+00 4.57e-01 4.91e+01 angle pdb=" N GLY r 50 " pdb=" CA GLY r 50 " pdb=" C GLY r 50 " ideal model delta sigma weight residual 112.77 103.88 8.89 1.28e+00 6.10e-01 4.83e+01 ... (remaining 239672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 91894 35.96 - 71.93: 9736 71.93 - 107.89: 1065 107.89 - 143.86: 12 143.86 - 179.82: 14 Dihedral angle restraints: 102721 sinusoidal: 85295 harmonic: 17426 Sorted by residual: dihedral pdb=" C4' G 12286 " pdb=" C3' G 12286 " pdb=" C2' G 12286 " pdb=" C1' G 12286 " ideal model delta sinusoidal sigma weight residual -35.00 30.79 -65.79 1 8.00e+00 1.56e-02 8.85e+01 dihedral pdb=" O4' U 12580 " pdb=" C1' U 12580 " pdb=" N1 U 12580 " pdb=" C2 U 12580 " ideal model delta sinusoidal sigma weight residual 200.00 20.18 179.82 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 12457 " pdb=" C1' U 12457 " pdb=" N1 U 12457 " pdb=" C2 U 12457 " ideal model delta sinusoidal sigma weight residual 200.00 27.75 172.25 1 1.50e+01 4.44e-03 8.49e+01 ... (remaining 102718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 17960 0.074 - 0.148: 11310 0.148 - 0.222: 1163 0.222 - 0.296: 119 0.296 - 0.370: 17 Chirality restraints: 30569 Sorted by residual: chirality pdb=" C3' A 11020 " pdb=" C4' A 11020 " pdb=" O3' A 11020 " pdb=" C2' A 11020 " both_signs ideal model delta sigma weight residual False -2.74 -2.37 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CA VAL r 51 " pdb=" N VAL r 51 " pdb=" C VAL r 51 " pdb=" CB VAL r 51 " both_signs ideal model delta sigma weight residual False 2.44 2.81 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" C1' G 11930 " pdb=" O4' G 11930 " pdb=" C2' G 11930 " pdb=" N9 G 11930 " both_signs ideal model delta sigma weight residual False 2.46 2.10 0.36 2.00e-01 2.50e+01 3.19e+00 ... (remaining 30566 not shown) Planarity restraints: 13095 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 12061 " 0.231 2.00e-02 2.50e+03 9.55e-02 2.74e+02 pdb=" N9 G 12061 " -0.016 2.00e-02 2.50e+03 pdb=" C8 G 12061 " -0.106 2.00e-02 2.50e+03 pdb=" N7 G 12061 " -0.090 2.00e-02 2.50e+03 pdb=" C5 G 12061 " -0.040 2.00e-02 2.50e+03 pdb=" C6 G 12061 " 0.045 2.00e-02 2.50e+03 pdb=" O6 G 12061 " 0.143 2.00e-02 2.50e+03 pdb=" N1 G 12061 " 0.035 2.00e-02 2.50e+03 pdb=" C2 G 12061 " -0.025 2.00e-02 2.50e+03 pdb=" N2 G 12061 " -0.046 2.00e-02 2.50e+03 pdb=" N3 G 12061 " -0.065 2.00e-02 2.50e+03 pdb=" C4 G 12061 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 11647 " -0.151 2.00e-02 2.50e+03 7.97e-02 1.43e+02 pdb=" N1 U 11647 " 0.009 2.00e-02 2.50e+03 pdb=" C2 U 11647 " 0.029 2.00e-02 2.50e+03 pdb=" O2 U 11647 " 0.061 2.00e-02 2.50e+03 pdb=" N3 U 11647 " 0.016 2.00e-02 2.50e+03 pdb=" C4 U 11647 " 0.018 2.00e-02 2.50e+03 pdb=" O4 U 11647 " -0.133 2.00e-02 2.50e+03 pdb=" C5 U 11647 " 0.076 2.00e-02 2.50e+03 pdb=" C6 U 11647 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 11328 " -0.162 2.00e-02 2.50e+03 7.00e-02 1.35e+02 pdb=" N9 A 11328 " 0.013 2.00e-02 2.50e+03 pdb=" C8 A 11328 " 0.065 2.00e-02 2.50e+03 pdb=" N7 A 11328 " 0.054 2.00e-02 2.50e+03 pdb=" C5 A 11328 " 0.029 2.00e-02 2.50e+03 pdb=" C6 A 11328 " -0.024 2.00e-02 2.50e+03 pdb=" N6 A 11328 " -0.108 2.00e-02 2.50e+03 pdb=" N1 A 11328 " -0.009 2.00e-02 2.50e+03 pdb=" C2 A 11328 " 0.030 2.00e-02 2.50e+03 pdb=" N3 A 11328 " 0.059 2.00e-02 2.50e+03 pdb=" C4 A 11328 " 0.053 2.00e-02 2.50e+03 ... (remaining 13092 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 7847 2.69 - 3.24: 134465 3.24 - 3.80: 279945 3.80 - 4.35: 379501 4.35 - 4.90: 512175 Nonbonded interactions: 1313933 Sorted by model distance: nonbonded pdb=" O HIS G 14 " pdb=" O PHE G 15 " model vdw 2.140 3.040 nonbonded pdb=" O LYS g 8 " pdb=" O VAL g 9 " model vdw 2.230 3.040 nonbonded pdb=" O TYR e 142 " pdb=" N LYS e 144 " model vdw 2.250 2.520 nonbonded pdb=" O LYS l 29 " pdb=" OG1 THR l 30 " model vdw 2.286 2.440 nonbonded pdb=" O ASN l 93 " pdb=" OG1 THR l 94 " model vdw 2.303 2.440 ... (remaining 1313928 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 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: 0.120 Extract box with map and model: 12.920 Check model and map are aligned: 1.630 Set scattering table: 1.070 Process input model: 530.180 Find NCS groups from input model: 3.070 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: 0.040 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 553.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 160427 Z= 0.335 Angle : 0.896 10.795 239677 Z= 0.603 Chirality : 0.078 0.370 30569 Planarity : 0.008 0.096 13095 Dihedral : 22.029 179.819 91479 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 1.45 % Allowed : 11.41 % Favored : 87.14 % Rotamer: Outliers : 0.74 % Allowed : 4.25 % Favored : 95.01 % 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: -4.43 (0.09), residues: 6011 helix: -2.80 (0.09), residues: 1825 sheet: -2.64 (0.14), residues: 1073 loop : -3.17 (0.09), residues: 3113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.006 TRP U 60 HIS 0.001 0.000 HIS o 100 PHE 0.032 0.003 PHE e 172 TYR 0.048 0.005 TYR s 38 ARG 0.005 0.000 ARG D 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1530 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1493 time to evaluate : 6.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 115 ILE cc_start: 0.9271 (pt) cc_final: 0.8808 (mt) REVERT: b 116 GLN cc_start: 0.8706 (pt0) cc_final: 0.8378 (tt0) REVERT: b 129 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9020 (pp) REVERT: b 180 MET cc_start: 0.8568 (mmm) cc_final: 0.8203 (mmm) REVERT: b 239 PHE cc_start: 0.8015 (t80) cc_final: 0.7637 (t80) REVERT: c 103 ASP cc_start: 0.7933 (p0) cc_final: 0.7633 (p0) REVERT: d 101 TYR cc_start: 0.9065 (t80) cc_final: 0.8575 (t80) REVERT: d 118 LEU cc_start: 0.9194 (tp) cc_final: 0.8963 (tp) REVERT: d 124 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.8495 (t80) REVERT: e 82 TYR cc_start: 0.8950 (t80) cc_final: 0.8591 (t80) REVERT: e 127 TYR cc_start: 0.8595 (t80) cc_final: 0.8310 (t80) REVERT: e 137 PHE cc_start: 0.8180 (m-80) cc_final: 0.7819 (m-80) REVERT: f 61 TRP cc_start: 0.8905 (m100) cc_final: 0.8401 (m100) REVERT: f 68 ARG cc_start: 0.8907 (ttt-90) cc_final: 0.8670 (ttp80) REVERT: f 113 ASP cc_start: 0.8703 (m-30) cc_final: 0.8442 (m-30) REVERT: j 49 ASP cc_start: 0.7655 (t0) cc_final: 0.7430 (t0) REVERT: k 90 ASN cc_start: 0.8801 (p0) cc_final: 0.8551 (p0) REVERT: l 122 VAL cc_start: 0.9562 (t) cc_final: 0.9361 (p) REVERT: m 103 TYR cc_start: 0.8444 (m-80) cc_final: 0.8230 (m-80) REVERT: n 54 LEU cc_start: 0.9251 (tp) cc_final: 0.8972 (tp) REVERT: n 72 ASP cc_start: 0.8264 (t70) cc_final: 0.8061 (t70) REVERT: n 75 ILE cc_start: 0.9405 (mm) cc_final: 0.9079 (mm) REVERT: o 89 ASP cc_start: 0.7953 (t0) cc_final: 0.7698 (t0) REVERT: o 98 GLN cc_start: 0.8326 (tp40) cc_final: 0.7789 (tp-100) REVERT: o 116 GLN cc_start: 0.8714 (mt0) cc_final: 0.8174 (mt0) REVERT: p 39 LEU cc_start: 0.9343 (tp) cc_final: 0.9081 (tp) REVERT: p 54 LEU cc_start: 0.9224 (tp) cc_final: 0.8767 (tp) REVERT: q 96 ASP cc_start: 0.8461 (t0) cc_final: 0.8118 (t0) REVERT: r 60 LYS cc_start: 0.8977 (pttm) cc_final: 0.8593 (pttp) REVERT: r 85 LYS cc_start: 0.8942 (ttmt) cc_final: 0.8710 (ttmt) REVERT: r 95 ASP cc_start: 0.7838 (t0) cc_final: 0.7212 (t0) REVERT: r 99 THR cc_start: 0.8576 (p) cc_final: 0.8002 (p) REVERT: r 101 ILE cc_start: 0.9269 (mm) cc_final: 0.8430 (mm) REVERT: t 1 MET cc_start: 0.5285 (ttm) cc_final: 0.3977 (mpp) REVERT: t 8 LEU cc_start: 0.9314 (mt) cc_final: 0.9053 (mt) REVERT: t 42 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8125 (mt-10) REVERT: u 45 GLN cc_start: 0.9329 (tp-100) cc_final: 0.9033 (tp40) REVERT: u 101 THR cc_start: 0.9278 (m) cc_final: 0.8928 (m) REVERT: v 40 ILE cc_start: 0.9314 (mm) cc_final: 0.9104 (tp) REVERT: v 48 MET cc_start: 0.9136 (tpt) cc_final: 0.8884 (mmm) REVERT: v 63 ILE cc_start: 0.9555 (mm) cc_final: 0.9223 (tp) REVERT: w 64 LYS cc_start: 0.9104 (tptm) cc_final: 0.8863 (tptm) REVERT: x 5 GLN cc_start: 0.8842 (mt0) cc_final: 0.8601 (mt0) REVERT: y 2 LYS cc_start: 0.8912 (pttm) cc_final: 0.8639 (ptpp) REVERT: y 38 GLN cc_start: 0.8602 (pm20) cc_final: 0.8296 (pm20) REVERT: y 49 ASP cc_start: 0.8276 (m-30) cc_final: 0.7863 (m-30) REVERT: y 60 LYS cc_start: 0.9330 (mtpp) cc_final: 0.8997 (mtmt) REVERT: z 20 LYS cc_start: 0.9404 (mtpt) cc_final: 0.8746 (mttm) REVERT: z 55 LYS cc_start: 0.8998 (ttpt) cc_final: 0.8786 (ptmm) REVERT: C 36 LYS cc_start: 0.9447 (ttmt) cc_final: 0.9031 (ttpt) REVERT: C 37 LYS cc_start: 0.9290 (mmtm) cc_final: 0.9001 (mmtp) REVERT: E 39 ARG cc_start: 0.8725 (ttt180) cc_final: 0.8495 (ttt-90) REVERT: F 4 ARG cc_start: 0.8071 (ptp-170) cc_final: 0.7765 (ptp90) REVERT: F 36 ARG cc_start: 0.8497 (ptt90) cc_final: 0.7993 (ptm160) REVERT: G 21 TYR cc_start: 0.8570 (m-80) cc_final: 0.8142 (m-10) REVERT: G 112 ARG cc_start: 0.9230 (tpt170) cc_final: 0.9016 (tpt90) REVERT: G 119 GLN cc_start: 0.8716 (mm-40) cc_final: 0.8469 (mm-40) REVERT: H 7 ASN cc_start: 0.8965 (m110) cc_final: 0.8690 (t0) REVERT: H 18 ASN cc_start: 0.8435 (m-40) cc_final: 0.8097 (m-40) REVERT: H 22 PHE cc_start: 0.8275 (t80) cc_final: 0.7523 (t80) REVERT: H 166 TRP cc_start: 0.8965 (p-90) cc_final: 0.8754 (p-90) REVERT: H 184 ASN cc_start: 0.8789 (m-40) cc_final: 0.8293 (m110) REVERT: I 28 ASP cc_start: 0.7581 (p0) cc_final: 0.6873 (t0) REVERT: I 53 GLN cc_start: 0.9389 (mt0) cc_final: 0.8940 (mt0) REVERT: I 71 PHE cc_start: 0.8857 (m-80) cc_final: 0.8468 (m-10) REVERT: I 73 ASN cc_start: 0.9527 (m-40) cc_final: 0.9088 (m-40) REVERT: I 123 MET cc_start: 0.9388 (ttp) cc_final: 0.9092 (tpp) REVERT: I 181 PHE cc_start: 0.8628 (t80) cc_final: 0.8387 (t80) REVERT: J 59 ILE cc_start: 0.9641 (pt) cc_final: 0.9369 (pt) REVERT: J 115 GLU cc_start: 0.9401 (pt0) cc_final: 0.8907 (pt0) REVERT: K 13 ASP cc_start: 0.9234 (m-30) cc_final: 0.8910 (m-30) REVERT: K 70 VAL cc_start: 0.9107 (p) cc_final: 0.8808 (p) REVERT: L 30 MET cc_start: 0.8702 (ttp) cc_final: 0.7835 (tmm) REVERT: L 32 ASP cc_start: 0.8352 (m-30) cc_final: 0.8058 (m-30) REVERT: L 102 TRP cc_start: 0.9048 (m-10) cc_final: 0.8694 (m-90) REVERT: M 37 ASN cc_start: 0.8937 (m110) cc_final: 0.8640 (m110) REVERT: M 47 ASP cc_start: 0.8151 (t70) cc_final: 0.7691 (t0) REVERT: M 51 GLU cc_start: 0.8360 (mp0) cc_final: 0.8041 (mp0) REVERT: M 59 GLU cc_start: 0.8872 (pt0) cc_final: 0.8218 (pm20) REVERT: M 72 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8203 (mp0) REVERT: N 86 LEU cc_start: 0.9153 (mt) cc_final: 0.8682 (tt) REVERT: O 49 PHE cc_start: 0.9334 (m-80) cc_final: 0.9130 (m-80) REVERT: O 100 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8508 (tp) REVERT: R 10 ASP cc_start: 0.7560 (t0) cc_final: 0.7188 (t70) REVERT: R 11 HIS cc_start: 0.7836 (m-70) cc_final: 0.7617 (m-70) REVERT: R 26 LYS cc_start: 0.8913 (mttt) cc_final: 0.8698 (tptp) REVERT: R 51 GLN cc_start: 0.9340 (mt0) cc_final: 0.8947 (tp-100) REVERT: R 67 ASP cc_start: 0.9054 (t0) cc_final: 0.8773 (t70) REVERT: S 5 MET cc_start: 0.7242 (mmm) cc_final: 0.6883 (mmp) REVERT: S 88 MET cc_start: 0.9121 (tpp) cc_final: 0.8880 (tpp) REVERT: S 89 ARG cc_start: 0.8979 (ttm-80) cc_final: 0.8417 (tpm170) REVERT: T 20 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.5811 (m-30) REVERT: T 36 ASN cc_start: 0.9147 (m110) cc_final: 0.8946 (m110) REVERT: T 58 MET cc_start: 0.8587 (ptp) cc_final: 0.8374 (ptm) REVERT: U 56 ARG cc_start: 0.9209 (mmm160) cc_final: 0.8983 (mmm160) REVERT: U 76 LYS cc_start: 0.9395 (mmpt) cc_final: 0.9117 (ptmt) REVERT: W 20 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8057 (tp) REVERT: W 31 TYR cc_start: 0.8720 (m-80) cc_final: 0.8235 (m-80) REVERT: W 56 ARG cc_start: 0.8956 (ttm110) cc_final: 0.8278 (ttt-90) REVERT: X 19 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8503 (pm20) REVERT: X 39 ILE cc_start: 0.3422 (OUTLIER) cc_final: 0.2563 (mp) REVERT: X 43 MET cc_start: 0.7542 (mtt) cc_final: 0.7325 (mtt) REVERT: Y 2 ASN cc_start: 0.7144 (t0) cc_final: 0.6938 (t0) REVERT: Y 20 ASN cc_start: 0.9455 (m-40) cc_final: 0.9093 (m110) REVERT: Y 24 ARG cc_start: 0.9173 (mtm180) cc_final: 0.8831 (mtm180) REVERT: Y 26 MET cc_start: 0.9002 (ttp) cc_final: 0.8770 (mmt) REVERT: Y 58 ASP cc_start: 0.8850 (m-30) cc_final: 0.8289 (m-30) REVERT: Z 24 LYS cc_start: 0.8143 (tmmt) cc_final: 0.7909 (mtpp) REVERT: Z 36 PHE cc_start: 0.8741 (t80) cc_final: 0.8427 (t80) REVERT: Z 43 GLU cc_start: 0.8822 (tt0) cc_final: 0.8331 (tp30) REVERT: Z 45 LYS cc_start: 0.8788 (mtmt) cc_final: 0.8487 (mtmt) REVERT: a 8 MET cc_start: -0.1664 (mpp) cc_final: -0.2386 (mtt) REVERT: a 216 THR cc_start: 0.4245 (m) cc_final: 0.4001 (p) REVERT: 8 151 MET cc_start: 0.9310 (tmm) cc_final: 0.8858 (tmm) REVERT: 8 152 TYR cc_start: 0.9468 (m-80) cc_final: 0.9220 (m-80) REVERT: 8 221 PHE cc_start: 0.9205 (t80) cc_final: 0.8785 (t80) REVERT: 8 291 MET cc_start: 0.8527 (tpt) cc_final: 0.8070 (tpt) REVERT: 8 296 TYR cc_start: 0.9154 (t80) cc_final: 0.8578 (t80) outliers start: 37 outliers final: 7 residues processed: 1518 average time/residue: 1.3587 time to fit residues: 3500.2882 Evaluate side-chains 1022 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1009 time to evaluate : 5.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain d residue 124 PHE Chi-restraints excluded: chain f residue 102 ILE Chi-restraints excluded: chain g residue 143 ILE Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain G residue 108 GLN Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain T residue 20 ASP Chi-restraints excluded: chain W residue 20 ILE Chi-restraints excluded: chain X residue 39 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1053 random chunks: chunk 889 optimal weight: 10.0000 chunk 798 optimal weight: 20.0000 chunk 442 optimal weight: 20.0000 chunk 272 optimal weight: 20.0000 chunk 538 optimal weight: 9.9990 chunk 426 optimal weight: 9.9990 chunk 825 optimal weight: 10.0000 chunk 319 optimal weight: 30.0000 chunk 501 optimal weight: 6.9990 chunk 614 optimal weight: 30.0000 chunk 956 optimal weight: 10.0000 overall best weight: 9.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 45 ASN b 85 ASN ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 196 ASN b 225 ASN b 259 ASN c 49 GLN c 150 GLN c 167 ASN d 90 GLN d 97 ASN ** d 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 195 GLN ** e 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 100 ASN f 110 HIS ** g 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 66 ASN j 136 GLN ** k 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 38 GLN l 54 GLN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 17 ASN m 22 GLN ** n 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN o 100 HIS p 11 GLN p 65 ASN q 71 ASN r 43 ASN s 9 HIS s 57 ASN ** s 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 68 ASN u 73 ASN w 42 HIS x 22 ASN y 20 ASN y 27 ASN y 36 GLN y 58 ASN z 8 GLN B 5 ASN D 13 ASN D 29 GLN F 13 ASN ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN G 50 ASN G 57 ASN G 145 ASN G 202 ASN H 2 GLN H 101 ASN H 122 GLN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 GLN I 84 ASN I 88 ASN I 115 GLN I 125 ASN I 151 GLN I 197 HIS ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 ASN ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 145 ASN K 81 ASN L 129 ASN M 3 GLN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 ASN N 4 GLN N 30 ASN N 125 GLN O 35 GLN O 58 ASN ** O 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 111 GLN ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 59 GLN S 65 GLN T 36 ASN ** T 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 ASN ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 30 HIS W 30 ASN ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 54 GLN Y 67 HIS Y 69 ASN Z 8 ASN a 47 ASN ** a 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 172 HIS 8 9 ASN 8 38 ASN 8 43 GLN 8 255 ASN ** 8 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 355 GLN Total number of N/Q/H flips: 84 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 160427 Z= 0.356 Angle : 0.710 10.245 239677 Z= 0.368 Chirality : 0.038 0.252 30569 Planarity : 0.006 0.073 13095 Dihedral : 22.974 179.640 79475 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.35 % Favored : 90.45 % Rotamer: Outliers : 3.24 % Allowed : 13.44 % Favored : 83.32 % 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: -3.07 (0.10), residues: 6011 helix: -0.97 (0.11), residues: 1905 sheet: -2.16 (0.14), residues: 1104 loop : -2.74 (0.10), residues: 3002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP U 60 HIS 0.015 0.002 HIS H 189 PHE 0.032 0.002 PHE H 22 TYR 0.023 0.002 TYR g 25 ARG 0.014 0.001 ARG K 44 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1266 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1104 time to evaluate : 6.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 116 GLN cc_start: 0.8952 (pt0) cc_final: 0.8394 (tt0) REVERT: b 145 MET cc_start: 0.7832 (mtm) cc_final: 0.7556 (mtm) REVERT: c 103 ASP cc_start: 0.8098 (p0) cc_final: 0.7803 (p0) REVERT: d 100 MET cc_start: 0.8607 (tpp) cc_final: 0.8134 (mmt) REVERT: d 101 TYR cc_start: 0.8963 (t80) cc_final: 0.8581 (t80) REVERT: d 124 PHE cc_start: 0.8951 (OUTLIER) cc_final: 0.8397 (t80) REVERT: e 137 PHE cc_start: 0.8420 (m-80) cc_final: 0.8076 (m-80) REVERT: f 17 LYS cc_start: 0.8400 (ttmm) cc_final: 0.8150 (tmtt) REVERT: f 54 ARG cc_start: 0.7574 (ttm170) cc_final: 0.7328 (ttm170) REVERT: f 61 TRP cc_start: 0.8879 (m100) cc_final: 0.8367 (m100) REVERT: f 163 TYR cc_start: 0.7336 (m-80) cc_final: 0.7074 (m-80) REVERT: g 27 ARG cc_start: 0.8442 (ptt180) cc_final: 0.8166 (ptt-90) REVERT: g 112 LYS cc_start: 0.5814 (pttt) cc_final: 0.5344 (ptpt) REVERT: j 1 MET cc_start: 0.8416 (pmm) cc_final: 0.8015 (pmm) REVERT: j 49 ASP cc_start: 0.7674 (t0) cc_final: 0.7400 (t0) REVERT: j 118 MET cc_start: 0.8341 (ptp) cc_final: 0.8103 (ptp) REVERT: m 17 ASN cc_start: 0.8486 (OUTLIER) cc_final: 0.7938 (t0) REVERT: m 110 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8304 (tm-30) REVERT: m 112 LEU cc_start: 0.9358 (tp) cc_final: 0.8509 (tt) REVERT: n 75 ILE cc_start: 0.9464 (mm) cc_final: 0.9193 (mm) REVERT: o 89 ASP cc_start: 0.8044 (t0) cc_final: 0.7617 (t0) REVERT: o 98 GLN cc_start: 0.8317 (tp40) cc_final: 0.7793 (tp-100) REVERT: q 96 ASP cc_start: 0.8524 (t0) cc_final: 0.8305 (t0) REVERT: r 49 ILE cc_start: 0.6590 (pt) cc_final: 0.6262 (pt) REVERT: t 1 MET cc_start: 0.6196 (ttm) cc_final: 0.3714 (mpp) REVERT: t 87 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8872 (pp) REVERT: u 36 GLU cc_start: 0.9424 (pp20) cc_final: 0.8805 (pp20) REVERT: u 45 GLN cc_start: 0.9314 (tp-100) cc_final: 0.8980 (tp40) REVERT: u 87 GLU cc_start: 0.8531 (tp30) cc_final: 0.8330 (tp30) REVERT: v 62 THR cc_start: 0.8318 (p) cc_final: 0.8117 (p) REVERT: w 37 ARG cc_start: 0.9048 (tpp80) cc_final: 0.8782 (tpp80) REVERT: w 64 LYS cc_start: 0.8827 (tptm) cc_final: 0.8619 (tptm) REVERT: w 79 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7896 (mp0) REVERT: y 2 LYS cc_start: 0.8977 (pttm) cc_final: 0.8687 (ptpp) REVERT: y 36 GLN cc_start: 0.9104 (mm-40) cc_final: 0.8830 (mp10) REVERT: y 45 GLN cc_start: 0.8758 (pp30) cc_final: 0.8532 (pp30) REVERT: y 49 ASP cc_start: 0.8388 (m-30) cc_final: 0.8158 (m-30) REVERT: z 5 LYS cc_start: 0.8854 (mmmm) cc_final: 0.8294 (mmmm) REVERT: z 20 LYS cc_start: 0.9525 (mtpt) cc_final: 0.8624 (mttm) REVERT: z 55 LYS cc_start: 0.9144 (ttpt) cc_final: 0.8831 (ptmm) REVERT: C 32 LYS cc_start: 0.7874 (ptmm) cc_final: 0.7336 (tttm) REVERT: C 36 LYS cc_start: 0.9534 (ttmt) cc_final: 0.9145 (ttpt) REVERT: C 37 LYS cc_start: 0.9364 (mmtm) cc_final: 0.9146 (mmtp) REVERT: F 4 ARG cc_start: 0.8394 (ptp-170) cc_final: 0.7969 (ptp90) REVERT: F 36 ARG cc_start: 0.8878 (ptt90) cc_final: 0.8593 (ptm160) REVERT: G 21 TYR cc_start: 0.8548 (m-80) cc_final: 0.8124 (m-10) REVERT: G 103 TRP cc_start: 0.8540 (t-100) cc_final: 0.7990 (t-100) REVERT: G 112 ARG cc_start: 0.9268 (tpt170) cc_final: 0.8904 (tpt90) REVERT: G 119 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8564 (mm-40) REVERT: H 28 PHE cc_start: 0.8963 (OUTLIER) cc_final: 0.8526 (m-80) REVERT: H 41 TYR cc_start: 0.8829 (t80) cc_final: 0.8464 (t80) REVERT: H 79 LYS cc_start: 0.7906 (mmtm) cc_final: 0.7428 (mmmt) REVERT: H 99 GLN cc_start: 0.8432 (mp10) cc_final: 0.7751 (tm-30) REVERT: H 166 TRP cc_start: 0.9008 (p-90) cc_final: 0.8694 (p-90) REVERT: I 28 ASP cc_start: 0.7646 (p0) cc_final: 0.6896 (t0) REVERT: I 73 ASN cc_start: 0.9543 (m-40) cc_final: 0.9067 (m110) REVERT: I 123 MET cc_start: 0.9341 (ttp) cc_final: 0.8937 (mtp) REVERT: I 197 HIS cc_start: 0.8904 (OUTLIER) cc_final: 0.8682 (m-70) REVERT: J 63 MET cc_start: 0.8845 (tpp) cc_final: 0.8368 (tpp) REVERT: J 70 MET cc_start: 0.7985 (mmm) cc_final: 0.7487 (mmt) REVERT: J 85 LYS cc_start: 0.8978 (mmtt) cc_final: 0.8700 (tptp) REVERT: J 96 GLN cc_start: 0.8209 (tm-30) cc_final: 0.7712 (tm-30) REVERT: J 115 GLU cc_start: 0.9430 (pt0) cc_final: 0.9036 (pt0) REVERT: J 161 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8753 (mp0) REVERT: K 24 ARG cc_start: 0.8585 (mtm110) cc_final: 0.8383 (mtm110) REVERT: K 25 TYR cc_start: 0.9034 (m-80) cc_final: 0.8526 (m-10) REVERT: K 88 MET cc_start: 0.8032 (ppp) cc_final: 0.6655 (tmm) REVERT: L 30 MET cc_start: 0.8683 (ttp) cc_final: 0.7944 (ttt) REVERT: L 32 ASP cc_start: 0.8661 (m-30) cc_final: 0.8390 (m-30) REVERT: L 102 TRP cc_start: 0.9075 (m-10) cc_final: 0.8801 (m-90) REVERT: M 37 ASN cc_start: 0.8895 (m-40) cc_final: 0.8629 (m110) REVERT: M 47 ASP cc_start: 0.8363 (t70) cc_final: 0.7694 (t0) REVERT: M 60 LEU cc_start: 0.8827 (mp) cc_final: 0.8583 (mp) REVERT: M 72 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8168 (mp0) REVERT: M 95 MET cc_start: 0.9053 (mtp) cc_final: 0.8706 (mtm) REVERT: M 98 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8438 (pt) REVERT: M 125 ILE cc_start: 0.9286 (mm) cc_final: 0.9037 (tp) REVERT: N 59 LYS cc_start: 0.8777 (mtpp) cc_final: 0.8489 (mtpp) REVERT: N 86 LEU cc_start: 0.8951 (mt) cc_final: 0.8618 (tt) REVERT: O 40 ILE cc_start: 0.7631 (mm) cc_final: 0.7402 (mm) REVERT: P 45 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.7872 (m) REVERT: P 84 MET cc_start: 0.8480 (ttm) cc_final: 0.7903 (ppp) REVERT: Q 69 GLU cc_start: 0.7957 (tp30) cc_final: 0.7581 (mm-30) REVERT: R 11 HIS cc_start: 0.7698 (m-70) cc_final: 0.7332 (m-70) REVERT: R 47 LEU cc_start: 0.6043 (mt) cc_final: 0.5833 (mt) REVERT: R 51 GLN cc_start: 0.9187 (mt0) cc_final: 0.8903 (tp40) REVERT: R 67 ASP cc_start: 0.9057 (t70) cc_final: 0.8793 (t70) REVERT: S 5 MET cc_start: 0.7132 (mmm) cc_final: 0.6611 (mmp) REVERT: S 92 ILE cc_start: 0.9355 (mm) cc_final: 0.8863 (mm) REVERT: S 95 LEU cc_start: 0.9351 (tp) cc_final: 0.8838 (mp) REVERT: T 25 GLU cc_start: 0.8885 (pm20) cc_final: 0.8389 (pm20) REVERT: T 36 ASN cc_start: 0.9225 (m-40) cc_final: 0.8981 (m-40) REVERT: T 58 MET cc_start: 0.8619 (ptp) cc_final: 0.8411 (ptm) REVERT: U 32 PHE cc_start: 0.9290 (p90) cc_final: 0.9030 (p90) REVERT: U 53 ASP cc_start: 0.8548 (t0) cc_final: 0.8333 (t0) REVERT: W 31 TYR cc_start: 0.8803 (m-80) cc_final: 0.8265 (m-80) REVERT: W 51 GLN cc_start: 0.9026 (tp40) cc_final: 0.8741 (tm-30) REVERT: W 53 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8772 (mp10) REVERT: Y 20 ASN cc_start: 0.9498 (m-40) cc_final: 0.9061 (m110) REVERT: Y 28 ARG cc_start: 0.8569 (mmm-85) cc_final: 0.8206 (mtt180) REVERT: Y 58 ASP cc_start: 0.8791 (m-30) cc_final: 0.8284 (m-30) REVERT: Y 73 ARG cc_start: 0.9328 (ttp-110) cc_final: 0.8965 (ttm170) REVERT: Z 28 LEU cc_start: 0.9424 (mm) cc_final: 0.9137 (mm) REVERT: Z 36 PHE cc_start: 0.8886 (t80) cc_final: 0.8539 (t80) REVERT: Z 43 GLU cc_start: 0.8909 (tt0) cc_final: 0.8414 (tp30) REVERT: a 8 MET cc_start: -0.1702 (mpp) cc_final: -0.2643 (mtt) REVERT: 8 151 MET cc_start: 0.9378 (tmm) cc_final: 0.8954 (tmm) REVERT: 8 164 GLU cc_start: 0.9039 (tp30) cc_final: 0.8789 (tp30) REVERT: 8 207 PHE cc_start: 0.8126 (m-10) cc_final: 0.7815 (m-10) REVERT: 8 221 PHE cc_start: 0.9122 (t80) cc_final: 0.8693 (t80) REVERT: 8 300 MET cc_start: 0.8618 (mmp) cc_final: 0.8403 (mmp) REVERT: 8 310 MET cc_start: 0.8810 (mmm) cc_final: 0.8487 (mmm) outliers start: 162 outliers final: 93 residues processed: 1178 average time/residue: 1.3091 time to fit residues: 2670.0436 Evaluate side-chains 1031 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 930 time to evaluate : 5.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 34 GLU Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 202 ARG Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain d residue 124 PHE Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain f residue 25 ILE Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 91 ASP Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 17 ASN Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 65 LEU Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain o residue 20 GLU Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 99 LEU Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 103 VAL Chi-restraints excluded: chain r residue 26 ASP Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 34 GLU Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 59 GLU Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 85 ILE Chi-restraints excluded: chain s residue 94 ASP Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain v residue 7 GLU Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain y residue 6 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain I residue 197 HIS Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 75 GLU Chi-restraints excluded: chain K residue 79 ARG Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 51 PHE Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain S residue 61 ASN Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain W residue 53 GLN Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain 8 residue 227 ASP Chi-restraints excluded: chain 8 residue 271 VAL Chi-restraints excluded: chain 8 residue 340 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1053 random chunks: chunk 531 optimal weight: 7.9990 chunk 296 optimal weight: 20.0000 chunk 795 optimal weight: 50.0000 chunk 651 optimal weight: 40.0000 chunk 263 optimal weight: 8.9990 chunk 957 optimal weight: 10.0000 chunk 1034 optimal weight: 8.9990 chunk 853 optimal weight: 50.0000 chunk 949 optimal weight: 10.0000 chunk 326 optimal weight: 20.0000 chunk 768 optimal weight: 20.0000 overall best weight: 9.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 36 GLN c 134 HIS c 167 ASN d 136 GLN ** d 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 29 HIS ** q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 55 GLN ** q 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 15 HIS w 46 ASN ** x 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 GLN ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 ASN ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 GLN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 GLN ** O 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 HIS T 61 GLN ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 8 GLN ** W 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 57 GLN ** 8 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 54 GLN ** 8 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 160427 Z= 0.330 Angle : 0.653 16.378 239677 Z= 0.337 Chirality : 0.037 0.333 30569 Planarity : 0.005 0.075 13095 Dihedral : 23.282 179.264 79450 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.97 % Favored : 89.90 % Rotamer: Outliers : 3.95 % Allowed : 15.74 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.10), residues: 6011 helix: -0.37 (0.11), residues: 1919 sheet: -1.98 (0.15), residues: 1096 loop : -2.48 (0.10), residues: 2996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP U 60 HIS 0.057 0.002 HIS I 197 PHE 0.025 0.002 PHE m 117 TYR 0.022 0.002 TYR b 95 ARG 0.013 0.001 ARG m 114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1236 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1038 time to evaluate : 6.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 116 GLN cc_start: 0.8947 (pt0) cc_final: 0.8209 (tt0) REVERT: c 2 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8805 (mp) REVERT: c 103 ASP cc_start: 0.8197 (p0) cc_final: 0.7936 (p0) REVERT: d 100 MET cc_start: 0.8693 (tpp) cc_final: 0.8259 (mmt) REVERT: d 124 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8289 (t80) REVERT: d 188 MET cc_start: 0.8954 (tpp) cc_final: 0.8724 (tpp) REVERT: e 21 TYR cc_start: 0.8503 (m-10) cc_final: 0.8155 (m-10) REVERT: e 137 PHE cc_start: 0.8503 (m-80) cc_final: 0.8096 (m-80) REVERT: f 57 TYR cc_start: 0.8439 (m-80) cc_final: 0.8149 (m-80) REVERT: f 61 TRP cc_start: 0.8844 (m100) cc_final: 0.8340 (m100) REVERT: f 162 ARG cc_start: 0.8845 (ptp-170) cc_final: 0.8332 (mtp85) REVERT: g 29 PHE cc_start: 0.9031 (t80) cc_final: 0.8724 (t80) REVERT: g 35 LYS cc_start: 0.9361 (mttp) cc_final: 0.9131 (mttp) REVERT: g 112 LYS cc_start: 0.5760 (pttt) cc_final: 0.5219 (ptpt) REVERT: j 1 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8233 (pmm) REVERT: j 49 ASP cc_start: 0.7739 (t0) cc_final: 0.7437 (t0) REVERT: m 110 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8395 (tm-30) REVERT: m 112 LEU cc_start: 0.9373 (tp) cc_final: 0.8940 (tp) REVERT: m 136 MET cc_start: 0.7598 (ppp) cc_final: 0.6962 (ppp) REVERT: n 72 ASP cc_start: 0.8531 (t70) cc_final: 0.8298 (t70) REVERT: o 89 ASP cc_start: 0.7898 (t0) cc_final: 0.7455 (t0) REVERT: o 98 GLN cc_start: 0.8379 (tp40) cc_final: 0.7895 (tp-100) REVERT: p 70 GLU cc_start: 0.6651 (mp0) cc_final: 0.6428 (mp0) REVERT: r 22 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8780 (pp) REVERT: r 85 LYS cc_start: 0.9061 (ttmt) cc_final: 0.8815 (tttm) REVERT: t 1 MET cc_start: 0.6072 (ttm) cc_final: 0.2842 (mpp) REVERT: t 87 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8762 (pp) REVERT: u 87 GLU cc_start: 0.8610 (tp30) cc_final: 0.8347 (tp30) REVERT: w 17 LEU cc_start: 0.9176 (mm) cc_final: 0.8918 (mm) REVERT: w 37 ARG cc_start: 0.8984 (tpp80) cc_final: 0.8711 (tpp80) REVERT: w 64 LYS cc_start: 0.8897 (tptm) cc_final: 0.8635 (tptm) REVERT: w 79 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7933 (mp0) REVERT: x 32 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.9043 (mm) REVERT: y 1 MET cc_start: 0.8108 (tpp) cc_final: 0.7823 (tpp) REVERT: y 5 GLU cc_start: 0.8704 (mp0) cc_final: 0.8140 (mp0) REVERT: y 38 GLN cc_start: 0.8787 (pm20) cc_final: 0.8580 (pm20) REVERT: y 45 GLN cc_start: 0.8821 (pp30) cc_final: 0.8464 (pp30) REVERT: y 49 ASP cc_start: 0.8240 (m-30) cc_final: 0.7862 (m-30) REVERT: z 36 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7797 (mm-30) REVERT: z 39 ASP cc_start: 0.9008 (t0) cc_final: 0.8792 (m-30) REVERT: z 55 LYS cc_start: 0.9145 (ttpt) cc_final: 0.8791 (ptmm) REVERT: C 26 LYS cc_start: 0.9178 (mmmt) cc_final: 0.8616 (tppt) REVERT: C 32 LYS cc_start: 0.7998 (ptmm) cc_final: 0.7568 (tttm) REVERT: C 36 LYS cc_start: 0.9492 (ttmt) cc_final: 0.9076 (ttpt) REVERT: F 36 ARG cc_start: 0.8909 (ptt90) cc_final: 0.8655 (ptm160) REVERT: G 21 TYR cc_start: 0.8485 (m-80) cc_final: 0.8124 (m-10) REVERT: G 103 TRP cc_start: 0.8507 (t-100) cc_final: 0.7971 (t-100) REVERT: G 112 ARG cc_start: 0.9260 (tpt170) cc_final: 0.8834 (tpt90) REVERT: G 119 GLN cc_start: 0.8813 (mm-40) cc_final: 0.8576 (mm-40) REVERT: G 153 MET cc_start: 0.8543 (ttm) cc_final: 0.7929 (mtp) REVERT: H 28 PHE cc_start: 0.9055 (OUTLIER) cc_final: 0.8686 (m-80) REVERT: H 122 GLN cc_start: 0.9431 (mt0) cc_final: 0.8899 (mp10) REVERT: H 166 TRP cc_start: 0.9095 (p-90) cc_final: 0.8726 (p-90) REVERT: H 184 ASN cc_start: 0.8695 (m110) cc_final: 0.8065 (m110) REVERT: I 28 ASP cc_start: 0.7702 (p0) cc_final: 0.7035 (t0) REVERT: I 70 GLN cc_start: 0.9099 (mp10) cc_final: 0.8891 (pm20) REVERT: I 71 PHE cc_start: 0.9106 (m-80) cc_final: 0.8900 (m-80) REVERT: I 73 ASN cc_start: 0.9530 (m-40) cc_final: 0.8928 (m110) REVERT: I 123 MET cc_start: 0.9247 (ttp) cc_final: 0.8974 (mtp) REVERT: I 181 PHE cc_start: 0.8543 (t80) cc_final: 0.8325 (t80) REVERT: J 63 MET cc_start: 0.8809 (tpp) cc_final: 0.8503 (tpp) REVERT: J 96 GLN cc_start: 0.8481 (tm-30) cc_final: 0.7887 (tm-30) REVERT: J 115 GLU cc_start: 0.9476 (pt0) cc_final: 0.8930 (pt0) REVERT: J 122 VAL cc_start: 0.8625 (OUTLIER) cc_final: 0.8377 (m) REVERT: J 155 LYS cc_start: 0.9493 (pttt) cc_final: 0.9284 (ptmt) REVERT: J 161 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8837 (mm-30) REVERT: K 24 ARG cc_start: 0.8561 (mtm110) cc_final: 0.8146 (mtm110) REVERT: K 25 TYR cc_start: 0.8977 (m-80) cc_final: 0.8299 (m-10) REVERT: K 79 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7849 (mtp85) REVERT: K 80 PHE cc_start: 0.8744 (m-80) cc_final: 0.8389 (m-80) REVERT: K 88 MET cc_start: 0.8560 (ppp) cc_final: 0.8018 (tmm) REVERT: L 30 MET cc_start: 0.8804 (ttp) cc_final: 0.7964 (tmm) REVERT: L 32 ASP cc_start: 0.8814 (m-30) cc_final: 0.8500 (m-30) REVERT: L 102 TRP cc_start: 0.9056 (m-10) cc_final: 0.8734 (m-90) REVERT: M 2 MET cc_start: 0.9077 (tmm) cc_final: 0.8686 (tmm) REVERT: M 37 ASN cc_start: 0.8773 (m-40) cc_final: 0.8419 (m110) REVERT: M 47 ASP cc_start: 0.8446 (t70) cc_final: 0.7719 (t0) REVERT: M 51 GLU cc_start: 0.7711 (mp0) cc_final: 0.6842 (mp0) REVERT: M 59 GLU cc_start: 0.8962 (pt0) cc_final: 0.8561 (pm20) REVERT: M 98 LEU cc_start: 0.8644 (pt) cc_final: 0.8195 (pt) REVERT: N 86 LEU cc_start: 0.8937 (mt) cc_final: 0.8526 (tt) REVERT: O 46 LYS cc_start: 0.8307 (mtmm) cc_final: 0.7783 (mtmm) REVERT: O 65 TYR cc_start: 0.8255 (m-80) cc_final: 0.8025 (m-80) REVERT: P 30 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8461 (tp) REVERT: P 54 SER cc_start: 0.9276 (p) cc_final: 0.9049 (m) REVERT: P 93 GLU cc_start: 0.8387 (tm-30) cc_final: 0.8032 (tm-30) REVERT: Q 69 GLU cc_start: 0.7914 (tp30) cc_final: 0.7531 (tp30) REVERT: Q 111 GLN cc_start: 0.8408 (mt0) cc_final: 0.8201 (mt0) REVERT: R 47 LEU cc_start: 0.6235 (mt) cc_final: 0.5969 (mt) REVERT: R 51 GLN cc_start: 0.9176 (mt0) cc_final: 0.8864 (tp-100) REVERT: R 67 ASP cc_start: 0.9007 (t0) cc_final: 0.8737 (t70) REVERT: S 5 MET cc_start: 0.7036 (mmm) cc_final: 0.6507 (mmp) REVERT: S 30 ILE cc_start: 0.8662 (mt) cc_final: 0.8403 (tt) REVERT: S 92 ILE cc_start: 0.9377 (mm) cc_final: 0.8873 (mm) REVERT: S 95 LEU cc_start: 0.9352 (tp) cc_final: 0.8857 (mp) REVERT: T 25 GLU cc_start: 0.8923 (pm20) cc_final: 0.8494 (pm20) REVERT: U 29 ASN cc_start: 0.8086 (m-40) cc_final: 0.7837 (m-40) REVERT: U 32 PHE cc_start: 0.9287 (p90) cc_final: 0.9076 (p90) REVERT: U 53 ASP cc_start: 0.8585 (t0) cc_final: 0.8256 (t0) REVERT: W 31 TYR cc_start: 0.8813 (m-80) cc_final: 0.8288 (m-80) REVERT: W 51 GLN cc_start: 0.8984 (tp40) cc_final: 0.8718 (tm-30) REVERT: W 56 ARG cc_start: 0.9190 (ttm110) cc_final: 0.8714 (ttt-90) REVERT: X 18 VAL cc_start: 0.7109 (t) cc_final: 0.6557 (t) REVERT: X 19 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8260 (pt0) REVERT: Y 20 ASN cc_start: 0.9496 (m-40) cc_final: 0.9194 (m-40) REVERT: Y 28 ARG cc_start: 0.8614 (mmm-85) cc_final: 0.8110 (mtt180) REVERT: Y 58 ASP cc_start: 0.8639 (m-30) cc_final: 0.8089 (m-30) REVERT: Y 73 ARG cc_start: 0.9337 (ttp-110) cc_final: 0.9016 (ttm170) REVERT: Z 24 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7601 (mtpt) REVERT: Z 36 PHE cc_start: 0.8926 (t80) cc_final: 0.8635 (t80) REVERT: Z 43 GLU cc_start: 0.8930 (tt0) cc_final: 0.8433 (tp30) REVERT: a 8 MET cc_start: -0.1662 (mpp) cc_final: -0.2589 (mtt) REVERT: a 57 GLN cc_start: 0.1747 (OUTLIER) cc_final: 0.1393 (pt0) REVERT: 8 118 MET cc_start: 0.8565 (tpp) cc_final: 0.6944 (tpp) REVERT: 8 151 MET cc_start: 0.9490 (tmm) cc_final: 0.8971 (tmm) REVERT: 8 164 GLU cc_start: 0.9094 (tp30) cc_final: 0.8833 (tp30) REVERT: 8 207 PHE cc_start: 0.8125 (m-10) cc_final: 0.7772 (m-10) REVERT: 8 300 MET cc_start: 0.8663 (mmp) cc_final: 0.8412 (mmp) REVERT: 8 310 MET cc_start: 0.8819 (mmm) cc_final: 0.8518 (mmm) outliers start: 198 outliers final: 125 residues processed: 1138 average time/residue: 1.2788 time to fit residues: 2542.0143 Evaluate side-chains 1051 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 914 time to evaluate : 6.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 34 GLU Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 63 ILE Chi-restraints excluded: chain b residue 66 PHE Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 202 ARG Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 167 ASN Chi-restraints excluded: chain d residue 124 PHE Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain e residue 4 HIS Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain f residue 25 ILE Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain g residue 50 ARG Chi-restraints excluded: chain g residue 108 VAL Chi-restraints excluded: chain g residue 115 VAL Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 91 ASP Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain o residue 20 GLU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 103 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 26 ASP Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 98 ILE Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 94 ASP Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 53 VAL Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 46 ASN Chi-restraints excluded: chain w residue 72 ASN Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 59 ASP Chi-restraints excluded: chain y residue 6 LEU Chi-restraints excluded: chain z residue 26 LEU Chi-restraints excluded: chain z residue 43 ILE Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 75 GLU Chi-restraints excluded: chain K residue 79 ARG Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain S residue 61 ASN Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 24 LYS Chi-restraints excluded: chain Z residue 37 TYR Chi-restraints excluded: chain a residue 57 GLN Chi-restraints excluded: chain 8 residue 227 ASP Chi-restraints excluded: chain 8 residue 228 ASP Chi-restraints excluded: chain 8 residue 266 ILE Chi-restraints excluded: chain 8 residue 340 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1053 random chunks: chunk 946 optimal weight: 20.0000 chunk 720 optimal weight: 20.0000 chunk 497 optimal weight: 50.0000 chunk 106 optimal weight: 40.0000 chunk 457 optimal weight: 20.0000 chunk 643 optimal weight: 10.0000 chunk 961 optimal weight: 10.0000 chunk 1017 optimal weight: 30.0000 chunk 502 optimal weight: 7.9990 chunk 911 optimal weight: 10.0000 chunk 274 optimal weight: 8.9990 overall best weight: 9.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 164 GLN c 167 ASN d 136 GLN ** d 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 5 GLN ** n 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 62 ASN q 43 GLN q 55 GLN ** r 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 46 ASN B 3 GLN ** G 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 ASN ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 118 ASN ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 49 HIS T 79 GLN ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 52 ASN ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 160427 Z= 0.334 Angle : 0.643 13.021 239677 Z= 0.332 Chirality : 0.037 0.264 30569 Planarity : 0.005 0.052 13095 Dihedral : 23.442 179.274 79450 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 20.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.77 % Favored : 90.12 % Rotamer: Outliers : 4.23 % Allowed : 17.60 % Favored : 78.17 % 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: -2.33 (0.10), residues: 6011 helix: -0.20 (0.12), residues: 1913 sheet: -1.88 (0.15), residues: 1087 loop : -2.35 (0.10), residues: 3011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP U 60 HIS 0.007 0.001 HIS I 197 PHE 0.021 0.002 PHE H 36 TYR 0.036 0.002 TYR g 25 ARG 0.010 0.001 ARG G 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1187 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 975 time to evaluate : 6.772 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: c 103 ASP cc_start: 0.8254 (p0) cc_final: 0.8001 (p0) REVERT: d 124 PHE cc_start: 0.9077 (OUTLIER) cc_final: 0.8297 (m-80) REVERT: e 21 TYR cc_start: 0.8270 (m-10) cc_final: 0.8033 (m-10) REVERT: e 137 PHE cc_start: 0.8534 (m-80) cc_final: 0.8127 (m-80) REVERT: f 61 TRP cc_start: 0.8840 (m100) cc_final: 0.8319 (m100) REVERT: f 162 ARG cc_start: 0.8792 (ptp-170) cc_final: 0.8226 (mtp85) REVERT: g 29 PHE cc_start: 0.9034 (t80) cc_final: 0.8700 (t80) REVERT: g 112 LYS cc_start: 0.6690 (pttt) cc_final: 0.6319 (ptpt) REVERT: j 1 MET cc_start: 0.8535 (pmm) cc_final: 0.8261 (pmm) REVERT: k 82 ASN cc_start: 0.8253 (m-40) cc_final: 0.7993 (m-40) REVERT: m 110 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8266 (tm-30) REVERT: m 136 MET cc_start: 0.7350 (ppp) cc_final: 0.7107 (ppp) REVERT: o 56 LYS cc_start: 0.8049 (mmtm) cc_final: 0.7827 (mmtm) REVERT: o 60 GLU cc_start: 0.8802 (pp20) cc_final: 0.8590 (pm20) REVERT: o 80 GLU cc_start: 0.8747 (pp20) cc_final: 0.8547 (pp20) REVERT: o 89 ASP cc_start: 0.7845 (t0) cc_final: 0.7523 (t0) REVERT: r 22 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8835 (pp) REVERT: t 87 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8782 (pp) REVERT: u 87 GLU cc_start: 0.8571 (tp30) cc_final: 0.8324 (tp30) REVERT: w 17 LEU cc_start: 0.9186 (mm) cc_final: 0.8955 (mm) REVERT: w 51 ARG cc_start: 0.8949 (ptm160) cc_final: 0.8318 (tmm-80) REVERT: w 64 LYS cc_start: 0.8856 (tptm) cc_final: 0.8551 (tptm) REVERT: w 79 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8090 (mp0) REVERT: y 7 ARG cc_start: 0.8588 (mtm110) cc_final: 0.8324 (ptp90) REVERT: y 38 GLN cc_start: 0.8842 (pm20) cc_final: 0.8604 (pm20) REVERT: y 45 GLN cc_start: 0.8872 (pp30) cc_final: 0.8573 (pp30) REVERT: z 20 LYS cc_start: 0.9546 (mtpt) cc_final: 0.8670 (mttm) REVERT: z 55 LYS cc_start: 0.9221 (ttpt) cc_final: 0.8887 (ptmm) REVERT: C 24 LYS cc_start: 0.7712 (tppt) cc_final: 0.7474 (tppt) REVERT: C 26 LYS cc_start: 0.9126 (mmmt) cc_final: 0.8634 (tppt) REVERT: C 32 LYS cc_start: 0.7955 (ptmm) cc_final: 0.7518 (tttm) REVERT: C 36 LYS cc_start: 0.9418 (ttmt) cc_final: 0.9111 (ttpt) REVERT: C 46 VAL cc_start: 0.9347 (t) cc_final: 0.9094 (p) REVERT: F 4 ARG cc_start: 0.8619 (ptp-110) cc_final: 0.8189 (ptp-110) REVERT: F 36 ARG cc_start: 0.8963 (ptt90) cc_final: 0.8711 (ptm160) REVERT: G 21 TYR cc_start: 0.8386 (m-80) cc_final: 0.8091 (m-10) REVERT: G 103 TRP cc_start: 0.8495 (t-100) cc_final: 0.7847 (t-100) REVERT: G 112 ARG cc_start: 0.9240 (tpt170) cc_final: 0.8313 (mtp180) REVERT: G 153 MET cc_start: 0.8512 (ttm) cc_final: 0.7895 (mtp) REVERT: H 28 PHE cc_start: 0.9069 (OUTLIER) cc_final: 0.8684 (m-80) REVERT: H 79 LYS cc_start: 0.7827 (mmtm) cc_final: 0.7417 (mmmt) REVERT: H 166 TRP cc_start: 0.9097 (p-90) cc_final: 0.8759 (p-90) REVERT: H 184 ASN cc_start: 0.8766 (m110) cc_final: 0.8107 (m110) REVERT: I 28 ASP cc_start: 0.7878 (p0) cc_final: 0.7164 (t0) REVERT: I 70 GLN cc_start: 0.9123 (mp10) cc_final: 0.8854 (pm20) REVERT: I 71 PHE cc_start: 0.8932 (m-80) cc_final: 0.8625 (m-80) REVERT: I 123 MET cc_start: 0.9175 (ttp) cc_final: 0.8896 (mtm) REVERT: I 181 PHE cc_start: 0.8542 (t80) cc_final: 0.8270 (t80) REVERT: J 53 ARG cc_start: 0.8390 (mmm160) cc_final: 0.8017 (mmm160) REVERT: J 63 MET cc_start: 0.8755 (tpp) cc_final: 0.8408 (tpp) REVERT: J 96 GLN cc_start: 0.8338 (tm-30) cc_final: 0.7745 (tm-30) REVERT: J 115 GLU cc_start: 0.9475 (pt0) cc_final: 0.9228 (pt0) REVERT: J 155 LYS cc_start: 0.9502 (pttt) cc_final: 0.9214 (ptmt) REVERT: J 161 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8864 (mm-30) REVERT: K 24 ARG cc_start: 0.8673 (mtm110) cc_final: 0.8220 (mtm110) REVERT: K 25 TYR cc_start: 0.8978 (m-10) cc_final: 0.8230 (m-80) REVERT: K 88 MET cc_start: 0.8646 (ppp) cc_final: 0.8371 (ppp) REVERT: L 30 MET cc_start: 0.8720 (ttp) cc_final: 0.7978 (tmm) REVERT: L 32 ASP cc_start: 0.8855 (m-30) cc_final: 0.8483 (m-30) REVERT: L 102 TRP cc_start: 0.9051 (m-10) cc_final: 0.8786 (m-90) REVERT: L 129 ASN cc_start: 0.7572 (t0) cc_final: 0.7323 (m-40) REVERT: M 37 ASN cc_start: 0.8766 (m-40) cc_final: 0.8367 (m110) REVERT: M 98 LEU cc_start: 0.8768 (pt) cc_final: 0.8533 (pt) REVERT: N 67 LYS cc_start: 0.8413 (ptmm) cc_final: 0.8208 (tptt) REVERT: O 10 LEU cc_start: 0.8650 (mm) cc_final: 0.8447 (mm) REVERT: O 46 LYS cc_start: 0.8383 (mtmm) cc_final: 0.7939 (mppt) REVERT: P 54 SER cc_start: 0.9153 (p) cc_final: 0.8935 (m) REVERT: P 82 GLU cc_start: 0.7853 (pm20) cc_final: 0.6910 (pm20) REVERT: Q 69 GLU cc_start: 0.7924 (tp30) cc_final: 0.7600 (mm-30) REVERT: Q 111 GLN cc_start: 0.8276 (mt0) cc_final: 0.8005 (mt0) REVERT: R 47 LEU cc_start: 0.6359 (mt) cc_final: 0.6055 (mt) REVERT: R 51 GLN cc_start: 0.9156 (mt0) cc_final: 0.8865 (tp-100) REVERT: R 67 ASP cc_start: 0.8973 (t0) cc_final: 0.8705 (t70) REVERT: S 5 MET cc_start: 0.7040 (mmm) cc_final: 0.6513 (mmp) REVERT: S 95 LEU cc_start: 0.9326 (tp) cc_final: 0.8882 (mp) REVERT: T 25 GLU cc_start: 0.8896 (pm20) cc_final: 0.8500 (pm20) REVERT: T 47 LYS cc_start: 0.8352 (mtmm) cc_final: 0.8074 (mtmm) REVERT: U 14 ARG cc_start: 0.8702 (ttt180) cc_final: 0.8207 (ttp-170) REVERT: U 29 ASN cc_start: 0.7963 (m-40) cc_final: 0.7715 (m-40) REVERT: U 53 ASP cc_start: 0.8641 (t0) cc_final: 0.8321 (t0) REVERT: U 76 LYS cc_start: 0.9371 (mmmt) cc_final: 0.9163 (ptmt) REVERT: W 31 TYR cc_start: 0.8835 (m-80) cc_final: 0.8223 (m-80) REVERT: W 56 ARG cc_start: 0.9174 (ttm110) cc_final: 0.8684 (ttt-90) REVERT: X 18 VAL cc_start: 0.7264 (t) cc_final: 0.6801 (t) REVERT: X 19 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8100 (pt0) REVERT: Y 20 ASN cc_start: 0.9493 (m-40) cc_final: 0.9201 (m-40) REVERT: Y 26 MET cc_start: 0.8450 (mmt) cc_final: 0.8235 (mmt) REVERT: Y 28 ARG cc_start: 0.8627 (mmm-85) cc_final: 0.8217 (mtt180) REVERT: Y 31 ILE cc_start: 0.9653 (OUTLIER) cc_final: 0.9156 (pt) REVERT: Y 35 TYR cc_start: 0.9010 (m-80) cc_final: 0.8689 (m-80) REVERT: Y 58 ASP cc_start: 0.8588 (m-30) cc_final: 0.8085 (m-30) REVERT: Y 66 ILE cc_start: 0.8843 (mm) cc_final: 0.8490 (tt) REVERT: Y 73 ARG cc_start: 0.9321 (ttp-110) cc_final: 0.8699 (ptp-170) REVERT: Y 81 GLN cc_start: 0.9017 (mm-40) cc_final: 0.8730 (tm-30) REVERT: Z 24 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8043 (mtpp) REVERT: Z 36 PHE cc_start: 0.8912 (t80) cc_final: 0.8596 (t80) REVERT: Z 43 GLU cc_start: 0.8815 (tt0) cc_final: 0.8433 (tp30) REVERT: a 8 MET cc_start: -0.1566 (mpp) cc_final: -0.2362 (mtm) REVERT: a 57 GLN cc_start: 0.2058 (OUTLIER) cc_final: 0.1540 (pt0) REVERT: a 180 PHE cc_start: 0.2043 (OUTLIER) cc_final: 0.1787 (t80) REVERT: 8 118 MET cc_start: 0.8306 (tpp) cc_final: 0.7923 (tpp) REVERT: 8 151 MET cc_start: 0.9546 (tmm) cc_final: 0.9173 (tmm) REVERT: 8 207 PHE cc_start: 0.8126 (m-10) cc_final: 0.7634 (m-10) REVERT: 8 300 MET cc_start: 0.8658 (mmp) cc_final: 0.8383 (mmp) REVERT: 8 310 MET cc_start: 0.8843 (mmm) cc_final: 0.8547 (mmm) outliers start: 212 outliers final: 146 residues processed: 1090 average time/residue: 1.2825 time to fit residues: 2445.9312 Evaluate side-chains 1055 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 901 time to evaluate : 6.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 66 PHE Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 202 ARG Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 124 PHE Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain e residue 4 HIS Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain e residue 173 ASP Chi-restraints excluded: chain f residue 25 ILE Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain g residue 8 LYS Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 139 VAL Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 91 ASP Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 99 LEU Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain q residue 103 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 98 ILE Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 85 ILE Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 72 ASN Chi-restraints excluded: chain w residue 78 ILE Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 70 LEU Chi-restraints excluded: chain y residue 6 LEU Chi-restraints excluded: chain y residue 58 ASN Chi-restraints excluded: chain z residue 23 LEU Chi-restraints excluded: chain z residue 26 LEU Chi-restraints excluded: chain z residue 43 ILE Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 61 LYS Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 75 GLU Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 125 ASP Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 24 LYS Chi-restraints excluded: chain Z residue 27 VAL Chi-restraints excluded: chain Z residue 37 TYR Chi-restraints excluded: chain a residue 57 GLN Chi-restraints excluded: chain a residue 180 PHE Chi-restraints excluded: chain 8 residue 130 LEU Chi-restraints excluded: chain 8 residue 227 ASP Chi-restraints excluded: chain 8 residue 254 VAL Chi-restraints excluded: chain 8 residue 266 ILE Chi-restraints excluded: chain 8 residue 271 VAL Chi-restraints excluded: chain 8 residue 340 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1053 random chunks: chunk 847 optimal weight: 40.0000 chunk 577 optimal weight: 20.0000 chunk 14 optimal weight: 0.3980 chunk 757 optimal weight: 10.0000 chunk 419 optimal weight: 10.0000 chunk 868 optimal weight: 10.0000 chunk 703 optimal weight: 10.0000 chunk 1 optimal weight: 0.6980 chunk 519 optimal weight: 2.9990 chunk 913 optimal weight: 10.0000 chunk 256 optimal weight: 40.0000 overall best weight: 4.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 167 ASN d 97 ASN d 136 GLN d 156 ASN ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 18 GLN g 28 ASN ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 6 GLN q 43 GLN q 55 GLN ** r 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 49 ASN G 38 HIS ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 197 HIS ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 118 ASN ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 40 ASN ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 52 ASN Y 12 GLN ** Y 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 308 GLN ** 8 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 160427 Z= 0.194 Angle : 0.568 11.918 239677 Z= 0.293 Chirality : 0.033 0.265 30569 Planarity : 0.004 0.067 13095 Dihedral : 23.435 177.225 79450 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.77 % Favored : 91.12 % Rotamer: Outliers : 3.79 % Allowed : 18.81 % Favored : 77.39 % 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: -2.04 (0.10), residues: 6011 helix: -0.02 (0.12), residues: 1913 sheet: -1.65 (0.15), residues: 1086 loop : -2.15 (0.11), residues: 3012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP U 60 HIS 0.011 0.001 HIS T 45 PHE 0.024 0.001 PHE 8 115 TYR 0.043 0.001 TYR g 25 ARG 0.015 0.001 ARG P 36 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1209 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1019 time to evaluate : 6.661 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: c 103 ASP cc_start: 0.8181 (p0) cc_final: 0.7955 (p0) REVERT: d 101 TYR cc_start: 0.8788 (t80) cc_final: 0.8554 (t80) REVERT: d 156 ASN cc_start: 0.8825 (OUTLIER) cc_final: 0.8452 (t0) REVERT: d 164 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9140 (mm) REVERT: d 188 MET cc_start: 0.8879 (tpp) cc_final: 0.8668 (tpp) REVERT: e 137 PHE cc_start: 0.8496 (m-80) cc_final: 0.8103 (m-80) REVERT: f 61 TRP cc_start: 0.8866 (m100) cc_final: 0.8360 (m100) REVERT: f 148 ARG cc_start: 0.8505 (tmm-80) cc_final: 0.8275 (tmm160) REVERT: f 162 ARG cc_start: 0.8773 (ptp-170) cc_final: 0.8203 (mtp180) REVERT: g 29 PHE cc_start: 0.8992 (t80) cc_final: 0.8693 (t80) REVERT: g 35 LYS cc_start: 0.9430 (mttp) cc_final: 0.9204 (mttp) REVERT: j 1 MET cc_start: 0.8557 (pmm) cc_final: 0.8229 (pmm) REVERT: k 82 ASN cc_start: 0.8237 (m-40) cc_final: 0.7997 (m-40) REVERT: m 17 ASN cc_start: 0.8401 (t0) cc_final: 0.7878 (t0) REVERT: m 110 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8311 (tm-30) REVERT: m 135 VAL cc_start: 0.7969 (OUTLIER) cc_final: 0.7669 (p) REVERT: m 136 MET cc_start: 0.7224 (ppp) cc_final: 0.6968 (ppp) REVERT: n 43 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7689 (mp0) REVERT: o 98 GLN cc_start: 0.8245 (tp40) cc_final: 0.7776 (tp-100) REVERT: p 12 MET cc_start: 0.7339 (tpp) cc_final: 0.6778 (tpp) REVERT: p 70 GLU cc_start: 0.6505 (mp0) cc_final: 0.6259 (mp0) REVERT: q 96 ASP cc_start: 0.8528 (t0) cc_final: 0.8299 (t0) REVERT: r 85 LYS cc_start: 0.9072 (ttmt) cc_final: 0.8842 (tttt) REVERT: s 95 ARG cc_start: 0.8480 (ptm-80) cc_final: 0.8160 (ttp80) REVERT: t 1 MET cc_start: 0.5961 (OUTLIER) cc_final: 0.4533 (mmt) REVERT: t 79 ASP cc_start: 0.8906 (t0) cc_final: 0.8700 (t0) REVERT: t 87 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8798 (pp) REVERT: u 87 GLU cc_start: 0.8562 (tp30) cc_final: 0.8339 (tp30) REVERT: w 51 ARG cc_start: 0.8770 (ptm160) cc_final: 0.8244 (tmm-80) REVERT: w 64 LYS cc_start: 0.8967 (tptm) cc_final: 0.8708 (tptm) REVERT: x 42 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8405 (tm-30) REVERT: x 70 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8747 (tp) REVERT: x 75 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7211 (tm-30) REVERT: y 36 GLN cc_start: 0.9321 (mm110) cc_final: 0.8930 (mp10) REVERT: z 18 LYS cc_start: 0.8214 (mmtt) cc_final: 0.7895 (tppt) REVERT: z 20 LYS cc_start: 0.9515 (mtpt) cc_final: 0.8638 (mttm) REVERT: z 30 ARG cc_start: 0.7997 (mtm-85) cc_final: 0.7794 (ptp90) REVERT: C 24 LYS cc_start: 0.7602 (tppt) cc_final: 0.7067 (tppt) REVERT: C 32 LYS cc_start: 0.7895 (ptmm) cc_final: 0.7212 (tttm) REVERT: C 34 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8131 (mm-30) REVERT: C 36 LYS cc_start: 0.9284 (ttmt) cc_final: 0.9046 (ttpt) REVERT: F 4 ARG cc_start: 0.8633 (ptp-110) cc_final: 0.8192 (ptp-110) REVERT: F 36 ARG cc_start: 0.8954 (ptt90) cc_final: 0.8705 (ptm160) REVERT: G 21 TYR cc_start: 0.8334 (m-80) cc_final: 0.8037 (m-10) REVERT: G 103 TRP cc_start: 0.8483 (t-100) cc_final: 0.7939 (t-100) REVERT: G 112 ARG cc_start: 0.9268 (tpt170) cc_final: 0.8330 (mtp180) REVERT: G 153 MET cc_start: 0.8436 (ttm) cc_final: 0.7885 (mtp) REVERT: H 28 PHE cc_start: 0.9063 (OUTLIER) cc_final: 0.8691 (m-80) REVERT: H 41 TYR cc_start: 0.8927 (t80) cc_final: 0.8692 (t80) REVERT: H 117 ASP cc_start: 0.9030 (m-30) cc_final: 0.8360 (p0) REVERT: H 166 TRP cc_start: 0.9043 (p-90) cc_final: 0.8714 (p-90) REVERT: H 184 ASN cc_start: 0.8885 (m110) cc_final: 0.8413 (m110) REVERT: I 28 ASP cc_start: 0.7726 (p0) cc_final: 0.6977 (t0) REVERT: I 70 GLN cc_start: 0.9112 (mp10) cc_final: 0.8886 (pm20) REVERT: I 73 ASN cc_start: 0.9520 (m-40) cc_final: 0.8829 (m110) REVERT: I 123 MET cc_start: 0.9148 (ttp) cc_final: 0.8896 (mtp) REVERT: I 181 PHE cc_start: 0.8577 (t80) cc_final: 0.8373 (t80) REVERT: J 63 MET cc_start: 0.8686 (tpp) cc_final: 0.8417 (tpp) REVERT: J 70 MET cc_start: 0.7917 (mmt) cc_final: 0.7689 (tpt) REVERT: J 80 LEU cc_start: 0.9457 (mt) cc_final: 0.9084 (pp) REVERT: J 96 GLN cc_start: 0.8281 (tm-30) cc_final: 0.7928 (tm-30) REVERT: J 115 GLU cc_start: 0.9463 (pt0) cc_final: 0.9164 (pt0) REVERT: J 146 MET cc_start: 0.8673 (tmm) cc_final: 0.8251 (tmm) REVERT: J 155 LYS cc_start: 0.9507 (pttt) cc_final: 0.9225 (ptmt) REVERT: J 161 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8899 (mp0) REVERT: K 80 PHE cc_start: 0.8767 (m-80) cc_final: 0.8484 (m-80) REVERT: L 30 MET cc_start: 0.8694 (ttp) cc_final: 0.7997 (tmm) REVERT: L 32 ASP cc_start: 0.8838 (m-30) cc_final: 0.8464 (m-30) REVERT: L 102 TRP cc_start: 0.9065 (m-10) cc_final: 0.8728 (m-10) REVERT: M 37 ASN cc_start: 0.8744 (m-40) cc_final: 0.8312 (m110) REVERT: M 59 GLU cc_start: 0.8942 (pt0) cc_final: 0.8553 (pm20) REVERT: M 95 MET cc_start: 0.8918 (mtp) cc_final: 0.8581 (mtm) REVERT: M 98 LEU cc_start: 0.8718 (pt) cc_final: 0.8384 (pt) REVERT: N 51 LEU cc_start: 0.9459 (tp) cc_final: 0.9203 (tp) REVERT: N 67 LYS cc_start: 0.8378 (ptmm) cc_final: 0.8175 (tptt) REVERT: O 46 LYS cc_start: 0.8358 (mtmm) cc_final: 0.7361 (mptt) REVERT: O 47 GLU cc_start: 0.7230 (mm-30) cc_final: 0.6944 (mm-30) REVERT: O 88 MET cc_start: 0.8695 (mpp) cc_final: 0.8343 (tpp) REVERT: P 54 SER cc_start: 0.9183 (p) cc_final: 0.8951 (m) REVERT: P 84 MET cc_start: 0.8486 (ttm) cc_final: 0.7854 (ppp) REVERT: P 93 GLU cc_start: 0.8362 (tm-30) cc_final: 0.7850 (tm-30) REVERT: Q 69 GLU cc_start: 0.7780 (tp30) cc_final: 0.7566 (mm-30) REVERT: R 47 LEU cc_start: 0.6595 (mt) cc_final: 0.6363 (mt) REVERT: R 51 GLN cc_start: 0.9140 (mt0) cc_final: 0.8819 (tp-100) REVERT: R 67 ASP cc_start: 0.8982 (t0) cc_final: 0.8726 (t70) REVERT: S 5 MET cc_start: 0.7013 (mmm) cc_final: 0.6488 (mmp) REVERT: S 88 MET cc_start: 0.8939 (tpp) cc_final: 0.8702 (tpp) REVERT: T 25 GLU cc_start: 0.8819 (pm20) cc_final: 0.8401 (pm20) REVERT: T 47 LYS cc_start: 0.8358 (mtmm) cc_final: 0.8036 (mtmm) REVERT: U 14 ARG cc_start: 0.8688 (ttt180) cc_final: 0.8166 (ttp-170) REVERT: U 17 TYR cc_start: 0.8803 (m-80) cc_final: 0.8549 (m-10) REVERT: U 29 ASN cc_start: 0.8003 (m-40) cc_final: 0.7797 (m-40) REVERT: U 32 PHE cc_start: 0.9211 (p90) cc_final: 0.8048 (p90) REVERT: U 34 GLU cc_start: 0.8467 (pm20) cc_final: 0.8208 (pm20) REVERT: U 53 ASP cc_start: 0.8574 (t0) cc_final: 0.8252 (t0) REVERT: W 56 ARG cc_start: 0.9233 (ttm110) cc_final: 0.8753 (ttt-90) REVERT: X 70 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9158 (tp) REVERT: Y 20 ASN cc_start: 0.9456 (m-40) cc_final: 0.9178 (m-40) REVERT: Y 28 ARG cc_start: 0.8601 (mmm-85) cc_final: 0.8057 (mtt180) REVERT: Y 31 ILE cc_start: 0.9682 (OUTLIER) cc_final: 0.8911 (pt) REVERT: Y 35 TYR cc_start: 0.8962 (m-80) cc_final: 0.8728 (m-80) REVERT: Y 53 MET cc_start: 0.8717 (ppp) cc_final: 0.8508 (ppp) REVERT: Y 58 ASP cc_start: 0.8654 (m-30) cc_final: 0.8111 (m-30) REVERT: Y 66 ILE cc_start: 0.8771 (mm) cc_final: 0.8433 (tt) REVERT: Y 73 ARG cc_start: 0.9273 (ttp-110) cc_final: 0.9016 (ttm170) REVERT: Y 81 GLN cc_start: 0.8911 (mm-40) cc_final: 0.8635 (tm-30) REVERT: Z 24 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7491 (mtpt) REVERT: Z 36 PHE cc_start: 0.8854 (t80) cc_final: 0.8535 (t80) REVERT: Z 43 GLU cc_start: 0.8776 (tt0) cc_final: 0.8451 (tp30) REVERT: a 8 MET cc_start: -0.0913 (mpp) cc_final: -0.1876 (mtt) REVERT: a 180 PHE cc_start: 0.1920 (OUTLIER) cc_final: 0.1659 (t80) REVERT: 8 118 MET cc_start: 0.8114 (tpp) cc_final: 0.7907 (tpp) REVERT: 8 151 MET cc_start: 0.9565 (tmm) cc_final: 0.9074 (tmm) REVERT: 8 152 TYR cc_start: 0.9352 (m-80) cc_final: 0.8732 (m-80) REVERT: 8 207 PHE cc_start: 0.8060 (m-10) cc_final: 0.7575 (m-10) REVERT: 8 223 TYR cc_start: 0.9454 (p90) cc_final: 0.9093 (p90) REVERT: 8 300 MET cc_start: 0.8717 (mmp) cc_final: 0.8455 (mmp) REVERT: 8 310 MET cc_start: 0.8839 (mmm) cc_final: 0.8549 (mmm) outliers start: 190 outliers final: 127 residues processed: 1121 average time/residue: 1.2769 time to fit residues: 2504.4679 Evaluate side-chains 1058 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 920 time to evaluate : 6.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 66 PHE Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 156 ASN Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain e residue 4 HIS Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain f residue 25 ILE Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain g residue 108 VAL Chi-restraints excluded: chain g residue 115 VAL Chi-restraints excluded: chain j residue 139 VAL Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 91 ASP Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain q residue 103 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 26 ASP Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 1 MET Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 53 VAL Chi-restraints excluded: chain t residue 56 GLU Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 46 ASN Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 70 LEU Chi-restraints excluded: chain y residue 6 LEU Chi-restraints excluded: chain y residue 58 ASN Chi-restraints excluded: chain z residue 23 LEU Chi-restraints excluded: chain z residue 26 LEU Chi-restraints excluded: chain z residue 43 ILE Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 192 TYR Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 135 GLN Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 125 ASP Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 49 PHE Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 16 MET Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Z residue 24 LYS Chi-restraints excluded: chain Z residue 27 VAL Chi-restraints excluded: chain Z residue 37 TYR Chi-restraints excluded: chain a residue 180 PHE Chi-restraints excluded: chain 8 residue 227 ASP Chi-restraints excluded: chain 8 residue 228 ASP Chi-restraints excluded: chain 8 residue 271 VAL Chi-restraints excluded: chain 8 residue 340 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1053 random chunks: chunk 342 optimal weight: 0.8980 chunk 916 optimal weight: 50.0000 chunk 201 optimal weight: 7.9990 chunk 597 optimal weight: 40.0000 chunk 251 optimal weight: 1.9990 chunk 1018 optimal weight: 10.0000 chunk 845 optimal weight: 20.0000 chunk 471 optimal weight: 20.0000 chunk 84 optimal weight: 50.0000 chunk 337 optimal weight: 50.0000 chunk 534 optimal weight: 0.0980 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 136 GLN ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 37 ASN g 28 ASN ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 5 GLN ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 9 GLN ** o 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 9 GLN q 43 GLN q 55 GLN ** r 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 HIS H 122 GLN ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 125 ASN J 120 HIS ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 52 ASN ** Y 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 97 ASN ** 8 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 160427 Z= 0.184 Angle : 0.562 11.763 239677 Z= 0.288 Chirality : 0.033 0.407 30569 Planarity : 0.004 0.075 13095 Dihedral : 23.404 177.286 79448 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.80 % Favored : 91.10 % Rotamer: Outliers : 3.81 % Allowed : 20.23 % Favored : 75.95 % 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: -1.85 (0.11), residues: 6011 helix: 0.08 (0.12), residues: 1918 sheet: -1.46 (0.15), residues: 1084 loop : -2.03 (0.11), residues: 3009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP U 60 HIS 0.009 0.001 HIS K 11 PHE 0.033 0.001 PHE C 19 TYR 0.045 0.001 TYR g 25 ARG 0.009 0.001 ARG t 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1200 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1009 time to evaluate : 6.746 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: b 116 GLN cc_start: 0.8008 (tt0) cc_final: 0.7636 (tt0) REVERT: c 103 ASP cc_start: 0.8169 (p0) cc_final: 0.7940 (p0) REVERT: d 101 TYR cc_start: 0.8713 (t80) cc_final: 0.8479 (t80) REVERT: d 164 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9141 (mm) REVERT: d 188 MET cc_start: 0.8836 (tpp) cc_final: 0.8603 (tpp) REVERT: e 137 PHE cc_start: 0.8460 (m-80) cc_final: 0.8108 (m-80) REVERT: f 61 TRP cc_start: 0.8847 (m100) cc_final: 0.8298 (m100) REVERT: f 148 ARG cc_start: 0.8510 (tmm-80) cc_final: 0.8270 (tmm160) REVERT: f 162 ARG cc_start: 0.8740 (ptp-170) cc_final: 0.8138 (mtp85) REVERT: j 1 MET cc_start: 0.8665 (pmm) cc_final: 0.8337 (pmm) REVERT: k 82 ASN cc_start: 0.8295 (m-40) cc_final: 0.8029 (m-40) REVERT: m 75 GLU cc_start: 0.7932 (pm20) cc_final: 0.7159 (pm20) REVERT: m 103 TYR cc_start: 0.8367 (m-80) cc_final: 0.8089 (m-80) REVERT: m 110 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8355 (tm-30) REVERT: m 135 VAL cc_start: 0.7971 (OUTLIER) cc_final: 0.7667 (p) REVERT: m 136 MET cc_start: 0.7247 (ppp) cc_final: 0.6986 (ppp) REVERT: o 98 GLN cc_start: 0.8274 (tp40) cc_final: 0.7808 (tp-100) REVERT: p 12 MET cc_start: 0.7351 (tpp) cc_final: 0.6978 (tpp) REVERT: p 70 GLU cc_start: 0.6372 (mp0) cc_final: 0.6086 (mp0) REVERT: p 97 TYR cc_start: 0.8232 (m-80) cc_final: 0.8011 (m-80) REVERT: r 22 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8730 (pp) REVERT: s 94 ASP cc_start: 0.7293 (t0) cc_final: 0.6990 (t0) REVERT: s 95 ARG cc_start: 0.8608 (ptm-80) cc_final: 0.8229 (ttp80) REVERT: t 1 MET cc_start: 0.6184 (mtt) cc_final: 0.4492 (mmt) REVERT: t 12 ARG cc_start: 0.8919 (tpp80) cc_final: 0.8491 (tpp80) REVERT: t 79 ASP cc_start: 0.8847 (t0) cc_final: 0.8641 (t0) REVERT: t 87 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8572 (pp) REVERT: u 87 GLU cc_start: 0.8539 (tp30) cc_final: 0.8335 (tp30) REVERT: w 51 ARG cc_start: 0.8689 (ptm160) cc_final: 0.8244 (tmm-80) REVERT: x 42 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8366 (tm-30) REVERT: x 64 ASP cc_start: 0.8567 (p0) cc_final: 0.8347 (p0) REVERT: y 1 MET cc_start: 0.7929 (tpp) cc_final: 0.6869 (tpp) REVERT: y 2 LYS cc_start: 0.8807 (ptpp) cc_final: 0.8471 (ptpp) REVERT: y 17 GLU cc_start: 0.8911 (tp30) cc_final: 0.8703 (tp30) REVERT: y 36 GLN cc_start: 0.9120 (mm110) cc_final: 0.8766 (mp10) REVERT: z 20 LYS cc_start: 0.9510 (mtpt) cc_final: 0.8633 (mttm) REVERT: C 7 LYS cc_start: 0.8732 (mtmt) cc_final: 0.8338 (mtmt) REVERT: C 32 LYS cc_start: 0.7872 (ptmm) cc_final: 0.7178 (tttm) REVERT: C 34 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8114 (mm-30) REVERT: C 36 LYS cc_start: 0.9370 (ttmt) cc_final: 0.9058 (ttpt) REVERT: C 46 VAL cc_start: 0.9280 (t) cc_final: 0.9021 (p) REVERT: F 4 ARG cc_start: 0.8631 (ptp-110) cc_final: 0.8188 (ptp-110) REVERT: F 36 ARG cc_start: 0.8969 (ptt90) cc_final: 0.8567 (ptt-90) REVERT: G 5 MET cc_start: 0.9015 (tmm) cc_final: 0.8792 (tpt) REVERT: G 21 TYR cc_start: 0.8151 (m-80) cc_final: 0.7844 (m-80) REVERT: G 103 TRP cc_start: 0.8467 (t-100) cc_final: 0.7961 (t-100) REVERT: G 112 ARG cc_start: 0.9282 (tpt170) cc_final: 0.8407 (mtp180) REVERT: G 153 MET cc_start: 0.8407 (ttm) cc_final: 0.7869 (mtp) REVERT: H 28 PHE cc_start: 0.9037 (OUTLIER) cc_final: 0.8649 (m-80) REVERT: H 117 ASP cc_start: 0.9030 (m-30) cc_final: 0.8297 (p0) REVERT: H 122 GLN cc_start: 0.9431 (mt0) cc_final: 0.8915 (mp10) REVERT: H 166 TRP cc_start: 0.9022 (p-90) cc_final: 0.8700 (p-90) REVERT: H 184 ASN cc_start: 0.8879 (m110) cc_final: 0.8419 (m110) REVERT: I 28 ASP cc_start: 0.7691 (p0) cc_final: 0.6922 (t0) REVERT: I 70 GLN cc_start: 0.9117 (mp10) cc_final: 0.8916 (pm20) REVERT: I 73 ASN cc_start: 0.9517 (m-40) cc_final: 0.8770 (m110) REVERT: I 123 MET cc_start: 0.9156 (ttp) cc_final: 0.8879 (mtm) REVERT: J 53 ARG cc_start: 0.8138 (mmm160) cc_final: 0.7908 (mmm160) REVERT: J 63 MET cc_start: 0.8714 (tpp) cc_final: 0.8376 (tpp) REVERT: J 80 LEU cc_start: 0.9459 (mt) cc_final: 0.9071 (pp) REVERT: J 96 GLN cc_start: 0.8412 (tm-30) cc_final: 0.7924 (tm-30) REVERT: J 115 GLU cc_start: 0.9450 (pt0) cc_final: 0.9139 (pt0) REVERT: J 155 LYS cc_start: 0.9510 (pttt) cc_final: 0.9186 (ptmm) REVERT: J 161 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8867 (mm-30) REVERT: K 24 ARG cc_start: 0.8813 (mtm180) cc_final: 0.8515 (mtm110) REVERT: K 25 TYR cc_start: 0.8960 (m-10) cc_final: 0.8547 (m-80) REVERT: K 80 PHE cc_start: 0.8714 (m-80) cc_final: 0.8465 (m-80) REVERT: L 30 MET cc_start: 0.8582 (ttp) cc_final: 0.7934 (tmm) REVERT: L 32 ASP cc_start: 0.8840 (m-30) cc_final: 0.8469 (m-30) REVERT: L 102 TRP cc_start: 0.9056 (m-10) cc_final: 0.8744 (m-10) REVERT: M 37 ASN cc_start: 0.8790 (m-40) cc_final: 0.8304 (m110) REVERT: M 59 GLU cc_start: 0.8911 (pt0) cc_final: 0.8536 (pm20) REVERT: M 95 MET cc_start: 0.8894 (mtp) cc_final: 0.8483 (mtm) REVERT: M 110 MET cc_start: 0.7063 (pmm) cc_final: 0.6791 (pmm) REVERT: N 51 LEU cc_start: 0.9301 (tp) cc_final: 0.8678 (tp) REVERT: O 46 LYS cc_start: 0.8300 (mtmm) cc_final: 0.7536 (mptt) REVERT: O 47 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6969 (mm-30) REVERT: O 88 MET cc_start: 0.8701 (mpp) cc_final: 0.8326 (tpp) REVERT: P 84 MET cc_start: 0.8463 (ttm) cc_final: 0.7898 (ppp) REVERT: P 93 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7756 (tm-30) REVERT: R 47 LEU cc_start: 0.6577 (mt) cc_final: 0.6338 (mt) REVERT: R 51 GLN cc_start: 0.9129 (mt0) cc_final: 0.8793 (tp-100) REVERT: R 67 ASP cc_start: 0.9068 (t0) cc_final: 0.8786 (t70) REVERT: R 82 LEU cc_start: 0.8714 (tp) cc_final: 0.8436 (tp) REVERT: S 5 MET cc_start: 0.6991 (mmm) cc_final: 0.6465 (mmp) REVERT: S 91 GLU cc_start: 0.8869 (mp0) cc_final: 0.8517 (mp0) REVERT: T 25 GLU cc_start: 0.8849 (pm20) cc_final: 0.8417 (pm20) REVERT: T 47 LYS cc_start: 0.8369 (mtmm) cc_final: 0.8073 (mtmm) REVERT: U 14 ARG cc_start: 0.8682 (ttt180) cc_final: 0.8246 (ttp-170) REVERT: U 17 TYR cc_start: 0.8786 (m-80) cc_final: 0.8509 (m-10) REVERT: U 29 ASN cc_start: 0.7970 (m-40) cc_final: 0.7764 (m-40) REVERT: U 32 PHE cc_start: 0.9123 (p90) cc_final: 0.7957 (p90) REVERT: U 34 GLU cc_start: 0.8460 (pm20) cc_final: 0.8238 (pm20) REVERT: U 53 ASP cc_start: 0.8654 (t0) cc_final: 0.8334 (t0) REVERT: U 55 ASP cc_start: 0.8929 (t0) cc_final: 0.8417 (t0) REVERT: U 56 ARG cc_start: 0.8913 (mmm-85) cc_final: 0.8631 (mmm160) REVERT: U 76 LYS cc_start: 0.9381 (mmmt) cc_final: 0.9168 (mtpt) REVERT: W 56 ARG cc_start: 0.9207 (ttm110) cc_final: 0.8847 (mtp180) REVERT: X 19 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8113 (pt0) REVERT: X 20 LYS cc_start: 0.8818 (mtmt) cc_final: 0.8592 (pttm) REVERT: X 70 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9207 (tp) REVERT: Y 20 ASN cc_start: 0.9446 (m-40) cc_final: 0.8927 (p0) REVERT: Y 28 ARG cc_start: 0.8676 (mmm-85) cc_final: 0.8125 (mtt180) REVERT: Y 31 ILE cc_start: 0.9657 (OUTLIER) cc_final: 0.8773 (pt) REVERT: Y 35 TYR cc_start: 0.8958 (m-80) cc_final: 0.8705 (m-80) REVERT: Y 58 ASP cc_start: 0.8653 (m-30) cc_final: 0.8110 (m-30) REVERT: Y 66 ILE cc_start: 0.8759 (mm) cc_final: 0.8419 (tt) REVERT: Y 67 HIS cc_start: 0.7458 (t-90) cc_final: 0.7092 (t70) REVERT: Y 81 GLN cc_start: 0.8960 (mm-40) cc_final: 0.8713 (tm-30) REVERT: Z 24 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7746 (mtpt) REVERT: Z 36 PHE cc_start: 0.8836 (t80) cc_final: 0.8532 (t80) REVERT: Z 43 GLU cc_start: 0.8774 (tt0) cc_final: 0.8377 (tp30) REVERT: a 8 MET cc_start: -0.0983 (mpp) cc_final: -0.1768 (mtm) REVERT: a 180 PHE cc_start: 0.1896 (OUTLIER) cc_final: 0.1629 (t80) REVERT: 8 129 TYR cc_start: 0.8836 (m-80) cc_final: 0.8485 (m-80) REVERT: 8 151 MET cc_start: 0.9571 (tmm) cc_final: 0.9085 (tmm) REVERT: 8 152 TYR cc_start: 0.9356 (m-80) cc_final: 0.8737 (m-80) REVERT: 8 182 LYS cc_start: 0.9349 (tttt) cc_final: 0.9102 (tttm) REVERT: 8 207 PHE cc_start: 0.8042 (m-10) cc_final: 0.7559 (m-10) REVERT: 8 300 MET cc_start: 0.8749 (mmp) cc_final: 0.8457 (mmp) REVERT: 8 310 MET cc_start: 0.8851 (mmm) cc_final: 0.8574 (mmm) outliers start: 191 outliers final: 139 residues processed: 1115 average time/residue: 1.2739 time to fit residues: 2484.6048 Evaluate side-chains 1072 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 924 time to evaluate : 6.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 66 PHE Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 202 ARG Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain e residue 4 HIS Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain f residue 25 ILE Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain g residue 115 VAL Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 118 MET Chi-restraints excluded: chain j residue 139 VAL Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 91 ASP Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 119 LEU Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain o residue 76 LYS Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain q residue 55 GLN Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain q residue 103 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 26 ASP Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 53 VAL Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 7 ASP Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain w residue 46 ASN Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain y residue 6 LEU Chi-restraints excluded: chain y residue 58 ASN Chi-restraints excluded: chain z residue 23 LEU Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 192 TYR Chi-restraints excluded: chain I residue 135 GLN Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 125 ASP Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 49 PHE Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 16 MET Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain W residue 24 ASP Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Y residue 12 GLN Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 24 LYS Chi-restraints excluded: chain Z residue 37 TYR Chi-restraints excluded: chain a residue 180 PHE Chi-restraints excluded: chain 8 residue 227 ASP Chi-restraints excluded: chain 8 residue 228 ASP Chi-restraints excluded: chain 8 residue 254 VAL Chi-restraints excluded: chain 8 residue 271 VAL Chi-restraints excluded: chain 8 residue 340 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1053 random chunks: chunk 982 optimal weight: 20.0000 chunk 114 optimal weight: 0.0470 chunk 580 optimal weight: 30.0000 chunk 744 optimal weight: 20.0000 chunk 576 optimal weight: 20.0000 chunk 857 optimal weight: 50.0000 chunk 568 optimal weight: 30.0000 chunk 1014 optimal weight: 50.0000 chunk 635 optimal weight: 20.0000 chunk 618 optimal weight: 20.0000 chunk 468 optimal weight: 20.0000 overall best weight: 16.0094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 52 HIS ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 225 ASN c 67 HIS d 136 GLN ** d 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 58 GLN ** r 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 87 GLN w 46 ASN y 36 GLN ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 HIS ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 GLN ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 27 GLN ** T 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 12 GLN ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 188 ASN 8 5 ASN 8 8 ASN ** 8 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.5150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.161 160427 Z= 0.528 Angle : 0.825 13.883 239677 Z= 0.415 Chirality : 0.044 0.471 30569 Planarity : 0.006 0.068 13095 Dihedral : 23.804 178.602 79448 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 30.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.15 % Favored : 88.72 % Rotamer: Outliers : 5.05 % Allowed : 20.71 % Favored : 74.24 % 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: -2.29 (0.10), residues: 6011 helix: -0.45 (0.11), residues: 1930 sheet: -1.67 (0.15), residues: 1082 loop : -2.19 (0.11), residues: 2999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP U 60 HIS 0.014 0.002 HIS q 13 PHE 0.024 0.003 PHE m 117 TYR 0.052 0.003 TYR g 25 ARG 0.010 0.001 ARG j 99 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1119 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 866 time to evaluate : 5.953 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: b 116 GLN cc_start: 0.7836 (tt0) cc_final: 0.7428 (tt0) REVERT: c 103 ASP cc_start: 0.8468 (p0) cc_final: 0.8227 (p0) REVERT: c 156 PHE cc_start: 0.8746 (m-80) cc_final: 0.8523 (m-80) REVERT: d 101 TYR cc_start: 0.8983 (t80) cc_final: 0.8708 (t80) REVERT: d 164 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.8959 (mm) REVERT: d 188 MET cc_start: 0.8701 (tpp) cc_final: 0.8303 (tpp) REVERT: e 137 PHE cc_start: 0.8701 (m-80) cc_final: 0.8290 (m-80) REVERT: f 61 TRP cc_start: 0.8847 (m100) cc_final: 0.8346 (m100) REVERT: f 148 ARG cc_start: 0.8625 (tmm-80) cc_final: 0.8397 (tmm160) REVERT: f 162 ARG cc_start: 0.8719 (ptp-170) cc_final: 0.8238 (mtp85) REVERT: g 29 PHE cc_start: 0.9188 (t80) cc_final: 0.8850 (t80) REVERT: m 90 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7287 (mt-10) REVERT: m 110 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8364 (tm-30) REVERT: m 135 VAL cc_start: 0.8174 (OUTLIER) cc_final: 0.7823 (p) REVERT: m 136 MET cc_start: 0.7279 (ppp) cc_final: 0.6913 (ppp) REVERT: o 17 LYS cc_start: 0.9335 (tptp) cc_final: 0.9111 (tppt) REVERT: o 19 GLN cc_start: 0.9188 (pp30) cc_final: 0.8912 (pp30) REVERT: p 70 GLU cc_start: 0.6674 (mp0) cc_final: 0.6461 (mp0) REVERT: t 1 MET cc_start: 0.6652 (mtt) cc_final: 0.5183 (mmt) REVERT: v 38 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8941 (mm) REVERT: w 51 ARG cc_start: 0.9068 (ptm160) cc_final: 0.8259 (ttp80) REVERT: x 42 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8445 (tm-30) REVERT: y 17 GLU cc_start: 0.9013 (tp30) cc_final: 0.8743 (tp30) REVERT: z 18 LYS cc_start: 0.8332 (mmmt) cc_final: 0.7915 (tppt) REVERT: z 44 ARG cc_start: 0.8718 (tpp80) cc_final: 0.8448 (mpp80) REVERT: C 32 LYS cc_start: 0.7920 (ptmm) cc_final: 0.7283 (tttm) REVERT: C 34 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8066 (mm-30) REVERT: C 36 LYS cc_start: 0.9551 (ttmt) cc_final: 0.9183 (ttpt) REVERT: C 52 LYS cc_start: 0.7061 (tptp) cc_final: 0.6594 (tptp) REVERT: F 4 ARG cc_start: 0.8661 (ptp-110) cc_final: 0.8170 (ptp-110) REVERT: F 36 ARG cc_start: 0.8996 (ptt90) cc_final: 0.8497 (ptt180) REVERT: G 21 TYR cc_start: 0.8282 (m-80) cc_final: 0.7968 (m-10) REVERT: G 103 TRP cc_start: 0.8721 (t-100) cc_final: 0.8042 (t-100) REVERT: G 112 ARG cc_start: 0.9227 (tpt170) cc_final: 0.8121 (mtp180) REVERT: G 153 MET cc_start: 0.8516 (ttm) cc_final: 0.8007 (mtp) REVERT: H 28 PHE cc_start: 0.8965 (OUTLIER) cc_final: 0.8593 (m-80) REVERT: H 166 TRP cc_start: 0.9135 (p-90) cc_final: 0.8866 (p-90) REVERT: H 184 ASN cc_start: 0.8640 (m110) cc_final: 0.8106 (m110) REVERT: I 28 ASP cc_start: 0.7822 (p0) cc_final: 0.7130 (t0) REVERT: J 63 MET cc_start: 0.8657 (tpp) cc_final: 0.8305 (tpp) REVERT: J 96 GLN cc_start: 0.8372 (tm-30) cc_final: 0.7774 (tm-30) REVERT: J 115 GLU cc_start: 0.9519 (pt0) cc_final: 0.9233 (pt0) REVERT: K 24 ARG cc_start: 0.8829 (mtm180) cc_final: 0.8436 (mtm110) REVERT: K 25 TYR cc_start: 0.9001 (m-10) cc_final: 0.8517 (m-80) REVERT: K 88 MET cc_start: 0.8362 (ppp) cc_final: 0.7803 (tmm) REVERT: L 30 MET cc_start: 0.8757 (ttp) cc_final: 0.8263 (tmm) REVERT: L 32 ASP cc_start: 0.8898 (m-30) cc_final: 0.8505 (m-30) REVERT: M 37 ASN cc_start: 0.9038 (m-40) cc_final: 0.8596 (m110) REVERT: M 59 GLU cc_start: 0.8950 (pt0) cc_final: 0.8229 (pm20) REVERT: M 95 MET cc_start: 0.9060 (mtp) cc_final: 0.8786 (ptp) REVERT: N 51 LEU cc_start: 0.9527 (tp) cc_final: 0.9182 (tp) REVERT: O 11 LYS cc_start: 0.7426 (mmtp) cc_final: 0.7198 (mmmt) REVERT: O 14 ASP cc_start: 0.9392 (p0) cc_final: 0.9179 (p0) REVERT: O 46 LYS cc_start: 0.8113 (mtmm) cc_final: 0.7350 (mptt) REVERT: O 88 MET cc_start: 0.8752 (mpp) cc_final: 0.8350 (tpp) REVERT: Q 74 GLN cc_start: 0.8286 (mt0) cc_final: 0.7844 (mm110) REVERT: R 47 LEU cc_start: 0.6426 (mt) cc_final: 0.6109 (mt) REVERT: R 51 GLN cc_start: 0.9146 (mt0) cc_final: 0.8838 (tp-100) REVERT: R 67 ASP cc_start: 0.8869 (t0) cc_final: 0.8598 (t70) REVERT: R 82 LEU cc_start: 0.8710 (tp) cc_final: 0.8470 (tp) REVERT: S 88 MET cc_start: 0.8820 (tpp) cc_final: 0.8043 (tpp) REVERT: S 95 LEU cc_start: 0.9372 (tt) cc_final: 0.8958 (mp) REVERT: T 25 GLU cc_start: 0.8992 (pm20) cc_final: 0.8625 (pm20) REVERT: U 14 ARG cc_start: 0.8699 (ttt180) cc_final: 0.8183 (ttp-170) REVERT: U 32 PHE cc_start: 0.9199 (p90) cc_final: 0.8030 (p90) REVERT: U 34 GLU cc_start: 0.8590 (pm20) cc_final: 0.8371 (pm20) REVERT: U 53 ASP cc_start: 0.8741 (t0) cc_final: 0.8535 (t0) REVERT: U 76 LYS cc_start: 0.9388 (mmmt) cc_final: 0.9174 (mtpt) REVERT: V 42 LYS cc_start: 0.8867 (mtmm) cc_final: 0.8085 (ptmt) REVERT: V 47 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.8097 (p0) REVERT: Y 20 ASN cc_start: 0.9509 (m-40) cc_final: 0.8977 (p0) REVERT: Y 26 MET cc_start: 0.8493 (mmp) cc_final: 0.8133 (mmp) REVERT: Y 28 ARG cc_start: 0.8751 (mmm-85) cc_final: 0.8301 (mtt180) REVERT: Y 66 ILE cc_start: 0.8890 (mm) cc_final: 0.8504 (tt) REVERT: Y 67 HIS cc_start: 0.7457 (t-90) cc_final: 0.7152 (t-90) REVERT: Y 81 GLN cc_start: 0.9072 (mm-40) cc_final: 0.8671 (tm-30) REVERT: Z 36 PHE cc_start: 0.9011 (t80) cc_final: 0.8660 (t80) REVERT: Z 43 GLU cc_start: 0.8874 (tt0) cc_final: 0.8436 (tp30) REVERT: a 8 MET cc_start: -0.0845 (mpp) cc_final: -0.1693 (mtm) REVERT: a 180 PHE cc_start: 0.1934 (OUTLIER) cc_final: 0.1667 (t80) REVERT: 8 118 MET cc_start: 0.7898 (tpp) cc_final: 0.7684 (tpp) REVERT: 8 151 MET cc_start: 0.9509 (tmm) cc_final: 0.9075 (tmm) REVERT: 8 182 LYS cc_start: 0.9450 (tttt) cc_final: 0.9180 (tttm) REVERT: 8 207 PHE cc_start: 0.8088 (m-10) cc_final: 0.7586 (m-10) REVERT: 8 300 MET cc_start: 0.8702 (mmp) cc_final: 0.8374 (mmp) outliers start: 253 outliers final: 189 residues processed: 1029 average time/residue: 1.2492 time to fit residues: 2261.4744 Evaluate side-chains 1013 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 818 time to evaluate : 6.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 24 HIS Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 66 PHE Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 202 ARG Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain e residue 4 HIS Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 51 ASN Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 173 ASP Chi-restraints excluded: chain f residue 25 ILE Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain g residue 19 VAL Chi-restraints excluded: chain g residue 115 VAL Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 118 MET Chi-restraints excluded: chain j residue 139 VAL Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 86 GLU Chi-restraints excluded: chain l residue 103 ILE Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 119 LEU Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain o residue 61 GLN Chi-restraints excluded: chain o residue 88 LYS Chi-restraints excluded: chain o residue 112 GLU Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 43 GLN Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain q residue 103 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 25 LEU Chi-restraints excluded: chain r residue 26 ASP Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 36 LEU Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 52 GLU Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 85 ILE Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 53 VAL Chi-restraints excluded: chain t residue 59 ASN Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain v residue 38 LEU Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 26 SER Chi-restraints excluded: chain w residue 46 ASN Chi-restraints excluded: chain w residue 78 ILE Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 59 ASP Chi-restraints excluded: chain y residue 4 LYS Chi-restraints excluded: chain y residue 6 LEU Chi-restraints excluded: chain y residue 7 ARG Chi-restraints excluded: chain y residue 13 GLU Chi-restraints excluded: chain y residue 58 ASN Chi-restraints excluded: chain z residue 23 LEU Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain H residue 7 ASN Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 40 GLN Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 192 TYR Chi-restraints excluded: chain I residue 135 GLN Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 125 ASP Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 49 PHE Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 47 ASP Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain X residue 70 LEU 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 37 TYR Chi-restraints excluded: chain a residue 180 PHE Chi-restraints excluded: chain 8 residue 198 VAL Chi-restraints excluded: chain 8 residue 227 ASP Chi-restraints excluded: chain 8 residue 228 ASP Chi-restraints excluded: chain 8 residue 254 VAL Chi-restraints excluded: chain 8 residue 266 ILE Chi-restraints excluded: chain 8 residue 340 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1053 random chunks: chunk 627 optimal weight: 20.0000 chunk 405 optimal weight: 30.0000 chunk 606 optimal weight: 20.0000 chunk 305 optimal weight: 6.9990 chunk 199 optimal weight: 5.9990 chunk 196 optimal weight: 7.9990 chunk 645 optimal weight: 10.0000 chunk 691 optimal weight: 20.0000 chunk 501 optimal weight: 0.0270 chunk 94 optimal weight: 20.0000 chunk 797 optimal weight: 10.0000 overall best weight: 6.2048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 136 GLN ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 55 GLN ** r 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 HIS ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 ASN ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 36 ASN ** U 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.4995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 160427 Z= 0.239 Angle : 0.621 12.112 239677 Z= 0.317 Chirality : 0.035 0.280 30569 Planarity : 0.004 0.053 13095 Dihedral : 23.743 178.438 79448 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 20.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.22 % Favored : 90.67 % Rotamer: Outliers : 3.65 % Allowed : 22.55 % Favored : 73.80 % 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: -1.99 (0.11), residues: 6011 helix: -0.12 (0.12), residues: 1906 sheet: -1.58 (0.15), residues: 1095 loop : -2.03 (0.11), residues: 3010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP U 60 HIS 0.010 0.001 HIS K 11 PHE 0.025 0.002 PHE C 19 TYR 0.046 0.002 TYR g 25 ARG 0.017 0.001 ARG D 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1112 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 929 time to evaluate : 6.752 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: b 35 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8753 (tptt) REVERT: c 103 ASP cc_start: 0.8276 (p0) cc_final: 0.8004 (p0) REVERT: d 101 TYR cc_start: 0.8755 (t80) cc_final: 0.8517 (t80) REVERT: d 164 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9083 (mm) REVERT: d 188 MET cc_start: 0.8795 (tpp) cc_final: 0.8415 (tpp) REVERT: e 137 PHE cc_start: 0.8751 (m-80) cc_final: 0.8352 (m-80) REVERT: f 61 TRP cc_start: 0.8874 (m100) cc_final: 0.8359 (m100) REVERT: f 148 ARG cc_start: 0.8614 (tmm-80) cc_final: 0.8370 (tmm160) REVERT: f 162 ARG cc_start: 0.8710 (ptp-170) cc_final: 0.8142 (mtp85) REVERT: g 29 PHE cc_start: 0.9102 (t80) cc_final: 0.8697 (t80) REVERT: m 90 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7360 (mt-10) REVERT: m 103 TYR cc_start: 0.8502 (m-80) cc_final: 0.8272 (m-80) REVERT: m 135 VAL cc_start: 0.8082 (OUTLIER) cc_final: 0.7725 (p) REVERT: m 136 MET cc_start: 0.7376 (ppp) cc_final: 0.7012 (ppp) REVERT: n 43 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7684 (mp0) REVERT: p 70 GLU cc_start: 0.6607 (mp0) cc_final: 0.6368 (mp0) REVERT: r 22 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8826 (pp) REVERT: s 95 ARG cc_start: 0.8645 (ptm160) cc_final: 0.8308 (ttp80) REVERT: t 1 MET cc_start: 0.6305 (mtt) cc_final: 0.4739 (mmt) REVERT: u 87 GLU cc_start: 0.8336 (tp30) cc_final: 0.8084 (tp30) REVERT: w 51 ARG cc_start: 0.8824 (ptm160) cc_final: 0.8345 (tmm-80) REVERT: y 17 GLU cc_start: 0.9000 (tp30) cc_final: 0.8736 (tp30) REVERT: z 18 LYS cc_start: 0.8293 (mmmt) cc_final: 0.7936 (tppt) REVERT: z 36 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7836 (mm-30) REVERT: z 44 ARG cc_start: 0.8561 (tpp80) cc_final: 0.8329 (mpt-90) REVERT: C 7 LYS cc_start: 0.8807 (mtmt) cc_final: 0.8356 (mtmt) REVERT: C 32 LYS cc_start: 0.7839 (ptmm) cc_final: 0.7138 (tttm) REVERT: C 34 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8157 (mm-30) REVERT: C 36 LYS cc_start: 0.9439 (ttmt) cc_final: 0.9061 (ttpt) REVERT: C 46 VAL cc_start: 0.9336 (OUTLIER) cc_final: 0.9034 (p) REVERT: D 43 THR cc_start: 0.8669 (p) cc_final: 0.8285 (t) REVERT: F 4 ARG cc_start: 0.8637 (ptp-110) cc_final: 0.8106 (ptp-110) REVERT: F 27 CYS cc_start: 0.4703 (OUTLIER) cc_final: 0.3516 (t) REVERT: F 36 ARG cc_start: 0.8985 (ptt90) cc_final: 0.8517 (ptt180) REVERT: G 21 TYR cc_start: 0.8171 (m-80) cc_final: 0.7846 (m-80) REVERT: G 103 TRP cc_start: 0.8609 (t-100) cc_final: 0.7929 (t-100) REVERT: G 112 ARG cc_start: 0.9249 (tpt170) cc_final: 0.8287 (mtp180) REVERT: G 153 MET cc_start: 0.8440 (ttm) cc_final: 0.7947 (mtp) REVERT: H 28 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.8577 (m-80) REVERT: H 41 TYR cc_start: 0.8991 (t80) cc_final: 0.8734 (t80) REVERT: H 117 ASP cc_start: 0.9129 (m-30) cc_final: 0.8502 (p0) REVERT: H 166 TRP cc_start: 0.9094 (p-90) cc_final: 0.8803 (p-90) REVERT: H 184 ASN cc_start: 0.8846 (m110) cc_final: 0.8410 (m110) REVERT: I 28 ASP cc_start: 0.7796 (p0) cc_final: 0.7063 (t0) REVERT: I 73 ASN cc_start: 0.9523 (m-40) cc_final: 0.8825 (m110) REVERT: J 63 MET cc_start: 0.8738 (tpp) cc_final: 0.8397 (tpp) REVERT: J 65 LYS cc_start: 0.8759 (mmtm) cc_final: 0.8469 (mmtt) REVERT: J 96 GLN cc_start: 0.8403 (tm-30) cc_final: 0.7790 (tm-30) REVERT: J 115 GLU cc_start: 0.9489 (pt0) cc_final: 0.8821 (pt0) REVERT: J 146 MET cc_start: 0.8376 (tmm) cc_final: 0.7970 (tmm) REVERT: K 24 ARG cc_start: 0.8842 (mtm180) cc_final: 0.8574 (mtm180) REVERT: K 25 TYR cc_start: 0.8956 (m-10) cc_final: 0.8550 (m-80) REVERT: K 42 TRP cc_start: 0.7870 (m-90) cc_final: 0.6834 (m-90) REVERT: L 30 MET cc_start: 0.8562 (ttp) cc_final: 0.8117 (tmm) REVERT: L 32 ASP cc_start: 0.8873 (m-30) cc_final: 0.8399 (m-30) REVERT: M 2 MET cc_start: 0.9164 (tpp) cc_final: 0.8925 (tpp) REVERT: M 37 ASN cc_start: 0.8961 (m-40) cc_final: 0.8502 (m110) REVERT: M 59 GLU cc_start: 0.8940 (pt0) cc_final: 0.8401 (pm20) REVERT: O 11 LYS cc_start: 0.7376 (mmtp) cc_final: 0.7133 (mmmm) REVERT: O 46 LYS cc_start: 0.8243 (mtmm) cc_final: 0.7547 (mptt) REVERT: O 65 TYR cc_start: 0.8349 (m-80) cc_final: 0.8089 (m-80) REVERT: O 88 MET cc_start: 0.8790 (mpp) cc_final: 0.8408 (tpp) REVERT: R 47 LEU cc_start: 0.6525 (mt) cc_final: 0.6226 (mt) REVERT: R 51 GLN cc_start: 0.9082 (mt0) cc_final: 0.8763 (tp-100) REVERT: R 67 ASP cc_start: 0.9002 (t0) cc_final: 0.8732 (t70) REVERT: R 82 LEU cc_start: 0.8722 (tp) cc_final: 0.8434 (tp) REVERT: S 88 MET cc_start: 0.8846 (tpp) cc_final: 0.8058 (tpp) REVERT: S 95 LEU cc_start: 0.9411 (tt) cc_final: 0.8953 (mp) REVERT: T 25 GLU cc_start: 0.8835 (pm20) cc_final: 0.8410 (pm20) REVERT: U 32 PHE cc_start: 0.9156 (p90) cc_final: 0.7982 (p90) REVERT: U 34 GLU cc_start: 0.8504 (pm20) cc_final: 0.8304 (pm20) REVERT: U 53 ASP cc_start: 0.8752 (t0) cc_final: 0.8498 (t0) REVERT: V 47 ASP cc_start: 0.8554 (OUTLIER) cc_final: 0.8289 (p0) REVERT: V 56 ASP cc_start: 0.8333 (p0) cc_final: 0.8119 (p0) REVERT: W 56 ARG cc_start: 0.9056 (ttm110) cc_final: 0.8726 (mtp180) REVERT: X 19 GLU cc_start: 0.8640 (mm-30) cc_final: 0.7834 (pt0) REVERT: Y 20 ASN cc_start: 0.9451 (m-40) cc_final: 0.9187 (m-40) REVERT: Y 26 MET cc_start: 0.8476 (mmp) cc_final: 0.7818 (mmp) REVERT: Y 28 ARG cc_start: 0.8706 (mmm-85) cc_final: 0.8162 (mtt180) REVERT: Y 35 TYR cc_start: 0.9104 (m-80) cc_final: 0.8879 (m-80) REVERT: Y 58 ASP cc_start: 0.8570 (m-30) cc_final: 0.8224 (m-30) REVERT: Y 66 ILE cc_start: 0.8839 (mm) cc_final: 0.8489 (tt) REVERT: Y 67 HIS cc_start: 0.7492 (t-90) cc_final: 0.7127 (t-90) REVERT: Y 81 GLN cc_start: 0.9006 (mm-40) cc_final: 0.8711 (tm-30) REVERT: Z 36 PHE cc_start: 0.8926 (t80) cc_final: 0.8565 (t80) REVERT: Z 43 GLU cc_start: 0.8840 (tt0) cc_final: 0.8414 (tp30) REVERT: a 8 MET cc_start: -0.0835 (mpp) cc_final: -0.1693 (mtm) REVERT: a 180 PHE cc_start: 0.1638 (OUTLIER) cc_final: 0.1379 (t80) REVERT: 8 118 MET cc_start: 0.8378 (tpp) cc_final: 0.7412 (tpp) REVERT: 8 151 MET cc_start: 0.9567 (tmm) cc_final: 0.9092 (tmm) REVERT: 8 152 TYR cc_start: 0.9366 (m-80) cc_final: 0.8781 (m-80) REVERT: 8 207 PHE cc_start: 0.8029 (m-10) cc_final: 0.7536 (m-10) REVERT: 8 223 TYR cc_start: 0.9461 (p90) cc_final: 0.9137 (p90) REVERT: 8 300 MET cc_start: 0.8677 (mmp) cc_final: 0.8381 (mmp) outliers start: 183 outliers final: 143 residues processed: 1039 average time/residue: 1.2531 time to fit residues: 2279.3781 Evaluate side-chains 1015 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 863 time to evaluate : 6.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 35 LYS Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 51 ARG Chi-restraints excluded: chain b residue 66 PHE Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 202 ARG Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain e residue 4 HIS Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain f residue 25 ILE Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain g residue 115 VAL Chi-restraints excluded: chain j residue 118 MET Chi-restraints excluded: chain j residue 139 VAL Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 119 LEU Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain o residue 112 GLU Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 55 GLN Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain q residue 103 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 53 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 78 ILE Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain y residue 6 LEU Chi-restraints excluded: chain y residue 7 ARG Chi-restraints excluded: chain y residue 58 ASN Chi-restraints excluded: chain z residue 23 LEU Chi-restraints excluded: chain z residue 43 ILE Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 192 TYR Chi-restraints excluded: chain I residue 135 GLN Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 125 ASP Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 49 PHE Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 51 PHE Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 47 ASP Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 37 TYR Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 180 PHE Chi-restraints excluded: chain 8 residue 130 LEU Chi-restraints excluded: chain 8 residue 198 VAL Chi-restraints excluded: chain 8 residue 227 ASP Chi-restraints excluded: chain 8 residue 228 ASP Chi-restraints excluded: chain 8 residue 254 VAL Chi-restraints excluded: chain 8 residue 340 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1053 random chunks: chunk 923 optimal weight: 50.0000 chunk 972 optimal weight: 30.0000 chunk 887 optimal weight: 10.0000 chunk 945 optimal weight: 10.0000 chunk 569 optimal weight: 30.0000 chunk 412 optimal weight: 30.0000 chunk 742 optimal weight: 40.0000 chunk 290 optimal weight: 5.9990 chunk 854 optimal weight: 50.0000 chunk 894 optimal weight: 20.0000 chunk 942 optimal weight: 10.0000 overall best weight: 11.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 136 GLN ** d 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 55 GLN ** r 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 HIS ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 GLN ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 197 HIS ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 160427 Z= 0.389 Angle : 0.706 12.406 239677 Z= 0.358 Chirality : 0.039 0.282 30569 Planarity : 0.005 0.052 13095 Dihedral : 23.802 177.895 79448 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 26.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.76 % Favored : 89.12 % Rotamer: Outliers : 3.67 % Allowed : 22.97 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.11), residues: 6011 helix: -0.29 (0.12), residues: 1931 sheet: -1.58 (0.15), residues: 1096 loop : -2.08 (0.11), residues: 2984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP 8 191 HIS 0.011 0.002 HIS K 11 PHE 0.023 0.002 PHE C 19 TYR 0.074 0.002 TYR g 25 ARG 0.020 0.001 ARG R 70 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1046 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 862 time to evaluate : 6.607 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: b 35 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8713 (tptt) REVERT: b 116 GLN cc_start: 0.7971 (tt0) cc_final: 0.7654 (tt0) REVERT: c 103 ASP cc_start: 0.8419 (p0) cc_final: 0.8159 (p0) REVERT: d 101 TYR cc_start: 0.8807 (t80) cc_final: 0.8534 (t80) REVERT: d 164 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9007 (mm) REVERT: d 188 MET cc_start: 0.8835 (tpp) cc_final: 0.8412 (tpp) REVERT: e 137 PHE cc_start: 0.8792 (m-80) cc_final: 0.8384 (m-80) REVERT: f 61 TRP cc_start: 0.8865 (m100) cc_final: 0.8372 (m100) REVERT: f 162 ARG cc_start: 0.8724 (ptp-170) cc_final: 0.8251 (mtp85) REVERT: g 7 ASP cc_start: 0.8342 (t70) cc_final: 0.8119 (t70) REVERT: g 29 PHE cc_start: 0.9119 (t80) cc_final: 0.8815 (t80) REVERT: m 90 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7462 (mt-10) REVERT: m 135 VAL cc_start: 0.8191 (OUTLIER) cc_final: 0.7835 (p) REVERT: m 136 MET cc_start: 0.7220 (ppp) cc_final: 0.6858 (ppp) REVERT: n 74 GLU cc_start: 0.9077 (tp30) cc_final: 0.8711 (tm-30) REVERT: p 70 GLU cc_start: 0.6603 (mp0) cc_final: 0.6351 (mp0) REVERT: r 1 MET cc_start: 0.7951 (ppp) cc_final: 0.7715 (ppp) REVERT: r 22 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8919 (pp) REVERT: r 85 LYS cc_start: 0.9088 (ttmt) cc_final: 0.8783 (ttmm) REVERT: t 1 MET cc_start: 0.6394 (mtt) cc_final: 0.4794 (mmt) REVERT: u 87 GLU cc_start: 0.8373 (tp30) cc_final: 0.8158 (tp30) REVERT: v 38 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8870 (mm) REVERT: v 48 MET cc_start: 0.9166 (mmm) cc_final: 0.8717 (mmm) REVERT: w 74 LYS cc_start: 0.8567 (mmtp) cc_final: 0.8272 (mmtp) REVERT: y 17 GLU cc_start: 0.9033 (tp30) cc_final: 0.8759 (tp30) REVERT: z 18 LYS cc_start: 0.8326 (mmmt) cc_final: 0.7888 (tppt) REVERT: C 7 LYS cc_start: 0.8970 (mtmt) cc_final: 0.8433 (mtmt) REVERT: C 9 LYS cc_start: 0.8669 (tptm) cc_final: 0.8436 (tppt) REVERT: C 10 LEU cc_start: 0.9468 (mp) cc_final: 0.9234 (mt) REVERT: C 19 PHE cc_start: 0.9513 (p90) cc_final: 0.9253 (p90) REVERT: C 32 LYS cc_start: 0.7879 (ptmm) cc_final: 0.7257 (tttm) REVERT: C 34 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8061 (mm-30) REVERT: C 36 LYS cc_start: 0.9520 (ttmt) cc_final: 0.9166 (ttpt) REVERT: C 46 VAL cc_start: 0.9354 (OUTLIER) cc_final: 0.9051 (p) REVERT: F 4 ARG cc_start: 0.8649 (ptp-110) cc_final: 0.8168 (ptp-110) REVERT: F 27 CYS cc_start: 0.5188 (OUTLIER) cc_final: 0.3897 (t) REVERT: F 36 ARG cc_start: 0.8998 (ptt90) cc_final: 0.8524 (ptt180) REVERT: G 21 TYR cc_start: 0.8166 (m-80) cc_final: 0.7899 (m-10) REVERT: G 103 TRP cc_start: 0.8696 (t-100) cc_final: 0.8006 (t-100) REVERT: G 112 ARG cc_start: 0.9185 (tpt170) cc_final: 0.8199 (mtp180) REVERT: G 153 MET cc_start: 0.8423 (ttm) cc_final: 0.7987 (mtp) REVERT: H 28 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8554 (m-80) REVERT: H 41 TYR cc_start: 0.8963 (t80) cc_final: 0.8711 (t80) REVERT: H 166 TRP cc_start: 0.9118 (p-90) cc_final: 0.8833 (p-90) REVERT: H 184 ASN cc_start: 0.8843 (m110) cc_final: 0.8427 (m110) REVERT: I 28 ASP cc_start: 0.7808 (p0) cc_final: 0.7096 (t0) REVERT: I 73 ASN cc_start: 0.9452 (m-40) cc_final: 0.8758 (m110) REVERT: J 63 MET cc_start: 0.8739 (tpp) cc_final: 0.8389 (tpp) REVERT: J 96 GLN cc_start: 0.8348 (tm-30) cc_final: 0.7738 (tm-30) REVERT: J 115 GLU cc_start: 0.9497 (pt0) cc_final: 0.9192 (pt0) REVERT: K 24 ARG cc_start: 0.8649 (mtm180) cc_final: 0.8238 (mtm110) REVERT: K 25 TYR cc_start: 0.8952 (m-10) cc_final: 0.8334 (m-80) REVERT: L 30 MET cc_start: 0.8594 (ttp) cc_final: 0.8208 (tmm) REVERT: L 32 ASP cc_start: 0.8831 (m-30) cc_final: 0.8411 (m-30) REVERT: M 37 ASN cc_start: 0.9000 (m-40) cc_final: 0.8536 (m110) REVERT: M 59 GLU cc_start: 0.8982 (pt0) cc_final: 0.8484 (pm20) REVERT: M 95 MET cc_start: 0.9009 (mtm) cc_final: 0.8592 (ptp) REVERT: O 11 LYS cc_start: 0.7213 (mmtp) cc_final: 0.7012 (mmmm) REVERT: O 46 LYS cc_start: 0.8263 (mtmm) cc_final: 0.7708 (mptt) REVERT: P 78 ILE cc_start: 0.8652 (mp) cc_final: 0.8255 (mp) REVERT: Q 74 GLN cc_start: 0.8064 (mt0) cc_final: 0.7557 (mm110) REVERT: R 47 LEU cc_start: 0.6351 (mt) cc_final: 0.6083 (mt) REVERT: R 51 GLN cc_start: 0.9105 (mt0) cc_final: 0.8829 (tp-100) REVERT: R 67 ASP cc_start: 0.8996 (t0) cc_final: 0.8697 (t70) REVERT: S 88 MET cc_start: 0.8875 (tpp) cc_final: 0.8081 (tpp) REVERT: S 95 LEU cc_start: 0.9421 (tt) cc_final: 0.8973 (mp) REVERT: T 25 GLU cc_start: 0.8919 (pm20) cc_final: 0.8518 (pm20) REVERT: U 14 ARG cc_start: 0.8721 (ttt180) cc_final: 0.8040 (ttp-170) REVERT: U 32 PHE cc_start: 0.9134 (p90) cc_final: 0.8771 (p90) REVERT: U 53 ASP cc_start: 0.8632 (t0) cc_final: 0.8387 (t0) REVERT: V 10 ARG cc_start: 0.8915 (ttp80) cc_final: 0.8584 (tmm-80) REVERT: V 47 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.8075 (p0) REVERT: Y 20 ASN cc_start: 0.9474 (m-40) cc_final: 0.8971 (p0) REVERT: Y 26 MET cc_start: 0.8540 (mmp) cc_final: 0.7914 (mmp) REVERT: Y 28 ARG cc_start: 0.8728 (mmm-85) cc_final: 0.8175 (mtt180) REVERT: Y 35 TYR cc_start: 0.9108 (m-80) cc_final: 0.8880 (m-80) REVERT: Y 58 ASP cc_start: 0.8624 (m-30) cc_final: 0.8289 (m-30) REVERT: Y 66 ILE cc_start: 0.8921 (mm) cc_final: 0.8558 (tt) REVERT: Y 67 HIS cc_start: 0.7569 (t-90) cc_final: 0.7159 (t-90) REVERT: Y 81 GLN cc_start: 0.9062 (mm-40) cc_final: 0.8714 (tm-30) REVERT: Z 36 PHE cc_start: 0.8937 (t80) cc_final: 0.8591 (t80) REVERT: Z 43 GLU cc_start: 0.8850 (tt0) cc_final: 0.8420 (tp30) REVERT: a 8 MET cc_start: -0.0801 (mpp) cc_final: -0.1609 (mtm) REVERT: a 180 PHE cc_start: 0.1607 (OUTLIER) cc_final: 0.1327 (t80) REVERT: 8 118 MET cc_start: 0.7733 (tpp) cc_final: 0.7458 (tpp) REVERT: 8 151 MET cc_start: 0.9548 (tmm) cc_final: 0.9123 (tmm) REVERT: 8 207 PHE cc_start: 0.8077 (m-10) cc_final: 0.7576 (m-10) REVERT: 8 300 MET cc_start: 0.8689 (mmp) cc_final: 0.7956 (mmt) outliers start: 184 outliers final: 154 residues processed: 975 average time/residue: 1.2378 time to fit residues: 2115.4977 Evaluate side-chains 1002 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 838 time to evaluate : 6.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 24 HIS Chi-restraints excluded: chain b residue 35 LYS Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 51 ARG Chi-restraints excluded: chain b residue 66 PHE Chi-restraints excluded: chain b residue 71 ASP Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 202 ARG Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 64 GLU Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain e residue 4 HIS Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain f residue 25 ILE Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain g residue 19 VAL Chi-restraints excluded: chain g residue 115 VAL Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 118 MET Chi-restraints excluded: chain j residue 139 VAL Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain o residue 112 GLU Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 43 GLN Chi-restraints excluded: chain q residue 55 GLN Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain q residue 103 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 53 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain v residue 38 LEU Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 26 SER Chi-restraints excluded: chain w residue 78 ILE Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 59 ASP Chi-restraints excluded: chain y residue 6 LEU Chi-restraints excluded: chain y residue 7 ARG Chi-restraints excluded: chain y residue 58 ASN Chi-restraints excluded: chain z residue 23 LEU Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 40 GLN Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 192 TYR Chi-restraints excluded: chain I residue 135 GLN Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 155 LYS Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 125 ASP Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 49 PHE Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 51 PHE Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 47 ASP Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 37 TYR Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 180 PHE Chi-restraints excluded: chain 8 residue 130 LEU Chi-restraints excluded: chain 8 residue 198 VAL Chi-restraints excluded: chain 8 residue 227 ASP Chi-restraints excluded: chain 8 residue 228 ASP Chi-restraints excluded: chain 8 residue 254 VAL Chi-restraints excluded: chain 8 residue 340 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1053 random chunks: chunk 621 optimal weight: 20.0000 chunk 1000 optimal weight: 30.0000 chunk 610 optimal weight: 20.0000 chunk 474 optimal weight: 7.9990 chunk 695 optimal weight: 20.0000 chunk 1049 optimal weight: 20.0000 chunk 965 optimal weight: 10.0000 chunk 835 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 645 optimal weight: 20.0000 chunk 512 optimal weight: 20.0000 overall best weight: 11.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 97 ASN ** d 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 GLN ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 197 HIS ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 54 GLN ** 8 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.5535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.118 160427 Z= 0.392 Angle : 0.716 13.963 239677 Z= 0.364 Chirality : 0.039 0.283 30569 Planarity : 0.005 0.070 13095 Dihedral : 23.914 178.425 79448 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 26.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.36 % Favored : 89.52 % Rotamer: Outliers : 3.65 % Allowed : 23.45 % Favored : 72.90 % 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: -2.17 (0.10), residues: 6011 helix: -0.37 (0.12), residues: 1924 sheet: -1.64 (0.15), residues: 1096 loop : -2.08 (0.11), residues: 2991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP S 41 HIS 0.013 0.002 HIS K 11 PHE 0.045 0.002 PHE H 36 TYR 0.046 0.002 TYR g 25 ARG 0.015 0.001 ARG q 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1045 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 862 time to evaluate : 6.618 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: b 35 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8694 (tptt) REVERT: b 116 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7511 (tt0) REVERT: c 2 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8682 (mp) REVERT: c 103 ASP cc_start: 0.8393 (p0) cc_final: 0.8143 (p0) REVERT: d 101 TYR cc_start: 0.8843 (t80) cc_final: 0.8550 (t80) REVERT: d 164 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9015 (mm) REVERT: d 188 MET cc_start: 0.8849 (tpp) cc_final: 0.8417 (tpp) REVERT: e 137 PHE cc_start: 0.8850 (m-80) cc_final: 0.8382 (m-80) REVERT: f 61 TRP cc_start: 0.8866 (m100) cc_final: 0.8383 (m100) REVERT: f 162 ARG cc_start: 0.8736 (ptp-170) cc_final: 0.8145 (mtp85) REVERT: g 7 ASP cc_start: 0.8326 (t70) cc_final: 0.8110 (t70) REVERT: g 29 PHE cc_start: 0.9143 (t80) cc_final: 0.8852 (t80) REVERT: m 90 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7426 (mt-10) REVERT: m 135 VAL cc_start: 0.8272 (OUTLIER) cc_final: 0.7974 (p) REVERT: m 136 MET cc_start: 0.7233 (ppp) cc_final: 0.6870 (ppp) REVERT: n 74 GLU cc_start: 0.9130 (tp30) cc_final: 0.8831 (tm-30) REVERT: o 17 LYS cc_start: 0.9357 (tptp) cc_final: 0.9156 (tppt) REVERT: p 70 GLU cc_start: 0.6641 (mp0) cc_final: 0.6400 (mp0) REVERT: r 22 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8944 (pp) REVERT: r 85 LYS cc_start: 0.9071 (ttmt) cc_final: 0.8745 (ttmm) REVERT: s 95 ARG cc_start: 0.8641 (ptm-80) cc_final: 0.8293 (ttp80) REVERT: t 1 MET cc_start: 0.6225 (mtt) cc_final: 0.4566 (mmt) REVERT: t 12 ARG cc_start: 0.9049 (tpp80) cc_final: 0.8562 (tpp80) REVERT: v 38 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8909 (mm) REVERT: v 48 MET cc_start: 0.9148 (mmm) cc_final: 0.8727 (mmm) REVERT: w 74 LYS cc_start: 0.8581 (mmtp) cc_final: 0.8372 (mmtp) REVERT: y 17 GLU cc_start: 0.9050 (tp30) cc_final: 0.8782 (tp30) REVERT: z 18 LYS cc_start: 0.8410 (mmmt) cc_final: 0.7844 (tppt) REVERT: z 55 LYS cc_start: 0.8527 (ptmm) cc_final: 0.8016 (tmtt) REVERT: z 57 GLU cc_start: 0.9009 (pm20) cc_final: 0.8779 (pm20) REVERT: B 51 ARG cc_start: 0.8303 (ptm-80) cc_final: 0.7910 (ptm-80) REVERT: C 6 GLU cc_start: 0.8190 (pm20) cc_final: 0.6711 (pm20) REVERT: C 7 LYS cc_start: 0.8983 (mtmt) cc_final: 0.8511 (mtmt) REVERT: C 10 LEU cc_start: 0.9470 (mp) cc_final: 0.9088 (mt) REVERT: C 32 LYS cc_start: 0.7889 (ptmm) cc_final: 0.7275 (tttm) REVERT: C 34 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8080 (mm-30) REVERT: C 36 LYS cc_start: 0.9492 (ttmt) cc_final: 0.9218 (ttpt) REVERT: C 46 VAL cc_start: 0.9371 (OUTLIER) cc_final: 0.9031 (p) REVERT: F 4 ARG cc_start: 0.8665 (ptp-110) cc_final: 0.8159 (ptp-110) REVERT: F 12 ARG cc_start: 0.8801 (mmp-170) cc_final: 0.8488 (mmp-170) REVERT: F 27 CYS cc_start: 0.5155 (OUTLIER) cc_final: 0.3829 (t) REVERT: F 36 ARG cc_start: 0.8998 (ptt90) cc_final: 0.8617 (ptt180) REVERT: G 5 MET cc_start: 0.9036 (ppp) cc_final: 0.8742 (tpt) REVERT: G 21 TYR cc_start: 0.8174 (m-80) cc_final: 0.7906 (m-10) REVERT: G 103 TRP cc_start: 0.8680 (t-100) cc_final: 0.7996 (t-100) REVERT: G 112 ARG cc_start: 0.9190 (tpt170) cc_final: 0.8215 (mtp180) REVERT: G 153 MET cc_start: 0.8455 (ttm) cc_final: 0.8205 (mtp) REVERT: H 28 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.8546 (m-80) REVERT: H 184 ASN cc_start: 0.8861 (m110) cc_final: 0.8442 (m110) REVERT: I 28 ASP cc_start: 0.7419 (p0) cc_final: 0.6966 (t0) REVERT: I 73 ASN cc_start: 0.9500 (m-40) cc_final: 0.8928 (m110) REVERT: J 63 MET cc_start: 0.8761 (tpp) cc_final: 0.8397 (tpp) REVERT: J 96 GLN cc_start: 0.8290 (tm-30) cc_final: 0.7793 (tm-30) REVERT: J 115 GLU cc_start: 0.9497 (pt0) cc_final: 0.9191 (pt0) REVERT: K 24 ARG cc_start: 0.8670 (mtm180) cc_final: 0.8276 (mtm110) REVERT: K 25 TYR cc_start: 0.8988 (m-10) cc_final: 0.8405 (m-80) REVERT: K 42 TRP cc_start: 0.7954 (m-90) cc_final: 0.6924 (m-90) REVERT: L 30 MET cc_start: 0.8554 (ttp) cc_final: 0.8266 (tmm) REVERT: L 32 ASP cc_start: 0.8851 (m-30) cc_final: 0.8437 (m-30) REVERT: M 37 ASN cc_start: 0.9015 (m-40) cc_final: 0.8551 (m110) REVERT: M 39 LEU cc_start: 0.9478 (mp) cc_final: 0.9123 (pt) REVERT: M 59 GLU cc_start: 0.9002 (pt0) cc_final: 0.8496 (pm20) REVERT: M 95 MET cc_start: 0.9105 (mtm) cc_final: 0.8857 (ptp) REVERT: O 46 LYS cc_start: 0.8301 (mtmm) cc_final: 0.7943 (mptt) REVERT: P 78 ILE cc_start: 0.8762 (mp) cc_final: 0.8459 (mp) REVERT: Q 74 GLN cc_start: 0.8055 (mt0) cc_final: 0.7582 (mm110) REVERT: R 47 LEU cc_start: 0.6476 (mt) cc_final: 0.6189 (mt) REVERT: R 51 GLN cc_start: 0.9187 (mt0) cc_final: 0.8790 (tp-100) REVERT: R 67 ASP cc_start: 0.8885 (t0) cc_final: 0.8578 (t70) REVERT: S 88 MET cc_start: 0.8828 (tpp) cc_final: 0.8029 (tpp) REVERT: S 95 LEU cc_start: 0.9343 (tt) cc_final: 0.8967 (mp) REVERT: T 14 PHE cc_start: 0.8727 (m-80) cc_final: 0.8491 (m-80) REVERT: T 25 GLU cc_start: 0.8896 (pm20) cc_final: 0.8476 (pm20) REVERT: U 32 PHE cc_start: 0.9142 (p90) cc_final: 0.8766 (p90) REVERT: U 53 ASP cc_start: 0.8593 (t0) cc_final: 0.8319 (t0) REVERT: V 47 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.7964 (p0) REVERT: X 28 LYS cc_start: 0.7922 (pptt) cc_final: 0.7343 (ptpp) REVERT: Y 20 ASN cc_start: 0.9466 (m-40) cc_final: 0.9209 (m-40) REVERT: Y 26 MET cc_start: 0.8684 (mmp) cc_final: 0.8062 (mmp) REVERT: Y 28 ARG cc_start: 0.8730 (mmm-85) cc_final: 0.8156 (mtt180) REVERT: Y 35 TYR cc_start: 0.9118 (m-80) cc_final: 0.8917 (m-80) REVERT: Y 58 ASP cc_start: 0.8527 (m-30) cc_final: 0.8042 (m-30) REVERT: Y 66 ILE cc_start: 0.8906 (mm) cc_final: 0.8542 (tt) REVERT: Y 67 HIS cc_start: 0.7577 (t-90) cc_final: 0.7129 (t-90) REVERT: Y 81 GLN cc_start: 0.9050 (mm-40) cc_final: 0.8732 (tm-30) REVERT: Z 36 PHE cc_start: 0.8944 (t80) cc_final: 0.8586 (t80) REVERT: Z 43 GLU cc_start: 0.8823 (tt0) cc_final: 0.8380 (tp30) REVERT: a 8 MET cc_start: -0.0619 (mpp) cc_final: -0.1421 (mtm) REVERT: a 180 PHE cc_start: 0.1620 (OUTLIER) cc_final: 0.1337 (t80) REVERT: 8 118 MET cc_start: 0.7777 (tpp) cc_final: 0.7561 (tpp) REVERT: 8 151 MET cc_start: 0.9550 (tmm) cc_final: 0.9085 (tmm) REVERT: 8 152 TYR cc_start: 0.9339 (m-80) cc_final: 0.8763 (m-80) REVERT: 8 207 PHE cc_start: 0.8080 (m-10) cc_final: 0.7578 (m-10) REVERT: 8 300 MET cc_start: 0.8702 (mmp) cc_final: 0.7966 (mmt) outliers start: 183 outliers final: 158 residues processed: 983 average time/residue: 1.2769 time to fit residues: 2201.4563 Evaluate side-chains 1006 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 836 time to evaluate : 6.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 24 HIS Chi-restraints excluded: chain b residue 35 LYS Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 51 ARG Chi-restraints excluded: chain b residue 66 PHE Chi-restraints excluded: chain b residue 71 ASP Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain b residue 116 GLN Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 202 ARG Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 64 GLU Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain e residue 4 HIS Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain f residue 25 ILE Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain g residue 19 VAL Chi-restraints excluded: chain g residue 115 VAL Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 118 MET Chi-restraints excluded: chain j residue 139 VAL Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 119 LEU Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain o residue 90 VAL Chi-restraints excluded: chain o residue 112 GLU Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 43 GLN Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain q residue 103 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 52 GLU Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 85 ILE Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 53 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain v residue 38 LEU Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 26 SER Chi-restraints excluded: chain w residue 78 ILE Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 59 ASP Chi-restraints excluded: chain y residue 6 LEU Chi-restraints excluded: chain y residue 58 ASN Chi-restraints excluded: chain z residue 23 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 40 GLN Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 192 TYR Chi-restraints excluded: chain I residue 135 GLN Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 155 LYS Chi-restraints excluded: chain K residue 30 THR 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 17 PHE Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 125 ASP Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 26 MET Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 49 PHE Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 51 PHE Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 61 ASN Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 47 ASP Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 37 TYR Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 180 PHE Chi-restraints excluded: chain 8 residue 124 ASP Chi-restraints excluded: chain 8 residue 130 LEU Chi-restraints excluded: chain 8 residue 198 VAL Chi-restraints excluded: chain 8 residue 227 ASP Chi-restraints excluded: chain 8 residue 228 ASP Chi-restraints excluded: chain 8 residue 254 VAL Chi-restraints excluded: chain 8 residue 266 ILE Chi-restraints excluded: chain 8 residue 340 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1053 random chunks: chunk 663 optimal weight: 30.0000 chunk 889 optimal weight: 10.0000 chunk 255 optimal weight: 10.0000 chunk 770 optimal weight: 20.0000 chunk 123 optimal weight: 9.9990 chunk 232 optimal weight: 9.9990 chunk 836 optimal weight: 10.0000 chunk 350 optimal weight: 20.0000 chunk 859 optimal weight: 50.0000 chunk 105 optimal weight: 0.9980 chunk 154 optimal weight: 6.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 5 GLN k 93 GLN ** o 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 55 GLN ** r 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 HIS ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 GLN ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 GLN ** S 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 54 GLN ** 8 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.059034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.037224 restraints weight = 977775.323| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.16 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.5531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 160427 Z= 0.279 Angle : 0.650 13.846 239677 Z= 0.331 Chirality : 0.036 0.276 30569 Planarity : 0.005 0.048 13095 Dihedral : 23.879 179.452 79448 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 23.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.05 % Favored : 89.84 % Rotamer: Outliers : 3.38 % Allowed : 23.79 % Favored : 72.84 % 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: -1.99 (0.11), residues: 6011 helix: -0.15 (0.12), residues: 1929 sheet: -1.55 (0.15), residues: 1093 loop : -2.03 (0.11), residues: 2989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP H 166 HIS 0.010 0.001 HIS K 11 PHE 0.023 0.002 PHE L 61 TYR 0.042 0.002 TYR g 25 ARG 0.011 0.001 ARG H 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 37651.59 seconds wall clock time: 661 minutes 36.00 seconds (39696.00 seconds total)