Starting phenix.real_space_refine on Tue Mar 19 09:39:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl4_12217/03_2024/7bl4_12217_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl4_12217/03_2024/7bl4_12217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl4_12217/03_2024/7bl4_12217.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl4_12217/03_2024/7bl4_12217.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl4_12217/03_2024/7bl4_12217_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl4_12217/03_2024/7bl4_12217_updated.pdb" } resolution = 2.4 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= -0.044 sd= 0.814 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 3018 5.49 5 Mg 6 5.21 5 S 99 5.16 5 C 46910 2.51 5 N 17384 2.21 5 O 26141 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "g ARG 24": "NH1" <-> "NH2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C GLU 34": "OE1" <-> "OE2" Residue "C ARG 51": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C ASP 65": "OD1" <-> "OD2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C ASP 83": "OD1" <-> "OD2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C ARG 166": "NH1" <-> "NH2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 176": "NH1" <-> "NH2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C ARG 181": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "C ASP 228": "OD1" <-> "OD2" Residue "C GLU 235": "OE1" <-> "OE2" Residue "C ASP 263": "OD1" <-> "OD2" Residue "C PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D ASP 108": "OD1" <-> "OD2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ASP 7": "OD1" <-> "OD2" Residue "E GLU 16": "OE1" <-> "OE2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ASP 22": "OD1" <-> "OD2" Residue "E PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ASP 140": "OD1" <-> "OD2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E ASP 171": "OD1" <-> "OD2" Residue "F ASP 5": "OD1" <-> "OD2" Residue "F ASP 9": "OD1" <-> "OD2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F GLU 97": "OE1" <-> "OE2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F ASP 112": "OD1" <-> "OD2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F ASP 122": "OD1" <-> "OD2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "G ARG 2": "NH1" <-> "NH2" Residue "G PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G GLU 166": "OE1" <-> "OE2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ASP 52": "OD1" <-> "OD2" Residue "J TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 60": "OD1" <-> "OD2" Residue "J TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 90": "OE1" <-> "OE2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L GLU 115": "OE1" <-> "OE2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N GLU 32": "OE1" <-> "OE2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ASP 58": "OD1" <-> "OD2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N ASP 72": "OD1" <-> "OD2" Residue "N PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 82": "OE1" <-> "OE2" Residue "N PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ASP 106": "OD1" <-> "OD2" Residue "N TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 114": "OE1" <-> "OE2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "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 TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 62": "OE1" <-> "OE2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "R ASP 95": "OD1" <-> "OD2" Residue "S GLU 59": "OE1" <-> "OE2" Residue "S PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T GLU 5": "OE1" <-> "OE2" Residue "T PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 56": "OE1" <-> "OE2" Residue "T ASP 79": "OD1" <-> "OD2" Residue "T GLU 89": "OE1" <-> "OE2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ASP 8": "OD1" <-> "OD2" Residue "U ARG 81": "NH1" <-> "NH2" Residue "U PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U ARG 93": "NH1" <-> "NH2" Residue "U PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 100": "OE1" <-> "OE2" Residue "V GLU 7": "OE1" <-> "OE2" Residue "V GLU 41": "OE1" <-> "OE2" Residue "V ASP 45": "OD1" <-> "OD2" Residue "V TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 76": "OD1" <-> "OD2" Residue "V TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 7": "NH1" <-> "NH2" Residue "W GLU 25": "OE1" <-> "OE2" Residue "W ASP 52": "OD1" <-> "OD2" Residue "W PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 79": "OE1" <-> "OE2" Residue "X ARG 2": "NH1" <-> "NH2" Residue "X ARG 10": "NH1" <-> "NH2" Residue "X ARG 17": "NH1" <-> "NH2" Residue "X ARG 36": "NH1" <-> "NH2" Residue "X ARG 49": "NH1" <-> "NH2" Residue "X ARG 56": "NH1" <-> "NH2" Residue "X ARG 73": "NH1" <-> "NH2" Residue "Y GLU 5": "OE1" <-> "OE2" Residue "Y GLU 12": "OE1" <-> "OE2" Residue "Y GLU 13": "OE1" <-> "OE2" Residue "Y PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ASP 49": "OD1" <-> "OD2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "Z PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 9": "NH1" <-> "NH2" Residue "0 ARG 15": "NH1" <-> "NH2" Residue "0 ASP 19": "OD1" <-> "OD2" Residue "0 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 5": "NH1" <-> "NH2" Residue "1 PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 39": "OD1" <-> "OD2" Residue "1 ARG 43": "NH1" <-> "NH2" Residue "1 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 3": "NH1" <-> "NH2" Residue "2 ARG 12": "NH1" <-> "NH2" Residue "2 ARG 14": "NH1" <-> "NH2" Residue "2 ARG 19": "NH1" <-> "NH2" Residue "2 ARG 21": "NH1" <-> "NH2" Residue "2 ARG 33": "NH1" <-> "NH2" Residue "2 ARG 41": "NH1" <-> "NH2" Residue "K GLU 110": "OE1" <-> "OE2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P GLU 70": "OE1" <-> "OE2" Residue "P ASP 81": "OD1" <-> "OD2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 38": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 51": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 104": "OE1" <-> "OE2" Residue "M ASP 106": "OD1" <-> "OD2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "M PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 7": "OD1" <-> "OD2" Residue "H ARG 27": "NH1" <-> "NH2" Residue "6 ASP 16": "OD1" <-> "OD2" Residue "6 GLU 72": "OE1" <-> "OE2" Residue "9 PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 60": "NH1" <-> "NH2" Residue "9 GLU 62": "OE1" <-> "OE2" Residue "9 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 66": "NH1" <-> "NH2" Residue "9 ASP 98": "OD1" <-> "OD2" Residue "9 GLU 103": "OE1" <-> "OE2" Residue "9 ARG 114": "NH1" <-> "NH2" Residue "9 ARG 139": "NH1" <-> "NH2" Residue "9 ARG 150": "NH1" <-> "NH2" Residue "9 GLU 155": "OE1" <-> "OE2" Residue "9 PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 177": "NH1" <-> "NH2" Residue "9 TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 219": "OE1" <-> "OE2" Residue "9 GLU 223": "OE1" <-> "OE2" Residue "9 ARG 230": "NH1" <-> "NH2" Residue "9 PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 239": "NH1" <-> "NH2" Residue "9 ASP 246": "OD1" <-> "OD2" Residue "9 ASP 248": "OD1" <-> "OD2" Residue "9 ASP 254": "OD1" <-> "OD2" Residue "9 ARG 278": "NH1" <-> "NH2" Residue "9 ASP 289": "OD1" <-> "OD2" Residue "9 GLU 292": "OE1" <-> "OE2" Residue "9 TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 327": "OD1" <-> "OD2" Residue "3 ARG 12": "NH1" <-> "NH2" Residue "3 ARG 29": "NH1" <-> "NH2" Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 41": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 93560 Number of models: 1 Model: "" Number of chains: 47 Chain: "g" 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: "C" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" 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: "E" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1483 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain breaks: 1 Chain: "F" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" 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: "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: "L" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 90} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 577 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 4 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: "0" 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: "1" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "2" 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: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "P" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 911 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} 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: "H" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1110 Classifications: {'peptide': 149} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 144} Chain: "d" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 364 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "A" Number of atoms: 62195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2897, 62195 Classifications: {'RNA': 2897} Modifications used: {'rna2p_pur': 273, 'rna2p_pyr': 144, 'rna3p_pur': 1399, 'rna3p_pyr': 1081} Link IDs: {'rna2p': 417, 'rna3p': 2479} Chain breaks: 1 Chain: "B" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2548 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 105} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "6" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain: "9" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2582 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 14, 'TRANS': 323} Chain: "3" 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: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "9" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "6" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "9" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 85 SG CYS g 11 126.948 187.327 160.647 1.00111.00 S ATOM 110 SG CYS g 14 123.736 186.714 158.792 1.00109.54 S ATOM 213 SG CYS g 27 125.988 189.654 157.779 1.00109.91 S ATOM 24642 SG CYS d 16 153.723 88.741 206.750 1.00233.54 S ATOM 24796 SG CYS d 37 152.658 92.221 208.043 1.00231.77 S Time building chain proxies: 37.04, per 1000 atoms: 0.40 Number of scatterers: 93560 At special positions: 0 Unit cell: (197.96, 236.34, 234.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 99 16.00 P 3018 15.00 Mg 6 11.99 O 26141 8.00 N 17384 7.00 C 46910 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: 42.56 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN d 100 " pdb="ZN ZN d 100 " - pdb=" SG CYS d 37 " pdb="ZN ZN d 100 " - pdb=" SG CYS d 16 " pdb=" ZN g 101 " pdb="ZN ZN g 101 " - pdb=" ND1 HIS g 33 " pdb="ZN ZN g 101 " - pdb=" SG CYS g 11 " pdb="ZN ZN g 101 " - pdb=" SG CYS g 14 " pdb="ZN ZN g 101 " - pdb=" SG CYS g 27 " Number of angles added : 3 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6736 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 107 helices and 49 sheets defined 24.8% alpha, 17.8% beta 978 base pairs and 1538 stacking pairs defined. Time for finding SS restraints: 45.49 Creating SS restraints... Processing helix chain 'g' and resid 31 through 33 No H-bonds generated for 'chain 'g' and resid 31 through 33' Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 131 through 133 No H-bonds generated for 'chain 'C' and resid 131 through 133' Processing helix chain 'C' and resid 198 through 200 No H-bonds generated for 'chain 'C' and resid 198 through 200' Processing helix chain 'C' and resid 207 through 211 Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing helix chain 'C' and resid 263 through 265 No H-bonds generated for 'chain 'C' and resid 263 through 265' Processing helix chain 'D' and resid 62 through 70 Processing helix chain 'D' and resid 99 through 102 Processing helix chain 'D' and resid 121 through 125 Processing helix chain 'E' and resid 16 through 20 Processing helix chain 'E' and resid 25 through 39 Processing helix chain 'E' and resid 98 through 114 Processing helix chain 'E' and resid 131 through 140 Processing helix chain 'E' and resid 155 through 161 Processing helix chain 'E' and resid 177 through 182 Processing helix chain 'E' and resid 190 through 200 Processing helix chain 'F' and resid 2 through 9 removed outlier: 3.918A pdb=" N LYS F 8 " --> pdb=" O HIS F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 18 Processing helix chain 'F' and resid 41 through 43 No H-bonds generated for 'chain 'F' and resid 41 through 43' Processing helix chain 'F' and resid 47 through 59 Processing helix chain 'F' and resid 92 through 104 removed outlier: 4.398A pdb=" N GLU F 97 " --> pdb=" O ARG F 94 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE F 98 " --> pdb=" O MET F 95 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU F 100 " --> pdb=" O GLU F 97 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR F 104 " --> pdb=" O ARG F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 109 No H-bonds generated for 'chain 'F' and resid 107 through 109' Processing helix chain 'F' and resid 134 through 136 No H-bonds generated for 'chain 'F' and resid 134 through 136' Processing helix chain 'F' and resid 142 through 144 No H-bonds generated for 'chain 'F' and resid 142 through 144' Processing helix chain 'F' and resid 162 through 171 Processing helix chain 'G' and resid 60 through 79 removed outlier: 3.575A pdb=" N GLN G 63 " --> pdb=" O GLY G 60 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLY G 65 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU G 71 " --> pdb=" O ARG G 68 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL G 75 " --> pdb=" O ASN G 72 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL G 78 " --> pdb=" O VAL G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 151 removed outlier: 3.828A pdb=" N TYR G 150 " --> pdb=" O ASP G 146 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 37 removed outlier: 3.970A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 61 No H-bonds generated for 'chain 'J' and resid 59 through 61' Processing helix chain 'J' and resid 68 through 71 No H-bonds generated for 'chain 'J' and resid 68 through 71' Processing helix chain 'J' and resid 89 through 95 Processing helix chain 'J' and resid 97 through 108 removed outlier: 4.276A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU J 102 " --> pdb=" O GLU J 98 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA J 104 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 121 removed outlier: 3.750A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 135 No H-bonds generated for 'chain 'J' and resid 133 through 135' Processing helix chain 'L' and resid 57 through 60 No H-bonds generated for 'chain 'L' and resid 57 through 60' Processing helix chain 'L' and resid 70 through 73 Processing helix chain 'L' and resid 79 through 82 No H-bonds generated for 'chain 'L' and resid 79 through 82' Processing helix chain 'L' and resid 129 through 137 Processing helix chain 'N' and resid 14 through 31 Processing helix chain 'N' and resid 38 through 56 removed outlier: 4.281A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 60 through 68 Processing helix chain 'N' and resid 73 through 78 Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'O' and resid 4 through 10 Processing helix chain 'O' and resid 12 through 21 Processing helix chain 'O' and resid 56 through 61 removed outlier: 3.592A pdb=" N GLU O 60 " --> pdb=" O LYS O 56 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 56 through 61' Processing helix chain 'O' and resid 68 through 85 removed outlier: 3.554A pdb=" N LYS O 85 " --> pdb=" O ARG O 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 102 through 113 Processing helix chain 'Q' and resid 6 through 19 removed outlier: 3.802A pdb=" N ARG Q 10 " --> pdb=" O GLY Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 28 Processing helix chain 'Q' and resid 31 through 71 removed outlier: 4.327A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 84 Processing helix chain 'Q' and resid 91 through 100 Processing helix chain 'Q' and resid 102 through 116 Processing helix chain 'S' and resid 14 through 23 removed outlier: 4.015A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 37 removed outlier: 4.086A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 60 removed outlier: 3.526A pdb=" N GLU S 59 " --> pdb=" O ILE S 55 " (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 4 through 8 Processing helix chain 'T' and resid 18 through 25 Processing helix chain 'T' and resid 40 through 50 Processing helix chain 'U' and resid 66 through 68 No H-bonds generated for 'chain 'U' and resid 66 through 68' Processing helix chain 'V' and resid 13 through 23 Processing helix chain 'V' and resid 44 through 51 removed outlier: 3.695A pdb=" N MET V 50 " --> pdb=" O LYS V 46 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 61 removed outlier: 3.651A pdb=" N ARG X 56 " --> pdb=" O ALA X 52 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS X 60 " --> pdb=" O ARG X 56 " (cutoff:3.500A) Processing helix chain 'X' and resid 63 through 72 Processing helix chain 'Y' and resid 5 through 7 No H-bonds generated for 'chain 'Y' and resid 5 through 7' Processing helix chain 'Y' and resid 11 through 22 removed outlier: 3.770A pdb=" N ASN Y 15 " --> pdb=" O VAL Y 11 " (cutoff:3.500A) Processing helix chain 'Y' and resid 25 through 33 removed outlier: 3.602A pdb=" N GLN Y 31 " --> pdb=" O ASN Y 27 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 55 removed outlier: 3.686A pdb=" N VAL Y 46 " --> pdb=" O LEU Y 43 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG Y 48 " --> pdb=" O GLN Y 45 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR Y 55 " --> pdb=" O ARG Y 52 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 26 Processing helix chain 'Z' and resid 41 through 49 Processing helix chain '0' and resid 9 through 18 removed outlier: 4.748A pdb=" N HIS 0 18 " --> pdb=" O MET 0 14 " (cutoff:3.500A) Processing helix chain '2' and resid 9 through 16 Processing helix chain '2' and resid 18 through 22 Processing helix chain '2' and resid 25 through 37 Processing helix chain 'K' and resid 105 through 109 Processing helix chain 'K' and resid 113 through 117 Processing helix chain 'P' and resid 3 through 9 removed outlier: 3.847A pdb=" N LEU P 7 " --> pdb=" O ILE P 3 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 55 No H-bonds generated for 'chain 'P' and resid 53 through 55' Processing helix chain 'P' and resid 97 through 100 Processing helix chain 'M' and resid 43 through 57 Processing helix chain 'M' and resid 110 through 123 removed outlier: 3.626A pdb=" N ALA M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 26 No H-bonds generated for 'chain 'H' and resid 23 through 26' Processing helix chain 'H' and resid 43 through 50 removed outlier: 4.087A pdb=" N ALA H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG H 50 " --> pdb=" O PHE H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 74 removed outlier: 3.650A pdb=" N GLU H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU H 62 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA H 63 " --> pdb=" O ALA H 59 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN H 73 " --> pdb=" O ALA H 69 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ALA H 74 " --> pdb=" O GLU H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 88 No H-bonds generated for 'chain 'H' and resid 86 through 88' Processing helix chain 'H' and resid 96 through 106 Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain '6' and resid 6 through 17 removed outlier: 3.542A pdb=" N LEU 6 17 " --> pdb=" O LYS 6 13 " (cutoff:3.500A) Processing helix chain '6' and resid 45 through 62 Processing helix chain '6' and resid 94 through 97 No H-bonds generated for 'chain '6' and resid 94 through 97' Processing helix chain '9' and resid 57 through 59 No H-bonds generated for 'chain '9' and resid 57 through 59' Processing helix chain '9' and resid 127 through 130 Processing helix chain '9' and resid 172 through 179 removed outlier: 3.633A pdb=" N ILE 9 176 " --> pdb=" O LYS 9 172 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG 9 177 " --> pdb=" O SER 9 173 " (cutoff:3.500A) Processing helix chain '9' and resid 219 through 221 No H-bonds generated for 'chain '9' and resid 219 through 221' Processing helix chain '9' and resid 230 through 232 No H-bonds generated for 'chain '9' and resid 230 through 232' Processing helix chain '9' and resid 255 through 259 Processing helix chain '9' and resid 261 through 268 removed outlier: 3.964A pdb=" N GLU 9 265 " --> pdb=" O ILE 9 261 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS 9 268 " --> pdb=" O SER 9 264 " (cutoff:3.500A) Processing helix chain '9' and resid 272 through 275 Processing helix chain '9' and resid 292 through 304 removed outlier: 3.627A pdb=" N ALA 9 299 " --> pdb=" O GLU 9 295 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA 9 303 " --> pdb=" O ALA 9 299 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU 9 304 " --> pdb=" O ILE 9 300 " (cutoff:3.500A) Processing helix chain '9' and resid 321 through 334 removed outlier: 4.382A pdb=" N TRP 9 326 " --> pdb=" O LYS 9 322 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU 9 334 " --> pdb=" O THR 9 330 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 12 removed outlier: 3.769A pdb=" N ARG 3 12 " --> pdb=" O GLY 3 8 " (cutoff:3.500A) Processing helix chain '3' and resid 32 through 34 No H-bonds generated for 'chain '3' and resid 32 through 34' Processing helix chain '3' and resid 37 through 44 removed outlier: 3.518A pdb=" N ARG 3 44 " --> pdb=" O LYS 3 40 " (cutoff:3.500A) Processing helix chain '3' and resid 52 through 60 removed outlier: 4.105A pdb=" N GLY 3 55 " --> pdb=" O GLY 3 52 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE 3 58 " --> pdb=" O GLY 3 55 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'g' and resid 14 through 19 Processing sheet with id= B, first strand: chain 'C' and resid 2 through 4 Processing sheet with id= C, first strand: chain 'C' and resid 114 through 117 removed outlier: 4.287A pdb=" N SER C 117 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE C 73 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LEU C 80 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE C 90 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 128 through 130 Processing sheet with id= E, first strand: chain 'C' and resid 180 through 184 removed outlier: 3.813A pdb=" N ALA C 165 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ARG C 174 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ILE C 163 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 169 through 172 removed outlier: 4.670A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL D 26 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N MET D 11 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL D 24 " --> pdb=" O MET D 11 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ARG D 13 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE D 22 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LYS D 190 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N VAL D 177 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 78 through 83 removed outlier: 4.296A pdb=" N GLY D 78 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR D 52 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 115 through 119 removed outlier: 5.729A pdb=" N MET D 165 " --> pdb=" O LYS D 116 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE D 118 " --> pdb=" O GLY D 163 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLY D 163 " --> pdb=" O PHE D 118 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 118 through 121 removed outlier: 6.712A pdb=" N VAL E 186 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N VAL E 121 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N MET E 188 " --> pdb=" O VAL E 121 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP E 168 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 127 through 130 removed outlier: 3.629A pdb=" N THR F 34 " --> pdb=" O THR F 154 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS F 32 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE F 33 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR F 67 " --> pdb=" O ILE F 84 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N CYS F 86 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU F 65 " --> pdb=" O CYS F 86 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 22 through 24 Processing sheet with id= L, first strand: chain 'G' and resid 40 through 43 removed outlier: 3.842A pdb=" N LYS G 43 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N THR G 50 " --> pdb=" O LYS G 43 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 160 through 163 Processing sheet with id= N, first strand: chain 'G' and resid 93 through 98 Processing sheet with id= O, first strand: chain 'J' and resid 138 through 140 removed outlier: 4.881A pdb=" N ASP J 19 " --> pdb=" O LEU J 140 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR J 53 " --> pdb=" O TYR J 16 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL J 18 " --> pdb=" O TYR J 53 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE J 55 " --> pdb=" O VAL J 18 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'J' and resid 73 through 77 Processing sheet with id= Q, first strand: chain 'L' and resid 74 through 76 removed outlier: 6.723A pdb=" N PHE L 107 " --> pdb=" O ALA L 75 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'L' and resid 121 through 123 removed outlier: 6.653A pdb=" N LYS L 141 " --> pdb=" O VAL L 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'N' and resid 33 through 37 Processing sheet with id= T, first strand: chain 'O' and resid 25 through 30 Processing sheet with id= U, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.555A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLN R 6 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL R 38 " --> pdb=" O GLN R 6 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'R' and resid 20 through 22 removed outlier: 3.542A pdb=" N VAL R 20 " --> pdb=" O VAL R 96 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL R 96 " --> pdb=" O VAL R 20 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY R 67 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA R 65 " --> pdb=" O ASP R 95 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'R' and resid 32 through 35 removed outlier: 3.628A pdb=" N VAL R 58 " --> pdb=" O SER R 102 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY R 100 " --> pdb=" O LYS R 60 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N GLU R 62 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ILE R 98 " --> pdb=" O GLU R 62 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'R' and resid 72 through 78 removed outlier: 4.039A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'S' and resid 3 through 7 removed outlier: 6.388A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'S' and resid 81 through 87 Processing sheet with id= AA, first strand: chain 'T' and resid 11 through 14 removed outlier: 6.809A pdb=" N LYS T 33 " --> pdb=" O ARG T 12 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL T 31 " --> pdb=" O PRO T 14 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL T 57 " --> pdb=" O THR T 86 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'T' and resid 67 through 69 Processing sheet with id= AC, first strand: chain 'U' and resid 21 through 23 Processing sheet with id= AD, first strand: chain 'U' and resid 63 through 65 removed outlier: 3.859A pdb=" N ASN U 26 " --> pdb=" O ILE U 34 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'U' and resid 40 through 44 Processing sheet with id= AF, first strand: chain 'U' and resid 82 through 84 Processing sheet with id= AG, first strand: chain 'V' and resid 3 through 6 removed outlier: 6.278A pdb=" N THR V 62 " --> pdb=" O ILE V 4 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ALA V 6 " --> pdb=" O THR V 62 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL V 64 " --> pdb=" O ALA V 6 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASP V 90 " --> pdb=" O GLN V 75 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N VAL V 77 " --> pdb=" O HIS V 88 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N HIS V 88 " --> pdb=" O VAL V 77 " (cutoff:3.500A) removed outlier: 9.912A pdb=" N ILE V 89 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N PHE V 91 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE V 29 " --> pdb=" O PHE V 91 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ARG V 93 " --> pdb=" O ILE V 29 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N TYR V 31 " --> pdb=" O ARG V 93 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'W' and resid 47 through 49 Processing sheet with id= AI, first strand: chain 'W' and resid 62 through 68 Processing sheet with id= AJ, first strand: chain 'X' and resid 12 through 15 Processing sheet with id= AK, first strand: chain 'X' and resid 32 through 39 removed outlier: 3.527A pdb=" N VAL X 39 " --> pdb=" O ARG X 44 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG X 44 " --> pdb=" O VAL X 39 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'Z' and resid 34 through 38 removed outlier: 3.524A pdb=" N ARG Z 37 " --> pdb=" O ILE Z 4 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain '1' and resid 19 through 25 removed outlier: 3.616A pdb=" N GLN 1 44 " --> pdb=" O ASP 1 39 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU 1 35 " --> pdb=" O TYR 1 48 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'K' and resid 6 through 8 removed outlier: 6.862A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS K 59 " --> pdb=" O LEU K 87 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'P' and resid 80 through 85 removed outlier: 6.627A pdb=" N LYS P 28 " --> pdb=" O ASP P 81 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE P 83 " --> pdb=" O GLU P 26 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU P 26 " --> pdb=" O ILE P 83 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL P 85 " --> pdb=" O THR P 24 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N THR P 24 " --> pdb=" O VAL P 85 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N GLU P 43 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE P 63 " --> pdb=" O GLU P 43 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR P 59 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ILE P 49 " --> pdb=" O ALA P 57 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA P 57 " --> pdb=" O ILE P 49 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'M' and resid 128 through 132 removed outlier: 6.309A pdb=" N ALA M 35 " --> pdb=" O VAL M 101 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL M 101 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'M' and resid 39 through 42 removed outlier: 3.837A pdb=" N GLY M 39 " --> pdb=" O ILE M 96 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE M 96 " --> pdb=" O GLY M 39 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE M 73 " --> pdb=" O GLU M 90 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N TRP M 92 " --> pdb=" O LYS M 71 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LYS M 71 " --> pdb=" O TRP M 92 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'H' and resid 77 through 83 removed outlier: 9.218A pdb=" N VAL H 78 " --> pdb=" O LYS H 141 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE H 143 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ILE H 80 " --> pdb=" O ILE H 143 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ASN H 145 " --> pdb=" O ILE H 80 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N SER H 82 " --> pdb=" O ASN H 145 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N VAL H 147 " --> pdb=" O SER H 82 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'd' and resid 11 through 15 Processing sheet with id= AT, first strand: chain '6' and resid 23 through 25 removed outlier: 3.761A pdb=" N ILE 6 86 " --> pdb=" O CYS 6 36 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain '9' and resid 64 through 66 removed outlier: 8.843A pdb=" N PHE 9 65 " --> pdb=" O SER 9 8 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU 9 10 " --> pdb=" O PHE 9 65 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain '9' and resid 86 through 90 removed outlier: 3.680A pdb=" N VAL 9 45 " --> pdb=" O ALA 9 118 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA 9 118 " --> pdb=" O VAL 9 45 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N MET 9 47 " --> pdb=" O LEU 9 116 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LEU 9 116 " --> pdb=" O MET 9 47 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ALA 9 49 " --> pdb=" O ARG 9 114 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ARG 9 114 " --> pdb=" O ALA 9 49 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain '9' and resid 162 through 166 removed outlier: 6.855A pdb=" N VAL 9 240 " --> pdb=" O GLY 9 163 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N LEU 9 165 " --> pdb=" O VAL 9 240 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU 9 242 " --> pdb=" O LEU 9 165 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL 9 281 " --> pdb=" O ILE 9 245 " (cutoff:3.500A) No H-bonds generated for sheet with id= AW 794 hydrogen bonds defined for protein. 2172 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2489 hydrogen bonds 3928 hydrogen bond angles 0 basepair planarities 978 basepair parallelities 1538 stacking parallelities Total time for adding SS restraints: 143.15 Time building geometry restraints manager: 45.75 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: 16150 1.33 - 1.46: 41916 1.46 - 1.58: 37401 1.58 - 1.70: 6031 1.70 - 1.82: 176 Bond restraints: 101674 Sorted by residual: bond pdb=" N3B GNP 9 402 " pdb=" PG GNP 9 402 " ideal model delta sigma weight residual 1.801 1.705 0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" O5' GNP 9 402 " pdb=" PA GNP 9 402 " ideal model delta sigma weight residual 1.660 1.572 0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C VAL H 31 " pdb=" N PRO H 32 " ideal model delta sigma weight residual 1.336 1.365 -0.029 1.20e-02 6.94e+03 5.86e+00 bond pdb=" O3A GNP 9 402 " pdb=" PB GNP 9 402 " ideal model delta sigma weight residual 1.687 1.641 0.046 2.00e-02 2.50e+03 5.32e+00 bond pdb=" N3B GNP 9 402 " pdb=" PB GNP 9 402 " ideal model delta sigma weight residual 1.681 1.636 0.045 2.00e-02 2.50e+03 5.03e+00 ... (remaining 101669 not shown) Histogram of bond angle deviations from ideal: 97.93 - 105.15: 13884 105.15 - 112.37: 58440 112.37 - 119.59: 32729 119.59 - 126.81: 38925 126.81 - 134.03: 8260 Bond angle restraints: 152238 Sorted by residual: angle pdb=" C PRO F 175 " pdb=" N PHE F 176 " pdb=" CA PHE F 176 " ideal model delta sigma weight residual 121.54 132.71 -11.17 1.91e+00 2.74e-01 3.42e+01 angle pdb=" CA MET F 95 " pdb=" CB MET F 95 " pdb=" CG MET F 95 " ideal model delta sigma weight residual 114.10 124.65 -10.55 2.00e+00 2.50e-01 2.78e+01 angle pdb=" N ILE E 181 " pdb=" CA ILE E 181 " pdb=" C ILE E 181 " ideal model delta sigma weight residual 112.96 108.36 4.60 1.00e+00 1.00e+00 2.12e+01 angle pdb=" C ILE T 2 " pdb=" N ARG T 3 " pdb=" CA ARG T 3 " ideal model delta sigma weight residual 121.70 129.07 -7.37 1.80e+00 3.09e-01 1.68e+01 angle pdb=" C3' G A2505 " pdb=" O3' G A2505 " pdb=" P U A2506 " ideal model delta sigma weight residual 120.20 125.65 -5.45 1.50e+00 4.44e-01 1.32e+01 ... (remaining 152233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.41: 57239 35.41 - 70.82: 6967 70.82 - 106.23: 808 106.23 - 141.64: 7 141.64 - 177.05: 10 Dihedral angle restraints: 65031 sinusoidal: 54560 harmonic: 10471 Sorted by residual: dihedral pdb=" O4' U A 545 " pdb=" C1' U A 545 " pdb=" N1 U A 545 " pdb=" C2 U A 545 " ideal model delta sinusoidal sigma weight residual 200.00 55.63 144.37 1 1.50e+01 4.44e-03 7.73e+01 dihedral pdb=" O4' U A1340 " pdb=" C1' U A1340 " pdb=" N1 U A1340 " pdb=" C2 U A1340 " ideal model delta sinusoidal sigma weight residual -128.00 49.05 -177.05 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U A1061 " pdb=" C1' U A1061 " pdb=" N1 U A1061 " pdb=" C2 U A1061 " ideal model delta sinusoidal sigma weight residual -128.00 48.90 -176.90 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 65028 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 17843 0.046 - 0.093: 1268 0.093 - 0.139: 346 0.139 - 0.185: 18 0.185 - 0.231: 4 Chirality restraints: 19479 Sorted by residual: chirality pdb=" C3' G A2505 " pdb=" C4' G A2505 " pdb=" O3' G A2505 " pdb=" C2' G A2505 " both_signs ideal model delta sigma weight residual False -2.74 -2.51 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C1' U A1736 " pdb=" O4' U A1736 " pdb=" C2' U A1736 " pdb=" N1 U A1736 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C3' A A1378 " pdb=" C4' A A1378 " pdb=" O3' A A1378 " pdb=" C2' A A1378 " both_signs ideal model delta sigma weight residual False -2.74 -2.54 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 19476 not shown) Planarity restraints: 8060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U A1736 " -0.036 2.00e-02 2.50e+03 1.90e-02 8.10e+00 pdb=" N1 U A1736 " 0.041 2.00e-02 2.50e+03 pdb=" C2 U A1736 " 0.002 2.00e-02 2.50e+03 pdb=" O2 U A1736 " 0.003 2.00e-02 2.50e+03 pdb=" N3 U A1736 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U A1736 " -0.006 2.00e-02 2.50e+03 pdb=" O4 U A1736 " -0.011 2.00e-02 2.50e+03 pdb=" C5 U A1736 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U A1736 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO F 175 " -0.012 2.00e-02 2.50e+03 2.52e-02 6.37e+00 pdb=" C PRO F 175 " 0.044 2.00e-02 2.50e+03 pdb=" O PRO F 175 " -0.016 2.00e-02 2.50e+03 pdb=" N PHE F 176 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A2564 " 0.028 2.00e-02 2.50e+03 1.36e-02 5.05e+00 pdb=" N9 A A2564 " -0.034 2.00e-02 2.50e+03 pdb=" C8 A A2564 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A A2564 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A A2564 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A A2564 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A A2564 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A A2564 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A A2564 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A A2564 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A A2564 " 0.000 2.00e-02 2.50e+03 ... (remaining 8057 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 1037 2.59 - 3.17: 71952 3.17 - 3.75: 186414 3.75 - 4.32: 252549 4.32 - 4.90: 336923 Nonbonded interactions: 848875 Sorted by model distance: nonbonded pdb="MG MG 9 401 " pdb=" O2G GNP 9 402 " model vdw 2.015 2.170 nonbonded pdb="MG MG 9 401 " pdb=" O1B GNP 9 402 " model vdw 2.037 2.170 nonbonded pdb=" OG SER 9 173 " pdb="MG MG 9 401 " model vdw 2.063 2.170 nonbonded pdb=" OP1 U B 5 " pdb=" O2' G B 61 " model vdw 2.130 2.440 nonbonded pdb=" OG1 THR J 3 " pdb=" O2 C A 995 " model vdw 2.137 2.440 ... (remaining 848870 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.010 Normalize map: mean=0, sd=1: 2.900 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: 0.110 Extract box with map and model: 13.800 Check model and map are aligned: 1.060 Set scattering table: 0.670 Process input model: 342.850 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.220 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: 0.010 Load rotamer database and sin/cos tables:13.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 376.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 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 : 0.002 0.096 101674 Z= 0.123 Angle : 0.453 11.173 152238 Z= 0.244 Chirality : 0.027 0.231 19479 Planarity : 0.003 0.046 8060 Dihedral : 22.632 177.047 58295 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.06 % Favored : 94.89 % Rotamer: Outliers : 0.03 % Allowed : 0.30 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -0.52 (0.14), residues: 3638 helix: 0.13 (0.18), residues: 883 sheet: 0.72 (0.20), residues: 719 loop : -0.95 (0.13), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 212 HIS 0.009 0.001 HIS M 13 PHE 0.020 0.001 PHE O 92 TYR 0.022 0.001 TYR F 127 ARG 0.015 0.001 ARG Q 12 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1096 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1095 time to evaluate : 4.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 97 ASP cc_start: 0.8502 (p0) cc_final: 0.7984 (t0) REVERT: C 255 LYS cc_start: 0.8558 (mtpt) cc_final: 0.8297 (mttm) REVERT: D 174 SER cc_start: 0.8275 (t) cc_final: 0.7903 (t) REVERT: D 185 ASN cc_start: 0.8723 (m-40) cc_final: 0.8458 (m110) REVERT: E 101 TYR cc_start: 0.9040 (t80) cc_final: 0.8816 (t80) REVERT: E 111 GLU cc_start: 0.8406 (tp30) cc_final: 0.7866 (tp30) REVERT: E 185 LYS cc_start: 0.8465 (mmtm) cc_final: 0.7850 (mmmm) REVERT: E 199 MET cc_start: 0.8393 (ppp) cc_final: 0.8128 (ppp) REVERT: F 2 LYS cc_start: 0.9004 (mptt) cc_final: 0.8723 (mmpt) REVERT: F 26 GLN cc_start: 0.8615 (tt0) cc_final: 0.8171 (tm-30) REVERT: F 89 THR cc_start: 0.8394 (m) cc_final: 0.8121 (t) REVERT: F 97 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7596 (pm20) REVERT: G 2 ARG cc_start: 0.7719 (tmm-80) cc_final: 0.6770 (tmm-80) REVERT: J 19 ASP cc_start: 0.7968 (t70) cc_final: 0.7674 (t70) REVERT: J 58 ASN cc_start: 0.8996 (m110) cc_final: 0.8609 (m110) REVERT: J 88 THR cc_start: 0.8941 (p) cc_final: 0.8694 (p) REVERT: L 1 MET cc_start: 0.7559 (ppp) cc_final: 0.7170 (ppp) REVERT: L 78 ARG cc_start: 0.8493 (mtt-85) cc_final: 0.8007 (mtt-85) REVERT: N 18 GLN cc_start: 0.7855 (tt0) cc_final: 0.7629 (tt0) REVERT: N 54 LEU cc_start: 0.9270 (tp) cc_final: 0.9057 (tp) REVERT: Q 58 GLN cc_start: 0.8386 (tt0) cc_final: 0.8143 (tp40) REVERT: R 60 LYS cc_start: 0.9006 (mtmm) cc_final: 0.8776 (mppt) REVERT: V 2 PHE cc_start: 0.7575 (m-10) cc_final: 0.7249 (m-10) REVERT: V 14 LYS cc_start: 0.8846 (ptmt) cc_final: 0.8581 (ttpt) REVERT: V 53 LYS cc_start: 0.8366 (mptt) cc_final: 0.8136 (mptt) REVERT: V 87 GLN cc_start: 0.8893 (mm-40) cc_final: 0.8683 (mm-40) REVERT: W 72 ASN cc_start: 0.7921 (m-40) cc_final: 0.7656 (m110) REVERT: K 51 LYS cc_start: 0.7804 (ttmm) cc_final: 0.7587 (ttmp) REVERT: P 95 LYS cc_start: 0.9288 (mmtm) cc_final: 0.9024 (mmtm) REVERT: M 30 SER cc_start: 0.8917 (p) cc_final: 0.8710 (p) REVERT: H 43 ASN cc_start: 0.8320 (m-40) cc_final: 0.7944 (p0) REVERT: 9 44 ASP cc_start: 0.7499 (t70) cc_final: 0.6879 (t0) REVERT: 9 48 GLU cc_start: 0.6263 (tp30) cc_final: 0.5907 (tm-30) REVERT: 9 77 ASP cc_start: 0.7960 (t0) cc_final: 0.7760 (t0) outliers start: 1 outliers final: 2 residues processed: 1095 average time/residue: 1.5482 time to fit residues: 2378.0772 Evaluate side-chains 936 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 934 time to evaluate : 4.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain K residue 95 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 553 optimal weight: 10.0000 chunk 497 optimal weight: 30.0000 chunk 275 optimal weight: 6.9990 chunk 169 optimal weight: 8.9990 chunk 335 optimal weight: 30.0000 chunk 265 optimal weight: 8.9990 chunk 514 optimal weight: 10.0000 chunk 198 optimal weight: 4.9990 chunk 312 optimal weight: 10.0000 chunk 382 optimal weight: 8.9990 chunk 595 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN E 41 GLN E 90 GLN E 115 GLN E 195 GLN F 36 ASN F 126 ASN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN L 104 GLN N 11 ASN O 38 GLN O 61 GLN Q 19 GLN Q 51 GLN Q 55 GLN R 11 GLN R 18 GLN S 15 GLN T 28 ASN T 70 HIS U 44 HIS ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 8 ASN X 15 ASN 1 25 ASN K 82 ASN K 88 ASN P 11 GLN H 33 GLN ** H 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 91 GLN ** 9 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.111 101674 Z= 0.541 Angle : 0.705 9.312 152238 Z= 0.357 Chirality : 0.041 0.329 19479 Planarity : 0.005 0.052 8060 Dihedral : 22.893 178.296 51124 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.88 % Favored : 94.04 % Rotamer: Outliers : 6.15 % Allowed : 17.80 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -0.85 (0.13), residues: 3638 helix: -0.18 (0.16), residues: 939 sheet: 0.16 (0.19), residues: 791 loop : -1.04 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 212 HIS 0.012 0.002 HIS M 13 PHE 0.037 0.002 PHE U 94 TYR 0.024 0.002 TYR Q 31 ARG 0.015 0.001 ARG S 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1236 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1051 time to evaluate : 4.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 36 ARG cc_start: 0.8777 (ttp80) cc_final: 0.8240 (ttm-80) REVERT: C 97 ASP cc_start: 0.8558 (p0) cc_final: 0.8299 (p0) REVERT: C 184 GLU cc_start: 0.7830 (pm20) cc_final: 0.7617 (pm20) REVERT: C 255 LYS cc_start: 0.8725 (mtpt) cc_final: 0.8342 (mttm) REVERT: D 174 SER cc_start: 0.8639 (t) cc_final: 0.8319 (t) REVERT: E 168 ASP cc_start: 0.8171 (t0) cc_final: 0.7804 (t0) REVERT: E 199 MET cc_start: 0.8597 (ppp) cc_final: 0.8391 (ppp) REVERT: F 26 GLN cc_start: 0.8755 (tt0) cc_final: 0.8316 (tm-30) REVERT: F 37 MET cc_start: 0.7154 (mmm) cc_final: 0.6842 (mmm) REVERT: F 95 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7522 (mmm) REVERT: G 2 ARG cc_start: 0.8239 (tmm-80) cc_final: 0.6843 (tmm-80) REVERT: G 68 ARG cc_start: 0.8966 (tpt90) cc_final: 0.8673 (tpt90) REVERT: G 100 ASN cc_start: 0.8071 (t0) cc_final: 0.7767 (t0) REVERT: G 148 ARG cc_start: 0.8625 (ttt-90) cc_final: 0.8346 (tmt90) REVERT: J 58 ASN cc_start: 0.9026 (m110) cc_final: 0.8572 (m110) REVERT: L 1 MET cc_start: 0.7745 (ppp) cc_final: 0.7343 (ppp) REVERT: L 76 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7366 (mt-10) REVERT: L 106 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7605 (mm-30) REVERT: N 54 LEU cc_start: 0.9397 (tp) cc_final: 0.9162 (tp) REVERT: O 97 PHE cc_start: 0.8430 (m-80) cc_final: 0.8141 (m-80) REVERT: U 85 ARG cc_start: 0.8958 (pmm-80) cc_final: 0.8696 (ptt90) REVERT: V 2 PHE cc_start: 0.7549 (m-10) cc_final: 0.7258 (m-10) REVERT: V 14 LYS cc_start: 0.8861 (ptmt) cc_final: 0.8528 (ttpt) REVERT: V 65 VAL cc_start: 0.8708 (p) cc_final: 0.8258 (p) REVERT: V 87 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8748 (mm-40) REVERT: W 74 LYS cc_start: 0.8845 (mtmp) cc_final: 0.8104 (mtpt) REVERT: Y 25 GLN cc_start: 0.9043 (tt0) cc_final: 0.8715 (tt0) REVERT: 0 12 ARG cc_start: 0.8958 (ttp-170) cc_final: 0.8690 (ttm170) REVERT: 0 35 GLU cc_start: 0.7935 (pm20) cc_final: 0.7428 (pm20) REVERT: 0 45 ASP cc_start: 0.8799 (OUTLIER) cc_final: 0.8258 (p0) REVERT: K 58 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8496 (pp) REVERT: K 59 LYS cc_start: 0.8985 (mttm) cc_final: 0.8747 (mttm) REVERT: K 113 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.6798 (mpp) REVERT: H 43 ASN cc_start: 0.8335 (m-40) cc_final: 0.7894 (p0) REVERT: 6 17 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8831 (tm) REVERT: 9 1 MET cc_start: 0.7183 (mpp) cc_final: 0.6508 (mpp) REVERT: 9 44 ASP cc_start: 0.7542 (t70) cc_final: 0.7246 (t0) outliers start: 185 outliers final: 99 residues processed: 1108 average time/residue: 1.6102 time to fit residues: 2483.2813 Evaluate side-chains 1101 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 997 time to evaluate : 4.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain O residue 13 ARG Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 38 GLN Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain Q residue 5 ARG Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain S residue 31 GLN Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 26 SER Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 25 LYS Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain Z residue 18 LYS Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 26 LEU Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 0 residue 53 VAL Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 28 THR Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 46 PHE Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 32 SER Chi-restraints excluded: chain 6 residue 56 VAL Chi-restraints excluded: chain 6 residue 65 LEU Chi-restraints excluded: chain 6 residue 70 GLU Chi-restraints excluded: chain 6 residue 89 VAL Chi-restraints excluded: chain 9 residue 29 ILE Chi-restraints excluded: chain 9 residue 58 ASP Chi-restraints excluded: chain 9 residue 71 GLN Chi-restraints excluded: chain 9 residue 135 ASN Chi-restraints excluded: chain 9 residue 143 ASN Chi-restraints excluded: chain 9 residue 321 VAL Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 28 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 331 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 495 optimal weight: 10.0000 chunk 405 optimal weight: 3.9990 chunk 164 optimal weight: 7.9990 chunk 596 optimal weight: 20.0000 chunk 644 optimal weight: 4.9990 chunk 531 optimal weight: 6.9990 chunk 591 optimal weight: 10.0000 chunk 203 optimal weight: 7.9990 chunk 478 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 13 ASN D 58 ASN D 130 GLN E 24 ASN E 90 GLN E 195 GLN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 135 GLN L 99 ASN O 38 GLN Q 19 GLN Q 43 GLN Q 51 GLN Q 55 GLN R 11 GLN T 28 ASN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 72 ASN X 15 ASN Z 19 HIS 1 25 ASN ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 29 GLN K 88 ASN ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN H 33 GLN H 43 ASN ** H 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 91 GLN 9 135 ASN ** 9 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 101674 Z= 0.305 Angle : 0.560 9.010 152238 Z= 0.289 Chirality : 0.035 0.276 19479 Planarity : 0.004 0.063 8060 Dihedral : 22.927 178.340 51122 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.47 % Favored : 94.47 % Rotamer: Outliers : 6.49 % Allowed : 22.26 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -0.76 (0.14), residues: 3638 helix: 0.09 (0.17), residues: 930 sheet: 0.09 (0.19), residues: 754 loop : -1.02 (0.13), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 212 HIS 0.008 0.001 HIS 3 30 PHE 0.021 0.002 PHE V 26 TYR 0.021 0.002 TYR Q 31 ARG 0.010 0.001 ARG W 7 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1235 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 1040 time to evaluate : 4.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 97 ASP cc_start: 0.8560 (p0) cc_final: 0.8250 (p0) REVERT: C 115 ILE cc_start: 0.8882 (pp) cc_final: 0.8563 (pt) REVERT: C 255 LYS cc_start: 0.8657 (mtpt) cc_final: 0.8278 (mttm) REVERT: D 174 SER cc_start: 0.8667 (t) cc_final: 0.8347 (t) REVERT: E 111 GLU cc_start: 0.8526 (tp30) cc_final: 0.7815 (tp30) REVERT: E 115 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7762 (tm-30) REVERT: E 168 ASP cc_start: 0.8130 (t0) cc_final: 0.7764 (t0) REVERT: F 26 GLN cc_start: 0.8733 (tt0) cc_final: 0.8309 (tm-30) REVERT: F 37 MET cc_start: 0.7243 (mmm) cc_final: 0.6896 (mmm) REVERT: F 95 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7696 (mmm) REVERT: F 111 ARG cc_start: 0.8047 (ppp80) cc_final: 0.7844 (ppp80) REVERT: G 100 ASN cc_start: 0.8109 (t0) cc_final: 0.7609 (t0) REVERT: G 148 ARG cc_start: 0.8608 (ttt-90) cc_final: 0.8311 (tmt90) REVERT: J 2 LYS cc_start: 0.8611 (mptt) cc_final: 0.8408 (mtpm) REVERT: J 58 ASN cc_start: 0.9014 (m110) cc_final: 0.8602 (m110) REVERT: L 78 ARG cc_start: 0.8571 (mtt-85) cc_final: 0.8130 (mtt-85) REVERT: N 35 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8605 (ttmm) REVERT: N 62 ASN cc_start: 0.9197 (m-40) cc_final: 0.8965 (m-40) REVERT: O 17 LYS cc_start: 0.9253 (tptp) cc_final: 0.9041 (tptp) REVERT: Q 108 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8797 (mm) REVERT: T 1 MET cc_start: 0.5873 (OUTLIER) cc_final: 0.5547 (ppp) REVERT: T 73 ARG cc_start: 0.7568 (ttp-170) cc_final: 0.7326 (ttm170) REVERT: U 100 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7628 (mm-30) REVERT: V 11 GLU cc_start: 0.7793 (tp30) cc_final: 0.7544 (tp30) REVERT: V 65 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8432 (p) REVERT: V 79 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.7747 (mtp180) REVERT: V 87 GLN cc_start: 0.8869 (mm-40) cc_final: 0.8585 (mm110) REVERT: W 26 SER cc_start: 0.9225 (OUTLIER) cc_final: 0.9017 (t) REVERT: W 74 LYS cc_start: 0.8904 (mtmp) cc_final: 0.8137 (mtpt) REVERT: X 61 LYS cc_start: 0.8854 (mmtt) cc_final: 0.8623 (mmpt) REVERT: 0 6 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8913 (tttm) REVERT: 0 12 ARG cc_start: 0.8821 (ttp-170) cc_final: 0.8537 (ttm170) REVERT: 0 45 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.8360 (p0) REVERT: 1 25 ASN cc_start: 0.8868 (t0) cc_final: 0.8663 (t0) REVERT: 1 27 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7865 (tpp80) REVERT: 1 49 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8385 (mmtm) REVERT: K 58 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8447 (pp) REVERT: P 12 MET cc_start: 0.8697 (mtp) cc_final: 0.8471 (mtm) REVERT: P 30 TRP cc_start: 0.8672 (m100) cc_final: 0.8157 (m100) REVERT: H 60 GLU cc_start: 0.7787 (pt0) cc_final: 0.7339 (pm20) REVERT: 6 96 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7624 (mpp80) REVERT: 9 1 MET cc_start: 0.7047 (mpp) cc_final: 0.6751 (mpp) REVERT: 9 44 ASP cc_start: 0.7739 (t70) cc_final: 0.7306 (t0) REVERT: 9 57 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8670 (pp) REVERT: 9 77 ASP cc_start: 0.8114 (t0) cc_final: 0.7838 (t0) REVERT: 9 131 LYS cc_start: 0.8494 (pttp) cc_final: 0.8148 (pmtt) REVERT: 9 141 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7623 (pptt) REVERT: 3 18 LYS cc_start: 0.9026 (mtpp) cc_final: 0.8663 (mtpp) outliers start: 195 outliers final: 104 residues processed: 1109 average time/residue: 1.5918 time to fit residues: 2463.3690 Evaluate side-chains 1099 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 979 time to evaluate : 4.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 115 GLN Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 35 LYS Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain Q residue 5 ARG Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain S residue 31 GLN Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 73 LYS Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 79 ARG Chi-restraints excluded: chain W residue 26 SER Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 25 LYS Chi-restraints excluded: chain X residue 53 LYS Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 39 ASP Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 6 LYS Chi-restraints excluded: chain 0 residue 33 SER Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 0 residue 53 VAL Chi-restraints excluded: chain 1 residue 13 SER Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 23 THR Chi-restraints excluded: chain 1 residue 27 ARG Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 49 LYS Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 96 LEU Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 32 SER Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 6 residue 56 VAL Chi-restraints excluded: chain 6 residue 64 LEU Chi-restraints excluded: chain 6 residue 65 LEU Chi-restraints excluded: chain 6 residue 70 GLU Chi-restraints excluded: chain 6 residue 89 VAL Chi-restraints excluded: chain 6 residue 96 ARG Chi-restraints excluded: chain 9 residue 5 ASP Chi-restraints excluded: chain 9 residue 26 GLU Chi-restraints excluded: chain 9 residue 29 ILE Chi-restraints excluded: chain 9 residue 35 ASP Chi-restraints excluded: chain 9 residue 45 VAL Chi-restraints excluded: chain 9 residue 52 ASN Chi-restraints excluded: chain 9 residue 57 ILE Chi-restraints excluded: chain 9 residue 58 ASP Chi-restraints excluded: chain 9 residue 141 LYS Chi-restraints excluded: chain 9 residue 321 VAL Chi-restraints excluded: chain 9 residue 333 ILE Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 28 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 589 optimal weight: 10.0000 chunk 448 optimal weight: 10.0000 chunk 309 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 284 optimal weight: 7.9990 chunk 400 optimal weight: 7.9990 chunk 598 optimal weight: 20.0000 chunk 634 optimal weight: 1.9990 chunk 312 optimal weight: 8.9990 chunk 567 optimal weight: 8.9990 chunk 170 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN D 130 GLN E 90 GLN E 195 GLN F 51 ASN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 HIS L 99 ASN L 104 GLN O 38 GLN Q 19 GLN Q 51 GLN Q 55 GLN R 11 GLN R 86 GLN T 28 ASN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 24 ASN ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 42 HIS W 72 ASN X 15 ASN 2 26 ASN K 88 ASN ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN 9 135 ASN ** 9 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 101674 Z= 0.450 Angle : 0.659 10.487 152238 Z= 0.337 Chirality : 0.039 0.320 19479 Planarity : 0.005 0.053 8060 Dihedral : 22.954 177.916 51120 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.65 % Favored : 93.27 % Rotamer: Outliers : 8.25 % Allowed : 24.35 % Favored : 67.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.98 (0.13), residues: 3638 helix: -0.03 (0.17), residues: 916 sheet: -0.15 (0.18), residues: 788 loop : -1.15 (0.13), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 61 HIS 0.008 0.002 HIS 3 25 PHE 0.022 0.002 PHE V 26 TYR 0.022 0.002 TYR E 101 ARG 0.015 0.001 ARG S 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1291 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 1043 time to evaluate : 4.270 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: C 97 ASP cc_start: 0.8642 (p0) cc_final: 0.8321 (p0) REVERT: C 131 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8269 (mpp) REVERT: D 174 SER cc_start: 0.8557 (t) cc_final: 0.8251 (t) REVERT: E 115 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7909 (tm-30) REVERT: E 168 ASP cc_start: 0.8132 (t0) cc_final: 0.7756 (t0) REVERT: E 185 LYS cc_start: 0.8766 (mmtp) cc_final: 0.8162 (mmmm) REVERT: F 26 GLN cc_start: 0.8784 (tt0) cc_final: 0.8408 (tm-30) REVERT: F 37 MET cc_start: 0.6900 (mmm) cc_final: 0.6557 (mmm) REVERT: F 95 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7643 (mmm) REVERT: F 111 ARG cc_start: 0.8161 (ppp80) cc_final: 0.7894 (ppp80) REVERT: F 112 ASP cc_start: 0.7569 (t70) cc_final: 0.7283 (t70) REVERT: F 145 VAL cc_start: 0.5807 (m) cc_final: 0.5577 (t) REVERT: G 100 ASN cc_start: 0.8095 (t0) cc_final: 0.7530 (t0) REVERT: G 142 GLN cc_start: 0.8236 (tp40) cc_final: 0.7970 (tp40) REVERT: G 148 ARG cc_start: 0.8657 (ttt-90) cc_final: 0.8377 (tmt90) REVERT: G 151 ARG cc_start: 0.8824 (mmt-90) cc_final: 0.8597 (tpt170) REVERT: J 58 ASN cc_start: 0.9010 (m110) cc_final: 0.8568 (m110) REVERT: L 78 ARG cc_start: 0.8571 (mtt-85) cc_final: 0.8113 (mtt-85) REVERT: N 62 ASN cc_start: 0.9210 (m-40) cc_final: 0.8978 (m-40) REVERT: N 99 LYS cc_start: 0.8950 (mttp) cc_final: 0.8664 (mttp) REVERT: O 52 SER cc_start: 0.9171 (OUTLIER) cc_final: 0.8678 (m) REVERT: O 104 GLN cc_start: 0.8158 (mp10) cc_final: 0.7866 (mp10) REVERT: Q 55 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8128 (mt0) REVERT: Q 108 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8795 (mm) REVERT: R 21 ARG cc_start: 0.9041 (mmm160) cc_final: 0.8448 (mmt180) REVERT: R 97 LYS cc_start: 0.7458 (OUTLIER) cc_final: 0.6883 (tppt) REVERT: S 62 ASP cc_start: 0.7695 (m-30) cc_final: 0.6885 (m-30) REVERT: T 1 MET cc_start: 0.6050 (OUTLIER) cc_final: 0.5834 (ppp) REVERT: T 73 ARG cc_start: 0.7587 (ttp-170) cc_final: 0.7362 (ttm170) REVERT: V 24 ASN cc_start: 0.8862 (OUTLIER) cc_final: 0.8489 (t0) REVERT: V 31 TYR cc_start: 0.8855 (p90) cc_final: 0.8075 (p90) REVERT: V 61 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8465 (tt) REVERT: V 90 ASP cc_start: 0.8681 (m-30) cc_final: 0.8147 (t0) REVERT: W 74 LYS cc_start: 0.8865 (mtmp) cc_final: 0.8112 (mtpt) REVERT: X 61 LYS cc_start: 0.8834 (mmtt) cc_final: 0.8632 (mmpt) REVERT: Z 39 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7574 (m-30) REVERT: 0 12 ARG cc_start: 0.8890 (ttp-170) cc_final: 0.8617 (ttm170) REVERT: K 51 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7543 (ttmm) REVERT: K 58 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8451 (pp) REVERT: K 82 ASN cc_start: 0.9118 (OUTLIER) cc_final: 0.8683 (m110) REVERT: P 30 TRP cc_start: 0.8668 (m100) cc_final: 0.7971 (m100) REVERT: P 81 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7539 (m-30) REVERT: H 44 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.7987 (tp) REVERT: H 53 GLU cc_start: 0.7443 (pm20) cc_final: 0.7107 (pm20) REVERT: H 60 GLU cc_start: 0.7790 (pt0) cc_final: 0.7404 (pm20) REVERT: 6 96 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7271 (mpp80) REVERT: 9 44 ASP cc_start: 0.7796 (t70) cc_final: 0.7224 (t0) REVERT: 9 57 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8671 (pp) REVERT: 9 71 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8167 (tt0) REVERT: 9 149 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8228 (mmmm) REVERT: 9 167 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.7900 (mtm) REVERT: 9 223 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7917 (pm20) REVERT: 9 254 ASP cc_start: 0.7089 (m-30) cc_final: 0.6053 (p0) outliers start: 248 outliers final: 138 residues processed: 1141 average time/residue: 1.5758 time to fit residues: 2510.5928 Evaluate side-chains 1172 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1012 time to evaluate : 4.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 115 GLN Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 38 GLN Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain O residue 98 GLN Chi-restraints excluded: chain Q residue 5 ARG Chi-restraints excluded: chain Q residue 55 GLN Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain S residue 31 GLN Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 73 LYS Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 24 ASN Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 26 SER Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain W residue 49 CYS Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 25 LYS Chi-restraints excluded: chain X residue 53 LYS Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 18 LYS Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 39 ASP Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 33 SER Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 0 residue 53 VAL Chi-restraints excluded: chain 1 residue 12 SER Chi-restraints excluded: chain 1 residue 13 SER Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 23 THR Chi-restraints excluded: chain 1 residue 27 ARG Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 2 residue 9 VAL Chi-restraints excluded: chain 2 residue 10 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 51 LYS Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 96 LEU Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 127 LYS Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 43 ASN Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 32 SER Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 6 residue 56 VAL Chi-restraints excluded: chain 6 residue 64 LEU Chi-restraints excluded: chain 6 residue 65 LEU Chi-restraints excluded: chain 6 residue 70 GLU Chi-restraints excluded: chain 6 residue 89 VAL Chi-restraints excluded: chain 6 residue 96 ARG Chi-restraints excluded: chain 9 residue 26 GLU Chi-restraints excluded: chain 9 residue 29 ILE Chi-restraints excluded: chain 9 residue 35 ASP Chi-restraints excluded: chain 9 residue 45 VAL Chi-restraints excluded: chain 9 residue 57 ILE Chi-restraints excluded: chain 9 residue 58 ASP Chi-restraints excluded: chain 9 residue 71 GLN Chi-restraints excluded: chain 9 residue 90 VAL Chi-restraints excluded: chain 9 residue 135 ASN Chi-restraints excluded: chain 9 residue 140 GLN Chi-restraints excluded: chain 9 residue 149 LYS Chi-restraints excluded: chain 9 residue 167 MET Chi-restraints excluded: chain 9 residue 214 ILE Chi-restraints excluded: chain 9 residue 223 GLU Chi-restraints excluded: chain 9 residue 247 ILE Chi-restraints excluded: chain 9 residue 321 VAL Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 50 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 528 optimal weight: 10.0000 chunk 359 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 472 optimal weight: 6.9990 chunk 261 optimal weight: 0.8980 chunk 541 optimal weight: 8.9990 chunk 438 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 323 optimal weight: 10.0000 chunk 569 optimal weight: 10.0000 chunk 160 optimal weight: 4.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN D 130 GLN E 24 ASN E 90 GLN E 195 GLN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN Q 19 GLN Q 43 GLN Q 51 GLN Q 55 GLN R 11 GLN U 68 ASN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 72 ASN X 15 ASN ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 ASN K 88 ASN P 11 GLN ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 101674 Z= 0.333 Angle : 0.592 10.705 152238 Z= 0.305 Chirality : 0.036 0.285 19479 Planarity : 0.004 0.058 8060 Dihedral : 22.976 179.397 51120 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.83 % Favored : 94.09 % Rotamer: Outliers : 7.52 % Allowed : 27.54 % Favored : 64.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.92 (0.13), residues: 3638 helix: 0.08 (0.17), residues: 914 sheet: -0.11 (0.19), residues: 761 loop : -1.13 (0.13), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 61 HIS 0.006 0.001 HIS E 165 PHE 0.025 0.002 PHE V 26 TYR 0.024 0.002 TYR F 127 ARG 0.013 0.001 ARG W 7 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1268 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1042 time to evaluate : 4.136 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: C 97 ASP cc_start: 0.8619 (p0) cc_final: 0.8279 (p0) REVERT: D 174 SER cc_start: 0.8624 (t) cc_final: 0.8319 (t) REVERT: E 111 GLU cc_start: 0.8544 (tp30) cc_final: 0.7789 (tp30) REVERT: E 115 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7878 (tm-30) REVERT: E 162 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8009 (mtm-85) REVERT: E 168 ASP cc_start: 0.8131 (t0) cc_final: 0.7839 (t0) REVERT: E 185 LYS cc_start: 0.8740 (mmtp) cc_final: 0.8132 (mmmm) REVERT: F 26 GLN cc_start: 0.8771 (tt0) cc_final: 0.8436 (tm-30) REVERT: F 37 MET cc_start: 0.7072 (mmm) cc_final: 0.6637 (mmm) REVERT: F 95 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7756 (mpm) REVERT: F 111 ARG cc_start: 0.8155 (ppp80) cc_final: 0.7860 (ppp80) REVERT: F 112 ASP cc_start: 0.7568 (t70) cc_final: 0.7267 (t70) REVERT: F 145 VAL cc_start: 0.5629 (m) cc_final: 0.5287 (t) REVERT: G 100 ASN cc_start: 0.8058 (t0) cc_final: 0.7601 (t0) REVERT: G 142 GLN cc_start: 0.8202 (tp40) cc_final: 0.7927 (tp40) REVERT: G 148 ARG cc_start: 0.8660 (ttt-90) cc_final: 0.8371 (tmt90) REVERT: G 151 ARG cc_start: 0.8830 (mmt-90) cc_final: 0.8611 (tpt170) REVERT: J 58 ASN cc_start: 0.9007 (m110) cc_final: 0.8560 (m110) REVERT: L 78 ARG cc_start: 0.8586 (mtt-85) cc_final: 0.8141 (mtt-85) REVERT: N 62 ASN cc_start: 0.9201 (m-40) cc_final: 0.8944 (m-40) REVERT: N 99 LYS cc_start: 0.8909 (mttp) cc_final: 0.8703 (mttp) REVERT: O 52 SER cc_start: 0.9131 (OUTLIER) cc_final: 0.8651 (m) REVERT: O 104 GLN cc_start: 0.8299 (mp10) cc_final: 0.7980 (mp10) REVERT: Q 108 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8837 (mm) REVERT: R 97 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.6759 (tppt) REVERT: V 24 ASN cc_start: 0.8874 (t0) cc_final: 0.8527 (t0) REVERT: V 31 TYR cc_start: 0.8785 (p90) cc_final: 0.7936 (p90) REVERT: V 61 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8454 (tt) REVERT: V 79 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.7779 (mtp180) REVERT: V 87 GLN cc_start: 0.8981 (mm-40) cc_final: 0.8666 (mm110) REVERT: V 90 ASP cc_start: 0.8663 (m-30) cc_final: 0.8134 (t0) REVERT: W 74 LYS cc_start: 0.8868 (mtmp) cc_final: 0.8104 (mtpt) REVERT: X 61 LYS cc_start: 0.8935 (mmtt) cc_final: 0.8662 (mmpt) REVERT: Y 25 GLN cc_start: 0.9053 (tt0) cc_final: 0.8738 (tt0) REVERT: 0 12 ARG cc_start: 0.8827 (ttp-170) cc_final: 0.8578 (ttm170) REVERT: 0 36 LYS cc_start: 0.7982 (mmmt) cc_final: 0.7599 (tptm) REVERT: 1 49 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8386 (mmtm) REVERT: K 51 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7527 (ttmm) REVERT: K 58 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8410 (pp) REVERT: K 66 LYS cc_start: 0.8926 (tptt) cc_final: 0.8722 (tptt) REVERT: P 12 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8407 (mtm) REVERT: P 30 TRP cc_start: 0.8641 (m100) cc_final: 0.8115 (m100) REVERT: P 81 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7454 (m-30) REVERT: H 44 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.7946 (tp) REVERT: H 53 GLU cc_start: 0.7394 (pm20) cc_final: 0.7169 (pm20) REVERT: H 60 GLU cc_start: 0.7724 (pt0) cc_final: 0.7320 (pm20) REVERT: d 25 ARG cc_start: 0.8404 (mtt180) cc_final: 0.8203 (tpp80) REVERT: 6 18 LYS cc_start: 0.8790 (mmmm) cc_final: 0.8509 (mtpp) REVERT: 9 44 ASP cc_start: 0.7826 (t70) cc_final: 0.7224 (t0) REVERT: 9 57 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8708 (pp) REVERT: 9 131 LYS cc_start: 0.8524 (pttp) cc_final: 0.8100 (pmtt) REVERT: 9 158 LEU cc_start: 0.8850 (tp) cc_final: 0.8605 (tp) REVERT: 9 167 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.7861 (mtm) REVERT: 9 254 ASP cc_start: 0.7004 (m-30) cc_final: 0.5970 (p0) outliers start: 226 outliers final: 133 residues processed: 1121 average time/residue: 1.6058 time to fit residues: 2513.3733 Evaluate side-chains 1164 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1015 time to evaluate : 4.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 115 GLN Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain O residue 98 GLN Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain Q residue 5 ARG Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 79 ARG Chi-restraints excluded: chain W residue 26 SER Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 53 LYS Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 31 GLN Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 18 LYS Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 39 ASP Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 0 residue 53 VAL Chi-restraints excluded: chain 1 residue 12 SER Chi-restraints excluded: chain 1 residue 13 SER Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 23 THR Chi-restraints excluded: chain 1 residue 33 LEU Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 49 LYS Chi-restraints excluded: chain 2 residue 10 LEU Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 51 LYS Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 43 ASN Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain 6 residue 10 VAL Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 21 ASP Chi-restraints excluded: chain 6 residue 32 SER Chi-restraints excluded: chain 6 residue 34 THR Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 6 residue 56 VAL Chi-restraints excluded: chain 6 residue 64 LEU Chi-restraints excluded: chain 6 residue 65 LEU Chi-restraints excluded: chain 6 residue 70 GLU Chi-restraints excluded: chain 6 residue 89 VAL Chi-restraints excluded: chain 6 residue 100 LEU Chi-restraints excluded: chain 9 residue 29 ILE Chi-restraints excluded: chain 9 residue 35 ASP Chi-restraints excluded: chain 9 residue 45 VAL Chi-restraints excluded: chain 9 residue 52 ASN Chi-restraints excluded: chain 9 residue 57 ILE Chi-restraints excluded: chain 9 residue 58 ASP Chi-restraints excluded: chain 9 residue 76 ARG Chi-restraints excluded: chain 9 residue 135 ASN Chi-restraints excluded: chain 9 residue 140 GLN Chi-restraints excluded: chain 9 residue 167 MET Chi-restraints excluded: chain 9 residue 214 ILE Chi-restraints excluded: chain 9 residue 285 ILE Chi-restraints excluded: chain 9 residue 321 VAL Chi-restraints excluded: chain 9 residue 333 ILE Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 28 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 213 optimal weight: 8.9990 chunk 571 optimal weight: 10.0000 chunk 125 optimal weight: 0.9990 chunk 372 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 chunk 634 optimal weight: 0.7980 chunk 526 optimal weight: 10.0000 chunk 293 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 209 optimal weight: 4.9990 chunk 333 optimal weight: 10.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN D 130 GLN E 24 ASN E 90 GLN E 195 GLN F 51 ASN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN L 35 HIS L 99 ASN O 38 GLN Q 19 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN Q 55 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 HIS R 86 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 72 ASN X 15 ASN 1 25 ASN ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 135 ASN ** 9 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 101674 Z= 0.260 Angle : 0.562 9.850 152238 Z= 0.289 Chirality : 0.034 0.264 19479 Planarity : 0.004 0.065 8060 Dihedral : 22.966 178.015 51120 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.18 % Favored : 93.73 % Rotamer: Outliers : 7.05 % Allowed : 28.94 % Favored : 64.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.89 (0.13), residues: 3638 helix: 0.10 (0.17), residues: 922 sheet: -0.13 (0.19), residues: 734 loop : -1.09 (0.13), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 61 HIS 0.005 0.001 HIS V 80 PHE 0.025 0.002 PHE V 26 TYR 0.021 0.002 TYR F 127 ARG 0.017 0.001 ARG W 7 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1245 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1033 time to evaluate : 4.489 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: C 97 ASP cc_start: 0.8678 (p0) cc_final: 0.8355 (p0) REVERT: D 174 SER cc_start: 0.8567 (t) cc_final: 0.8247 (t) REVERT: E 115 GLN cc_start: 0.8219 (mt0) cc_final: 0.7929 (tm-30) REVERT: E 168 ASP cc_start: 0.8094 (t0) cc_final: 0.7744 (t0) REVERT: E 185 LYS cc_start: 0.8747 (mmtp) cc_final: 0.8156 (mmmm) REVERT: F 16 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7595 (tpt) REVERT: F 26 GLN cc_start: 0.8736 (tt0) cc_final: 0.8444 (tm-30) REVERT: F 37 MET cc_start: 0.7147 (mmm) cc_final: 0.6676 (mmm) REVERT: F 95 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7760 (mpm) REVERT: F 111 ARG cc_start: 0.8159 (ppp80) cc_final: 0.7930 (ppp80) REVERT: G 29 ASN cc_start: 0.9195 (t0) cc_final: 0.8839 (m110) REVERT: G 41 GLU cc_start: 0.6482 (mp0) cc_final: 0.6178 (mp0) REVERT: G 68 ARG cc_start: 0.8800 (tpt90) cc_final: 0.8585 (tpt170) REVERT: G 100 ASN cc_start: 0.8060 (t0) cc_final: 0.7620 (t0) REVERT: G 142 GLN cc_start: 0.8207 (tp40) cc_final: 0.7523 (tp40) REVERT: G 146 ASP cc_start: 0.8518 (m-30) cc_final: 0.8137 (m-30) REVERT: G 148 ARG cc_start: 0.8653 (ttt-90) cc_final: 0.8338 (tmt90) REVERT: G 151 ARG cc_start: 0.8829 (mmt-90) cc_final: 0.8614 (tpt170) REVERT: J 58 ASN cc_start: 0.9005 (m110) cc_final: 0.8569 (m110) REVERT: J 98 GLU cc_start: 0.8328 (mp0) cc_final: 0.8091 (mp0) REVERT: L 78 ARG cc_start: 0.8540 (mtt-85) cc_final: 0.8124 (mtt-85) REVERT: N 62 ASN cc_start: 0.9206 (m-40) cc_final: 0.8952 (m-40) REVERT: O 52 SER cc_start: 0.9078 (OUTLIER) cc_final: 0.8553 (m) REVERT: O 61 GLN cc_start: 0.8793 (mp10) cc_final: 0.8499 (mp10) REVERT: O 104 GLN cc_start: 0.8337 (mp10) cc_final: 0.7980 (mp10) REVERT: Q 108 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8826 (mm) REVERT: R 21 ARG cc_start: 0.8944 (mmm160) cc_final: 0.8315 (mtt180) REVERT: R 101 ILE cc_start: 0.8749 (pt) cc_final: 0.8433 (pp) REVERT: S 57 ASN cc_start: 0.9061 (OUTLIER) cc_final: 0.8842 (t0) REVERT: U 25 LYS cc_start: 0.8772 (mtmt) cc_final: 0.8556 (mtpp) REVERT: V 19 ARG cc_start: 0.8993 (mtm110) cc_final: 0.8707 (mtm110) REVERT: V 24 ASN cc_start: 0.8969 (t0) cc_final: 0.8712 (t0) REVERT: V 31 TYR cc_start: 0.8752 (p90) cc_final: 0.7887 (p90) REVERT: V 61 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8331 (tt) REVERT: V 79 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.7716 (mtp180) REVERT: V 87 GLN cc_start: 0.8967 (mm-40) cc_final: 0.8659 (mm110) REVERT: V 90 ASP cc_start: 0.8538 (m-30) cc_final: 0.8035 (t0) REVERT: W 74 LYS cc_start: 0.8836 (mtmp) cc_final: 0.8091 (mtpt) REVERT: X 61 LYS cc_start: 0.8958 (mmtt) cc_final: 0.8704 (mmpt) REVERT: Y 25 GLN cc_start: 0.9055 (tt0) cc_final: 0.8736 (tt0) REVERT: 0 12 ARG cc_start: 0.8783 (ttp-170) cc_final: 0.8535 (ttm170) REVERT: 1 25 ASN cc_start: 0.8223 (t0) cc_final: 0.7986 (t0) REVERT: 1 49 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8428 (mmtm) REVERT: K 54 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8463 (tptm) REVERT: K 58 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8418 (pp) REVERT: K 113 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.6653 (mpp) REVERT: P 12 MET cc_start: 0.8629 (mtp) cc_final: 0.8331 (mtm) REVERT: P 30 TRP cc_start: 0.8573 (m100) cc_final: 0.8028 (m100) REVERT: P 81 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7519 (m-30) REVERT: P 95 LYS cc_start: 0.9395 (mmtm) cc_final: 0.9152 (mmtm) REVERT: H 44 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.7921 (tp) REVERT: H 53 GLU cc_start: 0.7369 (pm20) cc_final: 0.7122 (pm20) REVERT: H 60 GLU cc_start: 0.7731 (pt0) cc_final: 0.7322 (pm20) REVERT: 9 44 ASP cc_start: 0.7809 (t70) cc_final: 0.7153 (t0) REVERT: 9 131 LYS cc_start: 0.8535 (pttp) cc_final: 0.8168 (pmtt) REVERT: 9 158 LEU cc_start: 0.8870 (tp) cc_final: 0.8629 (tp) REVERT: 9 167 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.7753 (mtm) REVERT: 9 254 ASP cc_start: 0.6852 (m-30) cc_final: 0.5787 (p0) outliers start: 212 outliers final: 135 residues processed: 1116 average time/residue: 1.5929 time to fit residues: 2488.9058 Evaluate side-chains 1158 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1009 time to evaluate : 4.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 152 GLU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 38 GLN Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain Q residue 5 ARG Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain S residue 57 ASN Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 73 LYS Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 79 ARG Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 26 SER Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 53 LYS Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 39 ASP Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 0 residue 53 VAL Chi-restraints excluded: chain 1 residue 12 SER Chi-restraints excluded: chain 1 residue 13 SER Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 23 THR Chi-restraints excluded: chain 1 residue 28 THR Chi-restraints excluded: chain 1 residue 33 LEU Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 49 LYS Chi-restraints excluded: chain 2 residue 10 LEU Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain K residue 54 LYS Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 43 ASN Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 21 ASP Chi-restraints excluded: chain 6 residue 32 SER Chi-restraints excluded: chain 6 residue 34 THR Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 6 residue 56 VAL Chi-restraints excluded: chain 6 residue 64 LEU Chi-restraints excluded: chain 6 residue 65 LEU Chi-restraints excluded: chain 6 residue 70 GLU Chi-restraints excluded: chain 6 residue 100 LEU Chi-restraints excluded: chain 9 residue 26 GLU Chi-restraints excluded: chain 9 residue 29 ILE Chi-restraints excluded: chain 9 residue 35 ASP Chi-restraints excluded: chain 9 residue 45 VAL Chi-restraints excluded: chain 9 residue 52 ASN Chi-restraints excluded: chain 9 residue 58 ASP Chi-restraints excluded: chain 9 residue 167 MET Chi-restraints excluded: chain 9 residue 205 ASN Chi-restraints excluded: chain 9 residue 285 ILE Chi-restraints excluded: chain 9 residue 321 VAL Chi-restraints excluded: chain 9 residue 333 ILE Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 50 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 611 optimal weight: 0.7980 chunk 71 optimal weight: 9.9990 chunk 361 optimal weight: 10.0000 chunk 463 optimal weight: 10.0000 chunk 359 optimal weight: 10.0000 chunk 534 optimal weight: 10.0000 chunk 354 optimal weight: 10.0000 chunk 632 optimal weight: 3.9990 chunk 395 optimal weight: 40.0000 chunk 385 optimal weight: 6.9990 chunk 291 optimal weight: 0.4980 overall best weight: 4.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN E 90 GLN E 195 GLN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN N 81 ASN Q 19 GLN Q 43 GLN Q 51 GLN Q 55 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 72 ASN X 15 ASN ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 ASN ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN H 28 ASN H 66 ASN 9 135 ASN ** 9 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 101674 Z= 0.314 Angle : 0.587 10.457 152238 Z= 0.301 Chirality : 0.035 0.278 19479 Planarity : 0.004 0.072 8060 Dihedral : 22.952 178.662 51120 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.40 % Favored : 93.51 % Rotamer: Outliers : 6.95 % Allowed : 29.77 % Favored : 63.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.93 (0.13), residues: 3638 helix: 0.08 (0.17), residues: 922 sheet: -0.16 (0.19), residues: 747 loop : -1.12 (0.13), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 61 HIS 0.006 0.001 HIS 6 88 PHE 0.030 0.002 PHE U 72 TYR 0.022 0.002 TYR Q 31 ARG 0.017 0.001 ARG W 7 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1240 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1031 time to evaluate : 4.349 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: C 97 ASP cc_start: 0.8650 (p0) cc_final: 0.8325 (p0) REVERT: D 174 SER cc_start: 0.8575 (t) cc_final: 0.8268 (t) REVERT: E 111 GLU cc_start: 0.8507 (tp30) cc_final: 0.7826 (tp30) REVERT: E 115 GLN cc_start: 0.8199 (mt0) cc_final: 0.7895 (tm-30) REVERT: E 168 ASP cc_start: 0.8101 (t0) cc_final: 0.7745 (t0) REVERT: E 185 LYS cc_start: 0.8707 (mmtp) cc_final: 0.8142 (mmmm) REVERT: F 2 LYS cc_start: 0.8833 (mmpt) cc_final: 0.8587 (mmpt) REVERT: F 16 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7619 (mmm) REVERT: F 26 GLN cc_start: 0.8688 (tt0) cc_final: 0.8414 (tm-30) REVERT: F 37 MET cc_start: 0.7117 (mmm) cc_final: 0.6626 (mmm) REVERT: F 95 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7759 (mpm) REVERT: F 111 ARG cc_start: 0.8162 (ppp80) cc_final: 0.7813 (ppp80) REVERT: F 112 ASP cc_start: 0.7676 (t70) cc_final: 0.7428 (t70) REVERT: F 168 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7684 (mt) REVERT: G 29 ASN cc_start: 0.9228 (t0) cc_final: 0.8889 (m110) REVERT: G 142 GLN cc_start: 0.8216 (tp40) cc_final: 0.7552 (tp40) REVERT: G 146 ASP cc_start: 0.8536 (m-30) cc_final: 0.8159 (m-30) REVERT: G 148 ARG cc_start: 0.8665 (ttt-90) cc_final: 0.8348 (tmt90) REVERT: G 151 ARG cc_start: 0.8832 (mmt-90) cc_final: 0.8607 (tpt170) REVERT: J 58 ASN cc_start: 0.9009 (m110) cc_final: 0.8589 (m110) REVERT: L 1 MET cc_start: 0.7633 (ppp) cc_final: 0.7403 (ppp) REVERT: L 78 ARG cc_start: 0.8513 (mtt-85) cc_final: 0.8076 (mtt-85) REVERT: N 62 ASN cc_start: 0.9222 (m-40) cc_final: 0.8974 (m-40) REVERT: O 52 SER cc_start: 0.9173 (OUTLIER) cc_final: 0.8641 (m) REVERT: O 61 GLN cc_start: 0.8810 (mp10) cc_final: 0.8414 (mp10) REVERT: O 104 GLN cc_start: 0.8386 (mp10) cc_final: 0.8024 (mp10) REVERT: R 101 ILE cc_start: 0.8733 (pt) cc_final: 0.8435 (pp) REVERT: S 57 ASN cc_start: 0.9063 (OUTLIER) cc_final: 0.8835 (t0) REVERT: S 66 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8274 (mp) REVERT: T 1 MET cc_start: 0.5936 (OUTLIER) cc_final: 0.5512 (ppp) REVERT: T 70 HIS cc_start: 0.8711 (t-90) cc_final: 0.8453 (t-90) REVERT: U 25 LYS cc_start: 0.8756 (mtmt) cc_final: 0.8529 (mtpp) REVERT: V 19 ARG cc_start: 0.8992 (mtm110) cc_final: 0.8606 (mtm110) REVERT: V 24 ASN cc_start: 0.8972 (t0) cc_final: 0.8711 (t0) REVERT: V 31 TYR cc_start: 0.8754 (p90) cc_final: 0.8032 (p90) REVERT: V 61 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8382 (tt) REVERT: V 87 GLN cc_start: 0.8968 (mm-40) cc_final: 0.8717 (mm110) REVERT: V 90 ASP cc_start: 0.8545 (m-30) cc_final: 0.8108 (t0) REVERT: W 74 LYS cc_start: 0.8819 (mtmp) cc_final: 0.8080 (mtpt) REVERT: X 61 LYS cc_start: 0.8874 (mmtt) cc_final: 0.8549 (mmpt) REVERT: Y 25 GLN cc_start: 0.9063 (tt0) cc_final: 0.8745 (tt0) REVERT: Z 6 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8254 (pp) REVERT: 0 12 ARG cc_start: 0.8769 (ttp-170) cc_final: 0.8530 (ttm170) REVERT: 1 49 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8400 (mmtm) REVERT: K 22 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8520 (pt) REVERT: K 54 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8479 (tptm) REVERT: K 58 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8431 (pp) REVERT: K 66 LYS cc_start: 0.8884 (tptt) cc_final: 0.8523 (tptt) REVERT: K 82 ASN cc_start: 0.9013 (OUTLIER) cc_final: 0.8511 (m-40) REVERT: K 113 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.6696 (mpp) REVERT: P 12 MET cc_start: 0.8655 (mtp) cc_final: 0.8362 (mtm) REVERT: P 30 TRP cc_start: 0.8580 (m100) cc_final: 0.8136 (m100) REVERT: P 81 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.7505 (m-30) REVERT: H 44 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.7791 (tp) REVERT: H 60 GLU cc_start: 0.7714 (pt0) cc_final: 0.7315 (pm20) REVERT: 6 17 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8774 (tm) REVERT: 6 18 LYS cc_start: 0.8580 (mtpm) cc_final: 0.8295 (mmmm) REVERT: 6 96 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7248 (mpp80) REVERT: 9 44 ASP cc_start: 0.7811 (t70) cc_final: 0.7142 (t0) REVERT: 9 57 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8602 (pp) REVERT: 9 131 LYS cc_start: 0.8560 (pttp) cc_final: 0.8180 (pmtt) REVERT: 9 158 LEU cc_start: 0.8887 (tp) cc_final: 0.8655 (tp) REVERT: 9 167 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.7828 (mtm) outliers start: 209 outliers final: 140 residues processed: 1117 average time/residue: 1.6040 time to fit residues: 2504.4391 Evaluate side-chains 1158 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 997 time to evaluate : 4.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 176 PHE Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain O residue 98 GLN Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain Q residue 5 ARG Chi-restraints excluded: chain Q residue 55 GLN Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain S residue 57 ASN Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain S residue 73 LYS Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 59 GLU Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 53 LYS Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 39 ASP Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 1 residue 12 SER Chi-restraints excluded: chain 1 residue 13 SER Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 23 THR Chi-restraints excluded: chain 1 residue 33 LEU Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 49 LYS Chi-restraints excluded: chain 2 residue 10 LEU Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 54 LYS Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 43 ASN Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain 6 residue 10 VAL Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 21 ASP Chi-restraints excluded: chain 6 residue 32 SER Chi-restraints excluded: chain 6 residue 34 THR Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 6 residue 56 VAL Chi-restraints excluded: chain 6 residue 64 LEU Chi-restraints excluded: chain 6 residue 65 LEU Chi-restraints excluded: chain 6 residue 70 GLU Chi-restraints excluded: chain 6 residue 96 ARG Chi-restraints excluded: chain 6 residue 100 LEU Chi-restraints excluded: chain 9 residue 15 ASP Chi-restraints excluded: chain 9 residue 29 ILE Chi-restraints excluded: chain 9 residue 35 ASP Chi-restraints excluded: chain 9 residue 45 VAL Chi-restraints excluded: chain 9 residue 52 ASN Chi-restraints excluded: chain 9 residue 57 ILE Chi-restraints excluded: chain 9 residue 58 ASP Chi-restraints excluded: chain 9 residue 167 MET Chi-restraints excluded: chain 9 residue 205 ASN Chi-restraints excluded: chain 9 residue 211 VAL Chi-restraints excluded: chain 9 residue 214 ILE Chi-restraints excluded: chain 9 residue 321 VAL Chi-restraints excluded: chain 9 residue 333 ILE Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 50 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 391 optimal weight: 10.0000 chunk 252 optimal weight: 3.9990 chunk 377 optimal weight: 10.0000 chunk 190 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 122 optimal weight: 0.5980 chunk 401 optimal weight: 7.9990 chunk 430 optimal weight: 10.0000 chunk 312 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 496 optimal weight: 10.0000 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN E 90 GLN E 195 GLN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 ASN ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN N 23 ASN O 38 GLN Q 19 GLN Q 51 GLN Q 55 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 72 ASN X 15 ASN 1 25 ASN ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 ASN K 88 ASN ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN H 66 ASN 9 135 ASN ** 9 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 101674 Z= 0.318 Angle : 0.597 12.661 152238 Z= 0.306 Chirality : 0.036 0.276 19479 Planarity : 0.005 0.101 8060 Dihedral : 22.956 178.611 51120 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.40 % Favored : 93.54 % Rotamer: Outliers : 7.25 % Allowed : 30.17 % Favored : 62.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.97 (0.13), residues: 3638 helix: 0.04 (0.17), residues: 916 sheet: -0.24 (0.19), residues: 736 loop : -1.11 (0.13), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 61 HIS 0.005 0.001 HIS E 165 PHE 0.045 0.002 PHE U 72 TYR 0.035 0.002 TYR F 127 ARG 0.018 0.001 ARG W 7 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1243 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 1025 time to evaluate : 4.207 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: C 97 ASP cc_start: 0.8647 (p0) cc_final: 0.8328 (p0) REVERT: D 174 SER cc_start: 0.8571 (t) cc_final: 0.8269 (t) REVERT: E 115 GLN cc_start: 0.8176 (mt0) cc_final: 0.7952 (tm-30) REVERT: E 168 ASP cc_start: 0.8098 (t0) cc_final: 0.7743 (t0) REVERT: F 2 LYS cc_start: 0.8829 (mmpt) cc_final: 0.8581 (mmpt) REVERT: F 16 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7610 (mmm) REVERT: F 37 MET cc_start: 0.7224 (mmm) cc_final: 0.6771 (mmm) REVERT: F 95 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7778 (mpm) REVERT: F 111 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7803 (ppp80) REVERT: F 112 ASP cc_start: 0.7677 (t70) cc_final: 0.7415 (t70) REVERT: F 168 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7675 (mt) REVERT: G 29 ASN cc_start: 0.9234 (t0) cc_final: 0.8884 (m110) REVERT: G 142 GLN cc_start: 0.8225 (tp40) cc_final: 0.7634 (tp40) REVERT: G 146 ASP cc_start: 0.8564 (m-30) cc_final: 0.8294 (m-30) REVERT: G 148 ARG cc_start: 0.8668 (ttt-90) cc_final: 0.8353 (tmt90) REVERT: G 151 ARG cc_start: 0.8835 (mmt-90) cc_final: 0.8612 (tpt170) REVERT: J 58 ASN cc_start: 0.9049 (m110) cc_final: 0.8611 (m110) REVERT: L 1 MET cc_start: 0.7730 (ppp) cc_final: 0.7492 (ppp) REVERT: L 78 ARG cc_start: 0.8521 (mtt-85) cc_final: 0.8068 (mtt-85) REVERT: N 62 ASN cc_start: 0.9226 (m-40) cc_final: 0.8982 (m-40) REVERT: N 99 LYS cc_start: 0.8909 (mttp) cc_final: 0.8682 (mttp) REVERT: O 52 SER cc_start: 0.9162 (OUTLIER) cc_final: 0.8620 (m) REVERT: O 61 GLN cc_start: 0.8833 (mp10) cc_final: 0.8547 (mp10) REVERT: O 104 GLN cc_start: 0.8376 (mp10) cc_final: 0.7987 (mp10) REVERT: R 86 GLN cc_start: 0.7971 (mt0) cc_final: 0.7662 (tt0) REVERT: R 101 ILE cc_start: 0.8740 (pt) cc_final: 0.8224 (mt) REVERT: S 57 ASN cc_start: 0.9044 (OUTLIER) cc_final: 0.8824 (t0) REVERT: S 66 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8280 (mp) REVERT: T 1 MET cc_start: 0.5950 (OUTLIER) cc_final: 0.5530 (ppp) REVERT: T 70 HIS cc_start: 0.8751 (t-90) cc_final: 0.8524 (t-90) REVERT: U 25 LYS cc_start: 0.8760 (mtmt) cc_final: 0.8550 (mtpp) REVERT: V 24 ASN cc_start: 0.8967 (t0) cc_final: 0.8724 (t0) REVERT: V 31 TYR cc_start: 0.8774 (p90) cc_final: 0.8078 (p90) REVERT: V 61 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8337 (tt) REVERT: V 87 GLN cc_start: 0.8990 (mm-40) cc_final: 0.8679 (mm110) REVERT: V 90 ASP cc_start: 0.8527 (m-30) cc_final: 0.8118 (t0) REVERT: W 74 LYS cc_start: 0.8819 (mtmp) cc_final: 0.8084 (mtpt) REVERT: X 61 LYS cc_start: 0.8890 (mmtt) cc_final: 0.8474 (mmtm) REVERT: Y 25 GLN cc_start: 0.9061 (tt0) cc_final: 0.8744 (tt0) REVERT: Z 6 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8252 (pp) REVERT: 0 3 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8505 (pt0) REVERT: 0 12 ARG cc_start: 0.8795 (ttp-170) cc_final: 0.8537 (ttm170) REVERT: 1 49 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8392 (mmtm) REVERT: K 20 MET cc_start: 0.8541 (ttp) cc_final: 0.8318 (ttm) REVERT: K 22 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8521 (pt) REVERT: K 54 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8474 (tptm) REVERT: K 58 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8438 (pp) REVERT: K 66 LYS cc_start: 0.8861 (tptt) cc_final: 0.8581 (tptt) REVERT: K 82 ASN cc_start: 0.8948 (OUTLIER) cc_final: 0.8561 (m-40) REVERT: P 12 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8355 (mtm) REVERT: P 30 TRP cc_start: 0.8553 (m100) cc_final: 0.8114 (m100) REVERT: P 81 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.7558 (m-30) REVERT: P 95 LYS cc_start: 0.9375 (mmtm) cc_final: 0.9142 (mmtm) REVERT: H 44 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.7701 (tp) REVERT: H 60 GLU cc_start: 0.7666 (pt0) cc_final: 0.7282 (pm20) REVERT: d 1 MET cc_start: 0.5087 (tpt) cc_final: 0.4716 (tpp) REVERT: 6 18 LYS cc_start: 0.8587 (mtpm) cc_final: 0.8296 (mmmm) REVERT: 6 96 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7205 (mpp80) REVERT: 9 44 ASP cc_start: 0.7790 (t70) cc_final: 0.7124 (t0) REVERT: 9 57 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8613 (pp) REVERT: 9 131 LYS cc_start: 0.8552 (pttp) cc_final: 0.8165 (pmtt) REVERT: 9 158 LEU cc_start: 0.8895 (tp) cc_final: 0.8695 (tp) REVERT: 9 167 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7795 (mtm) REVERT: 9 223 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7724 (pm20) outliers start: 218 outliers final: 150 residues processed: 1115 average time/residue: 1.6155 time to fit residues: 2519.1149 Evaluate side-chains 1184 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 1011 time to evaluate : 4.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 111 ARG Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 176 PHE Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 38 GLN Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain O residue 98 GLN Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain Q residue 5 ARG Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain S residue 57 ASN Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain S residue 73 LYS Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 59 GLU Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 53 LYS Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 39 ASP Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 3 GLN Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 1 residue 12 SER Chi-restraints excluded: chain 1 residue 13 SER Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 23 THR Chi-restraints excluded: chain 1 residue 28 THR Chi-restraints excluded: chain 1 residue 33 LEU Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 49 LYS Chi-restraints excluded: chain 2 residue 10 LEU Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 54 LYS Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 43 ASN Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain 6 residue 10 VAL Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 21 ASP Chi-restraints excluded: chain 6 residue 32 SER Chi-restraints excluded: chain 6 residue 34 THR Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 6 residue 56 VAL Chi-restraints excluded: chain 6 residue 64 LEU Chi-restraints excluded: chain 6 residue 65 LEU Chi-restraints excluded: chain 6 residue 70 GLU Chi-restraints excluded: chain 6 residue 96 ARG Chi-restraints excluded: chain 6 residue 100 LEU Chi-restraints excluded: chain 9 residue 10 LEU Chi-restraints excluded: chain 9 residue 15 ASP Chi-restraints excluded: chain 9 residue 29 ILE Chi-restraints excluded: chain 9 residue 35 ASP Chi-restraints excluded: chain 9 residue 45 VAL Chi-restraints excluded: chain 9 residue 52 ASN Chi-restraints excluded: chain 9 residue 57 ILE Chi-restraints excluded: chain 9 residue 58 ASP Chi-restraints excluded: chain 9 residue 167 MET Chi-restraints excluded: chain 9 residue 205 ASN Chi-restraints excluded: chain 9 residue 211 VAL Chi-restraints excluded: chain 9 residue 214 ILE Chi-restraints excluded: chain 9 residue 223 GLU Chi-restraints excluded: chain 9 residue 321 VAL Chi-restraints excluded: chain 9 residue 333 ILE Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 32 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 575 optimal weight: 10.0000 chunk 605 optimal weight: 10.0000 chunk 552 optimal weight: 10.0000 chunk 589 optimal weight: 10.0000 chunk 354 optimal weight: 10.0000 chunk 256 optimal weight: 2.9990 chunk 462 optimal weight: 10.0000 chunk 180 optimal weight: 6.9990 chunk 532 optimal weight: 8.9990 chunk 557 optimal weight: 8.9990 chunk 587 optimal weight: 10.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN E 90 GLN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN N 81 ASN O 38 GLN Q 19 GLN Q 43 GLN Q 51 GLN Q 55 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 72 ASN X 15 ASN 2 26 ASN K 82 ASN K 88 ASN ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN H 66 ASN 9 99 GLN 9 135 ASN ** 9 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.102 101674 Z= 0.512 Angle : 0.712 12.197 152238 Z= 0.361 Chirality : 0.042 0.336 19479 Planarity : 0.005 0.091 8060 Dihedral : 22.992 178.099 51120 Min Nonbonded Distance : 1.677 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.53 % Favored : 92.39 % Rotamer: Outliers : 6.65 % Allowed : 31.20 % Favored : 62.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.21 (0.13), residues: 3638 helix: -0.19 (0.17), residues: 915 sheet: -0.38 (0.18), residues: 773 loop : -1.26 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP G 61 HIS 0.009 0.002 HIS E 165 PHE 0.042 0.002 PHE M 68 TYR 0.034 0.003 TYR 9 189 ARG 0.020 0.001 ARG W 7 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1231 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 1031 time to evaluate : 4.168 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: C 97 ASP cc_start: 0.8650 (p0) cc_final: 0.8346 (p0) REVERT: C 162 GLN cc_start: 0.7813 (tt0) cc_final: 0.7459 (mt0) REVERT: D 174 SER cc_start: 0.8714 (t) cc_final: 0.8424 (t) REVERT: E 111 GLU cc_start: 0.8602 (tp30) cc_final: 0.7886 (tp30) REVERT: E 115 GLN cc_start: 0.8227 (mt0) cc_final: 0.7871 (tm-30) REVERT: E 168 ASP cc_start: 0.8099 (t0) cc_final: 0.7723 (t0) REVERT: E 184 ASP cc_start: 0.8876 (m-30) cc_final: 0.8652 (m-30) REVERT: E 185 LYS cc_start: 0.8741 (mmtp) cc_final: 0.8161 (mmmm) REVERT: F 2 LYS cc_start: 0.8803 (mmpt) cc_final: 0.8541 (mmpt) REVERT: F 16 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7831 (tpt) REVERT: F 37 MET cc_start: 0.7033 (mmm) cc_final: 0.6505 (mmm) REVERT: F 111 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7897 (ppp80) REVERT: F 134 GLN cc_start: 0.6317 (pm20) cc_final: 0.5991 (pm20) REVERT: G 29 ASN cc_start: 0.9233 (t0) cc_final: 0.8771 (m110) REVERT: G 136 ASP cc_start: 0.8603 (t0) cc_final: 0.8011 (p0) REVERT: G 142 GLN cc_start: 0.8251 (tp40) cc_final: 0.7571 (tp40) REVERT: G 146 ASP cc_start: 0.8597 (m-30) cc_final: 0.8246 (m-30) REVERT: G 148 ARG cc_start: 0.8691 (ttt-90) cc_final: 0.8396 (tmt90) REVERT: J 58 ASN cc_start: 0.9070 (m110) cc_final: 0.8630 (m110) REVERT: J 118 MET cc_start: 0.8406 (mtt) cc_final: 0.8025 (mtt) REVERT: L 1 MET cc_start: 0.7772 (ppp) cc_final: 0.7495 (ppp) REVERT: N 99 LYS cc_start: 0.8956 (mttp) cc_final: 0.8731 (mttp) REVERT: O 52 SER cc_start: 0.9199 (OUTLIER) cc_final: 0.8633 (m) REVERT: O 104 GLN cc_start: 0.8379 (mp10) cc_final: 0.7928 (mp10) REVERT: Q 108 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8780 (mm) REVERT: R 101 ILE cc_start: 0.8885 (pt) cc_final: 0.8394 (mt) REVERT: S 66 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8283 (mp) REVERT: U 25 LYS cc_start: 0.8699 (mtmt) cc_final: 0.8476 (mtpp) REVERT: V 7 GLU cc_start: 0.8393 (pm20) cc_final: 0.8186 (pm20) REVERT: V 24 ASN cc_start: 0.8966 (t0) cc_final: 0.8701 (t0) REVERT: V 31 TYR cc_start: 0.8823 (p90) cc_final: 0.8069 (p90) REVERT: V 61 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8483 (tt) REVERT: V 87 GLN cc_start: 0.9010 (mm-40) cc_final: 0.8773 (mm110) REVERT: V 90 ASP cc_start: 0.8651 (m-30) cc_final: 0.8156 (t0) REVERT: W 74 LYS cc_start: 0.8842 (mtmp) cc_final: 0.8078 (mtpt) REVERT: Y 5 GLU cc_start: 0.9146 (mp0) cc_final: 0.8717 (mp0) REVERT: Y 25 GLN cc_start: 0.9098 (tt0) cc_final: 0.8789 (tt0) REVERT: Z 6 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8333 (pp) REVERT: 0 3 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8568 (pt0) REVERT: 0 12 ARG cc_start: 0.8891 (ttp-170) cc_final: 0.8616 (ttm170) REVERT: 1 43 ARG cc_start: 0.8260 (mtp85) cc_final: 0.8006 (mtp85) REVERT: K 51 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7540 (ttmm) REVERT: K 54 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8465 (tptm) REVERT: K 58 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8507 (pp) REVERT: K 66 LYS cc_start: 0.8965 (tptt) cc_final: 0.8496 (tptt) REVERT: K 82 ASN cc_start: 0.9207 (OUTLIER) cc_final: 0.8423 (m-40) REVERT: K 113 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.6755 (mpp) REVERT: P 12 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8462 (mtm) REVERT: P 30 TRP cc_start: 0.8628 (m100) cc_final: 0.8272 (m100) REVERT: P 81 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.7600 (m-30) REVERT: P 95 LYS cc_start: 0.9416 (mmtm) cc_final: 0.9181 (mmtm) REVERT: H 44 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7745 (tp) REVERT: H 60 GLU cc_start: 0.7650 (pt0) cc_final: 0.7308 (pm20) REVERT: 6 17 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8769 (tm) REVERT: 6 18 LYS cc_start: 0.8636 (mtpm) cc_final: 0.8362 (mmmm) REVERT: 6 96 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7217 (mpp80) REVERT: 9 44 ASP cc_start: 0.7771 (t70) cc_final: 0.7101 (t0) REVERT: 9 57 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8756 (pp) REVERT: 9 223 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7520 (pm20) REVERT: 9 254 ASP cc_start: 0.7131 (m-30) cc_final: 0.5916 (p0) outliers start: 200 outliers final: 143 residues processed: 1115 average time/residue: 1.6326 time to fit residues: 2537.0693 Evaluate side-chains 1155 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 992 time to evaluate : 4.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 111 ARG Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain O residue 98 GLN Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain O residue 117 PHE Chi-restraints excluded: chain Q residue 5 ARG Chi-restraints excluded: chain Q residue 55 GLN Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 73 LYS Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 53 LYS Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 31 GLN Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 18 LYS Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 3 GLN Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 1 residue 4 ILE Chi-restraints excluded: chain 1 residue 12 SER Chi-restraints excluded: chain 1 residue 13 SER Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 23 THR Chi-restraints excluded: chain 1 residue 33 LEU Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 2 residue 10 LEU Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 51 LYS Chi-restraints excluded: chain K residue 54 LYS Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 43 ASN Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 21 ASP Chi-restraints excluded: chain 6 residue 32 SER Chi-restraints excluded: chain 6 residue 34 THR Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 6 residue 56 VAL Chi-restraints excluded: chain 6 residue 64 LEU Chi-restraints excluded: chain 6 residue 65 LEU Chi-restraints excluded: chain 6 residue 70 GLU Chi-restraints excluded: chain 6 residue 96 ARG Chi-restraints excluded: chain 6 residue 100 LEU Chi-restraints excluded: chain 9 residue 29 ILE Chi-restraints excluded: chain 9 residue 35 ASP Chi-restraints excluded: chain 9 residue 45 VAL Chi-restraints excluded: chain 9 residue 57 ILE Chi-restraints excluded: chain 9 residue 58 ASP Chi-restraints excluded: chain 9 residue 211 VAL Chi-restraints excluded: chain 9 residue 214 ILE Chi-restraints excluded: chain 9 residue 223 GLU Chi-restraints excluded: chain 9 residue 321 VAL Chi-restraints excluded: chain 9 residue 333 ILE Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 32 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 386 optimal weight: 0.6980 chunk 623 optimal weight: 4.9990 chunk 380 optimal weight: 5.9990 chunk 295 optimal weight: 20.0000 chunk 433 optimal weight: 4.9990 chunk 653 optimal weight: 3.9990 chunk 601 optimal weight: 20.0000 chunk 520 optimal weight: 50.0000 chunk 54 optimal weight: 5.9990 chunk 401 optimal weight: 3.9990 chunk 319 optimal weight: 6.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 20 ASN C 116 GLN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN E 24 ASN E 90 GLN E 195 GLN F 26 GLN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN O 38 GLN Q 19 GLN Q 51 GLN Q 55 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 72 ASN X 15 ASN K 82 ASN K 88 ASN ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN H 66 ASN 9 135 ASN ** 9 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 101674 Z= 0.274 Angle : 0.607 13.828 152238 Z= 0.311 Chirality : 0.035 0.299 19479 Planarity : 0.005 0.094 8060 Dihedral : 23.033 178.031 51120 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.76 % Favored : 93.16 % Rotamer: Outliers : 5.62 % Allowed : 33.17 % Favored : 61.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.13 (0.13), residues: 3638 helix: -0.15 (0.17), residues: 925 sheet: -0.39 (0.18), residues: 736 loop : -1.16 (0.13), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 61 HIS 0.007 0.001 HIS E 165 PHE 0.033 0.002 PHE M 68 TYR 0.036 0.002 TYR F 127 ARG 0.021 0.001 ARG W 7 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1206 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1037 time to evaluate : 4.299 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: C 97 ASP cc_start: 0.8682 (p0) cc_final: 0.8335 (p0) REVERT: D 174 SER cc_start: 0.8550 (t) cc_final: 0.8252 (t) REVERT: E 115 GLN cc_start: 0.8159 (mt0) cc_final: 0.7790 (tm-30) REVERT: E 136 GLN cc_start: 0.8742 (tp40) cc_final: 0.8372 (tp40) REVERT: E 168 ASP cc_start: 0.8120 (t0) cc_final: 0.7764 (t0) REVERT: F 16 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7677 (tpt) REVERT: F 26 GLN cc_start: 0.8634 (tt0) cc_final: 0.8264 (tm-30) REVERT: F 37 MET cc_start: 0.7252 (mmm) cc_final: 0.6758 (mmm) REVERT: F 95 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7743 (mpm) REVERT: F 111 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7822 (ppp80) REVERT: G 29 ASN cc_start: 0.9243 (t0) cc_final: 0.8878 (m110) REVERT: G 106 LEU cc_start: 0.9049 (mp) cc_final: 0.8827 (mm) REVERT: G 136 ASP cc_start: 0.8586 (t0) cc_final: 0.8026 (p0) REVERT: G 142 GLN cc_start: 0.8181 (tp40) cc_final: 0.7638 (tp40) REVERT: G 146 ASP cc_start: 0.8436 (m-30) cc_final: 0.8168 (m-30) REVERT: G 148 ARG cc_start: 0.8643 (ttt-90) cc_final: 0.8312 (tmt90) REVERT: J 58 ASN cc_start: 0.9057 (m110) cc_final: 0.8621 (m110) REVERT: J 118 MET cc_start: 0.8373 (mtt) cc_final: 0.8047 (mtt) REVERT: L 1 MET cc_start: 0.7722 (ppp) cc_final: 0.7466 (ppp) REVERT: L 78 ARG cc_start: 0.8500 (mtt-85) cc_final: 0.8116 (mtt-85) REVERT: N 99 LYS cc_start: 0.8869 (mttp) cc_final: 0.8637 (mttp) REVERT: O 52 SER cc_start: 0.9110 (OUTLIER) cc_final: 0.8572 (m) REVERT: O 61 GLN cc_start: 0.8784 (mp10) cc_final: 0.8478 (mp10) REVERT: O 104 GLN cc_start: 0.8394 (mp10) cc_final: 0.7994 (mp10) REVERT: R 6 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8228 (tp-100) REVERT: R 101 ILE cc_start: 0.8739 (pt) cc_final: 0.8295 (mt) REVERT: V 24 ASN cc_start: 0.8944 (t0) cc_final: 0.8713 (t0) REVERT: V 31 TYR cc_start: 0.8752 (p90) cc_final: 0.8043 (p90) REVERT: V 61 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8364 (tt) REVERT: V 87 GLN cc_start: 0.8978 (mm-40) cc_final: 0.7839 (mp10) REVERT: V 90 ASP cc_start: 0.8558 (m-30) cc_final: 0.8139 (t0) REVERT: W 74 LYS cc_start: 0.8832 (mtmp) cc_final: 0.8096 (mtpt) REVERT: Y 25 GLN cc_start: 0.9028 (tt0) cc_final: 0.8739 (tt0) REVERT: Z 6 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8296 (pp) REVERT: 0 3 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8505 (pt0) REVERT: 0 12 ARG cc_start: 0.8762 (ttp-170) cc_final: 0.8532 (ttm170) REVERT: 0 36 LYS cc_start: 0.7955 (mmmt) cc_final: 0.7464 (tmtm) REVERT: K 54 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8478 (tptm) REVERT: K 58 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8429 (pp) REVERT: K 66 LYS cc_start: 0.8915 (tptt) cc_final: 0.8659 (tptt) REVERT: K 113 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.6659 (mpp) REVERT: P 12 MET cc_start: 0.8636 (mtp) cc_final: 0.8341 (mtm) REVERT: P 30 TRP cc_start: 0.8554 (m100) cc_final: 0.8069 (m100) REVERT: P 81 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.7517 (m-30) REVERT: P 95 LYS cc_start: 0.9411 (mmtm) cc_final: 0.9143 (mmtm) REVERT: H 44 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.7754 (tp) REVERT: 6 18 LYS cc_start: 0.8602 (mtpm) cc_final: 0.8326 (mmmm) REVERT: 6 96 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7246 (mpp80) REVERT: 9 44 ASP cc_start: 0.7785 (t70) cc_final: 0.7124 (t0) REVERT: 9 57 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8609 (pp) REVERT: 9 167 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.7793 (mtm) REVERT: 9 254 ASP cc_start: 0.6948 (m-30) cc_final: 0.5766 (p0) outliers start: 169 outliers final: 128 residues processed: 1103 average time/residue: 1.5929 time to fit residues: 2468.7394 Evaluate side-chains 1150 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1007 time to evaluate : 4.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 111 ARG Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 38 GLN Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain O residue 117 PHE Chi-restraints excluded: chain Q residue 5 ARG Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 73 LYS Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 53 LYS Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 18 LYS Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 3 GLN Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 1 residue 12 SER Chi-restraints excluded: chain 1 residue 13 SER Chi-restraints excluded: chain 1 residue 23 THR Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 2 residue 10 LEU Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 54 LYS Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 43 ASN Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 21 ASP Chi-restraints excluded: chain 6 residue 32 SER Chi-restraints excluded: chain 6 residue 34 THR Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 6 residue 56 VAL Chi-restraints excluded: chain 6 residue 64 LEU Chi-restraints excluded: chain 6 residue 65 LEU Chi-restraints excluded: chain 6 residue 70 GLU Chi-restraints excluded: chain 6 residue 96 ARG Chi-restraints excluded: chain 6 residue 100 LEU Chi-restraints excluded: chain 9 residue 29 ILE Chi-restraints excluded: chain 9 residue 45 VAL Chi-restraints excluded: chain 9 residue 57 ILE Chi-restraints excluded: chain 9 residue 58 ASP Chi-restraints excluded: chain 9 residue 167 MET Chi-restraints excluded: chain 9 residue 211 VAL Chi-restraints excluded: chain 9 residue 214 ILE Chi-restraints excluded: chain 9 residue 256 VAL Chi-restraints excluded: chain 9 residue 333 ILE Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 32 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 413 optimal weight: 20.0000 chunk 554 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 chunk 479 optimal weight: 20.0000 chunk 76 optimal weight: 7.9990 chunk 144 optimal weight: 9.9990 chunk 521 optimal weight: 50.0000 chunk 218 optimal weight: 2.9990 chunk 535 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 GLN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN E 90 GLN E 195 GLN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN N 81 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN Q 19 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN Q 55 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 HIS ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 72 ASN X 15 ASN K 88 ASN ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN 9 135 ASN ** 9 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.113310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.078426 restraints weight = 177956.724| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.39 r_work: 0.2942 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 101674 Z= 0.439 Angle : 0.676 13.598 152238 Z= 0.343 Chirality : 0.040 0.307 19479 Planarity : 0.005 0.068 8060 Dihedral : 22.996 179.936 51120 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.75 % Favored : 92.17 % Rotamer: Outliers : 5.59 % Allowed : 33.13 % Favored : 61.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.25 (0.13), residues: 3638 helix: -0.29 (0.17), residues: 928 sheet: -0.47 (0.18), residues: 758 loop : -1.21 (0.13), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP G 61 HIS 0.007 0.001 HIS E 165 PHE 0.030 0.002 PHE U 72 TYR 0.040 0.002 TYR 9 189 ARG 0.016 0.001 ARG Q 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 35716.23 seconds wall clock time: 620 minutes 43.59 seconds (37243.59 seconds total)