Starting phenix.real_space_refine on Mon Mar 25 19:46:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxu_23575/03_2024/7lxu_23575_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxu_23575/03_2024/7lxu_23575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxu_23575/03_2024/7lxu_23575.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxu_23575/03_2024/7lxu_23575.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxu_23575/03_2024/7lxu_23575_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxu_23575/03_2024/7lxu_23575_updated.pdb" } resolution = 3.1 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= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 276 5.16 5 B 2 2.79 5 C 32338 2.51 5 N 8458 2.21 5 O 9704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 45": "OE1" <-> "OE2" Residue "A ASP 80": "OD1" <-> "OD2" Residue "A GLU 103": "OE1" <-> "OE2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "A GLU 118": "OE1" <-> "OE2" Residue "A GLU 151": "OE1" <-> "OE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A ASP 161": "OD1" <-> "OD2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A ARG 187": "NH1" <-> "NH2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 228": "OE1" <-> "OE2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A GLU 248": "OE1" <-> "OE2" Residue "A TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 82": "OD1" <-> "OD2" Residue "B TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 166": "OD1" <-> "OD2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B ASP 215": "OD1" <-> "OD2" Residue "B GLU 233": "OE1" <-> "OE2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 4": "OD1" <-> "OD2" Residue "D TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 178": "OE1" <-> "OE2" Residue "D GLU 181": "OE1" <-> "OE2" Residue "D PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 198": "OE1" <-> "OE2" Residue "D GLU 211": "OE1" <-> "OE2" Residue "D PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 218": "OE1" <-> "OE2" Residue "E TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 18": "OE1" <-> "OE2" Residue "E ASP 122": "OD1" <-> "OD2" Residue "E PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 209": "OE1" <-> "OE2" Residue "E GLU 218": "OE1" <-> "OE2" Residue "E TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 236": "OD1" <-> "OD2" Residue "E TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 9": "OD1" <-> "OD2" Residue "F GLU 61": "OE1" <-> "OE2" Residue "F PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 114": "OD1" <-> "OD2" Residue "F TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "F PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 154": "OE1" <-> "OE2" Residue "F ARG 163": "NH1" <-> "NH2" Residue "F TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 180": "OE1" <-> "OE2" Residue "G TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G ASP 44": "OD1" <-> "OD2" Residue "G GLU 97": "OE1" <-> "OE2" Residue "G GLU 145": "OE1" <-> "OE2" Residue "G GLU 155": "OE1" <-> "OE2" Residue "G TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 194": "OE1" <-> "OE2" Residue "G TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 224": "OE1" <-> "OE2" Residue "G GLU 228": "OE1" <-> "OE2" Residue "H ARG 32": "NH1" <-> "NH2" Residue "H TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 69": "OE1" <-> "OE2" Residue "H ARG 75": "NH1" <-> "NH2" Residue "H PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 78": "OE1" <-> "OE2" Residue "H GLU 119": "OE1" <-> "OE2" Residue "H GLU 130": "OE1" <-> "OE2" Residue "H TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 157": "OD1" <-> "OD2" Residue "H ASP 178": "OD1" <-> "OD2" Residue "H ASP 195": "OD1" <-> "OD2" Residue "H TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 221": "OD1" <-> "OD2" Residue "H PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 239": "OE1" <-> "OE2" Residue "I GLU 64": "OE1" <-> "OE2" Residue "I GLU 86": "OE1" <-> "OE2" Residue "I TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 139": "OE1" <-> "OE2" Residue "I ASP 144": "OD1" <-> "OD2" Residue "I GLU 150": "OE1" <-> "OE2" Residue "I TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 61": "OD1" <-> "OD2" Residue "J GLU 67": "OE1" <-> "OE2" Residue "J GLU 77": "OE1" <-> "OE2" Residue "J GLU 87": "OE1" <-> "OE2" Residue "J ASP 138": "OD1" <-> "OD2" Residue "J GLU 145": "OE1" <-> "OE2" Residue "J ASP 148": "OD1" <-> "OD2" Residue "J GLU 178": "OE1" <-> "OE2" Residue "J ASP 191": "OD1" <-> "OD2" Residue "J GLU 199": "OE1" <-> "OE2" Residue "J GLU 206": "OE1" <-> "OE2" Residue "K TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 108": "OD1" <-> "OD2" Residue "K TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 155": "OE1" <-> "OE2" Residue "K GLU 189": "OE1" <-> "OE2" Residue "L GLU 32": "OE1" <-> "OE2" Residue "L TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 67": "OE1" <-> "OE2" Residue "L PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 115": "OD1" <-> "OD2" Residue "L GLU 122": "OE1" <-> "OE2" Residue "L TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 150": "OD1" <-> "OD2" Residue "L GLU 154": "OE1" <-> "OE2" Residue "L GLU 204": "OE1" <-> "OE2" Residue "L TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 106": "OE1" <-> "OE2" Residue "M TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 180": "NH1" <-> "NH2" Residue "M GLU 182": "OE1" <-> "OE2" Residue "M ASP 218": "OD1" <-> "OD2" Residue "M ASP 236": "OD1" <-> "OD2" Residue "N GLU 57": "OE1" <-> "OE2" Residue "N TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 78": "OE1" <-> "OE2" Residue "N ARG 97": "NH1" <-> "NH2" Residue "N PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 201": "OE1" <-> "OE2" Residue "N ASP 217": "OD1" <-> "OD2" Residue "N PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 45": "OE1" <-> "OE2" Residue "O ASP 80": "OD1" <-> "OD2" Residue "O GLU 103": "OE1" <-> "OE2" Residue "O GLU 106": "OE1" <-> "OE2" Residue "O GLU 118": "OE1" <-> "OE2" Residue "O GLU 151": "OE1" <-> "OE2" Residue "O GLU 156": "OE1" <-> "OE2" Residue "O ASP 161": "OD1" <-> "OD2" Residue "O GLU 186": "OE1" <-> "OE2" Residue "O ARG 187": "NH1" <-> "NH2" Residue "O GLU 214": "OE1" <-> "OE2" Residue "O PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 228": "OE1" <-> "OE2" Residue "O GLU 246": "OE1" <-> "OE2" Residue "O GLU 248": "OE1" <-> "OE2" Residue "O TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 82": "OD1" <-> "OD2" Residue "P TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 166": "OD1" <-> "OD2" Residue "P ARG 177": "NH1" <-> "NH2" Residue "P GLU 185": "OE1" <-> "OE2" Residue "P GLU 205": "OE1" <-> "OE2" Residue "P ASP 215": "OD1" <-> "OD2" Residue "P GLU 233": "OE1" <-> "OE2" Residue "Q ARG 3": "NH1" <-> "NH2" Residue "Q GLU 22": "OE1" <-> "OE2" Residue "Q TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 4": "OD1" <-> "OD2" Residue "R TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 178": "OE1" <-> "OE2" Residue "R GLU 181": "OE1" <-> "OE2" Residue "R PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 198": "OE1" <-> "OE2" Residue "R GLU 211": "OE1" <-> "OE2" Residue "R PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 218": "OE1" <-> "OE2" Residue "S TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 18": "OE1" <-> "OE2" Residue "S ASP 122": "OD1" <-> "OD2" Residue "S PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 209": "OE1" <-> "OE2" Residue "S GLU 218": "OE1" <-> "OE2" Residue "S TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 236": "OD1" <-> "OD2" Residue "S TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 9": "OD1" <-> "OD2" Residue "T GLU 61": "OE1" <-> "OE2" Residue "T PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 114": "OD1" <-> "OD2" Residue "T TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 140": "OE1" <-> "OE2" Residue "T PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 154": "OE1" <-> "OE2" Residue "T ARG 163": "NH1" <-> "NH2" Residue "T TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 180": "OE1" <-> "OE2" Residue "U TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 41": "OE1" <-> "OE2" Residue "U ASP 44": "OD1" <-> "OD2" Residue "U GLU 97": "OE1" <-> "OE2" Residue "U GLU 145": "OE1" <-> "OE2" Residue "U GLU 155": "OE1" <-> "OE2" Residue "U TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 194": "OE1" <-> "OE2" Residue "U TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 224": "OE1" <-> "OE2" Residue "U GLU 228": "OE1" <-> "OE2" Residue "V ARG 32": "NH1" <-> "NH2" Residue "V TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 57": "OE1" <-> "OE2" Residue "V TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 69": "OE1" <-> "OE2" Residue "V ARG 75": "NH1" <-> "NH2" Residue "V PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 78": "OE1" <-> "OE2" Residue "V GLU 119": "OE1" <-> "OE2" Residue "V GLU 130": "OE1" <-> "OE2" Residue "V TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 157": "OD1" <-> "OD2" Residue "V ASP 178": "OD1" <-> "OD2" Residue "V ASP 195": "OD1" <-> "OD2" Residue "V TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 221": "OD1" <-> "OD2" Residue "V PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 239": "OE1" <-> "OE2" Residue "W GLU 64": "OE1" <-> "OE2" Residue "W GLU 86": "OE1" <-> "OE2" Residue "W TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 139": "OE1" <-> "OE2" Residue "W ASP 144": "OD1" <-> "OD2" Residue "W GLU 150": "OE1" <-> "OE2" Residue "W TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 61": "OD1" <-> "OD2" Residue "X GLU 67": "OE1" <-> "OE2" Residue "X GLU 77": "OE1" <-> "OE2" Residue "X GLU 87": "OE1" <-> "OE2" Residue "X ASP 138": "OD1" <-> "OD2" Residue "X GLU 145": "OE1" <-> "OE2" Residue "X ASP 148": "OD1" <-> "OD2" Residue "X GLU 178": "OE1" <-> "OE2" Residue "X ASP 191": "OD1" <-> "OD2" Residue "X GLU 199": "OE1" <-> "OE2" Residue "X GLU 206": "OE1" <-> "OE2" Residue "Y TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 108": "OD1" <-> "OD2" Residue "Y TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 155": "OE1" <-> "OE2" Residue "Y GLU 189": "OE1" <-> "OE2" Residue "Z GLU 32": "OE1" <-> "OE2" Residue "Z TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 67": "OE1" <-> "OE2" Residue "Z PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 115": "OD1" <-> "OD2" Residue "Z GLU 122": "OE1" <-> "OE2" Residue "Z TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 150": "OD1" <-> "OD2" Residue "Z GLU 154": "OE1" <-> "OE2" Residue "Z GLU 204": "OE1" <-> "OE2" Residue "Z TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 106": "OE1" <-> "OE2" Residue "a TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 180": "NH1" <-> "NH2" Residue "a GLU 182": "OE1" <-> "OE2" Residue "a ASP 218": "OD1" <-> "OD2" Residue "a ASP 236": "OD1" <-> "OD2" Residue "b GLU 57": "OE1" <-> "OE2" Residue "b TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 78": "OE1" <-> "OE2" Residue "b ARG 97": "NH1" <-> "NH2" Residue "b PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 201": "OE1" <-> "OE2" Residue "b ASP 217": "OD1" <-> "OD2" Residue "b PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 50778 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 1986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1986 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain: "B" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1826 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 7, 'TRANS': 221} Chain: "C" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1934 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 5, 'TRANS': 236} Chain: "D" Number of atoms: 1845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1845 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 7, 'TRANS': 225} Chain: "E" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1830 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 1 Chain: "F" Number of atoms: 1866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1866 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 5, 'TRANS': 229} Chain: "G" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1979 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 5, 'TRANS': 236} Chain: "H" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1846 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 1, 'TRANS': 227} Chain breaks: 1 Chain: "I" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1676 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 11, 'TRANS': 207} Chain: "J" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1698 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 210} Chain: "K" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1614 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 193} Chain: "L" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1647 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 1, 'TRANS': 207} Chain: "M" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1696 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "N" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1920 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 5, 'TRANS': 228} Chain breaks: 1 Chain: "O" Number of atoms: 1986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1986 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain: "P" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1826 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 7, 'TRANS': 221} Chain: "Q" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1934 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 5, 'TRANS': 236} Chain: "R" Number of atoms: 1845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1845 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 7, 'TRANS': 225} Chain: "S" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1830 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 1 Chain: "T" Number of atoms: 1866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1866 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 5, 'TRANS': 229} Chain: "U" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1979 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 5, 'TRANS': 236} Chain: "V" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1846 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 1, 'TRANS': 227} Chain breaks: 1 Chain: "W" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1676 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 11, 'TRANS': 207} Chain: "X" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1698 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 210} Chain: "Y" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1614 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 193} Chain: "Z" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1647 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 1, 'TRANS': 207} Chain: "a" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1696 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "b" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1920 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 5, 'TRANS': 228} Chain breaks: 1 Chain: "L" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'YHD': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'YHD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 25.04, per 1000 atoms: 0.49 Number of scatterers: 50778 At special positions: 0 Unit cell: (174.23, 142.79, 134.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 276 16.00 O 9704 8.00 N 8458 7.00 C 32338 6.00 B 2 5.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 19.30 Conformation dependent library (CDL) restraints added in 8.9 seconds 12592 Ramachandran restraints generated. 6296 Oldfield, 0 Emsley, 6296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11948 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 166 helices and 58 sheets defined 33.3% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.88 Creating SS restraints... Processing helix chain 'A' and resid 23 through 35 removed outlier: 3.884A pdb=" N THR A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 111 removed outlier: 3.554A pdb=" N TYR A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 133 removed outlier: 3.930A pdb=" N CYS A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 194 removed outlier: 3.603A pdb=" N ILE A 182 " --> pdb=" O GLU A 178 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N SER A 183 " --> pdb=" O GLN A 179 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS A 191 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 207 No H-bonds generated for 'chain 'A' and resid 204 through 207' Processing helix chain 'A' and resid 209 through 219 Processing helix chain 'A' and resid 246 through 253 removed outlier: 4.056A pdb=" N ASN A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 31 removed outlier: 3.556A pdb=" N SER B 31 " --> pdb=" O ASN B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 61 No H-bonds generated for 'chain 'B' and resid 59 through 61' Processing helix chain 'B' and resid 80 through 100 removed outlier: 3.537A pdb=" N VAL B 85 " --> pdb=" O GLY B 81 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU B 93 " --> pdb=" O ARG B 89 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 123 removed outlier: 3.583A pdb=" N PHE B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR B 122 " --> pdb=" O VAL B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 177 removed outlier: 3.724A pdb=" N LYS B 176 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG B 177 " --> pdb=" O PHE B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 198 Processing helix chain 'B' and resid 224 through 230 removed outlier: 3.923A pdb=" N LYS B 228 " --> pdb=" O ASN B 225 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ASP B 229 " --> pdb=" O GLU B 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 5 No H-bonds generated for 'chain 'C' and resid 3 through 5' Processing helix chain 'C' and resid 19 through 28 Processing helix chain 'C' and resid 80 through 101 removed outlier: 3.806A pdb=" N ASN C 84 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 123 removed outlier: 3.787A pdb=" N VAL C 112 " --> pdb=" O SER C 108 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR C 121 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 178 removed outlier: 3.857A pdb=" N VAL C 174 " --> pdb=" O THR C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 199 Processing helix chain 'C' and resid 228 through 241 removed outlier: 3.765A pdb=" N ILE C 232 " --> pdb=" O THR C 228 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU C 234 " --> pdb=" O LYS C 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 27 removed outlier: 3.657A pdb=" N ALA D 22 " --> pdb=" O GLN D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 97 removed outlier: 3.675A pdb=" N ARG D 81 " --> pdb=" O ASN D 77 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 118 Processing helix chain 'D' and resid 165 through 172 Processing helix chain 'D' and resid 182 through 195 removed outlier: 3.691A pdb=" N ILE D 186 " --> pdb=" O GLN D 182 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 233 removed outlier: 4.027A pdb=" N GLN D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 30 removed outlier: 4.373A pdb=" N GLY E 29 " --> pdb=" O GLU E 25 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA E 30 " --> pdb=" O TYR E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 102 removed outlier: 4.202A pdb=" N THR E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 119 Processing helix chain 'E' and resid 122 through 124 No H-bonds generated for 'chain 'E' and resid 122 through 124' Processing helix chain 'E' and resid 176 through 186 removed outlier: 3.759A pdb=" N GLU E 185 " --> pdb=" O LEU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 207 Processing helix chain 'E' and resid 214 through 216 No H-bonds generated for 'chain 'E' and resid 214 through 216' Processing helix chain 'E' and resid 238 through 243 removed outlier: 4.388A pdb=" N VAL E 243 " --> pdb=" O ARG E 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 27 removed outlier: 3.869A pdb=" N ALA F 25 " --> pdb=" O GLN F 21 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'F' and resid 78 through 98 removed outlier: 3.572A pdb=" N SER F 94 " --> pdb=" O ASN F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 113 Processing helix chain 'F' and resid 115 through 121 removed outlier: 3.874A pdb=" N ASN F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR F 120 " --> pdb=" O TYR F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 172 removed outlier: 3.680A pdb=" N TYR F 170 " --> pdb=" O ALA F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 178 No H-bonds generated for 'chain 'F' and resid 176 through 178' Processing helix chain 'F' and resid 183 through 197 removed outlier: 3.769A pdb=" N HIS F 189 " --> pdb=" O GLU F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 236 removed outlier: 4.219A pdb=" N GLU F 230 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR F 231 " --> pdb=" O GLN F 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 33 Processing helix chain 'G' and resid 53 through 55 No H-bonds generated for 'chain 'G' and resid 53 through 55' Processing helix chain 'G' and resid 84 through 105 removed outlier: 3.597A pdb=" N ARG G 88 " --> pdb=" O ASP G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 125 removed outlier: 3.839A pdb=" N ASN G 116 " --> pdb=" O HIS G 112 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR G 125 " --> pdb=" O TYR G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 181 removed outlier: 3.585A pdb=" N THR G 177 " --> pdb=" O GLU G 173 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU G 178 " --> pdb=" O MET G 174 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LYS G 181 " --> pdb=" O THR G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 186 No H-bonds generated for 'chain 'G' and resid 184 through 186' Processing helix chain 'G' and resid 192 through 203 Processing helix chain 'G' and resid 223 through 225 No H-bonds generated for 'chain 'G' and resid 223 through 225' Processing helix chain 'G' and resid 234 through 240 removed outlier: 3.533A pdb=" N THR G 238 " --> pdb=" O GLU G 234 " (cutoff:3.500A) Proline residue: G 239 - end of helix No H-bonds generated for 'chain 'G' and resid 234 through 240' Processing helix chain 'H' and resid 49 through 69 Processing helix chain 'H' and resid 132 through 143 removed outlier: 3.621A pdb=" N LYS H 138 " --> pdb=" O HIS H 134 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE H 139 " --> pdb=" O ILE H 135 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE H 140 " --> pdb=" O THR H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 196 removed outlier: 3.884A pdb=" N ILE H 187 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N SER H 191 " --> pdb=" O TYR H 188 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR H 192 " --> pdb=" O ILE H 189 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU H 193 " --> pdb=" O GLN H 190 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN H 194 " --> pdb=" O SER H 191 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS H 196 " --> pdb=" O LEU H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 219 Processing helix chain 'I' and resid 49 through 69 Processing helix chain 'I' and resid 76 through 89 Processing helix chain 'I' and resid 131 through 141 removed outlier: 3.826A pdb=" N VAL I 137 " --> pdb=" O ASN I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 148 through 165 removed outlier: 3.634A pdb=" N GLY I 162 " --> pdb=" O ALA I 158 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 78 Processing helix chain 'J' and resid 86 through 100 removed outlier: 3.878A pdb=" N ASN J 100 " --> pdb=" O ILE J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 166 removed outlier: 3.585A pdb=" N GLY J 161 " --> pdb=" O GLU J 157 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET J 162 " --> pdb=" O GLN J 158 " (cutoff:3.500A) Processing helix chain 'J' and resid 173 through 188 removed outlier: 3.636A pdb=" N GLU J 178 " --> pdb=" O ASN J 174 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA J 187 " --> pdb=" O CYS J 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 71 removed outlier: 3.534A pdb=" N LEU K 55 " --> pdb=" O ILE K 51 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN K 56 " --> pdb=" O GLY K 52 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE K 60 " --> pdb=" O GLN K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 91 Processing helix chain 'K' and resid 134 through 145 removed outlier: 5.003A pdb=" N SER K 140 " --> pdb=" O TYR K 137 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ALA K 141 " --> pdb=" O LEU K 138 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE K 142 " --> pdb=" O VAL K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 169 removed outlier: 3.611A pdb=" N GLU K 166 " --> pdb=" O LEU K 162 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS K 169 " --> pdb=" O GLU K 165 " (cutoff:3.500A) Processing helix chain 'L' and resid 50 through 69 removed outlier: 4.374A pdb=" N TRP L 55 " --> pdb=" O ASP L 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 90 removed outlier: 4.358A pdb=" N TYR L 90 " --> pdb=" O ILE L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 141 removed outlier: 3.664A pdb=" N SER L 141 " --> pdb=" O SER L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 166 removed outlier: 3.680A pdb=" N GLU L 154 " --> pdb=" O ASP L 150 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 198 No H-bonds generated for 'chain 'L' and resid 195 through 198' Processing helix chain 'M' and resid 86 through 107 Processing helix chain 'M' and resid 113 through 130 removed outlier: 3.937A pdb=" N ARG M 127 " --> pdb=" O ILE M 123 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG M 128 " --> pdb=" O LEU M 124 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N PHE M 129 " --> pdb=" O TYR M 125 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N PHE M 130 " --> pdb=" O SER M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 181 removed outlier: 4.095A pdb=" N GLN M 171 " --> pdb=" O SER M 168 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE M 173 " --> pdb=" O SER M 170 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LEU M 174 " --> pdb=" O GLN M 171 " (cutoff:3.500A) Proline residue: M 175 - end of helix Processing helix chain 'M' and resid 195 through 212 Processing helix chain 'N' and resid 58 through 77 Processing helix chain 'N' and resid 82 through 84 No H-bonds generated for 'chain 'N' and resid 82 through 84' Processing helix chain 'N' and resid 88 through 104 Processing helix chain 'N' and resid 185 through 191 Processing helix chain 'N' and resid 199 through 216 removed outlier: 3.569A pdb=" N ILE N 212 " --> pdb=" O GLU N 208 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 35 removed outlier: 3.884A pdb=" N THR O 35 " --> pdb=" O ALA O 31 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 111 removed outlier: 3.553A pdb=" N TYR O 98 " --> pdb=" O LEU O 94 " (cutoff:3.500A) Processing helix chain 'O' and resid 117 through 133 removed outlier: 3.931A pdb=" N CYS O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL O 130 " --> pdb=" O ASP O 126 " (cutoff:3.500A) Processing helix chain 'O' and resid 178 through 194 removed outlier: 3.603A pdb=" N ILE O 182 " --> pdb=" O GLU O 178 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N SER O 183 " --> pdb=" O GLN O 179 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS O 191 " --> pdb=" O ARG O 187 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG O 192 " --> pdb=" O LEU O 188 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS O 193 " --> pdb=" O LEU O 189 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 207 No H-bonds generated for 'chain 'O' and resid 204 through 207' Processing helix chain 'O' and resid 209 through 219 Processing helix chain 'O' and resid 246 through 253 removed outlier: 4.056A pdb=" N ASN O 251 " --> pdb=" O LYS O 247 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 31 removed outlier: 3.555A pdb=" N SER P 31 " --> pdb=" O ASN P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 59 through 61 No H-bonds generated for 'chain 'P' and resid 59 through 61' Processing helix chain 'P' and resid 80 through 100 removed outlier: 3.537A pdb=" N VAL P 85 " --> pdb=" O GLY P 81 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU P 93 " --> pdb=" O ARG P 89 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER P 98 " --> pdb=" O ALA P 94 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN P 100 " --> pdb=" O ARG P 96 " (cutoff:3.500A) Processing helix chain 'P' and resid 107 through 123 removed outlier: 3.584A pdb=" N PHE P 121 " --> pdb=" O ILE P 117 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR P 122 " --> pdb=" O VAL P 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 177 removed outlier: 3.723A pdb=" N LYS P 176 " --> pdb=" O SER P 172 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG P 177 " --> pdb=" O PHE P 173 " (cutoff:3.500A) Processing helix chain 'P' and resid 184 through 198 Processing helix chain 'P' and resid 224 through 230 removed outlier: 3.924A pdb=" N LYS P 228 " --> pdb=" O ASN P 225 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ASP P 229 " --> pdb=" O GLU P 226 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 5 No H-bonds generated for 'chain 'Q' and resid 3 through 5' Processing helix chain 'Q' and resid 19 through 28 Processing helix chain 'Q' and resid 80 through 101 removed outlier: 3.806A pdb=" N ASN Q 84 " --> pdb=" O ASN Q 80 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE Q 85 " --> pdb=" O ALA Q 81 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU Q 98 " --> pdb=" O ALA Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 123 removed outlier: 3.786A pdb=" N VAL Q 112 " --> pdb=" O SER Q 108 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR Q 121 " --> pdb=" O ILE Q 117 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR Q 122 " --> pdb=" O LYS Q 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 168 through 178 removed outlier: 3.857A pdb=" N VAL Q 174 " --> pdb=" O THR Q 170 " (cutoff:3.500A) Processing helix chain 'Q' and resid 185 through 199 Processing helix chain 'Q' and resid 228 through 241 removed outlier: 3.766A pdb=" N ILE Q 232 " --> pdb=" O THR Q 228 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU Q 233 " --> pdb=" O GLU Q 229 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU Q 234 " --> pdb=" O LYS Q 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 27 removed outlier: 3.655A pdb=" N ALA R 22 " --> pdb=" O GLN R 18 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 97 removed outlier: 3.675A pdb=" N ARG R 81 " --> pdb=" O ASN R 77 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL R 82 " --> pdb=" O ALA R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 118 Processing helix chain 'R' and resid 165 through 172 Processing helix chain 'R' and resid 182 through 195 removed outlier: 3.691A pdb=" N ILE R 186 " --> pdb=" O GLN R 182 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE R 194 " --> pdb=" O LEU R 190 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU R 195 " --> pdb=" O LYS R 191 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 233 removed outlier: 4.027A pdb=" N GLN R 231 " --> pdb=" O GLU R 227 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU R 232 " --> pdb=" O LEU R 228 " (cutoff:3.500A) Processing helix chain 'S' and resid 22 through 30 removed outlier: 4.372A pdb=" N GLY S 29 " --> pdb=" O GLU S 25 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA S 30 " --> pdb=" O TYR S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 102 removed outlier: 4.202A pdb=" N THR S 87 " --> pdb=" O ALA S 83 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU S 88 " --> pdb=" O ASP S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 109 through 119 Processing helix chain 'S' and resid 122 through 124 No H-bonds generated for 'chain 'S' and resid 122 through 124' Processing helix chain 'S' and resid 176 through 186 removed outlier: 3.759A pdb=" N GLU S 185 " --> pdb=" O LEU S 181 " (cutoff:3.500A) Processing helix chain 'S' and resid 193 through 207 Processing helix chain 'S' and resid 214 through 216 No H-bonds generated for 'chain 'S' and resid 214 through 216' Processing helix chain 'S' and resid 238 through 243 removed outlier: 4.387A pdb=" N VAL S 243 " --> pdb=" O ARG S 239 " (cutoff:3.500A) Processing helix chain 'T' and resid 20 through 27 removed outlier: 3.870A pdb=" N ALA T 25 " --> pdb=" O GLN T 21 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU T 27 " --> pdb=" O GLU T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 29 through 31 No H-bonds generated for 'chain 'T' and resid 29 through 31' Processing helix chain 'T' and resid 78 through 98 removed outlier: 3.572A pdb=" N SER T 94 " --> pdb=" O ASN T 90 " (cutoff:3.500A) Processing helix chain 'T' and resid 105 through 113 Processing helix chain 'T' and resid 115 through 121 removed outlier: 3.874A pdb=" N ASN T 119 " --> pdb=" O LYS T 115 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR T 120 " --> pdb=" O TYR T 116 " (cutoff:3.500A) Processing helix chain 'T' and resid 164 through 172 removed outlier: 3.680A pdb=" N TYR T 170 " --> pdb=" O ALA T 166 " (cutoff:3.500A) Processing helix chain 'T' and resid 176 through 178 No H-bonds generated for 'chain 'T' and resid 176 through 178' Processing helix chain 'T' and resid 183 through 197 removed outlier: 3.769A pdb=" N HIS T 189 " --> pdb=" O GLU T 185 " (cutoff:3.500A) Processing helix chain 'T' and resid 225 through 236 removed outlier: 4.219A pdb=" N GLU T 230 " --> pdb=" O LEU T 226 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR T 231 " --> pdb=" O GLN T 227 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 33 Processing helix chain 'U' and resid 53 through 55 No H-bonds generated for 'chain 'U' and resid 53 through 55' Processing helix chain 'U' and resid 84 through 105 removed outlier: 3.598A pdb=" N ARG U 88 " --> pdb=" O ASP U 84 " (cutoff:3.500A) Processing helix chain 'U' and resid 111 through 125 removed outlier: 3.839A pdb=" N ASN U 116 " --> pdb=" O HIS U 112 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR U 125 " --> pdb=" O TYR U 121 " (cutoff:3.500A) Processing helix chain 'U' and resid 172 through 181 removed outlier: 3.585A pdb=" N THR U 177 " --> pdb=" O GLU U 173 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU U 178 " --> pdb=" O MET U 174 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS U 181 " --> pdb=" O THR U 177 " (cutoff:3.500A) Processing helix chain 'U' and resid 184 through 186 No H-bonds generated for 'chain 'U' and resid 184 through 186' Processing helix chain 'U' and resid 192 through 203 Processing helix chain 'U' and resid 223 through 225 No H-bonds generated for 'chain 'U' and resid 223 through 225' Processing helix chain 'U' and resid 234 through 240 removed outlier: 3.533A pdb=" N THR U 238 " --> pdb=" O GLU U 234 " (cutoff:3.500A) Proline residue: U 239 - end of helix No H-bonds generated for 'chain 'U' and resid 234 through 240' Processing helix chain 'V' and resid 49 through 69 Processing helix chain 'V' and resid 132 through 143 removed outlier: 3.620A pdb=" N LYS V 138 " --> pdb=" O HIS V 134 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE V 139 " --> pdb=" O ILE V 135 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE V 140 " --> pdb=" O THR V 136 " (cutoff:3.500A) Processing helix chain 'V' and resid 184 through 196 removed outlier: 3.884A pdb=" N ILE V 187 " --> pdb=" O SER V 184 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N SER V 191 " --> pdb=" O TYR V 188 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR V 192 " --> pdb=" O ILE V 189 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU V 193 " --> pdb=" O GLN V 190 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN V 194 " --> pdb=" O SER V 191 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS V 196 " --> pdb=" O LEU V 193 " (cutoff:3.500A) Processing helix chain 'V' and resid 203 through 219 Processing helix chain 'W' and resid 49 through 69 Processing helix chain 'W' and resid 76 through 89 Processing helix chain 'W' and resid 131 through 141 removed outlier: 3.825A pdb=" N VAL W 137 " --> pdb=" O ASN W 133 " (cutoff:3.500A) Processing helix chain 'W' and resid 148 through 165 removed outlier: 3.634A pdb=" N GLY W 162 " --> pdb=" O ALA W 158 " (cutoff:3.500A) Processing helix chain 'X' and resid 59 through 78 Processing helix chain 'X' and resid 86 through 100 removed outlier: 3.878A pdb=" N ASN X 100 " --> pdb=" O ILE X 96 " (cutoff:3.500A) Processing helix chain 'X' and resid 156 through 166 removed outlier: 3.585A pdb=" N GLY X 161 " --> pdb=" O GLU X 157 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET X 162 " --> pdb=" O GLN X 158 " (cutoff:3.500A) Processing helix chain 'X' and resid 173 through 188 removed outlier: 3.636A pdb=" N GLU X 178 " --> pdb=" O ASN X 174 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA X 187 " --> pdb=" O CYS X 183 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 71 removed outlier: 3.534A pdb=" N LEU Y 55 " --> pdb=" O ILE Y 51 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN Y 56 " --> pdb=" O GLY Y 52 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE Y 60 " --> pdb=" O GLN Y 56 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 91 Processing helix chain 'Y' and resid 134 through 145 removed outlier: 5.004A pdb=" N SER Y 140 " --> pdb=" O TYR Y 137 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ALA Y 141 " --> pdb=" O LEU Y 138 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE Y 142 " --> pdb=" O VAL Y 139 " (cutoff:3.500A) Processing helix chain 'Y' and resid 153 through 169 removed outlier: 3.611A pdb=" N GLU Y 166 " --> pdb=" O LEU Y 162 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS Y 169 " --> pdb=" O GLU Y 165 " (cutoff:3.500A) Processing helix chain 'Z' and resid 50 through 69 removed outlier: 4.373A pdb=" N TRP Z 55 " --> pdb=" O ASP Z 51 " (cutoff:3.500A) Processing helix chain 'Z' and resid 76 through 90 removed outlier: 4.360A pdb=" N TYR Z 90 " --> pdb=" O ILE Z 86 " (cutoff:3.500A) Processing helix chain 'Z' and resid 132 through 141 removed outlier: 3.664A pdb=" N SER Z 141 " --> pdb=" O SER Z 137 " (cutoff:3.500A) Processing helix chain 'Z' and resid 149 through 166 removed outlier: 3.680A pdb=" N GLU Z 154 " --> pdb=" O ASP Z 150 " (cutoff:3.500A) Processing helix chain 'Z' and resid 195 through 198 No H-bonds generated for 'chain 'Z' and resid 195 through 198' Processing helix chain 'a' and resid 86 through 107 Processing helix chain 'a' and resid 113 through 130 removed outlier: 3.937A pdb=" N ARG a 127 " --> pdb=" O ILE a 123 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG a 128 " --> pdb=" O LEU a 124 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N PHE a 129 " --> pdb=" O TYR a 125 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE a 130 " --> pdb=" O SER a 126 " (cutoff:3.500A) Processing helix chain 'a' and resid 168 through 181 removed outlier: 4.095A pdb=" N GLN a 171 " --> pdb=" O SER a 168 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE a 173 " --> pdb=" O SER a 170 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LEU a 174 " --> pdb=" O GLN a 171 " (cutoff:3.500A) Proline residue: a 175 - end of helix Processing helix chain 'a' and resid 195 through 212 Processing helix chain 'b' and resid 58 through 77 Processing helix chain 'b' and resid 82 through 84 No H-bonds generated for 'chain 'b' and resid 82 through 84' Processing helix chain 'b' and resid 88 through 104 Processing helix chain 'b' and resid 185 through 191 Processing helix chain 'b' and resid 199 through 216 removed outlier: 3.570A pdb=" N ILE b 212 " --> pdb=" O GLU b 208 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 171 through 174 removed outlier: 3.768A pdb=" N GLU A 230 " --> pdb=" O SER A 52 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 75 through 77 Processing sheet with id= C, first strand: chain 'B' and resid 160 through 162 removed outlier: 3.983A pdb=" N GLY B 43 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 72 through 78 removed outlier: 3.590A pdb=" N CYS B 137 " --> pdb=" O GLY B 73 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 34 through 38 Processing sheet with id= F, first strand: chain 'C' and resid 144 through 149 removed outlier: 6.633A pdb=" N CYS C 74 " --> pdb=" O LYS C 67 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LYS C 67 " --> pdb=" O CYS C 74 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N VAL C 76 " --> pdb=" O ILE C 65 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ILE C 65 " --> pdb=" O VAL C 76 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 158 through 161 Processing sheet with id= H, first strand: chain 'D' and resid 132 through 136 removed outlier: 4.014A pdb=" N ILE D 144 " --> pdb=" O TRP D 156 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 169 through 172 removed outlier: 3.795A pdb=" N VAL E 42 " --> pdb=" O GLY E 45 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS E 223 " --> pdb=" O THR E 228 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR E 228 " --> pdb=" O LYS E 223 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 68 through 71 removed outlier: 6.411A pdb=" N ILE E 74 " --> pdb=" O ILE E 70 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 35 through 39 Processing sheet with id= L, first strand: chain 'F' and resid 63 through 65 Processing sheet with id= M, first strand: chain 'F' and resid 135 through 137 removed outlier: 4.473A pdb=" N ILE F 143 " --> pdb=" O TYR F 155 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER F 151 " --> pdb=" O ARG F 147 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 47 through 51 removed outlier: 3.795A pdb=" N THR G 36 " --> pdb=" O ILE G 51 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 69 through 72 removed outlier: 3.565A pdb=" N SER G 137 " --> pdb=" O SER G 81 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 179 through 183 removed outlier: 5.783A pdb=" N THR H 2 " --> pdb=" O ASP H 17 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY H 11 " --> pdb=" O TYR H 8 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 34 through 36 removed outlier: 3.578A pdb=" N ILE H 174 " --> pdb=" O ALA H 166 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 19 through 21 removed outlier: 3.640A pdb=" N ASN H 28 " --> pdb=" O THR H 20 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 124 through 128 Processing sheet with id= T, first strand: chain 'I' and resid 109 through 112 removed outlier: 6.514A pdb=" N CYS I 43 " --> pdb=" O TYR I 36 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N TYR I 36 " --> pdb=" O CYS I 43 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N GLY I 45 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU I 34 " --> pdb=" O GLY I 45 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 150 through 153 removed outlier: 5.535A pdb=" N CYS J 11 " --> pdb=" O ASP J 26 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS J 25 " --> pdb=" O GLU J 199 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 144 through 146 removed outlier: 3.513A pdb=" N THR J 146 " --> pdb=" O LEU J 134 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU J 134 " --> pdb=" O THR J 146 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL J 53 " --> pdb=" O LYS J 46 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N LYS J 46 " --> pdb=" O VAL J 53 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'K' and resid 129 through 132 removed outlier: 3.784A pdb=" N GLN K 191 " --> pdb=" O LEU K 180 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'K' and resid 36 through 39 removed outlier: 3.704A pdb=" N LYS K 43 " --> pdb=" O ILE K 39 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'L' and resid 99 through 105 Processing sheet with id= Z, first strand: chain 'M' and resid 163 through 167 removed outlier: 6.049A pdb=" N THR M 39 " --> pdb=" O ASP M 54 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'M' and resid 158 through 160 removed outlier: 3.608A pdb=" N CYS M 159 " --> pdb=" O ASN M 151 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN M 151 " --> pdb=" O CYS M 159 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASN M 136 " --> pdb=" O TYR M 152 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS M 78 " --> pdb=" O THR M 75 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILE M 80 " --> pdb=" O LYS M 73 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LYS M 73 " --> pdb=" O ILE M 80 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N SER M 82 " --> pdb=" O ILE M 71 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ILE M 71 " --> pdb=" O SER M 82 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'N' and resid 175 through 177 Processing sheet with id= AC, first strand: chain 'N' and resid 170 through 172 removed outlier: 3.632A pdb=" N ASN N 47 " --> pdb=" O THR N 50 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N MET N 52 " --> pdb=" O LYS N 45 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N LYS N 45 " --> pdb=" O MET N 52 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'O' and resid 171 through 174 removed outlier: 3.768A pdb=" N GLU O 230 " --> pdb=" O SER O 52 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'O' and resid 75 through 77 Processing sheet with id= AF, first strand: chain 'P' and resid 160 through 162 removed outlier: 3.983A pdb=" N GLY P 43 " --> pdb=" O ALA P 40 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'P' and resid 72 through 78 removed outlier: 3.590A pdb=" N CYS P 137 " --> pdb=" O GLY P 73 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'Q' and resid 34 through 38 Processing sheet with id= AI, first strand: chain 'Q' and resid 144 through 149 removed outlier: 6.633A pdb=" N CYS Q 74 " --> pdb=" O LYS Q 67 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LYS Q 67 " --> pdb=" O CYS Q 74 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL Q 76 " --> pdb=" O ILE Q 65 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ILE Q 65 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'R' and resid 158 through 161 Processing sheet with id= AK, first strand: chain 'R' and resid 132 through 136 removed outlier: 4.014A pdb=" N ILE R 144 " --> pdb=" O TRP R 156 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'S' and resid 169 through 172 removed outlier: 3.796A pdb=" N VAL S 42 " --> pdb=" O GLY S 45 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS S 223 " --> pdb=" O THR S 228 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR S 228 " --> pdb=" O LYS S 223 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'S' and resid 68 through 71 removed outlier: 6.411A pdb=" N ILE S 74 " --> pdb=" O ILE S 70 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'T' and resid 35 through 39 Processing sheet with id= AO, first strand: chain 'T' and resid 63 through 65 Processing sheet with id= AP, first strand: chain 'T' and resid 135 through 137 removed outlier: 4.473A pdb=" N ILE T 143 " --> pdb=" O TYR T 155 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER T 151 " --> pdb=" O ARG T 147 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'U' and resid 47 through 51 removed outlier: 3.794A pdb=" N THR U 36 " --> pdb=" O ILE U 51 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'U' and resid 69 through 72 removed outlier: 3.564A pdb=" N SER U 137 " --> pdb=" O SER U 81 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'V' and resid 179 through 183 removed outlier: 5.783A pdb=" N THR V 2 " --> pdb=" O ASP V 17 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY V 11 " --> pdb=" O TYR V 8 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'V' and resid 34 through 36 removed outlier: 3.577A pdb=" N ILE V 174 " --> pdb=" O ALA V 166 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'V' and resid 19 through 21 removed outlier: 3.640A pdb=" N ASN V 28 " --> pdb=" O THR V 20 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'W' and resid 124 through 128 Processing sheet with id= AW, first strand: chain 'W' and resid 109 through 112 removed outlier: 6.514A pdb=" N CYS W 43 " --> pdb=" O TYR W 36 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N TYR W 36 " --> pdb=" O CYS W 43 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N GLY W 45 " --> pdb=" O LEU W 34 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU W 34 " --> pdb=" O GLY W 45 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'X' and resid 150 through 153 removed outlier: 5.536A pdb=" N CYS X 11 " --> pdb=" O ASP X 26 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS X 25 " --> pdb=" O GLU X 199 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'X' and resid 144 through 146 removed outlier: 3.513A pdb=" N THR X 146 " --> pdb=" O LEU X 134 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU X 134 " --> pdb=" O THR X 146 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL X 53 " --> pdb=" O LYS X 46 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LYS X 46 " --> pdb=" O VAL X 53 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'Y' and resid 129 through 132 removed outlier: 3.784A pdb=" N GLN Y 191 " --> pdb=" O LEU Y 180 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'Y' and resid 36 through 39 removed outlier: 3.704A pdb=" N LYS Y 43 " --> pdb=" O ILE Y 39 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'Z' and resid 99 through 105 Processing sheet with id= BC, first strand: chain 'a' and resid 163 through 167 removed outlier: 6.050A pdb=" N THR a 39 " --> pdb=" O ASP a 54 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'a' and resid 158 through 160 removed outlier: 3.608A pdb=" N CYS a 159 " --> pdb=" O ASN a 151 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN a 151 " --> pdb=" O CYS a 159 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASN a 136 " --> pdb=" O TYR a 152 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS a 78 " --> pdb=" O THR a 75 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILE a 80 " --> pdb=" O LYS a 73 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LYS a 73 " --> pdb=" O ILE a 80 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N SER a 82 " --> pdb=" O ILE a 71 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ILE a 71 " --> pdb=" O SER a 82 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'b' and resid 175 through 177 Processing sheet with id= BF, first strand: chain 'b' and resid 170 through 172 removed outlier: 3.633A pdb=" N ASN b 47 " --> pdb=" O THR b 50 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N MET b 52 " --> pdb=" O LYS b 45 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LYS b 45 " --> pdb=" O MET b 52 " (cutoff:3.500A) 1978 hydrogen bonds defined for protein. 5610 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 17.69 Time building geometry restraints manager: 20.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 16391 1.34 - 1.45: 8154 1.45 - 1.57: 26769 1.57 - 1.69: 6 1.69 - 1.81: 392 Bond restraints: 51712 Sorted by residual: bond pdb=" C13 YHD L 301 " pdb=" C14 YHD L 301 " ideal model delta sigma weight residual 1.477 1.623 -0.146 2.00e-02 2.50e+03 5.30e+01 bond pdb=" C13 YHD Z 301 " pdb=" C14 YHD Z 301 " ideal model delta sigma weight residual 1.477 1.623 -0.146 2.00e-02 2.50e+03 5.29e+01 bond pdb=" C09 YHD L 301 " pdb=" C10 YHD L 301 " ideal model delta sigma weight residual 1.505 1.562 -0.057 2.00e-02 2.50e+03 8.07e+00 bond pdb=" C09 YHD Z 301 " pdb=" C10 YHD Z 301 " ideal model delta sigma weight residual 1.505 1.561 -0.056 2.00e-02 2.50e+03 7.96e+00 bond pdb=" C04 YHD L 301 " pdb=" N23 YHD L 301 " ideal model delta sigma weight residual 1.464 1.518 -0.054 2.00e-02 2.50e+03 7.18e+00 ... (remaining 51707 not shown) Histogram of bond angle deviations from ideal: 97.94 - 105.18: 505 105.18 - 112.42: 26312 112.42 - 119.66: 17041 119.66 - 126.90: 25640 126.90 - 134.14: 338 Bond angle restraints: 69836 Sorted by residual: angle pdb=" CA ASN H 126 " pdb=" C ASN H 126 " pdb=" N PRO H 127 " ideal model delta sigma weight residual 118.16 121.71 -3.55 7.00e-01 2.04e+00 2.57e+01 angle pdb=" CA ASN V 126 " pdb=" C ASN V 126 " pdb=" N PRO V 127 " ideal model delta sigma weight residual 118.16 121.71 -3.55 7.00e-01 2.04e+00 2.57e+01 angle pdb=" N GLY Z 190 " pdb=" CA GLY Z 190 " pdb=" C GLY Z 190 " ideal model delta sigma weight residual 112.13 118.69 -6.56 1.34e+00 5.57e-01 2.40e+01 angle pdb=" N GLY L 190 " pdb=" CA GLY L 190 " pdb=" C GLY L 190 " ideal model delta sigma weight residual 112.13 118.69 -6.56 1.34e+00 5.57e-01 2.40e+01 angle pdb=" C ASP Z 192 " pdb=" N VAL Z 193 " pdb=" CA VAL Z 193 " ideal model delta sigma weight residual 121.65 117.34 4.31 9.40e-01 1.13e+00 2.10e+01 ... (remaining 69831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 27706 17.99 - 35.99: 2840 35.99 - 53.98: 456 53.98 - 71.98: 90 71.98 - 89.97: 42 Dihedral angle restraints: 31134 sinusoidal: 12452 harmonic: 18682 Sorted by residual: dihedral pdb=" CA PHE F 160 " pdb=" C PHE F 160 " pdb=" N GLY F 161 " pdb=" CA GLY F 161 " ideal model delta harmonic sigma weight residual 180.00 151.46 28.54 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA PHE T 160 " pdb=" C PHE T 160 " pdb=" N GLY T 161 " pdb=" CA GLY T 161 " ideal model delta harmonic sigma weight residual 180.00 151.48 28.52 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA ASN V 123 " pdb=" C ASN V 123 " pdb=" N ASP V 124 " pdb=" CA ASP V 124 " ideal model delta harmonic sigma weight residual -180.00 -152.53 -27.47 0 5.00e+00 4.00e-02 3.02e+01 ... (remaining 31131 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 7209 0.085 - 0.170: 596 0.170 - 0.256: 5 0.256 - 0.341: 2 0.341 - 0.426: 4 Chirality restraints: 7816 Sorted by residual: chirality pdb=" C04 YHD Z 301 " pdb=" C03 YHD Z 301 " pdb=" C08 YHD Z 301 " pdb=" N23 YHD Z 301 " both_signs ideal model delta sigma weight residual False 2.28 2.71 -0.43 2.00e-01 2.50e+01 4.53e+00 chirality pdb=" C04 YHD L 301 " pdb=" C03 YHD L 301 " pdb=" C08 YHD L 301 " pdb=" N23 YHD L 301 " both_signs ideal model delta sigma weight residual False 2.28 2.70 -0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" CB ILE U 221 " pdb=" CA ILE U 221 " pdb=" CG1 ILE U 221 " pdb=" CG2 ILE U 221 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.72e+00 ... (remaining 7813 not shown) Planarity restraints: 8908 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 220 " -0.036 2.00e-02 2.50e+03 3.47e-02 3.02e+01 pdb=" CG TRP G 220 " 0.092 2.00e-02 2.50e+03 pdb=" CD1 TRP G 220 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP G 220 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP G 220 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP G 220 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP G 220 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 220 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 220 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP G 220 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP U 220 " -0.036 2.00e-02 2.50e+03 3.47e-02 3.00e+01 pdb=" CG TRP U 220 " 0.092 2.00e-02 2.50e+03 pdb=" CD1 TRP U 220 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP U 220 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP U 220 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP U 220 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP U 220 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP U 220 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP U 220 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP U 220 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU N 242 " -0.088 5.00e-02 4.00e+02 1.34e-01 2.89e+01 pdb=" N PRO N 243 " 0.233 5.00e-02 4.00e+02 pdb=" CA PRO N 243 " -0.074 5.00e-02 4.00e+02 pdb=" CD PRO N 243 " -0.070 5.00e-02 4.00e+02 ... (remaining 8905 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 904 2.63 - 3.20: 48804 3.20 - 3.77: 78399 3.77 - 4.33: 115708 4.33 - 4.90: 190402 Nonbonded interactions: 434217 Sorted by model distance: nonbonded pdb=" OG SER a 62 " pdb=" NH2 ARG b 182 " model vdw 2.067 2.520 nonbonded pdb=" O ASP H 221 " pdb=" OG SER H 224 " model vdw 2.068 2.440 nonbonded pdb=" O ASP V 221 " pdb=" OG SER V 224 " model vdw 2.069 2.440 nonbonded pdb=" OE2 GLU D 90 " pdb=" OH TYR D 106 " model vdw 2.076 2.440 nonbonded pdb=" OE2 GLU R 90 " pdb=" OH TYR R 106 " model vdw 2.077 2.440 ... (remaining 434212 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 17.260 Check model and map are aligned: 0.820 Set scattering table: 0.510 Process input model: 125.460 Find NCS groups from input model: 5.310 Set up NCS constraints: 0.500 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 157.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.146 51712 Z= 0.388 Angle : 0.702 14.260 69836 Z= 0.385 Chirality : 0.047 0.426 7816 Planarity : 0.005 0.134 8908 Dihedral : 14.758 89.973 19186 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.46 % Allowed : 0.75 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.11), residues: 6296 helix: -0.24 (0.11), residues: 2108 sheet: -0.88 (0.14), residues: 1498 loop : -1.90 (0.12), residues: 2690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.092 0.003 TRP G 220 HIS 0.011 0.001 HIS A 12 PHE 0.036 0.002 PHE Q 73 TYR 0.027 0.002 TYR E 8 ARG 0.011 0.001 ARG U 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12592 Ramachandran restraints generated. 6296 Oldfield, 0 Emsley, 6296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12592 Ramachandran restraints generated. 6296 Oldfield, 0 Emsley, 6296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 5594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 864 time to evaluate : 5.895 Fit side-chains REVERT: B 79 MET cc_start: 0.8392 (mtp) cc_final: 0.8186 (mtp) REVERT: B 181 ASP cc_start: 0.8586 (p0) cc_final: 0.8368 (p0) REVERT: C 226 TYR cc_start: 0.7298 (m-10) cc_final: 0.6601 (m-10) REVERT: D 99 ASP cc_start: 0.8242 (t70) cc_final: 0.8031 (t0) REVERT: E 176 GLN cc_start: 0.8703 (pp30) cc_final: 0.8383 (pp30) REVERT: E 195 GLN cc_start: 0.7880 (mt0) cc_final: 0.7665 (mt0) REVERT: F 7 ASP cc_start: 0.7892 (t0) cc_final: 0.7681 (t0) REVERT: G 28 TYR cc_start: 0.8360 (m-10) cc_final: 0.8035 (m-80) REVERT: G 146 LYS cc_start: 0.8092 (pptt) cc_final: 0.7667 (mmtt) REVERT: H 53 GLN cc_start: 0.8832 (mt0) cc_final: 0.8623 (mt0) REVERT: J 26 ASP cc_start: 0.7984 (p0) cc_final: 0.7721 (p0) REVERT: L 67 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8018 (mt-10) REVERT: L 167 ASP cc_start: 0.7612 (t70) cc_final: 0.7239 (t0) REVERT: L 180 HIS cc_start: 0.7727 (m170) cc_final: 0.7328 (m170) REVERT: L 185 ASP cc_start: 0.8000 (p0) cc_final: 0.7742 (p0) REVERT: M 30 TRP cc_start: 0.7968 (t-100) cc_final: 0.7639 (t-100) REVERT: M 128 ARG cc_start: 0.9266 (tpt90) cc_final: 0.9010 (tpt90) REVERT: N 89 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8503 (tm-30) REVERT: O 129 GLN cc_start: 0.9036 (tm-30) cc_final: 0.8390 (tm-30) REVERT: Q 226 TYR cc_start: 0.7170 (m-10) cc_final: 0.6476 (m-10) REVERT: R 99 ASP cc_start: 0.8097 (t70) cc_final: 0.7891 (t0) REVERT: R 225 MET cc_start: 0.8285 (mtp) cc_final: 0.8023 (mtt) REVERT: S 114 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7229 (mm-30) REVERT: S 176 GLN cc_start: 0.8483 (pp30) cc_final: 0.8108 (pp30) REVERT: S 195 GLN cc_start: 0.7856 (mt0) cc_final: 0.7644 (mt0) REVERT: U 28 TYR cc_start: 0.8284 (m-10) cc_final: 0.7927 (m-80) REVERT: U 146 LYS cc_start: 0.7982 (pptt) cc_final: 0.7572 (mmtt) REVERT: V 53 GLN cc_start: 0.8747 (mt0) cc_final: 0.8496 (mt0) REVERT: X 26 ASP cc_start: 0.8071 (p0) cc_final: 0.7787 (p0) REVERT: Y 91 TYR cc_start: 0.8352 (t80) cc_final: 0.8092 (t80) REVERT: Z 17 ASP cc_start: 0.8243 (p0) cc_final: 0.8024 (p0) REVERT: Z 167 ASP cc_start: 0.7744 (t70) cc_final: 0.7483 (t0) REVERT: Z 180 HIS cc_start: 0.7593 (m170) cc_final: 0.7390 (m170) REVERT: b 89 GLN cc_start: 0.8734 (tm-30) cc_final: 0.8455 (tm-30) outliers start: 26 outliers final: 6 residues processed: 875 average time/residue: 0.6381 time to fit residues: 913.3786 Evaluate side-chains 724 residues out of total 5594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 718 time to evaluate : 6.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain K residue 59 GLU Chi-restraints excluded: chain M residue 143 GLU Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain Y residue 59 GLU Chi-restraints excluded: chain a residue 143 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 525 optimal weight: 3.9990 chunk 471 optimal weight: 8.9990 chunk 261 optimal weight: 0.8980 chunk 161 optimal weight: 0.9990 chunk 318 optimal weight: 2.9990 chunk 251 optimal weight: 1.9990 chunk 487 optimal weight: 0.7980 chunk 188 optimal weight: 2.9990 chunk 296 optimal weight: 4.9990 chunk 362 optimal weight: 1.9990 chunk 564 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN E 184 GLN ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 ASN ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 10 ASN I 66 HIS I 73 GLN J 8 ASN J 80 GLN K 114 GLN K 175 GLN L 197 HIS ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 34 ASN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 54 HIS W 73 GLN ** X 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 114 GLN Y 175 GLN Z 197 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 51712 Z= 0.274 Angle : 0.606 13.531 69836 Z= 0.325 Chirality : 0.046 0.183 7816 Planarity : 0.004 0.096 8908 Dihedral : 6.020 67.012 7032 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 1.54 % Allowed : 8.99 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.11), residues: 6296 helix: 0.43 (0.11), residues: 2166 sheet: -0.92 (0.14), residues: 1510 loop : -1.86 (0.12), residues: 2620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP U 220 HIS 0.010 0.001 HIS L 197 PHE 0.023 0.002 PHE Q 73 TYR 0.027 0.002 TYR H 118 ARG 0.005 0.000 ARG P 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12592 Ramachandran restraints generated. 6296 Oldfield, 0 Emsley, 6296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12592 Ramachandran restraints generated. 6296 Oldfield, 0 Emsley, 6296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 920 residues out of total 5594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 834 time to evaluate : 5.612 Fit side-chains REVERT: A 129 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8431 (tm-30) REVERT: B 79 MET cc_start: 0.8565 (mtp) cc_final: 0.8344 (mtm) REVERT: D 99 ASP cc_start: 0.8081 (t70) cc_final: 0.7803 (t0) REVERT: D 110 TYR cc_start: 0.8816 (t80) cc_final: 0.8602 (t80) REVERT: D 225 MET cc_start: 0.8295 (mtp) cc_final: 0.7959 (mtt) REVERT: E 176 GLN cc_start: 0.8354 (pp30) cc_final: 0.8010 (pp30) REVERT: E 195 GLN cc_start: 0.7702 (mt0) cc_final: 0.7446 (mt0) REVERT: F 121 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8382 (mm110) REVERT: F 227 GLN cc_start: 0.8424 (tp-100) cc_final: 0.8053 (tp-100) REVERT: G 100 THR cc_start: 0.9138 (m) cc_final: 0.8916 (m) REVERT: G 146 LYS cc_start: 0.8060 (pptt) cc_final: 0.7610 (mmtt) REVERT: H 53 GLN cc_start: 0.8706 (mt0) cc_final: 0.8381 (mt0) REVERT: K 27 LYS cc_start: 0.7971 (ptmm) cc_final: 0.7762 (pttp) REVERT: L 167 ASP cc_start: 0.7596 (t70) cc_final: 0.7395 (t70) REVERT: M 30 TRP cc_start: 0.7962 (t-100) cc_final: 0.7678 (t-100) REVERT: M 128 ARG cc_start: 0.9219 (tpt90) cc_final: 0.8993 (tpt90) REVERT: M 143 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6396 (mm-30) REVERT: M 171 GLN cc_start: 0.8749 (mm-40) cc_final: 0.8494 (mm110) REVERT: N 89 GLN cc_start: 0.8590 (tm-30) cc_final: 0.8304 (tm-30) REVERT: O 129 GLN cc_start: 0.9004 (tm-30) cc_final: 0.8352 (tm-30) REVERT: P 171 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8419 (mtp) REVERT: R 99 ASP cc_start: 0.8105 (t70) cc_final: 0.7822 (t0) REVERT: R 110 TYR cc_start: 0.8859 (t80) cc_final: 0.8656 (t80) REVERT: S 8 TYR cc_start: 0.5929 (p90) cc_final: 0.5039 (m-10) REVERT: S 176 GLN cc_start: 0.8271 (pp30) cc_final: 0.7941 (pp30) REVERT: S 195 GLN cc_start: 0.7676 (mt0) cc_final: 0.7435 (mt0) REVERT: T 227 GLN cc_start: 0.8390 (tp-100) cc_final: 0.8012 (tp-100) REVERT: U 146 LYS cc_start: 0.7978 (pptt) cc_final: 0.7567 (mmtt) REVERT: V 53 GLN cc_start: 0.8654 (mt0) cc_final: 0.8318 (mt0) REVERT: W 78 MET cc_start: 0.8748 (tmm) cc_final: 0.8410 (tmm) REVERT: Y 27 LYS cc_start: 0.7925 (ptmm) cc_final: 0.7699 (pttp) REVERT: Z 167 ASP cc_start: 0.7683 (t70) cc_final: 0.7428 (t0) REVERT: Z 180 HIS cc_start: 0.7586 (m170) cc_final: 0.7316 (m170) REVERT: a 143 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6386 (mm-30) REVERT: a 171 GLN cc_start: 0.8745 (mm-40) cc_final: 0.8501 (mm110) REVERT: b 89 GLN cc_start: 0.8536 (tm-30) cc_final: 0.8246 (tm-30) outliers start: 86 outliers final: 60 residues processed: 879 average time/residue: 0.6350 time to fit residues: 912.3897 Evaluate side-chains 821 residues out of total 5594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 757 time to evaluate : 5.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain G residue 34 ASN Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 240 GLU Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 124 MET Chi-restraints excluded: chain K residue 126 SER Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 197 HIS Chi-restraints excluded: chain M residue 143 GLU Chi-restraints excluded: chain M residue 232 VAL Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 169 TYR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 154 CYS Chi-restraints excluded: chain P residue 171 MET Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain R residue 2 SER Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 184 ASP Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain U residue 34 ASN Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain V residue 124 ASP Chi-restraints excluded: chain V residue 234 THR Chi-restraints excluded: chain V residue 240 GLU Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain W residue 174 ASP Chi-restraints excluded: chain W residue 204 ILE Chi-restraints excluded: chain X residue 115 LYS Chi-restraints excluded: chain X residue 134 LEU Chi-restraints excluded: chain Y residue 32 ASP Chi-restraints excluded: chain Y residue 124 MET Chi-restraints excluded: chain Y residue 126 SER Chi-restraints excluded: chain Z residue 121 VAL Chi-restraints excluded: chain Z residue 197 HIS Chi-restraints excluded: chain a residue 143 GLU Chi-restraints excluded: chain a residue 232 VAL Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 46 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 313 optimal weight: 0.7980 chunk 175 optimal weight: 0.9980 chunk 470 optimal weight: 5.9990 chunk 384 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 565 optimal weight: 3.9990 chunk 611 optimal weight: 3.9990 chunk 503 optimal weight: 0.9990 chunk 561 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 453 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN B 224 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 GLN ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 10 ASN I 54 HIS I 73 GLN ** J 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 197 HIS ** M 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 243 GLN P 169 ASN ** T 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 10 ASN W 69 ASN X 8 ASN ** X 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 175 GLN Z 197 HIS b 89 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 51712 Z= 0.261 Angle : 0.574 12.737 69836 Z= 0.307 Chirality : 0.045 0.186 7816 Planarity : 0.004 0.074 8908 Dihedral : 5.634 52.118 7026 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 2.25 % Allowed : 13.07 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.11), residues: 6296 helix: 0.66 (0.11), residues: 2176 sheet: -0.92 (0.14), residues: 1506 loop : -1.82 (0.12), residues: 2614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP U 220 HIS 0.011 0.001 HIS I 54 PHE 0.021 0.001 PHE N 54 TYR 0.026 0.001 TYR V 118 ARG 0.006 0.000 ARG a 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12592 Ramachandran restraints generated. 6296 Oldfield, 0 Emsley, 6296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12592 Ramachandran restraints generated. 6296 Oldfield, 0 Emsley, 6296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 947 residues out of total 5594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 821 time to evaluate : 6.548 Fit side-chains REVERT: A 129 GLN cc_start: 0.9012 (tm-30) cc_final: 0.8406 (tm-30) REVERT: D 144 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8330 (mp) REVERT: D 225 MET cc_start: 0.8155 (mtp) cc_final: 0.7855 (mtt) REVERT: E 195 GLN cc_start: 0.7709 (mt0) cc_final: 0.7364 (mt0) REVERT: F 121 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8277 (mp10) REVERT: F 227 GLN cc_start: 0.8404 (tp-100) cc_final: 0.8203 (tp-100) REVERT: G 28 TYR cc_start: 0.8312 (m-80) cc_final: 0.7885 (m-80) REVERT: G 146 LYS cc_start: 0.8061 (pptt) cc_final: 0.7591 (mmtt) REVERT: I 89 LYS cc_start: 0.9067 (ttmm) cc_final: 0.8766 (ttpp) REVERT: J 26 ASP cc_start: 0.7960 (p0) cc_final: 0.7754 (p0) REVERT: K 27 LYS cc_start: 0.8026 (ptmm) cc_final: 0.7654 (pttp) REVERT: M 97 GLN cc_start: 0.8384 (mt0) cc_final: 0.8151 (mt0) REVERT: M 128 ARG cc_start: 0.9216 (tpt90) cc_final: 0.8969 (tpt90) REVERT: N 89 GLN cc_start: 0.8548 (tm-30) cc_final: 0.8171 (tm-30) REVERT: O 61 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7544 (pt) REVERT: O 129 GLN cc_start: 0.8980 (tm-30) cc_final: 0.8378 (tm-30) REVERT: P 66 GLN cc_start: 0.8667 (mm110) cc_final: 0.8374 (mm110) REVERT: R 99 ASP cc_start: 0.8096 (t70) cc_final: 0.7769 (t0) REVERT: R 144 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8409 (mp) REVERT: R 225 MET cc_start: 0.8138 (mtp) cc_final: 0.7846 (mtt) REVERT: S 8 TYR cc_start: 0.5794 (p90) cc_final: 0.4988 (m-10) REVERT: S 82 MET cc_start: 0.8000 (mmm) cc_final: 0.7748 (mmm) REVERT: S 195 GLN cc_start: 0.7657 (mt0) cc_final: 0.7426 (mt0) REVERT: T 121 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8654 (mm-40) REVERT: U 28 TYR cc_start: 0.8297 (m-80) cc_final: 0.7835 (m-80) REVERT: U 146 LYS cc_start: 0.7960 (pptt) cc_final: 0.7473 (mmtt) REVERT: W 78 MET cc_start: 0.8837 (tmm) cc_final: 0.8510 (tmm) REVERT: W 89 LYS cc_start: 0.8977 (ttmm) cc_final: 0.8679 (ttpp) REVERT: Y 27 LYS cc_start: 0.8050 (ptmm) cc_final: 0.7702 (pttp) REVERT: Z 167 ASP cc_start: 0.7688 (t70) cc_final: 0.7388 (t0) REVERT: Z 180 HIS cc_start: 0.7619 (m170) cc_final: 0.7319 (m170) REVERT: a 97 GLN cc_start: 0.8378 (mt0) cc_final: 0.8152 (mt0) REVERT: a 171 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8509 (mm110) outliers start: 126 outliers final: 89 residues processed: 881 average time/residue: 0.6330 time to fit residues: 919.0194 Evaluate side-chains 832 residues out of total 5594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 738 time to evaluate : 5.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 226 TYR Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 160 PHE Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 240 GLU Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 174 ASP Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 126 SER Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 197 HIS Chi-restraints excluded: chain M residue 168 SER Chi-restraints excluded: chain M residue 232 VAL Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 154 CYS Chi-restraints excluded: chain Q residue 162 THR Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 226 TYR Chi-restraints excluded: chain R residue 2 SER Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 70 CYS Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 129 ILE Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 184 ASP Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain S residue 76 CYS Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 121 GLN Chi-restraints excluded: chain T residue 160 PHE Chi-restraints excluded: chain T residue 176 HIS Chi-restraints excluded: chain U residue 46 ILE Chi-restraints excluded: chain U residue 150 ASP Chi-restraints excluded: chain U residue 191 ASP Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain V residue 124 ASP Chi-restraints excluded: chain V residue 174 ILE Chi-restraints excluded: chain V residue 182 SER Chi-restraints excluded: chain V residue 234 THR Chi-restraints excluded: chain V residue 240 GLU Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 174 ASP Chi-restraints excluded: chain W residue 204 ILE Chi-restraints excluded: chain W residue 212 ILE Chi-restraints excluded: chain X residue 8 ASN Chi-restraints excluded: chain Y residue 32 ASP Chi-restraints excluded: chain Y residue 126 SER Chi-restraints excluded: chain Y residue 173 LEU Chi-restraints excluded: chain Z residue 121 VAL Chi-restraints excluded: chain a residue 232 VAL Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 12 VAL Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 242 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 559 optimal weight: 3.9990 chunk 425 optimal weight: 1.9990 chunk 293 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 270 optimal weight: 0.8980 chunk 379 optimal weight: 1.9990 chunk 567 optimal weight: 6.9990 chunk 601 optimal weight: 0.8980 chunk 296 optimal weight: 5.9990 chunk 538 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN B 224 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 HIS I 73 GLN ** J 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 175 GLN L 151 GLN L 197 HIS ** M 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 227 GLN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 163 GLN W 10 ASN W 35 HIS W 73 GLN X 8 ASN ** X 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 175 GLN Z 151 GLN Z 197 HIS b 119 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 51712 Z= 0.293 Angle : 0.574 12.643 69836 Z= 0.306 Chirality : 0.045 0.185 7816 Planarity : 0.004 0.063 8908 Dihedral : 5.510 56.322 7020 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 2.86 % Allowed : 14.46 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.11), residues: 6296 helix: 0.73 (0.11), residues: 2182 sheet: -0.94 (0.14), residues: 1510 loop : -1.82 (0.12), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 220 HIS 0.008 0.001 HIS L 197 PHE 0.022 0.002 PHE N 54 TYR 0.024 0.001 TYR V 118 ARG 0.005 0.000 ARG V 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12592 Ramachandran restraints generated. 6296 Oldfield, 0 Emsley, 6296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12592 Ramachandran restraints generated. 6296 Oldfield, 0 Emsley, 6296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 947 residues out of total 5594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 787 time to evaluate : 5.277 Fit side-chains REVERT: A 129 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8209 (tm-30) REVERT: B 70 GLU cc_start: 0.7846 (mp0) cc_final: 0.7596 (mp0) REVERT: B 181 ASP cc_start: 0.8581 (p0) cc_final: 0.8292 (p0) REVERT: B 209 GLU cc_start: 0.7537 (tp30) cc_final: 0.7187 (tp30) REVERT: D 99 ASP cc_start: 0.7962 (t0) cc_final: 0.7730 (t0) REVERT: D 144 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8323 (mp) REVERT: E 195 GLN cc_start: 0.7738 (mt0) cc_final: 0.7526 (mt0) REVERT: F 121 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8198 (mp10) REVERT: F 227 GLN cc_start: 0.8415 (tp-100) cc_final: 0.8197 (tp-100) REVERT: G 28 TYR cc_start: 0.8282 (m-80) cc_final: 0.7749 (m-80) REVERT: G 146 LYS cc_start: 0.8084 (pptt) cc_final: 0.7571 (mmtt) REVERT: H 78 GLU cc_start: 0.7810 (mp0) cc_final: 0.7029 (mm-30) REVERT: H 128 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7521 (mt) REVERT: I 89 LYS cc_start: 0.9118 (ttmm) cc_final: 0.8730 (ttpp) REVERT: J 217 MET cc_start: 0.7229 (mtt) cc_final: 0.6514 (mmt) REVERT: K 119 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7638 (m-30) REVERT: L 19 ARG cc_start: 0.8952 (ttm170) cc_final: 0.8607 (ttm170) REVERT: M 128 ARG cc_start: 0.9216 (tpt90) cc_final: 0.8954 (tpt90) REVERT: O 129 GLN cc_start: 0.8975 (tm-30) cc_final: 0.8367 (tm-30) REVERT: P 166 ASP cc_start: 0.7334 (t0) cc_final: 0.7125 (t0) REVERT: P 181 ASP cc_start: 0.8571 (p0) cc_final: 0.8284 (p0) REVERT: R 99 ASP cc_start: 0.8079 (t0) cc_final: 0.7779 (t0) REVERT: R 144 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8388 (mp) REVERT: S 82 MET cc_start: 0.7991 (mmm) cc_final: 0.7746 (mmm) REVERT: S 195 GLN cc_start: 0.7693 (mt0) cc_final: 0.7457 (mt0) REVERT: U 28 TYR cc_start: 0.8391 (m-80) cc_final: 0.7883 (m-80) REVERT: U 146 LYS cc_start: 0.7928 (pptt) cc_final: 0.7488 (mmtt) REVERT: V 128 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7556 (mt) REVERT: V 197 TYR cc_start: 0.8665 (t80) cc_final: 0.8303 (t80) REVERT: W 78 MET cc_start: 0.8904 (tmm) cc_final: 0.8610 (tmm) REVERT: W 89 LYS cc_start: 0.9062 (ttmm) cc_final: 0.8702 (ttpp) REVERT: Z 167 ASP cc_start: 0.7639 (t70) cc_final: 0.7327 (t0) REVERT: a 97 GLN cc_start: 0.8400 (mt0) cc_final: 0.8120 (mt0) REVERT: a 171 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8508 (mm-40) outliers start: 160 outliers final: 114 residues processed: 879 average time/residue: 0.6313 time to fit residues: 908.9973 Evaluate side-chains 874 residues out of total 5594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 754 time to evaluate : 6.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 226 TYR Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 220 CYS Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 160 PHE Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 221 ILE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 240 GLU Chi-restraints excluded: chain I residue 10 ASN Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 174 ASP Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 148 ASP Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain K residue 126 SER Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 168 SER Chi-restraints excluded: chain M residue 232 VAL Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 226 ILE Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain P residue 154 CYS Chi-restraints excluded: chain Q residue 162 THR Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 226 TYR Chi-restraints excluded: chain R residue 2 SER Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 70 CYS Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 129 ILE Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain S residue 76 CYS Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 160 PHE Chi-restraints excluded: chain T residue 176 HIS Chi-restraints excluded: chain U residue 46 ILE Chi-restraints excluded: chain U residue 140 ILE Chi-restraints excluded: chain U residue 191 ASP Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain U residue 221 ILE Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 124 ASP Chi-restraints excluded: chain V residue 128 LEU Chi-restraints excluded: chain V residue 234 THR Chi-restraints excluded: chain V residue 240 GLU Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 84 THR Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 174 ASP Chi-restraints excluded: chain W residue 204 ILE Chi-restraints excluded: chain W residue 212 ILE Chi-restraints excluded: chain X residue 134 LEU Chi-restraints excluded: chain X residue 148 ASP Chi-restraints excluded: chain Y residue 32 ASP Chi-restraints excluded: chain Y residue 126 SER Chi-restraints excluded: chain Y residue 173 LEU Chi-restraints excluded: chain Y residue 174 THR Chi-restraints excluded: chain Z residue 121 VAL Chi-restraints excluded: chain Z residue 194 PHE Chi-restraints excluded: chain a residue 162 THR Chi-restraints excluded: chain a residue 232 VAL Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 10 THR Chi-restraints excluded: chain b residue 12 VAL Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 119 ASN Chi-restraints excluded: chain b residue 226 ILE Chi-restraints excluded: chain b residue 242 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 500 optimal weight: 1.9990 chunk 341 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 447 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 513 optimal weight: 0.8980 chunk 415 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 307 optimal weight: 2.9990 chunk 539 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 GLN ** J 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 175 GLN L 197 HIS ** M 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 9 GLN W 73 GLN ** X 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 175 GLN Z 197 HIS ** Z 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 89 GLN b 119 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 51712 Z= 0.297 Angle : 0.581 12.351 69836 Z= 0.308 Chirality : 0.045 0.183 7816 Planarity : 0.004 0.062 8908 Dihedral : 5.482 57.502 7020 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 3.27 % Allowed : 15.46 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.11), residues: 6296 helix: 0.77 (0.11), residues: 2190 sheet: -0.90 (0.14), residues: 1516 loop : -1.82 (0.12), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 220 HIS 0.010 0.001 HIS Z 197 PHE 0.022 0.002 PHE b 54 TYR 0.023 0.001 TYR V 118 ARG 0.006 0.000 ARG C 17 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12592 Ramachandran restraints generated. 6296 Oldfield, 0 Emsley, 6296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12592 Ramachandran restraints generated. 6296 Oldfield, 0 Emsley, 6296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 990 residues out of total 5594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 807 time to evaluate : 5.936 Fit side-chains REVERT: A 61 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7372 (tt) REVERT: A 129 GLN cc_start: 0.9015 (tm-30) cc_final: 0.8267 (tm-30) REVERT: B 70 GLU cc_start: 0.7825 (mp0) cc_final: 0.7571 (mp0) REVERT: D 99 ASP cc_start: 0.8090 (t0) cc_final: 0.7774 (t0) REVERT: D 110 TYR cc_start: 0.8761 (t80) cc_final: 0.8517 (t80) REVERT: D 144 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8300 (mp) REVERT: E 176 GLN cc_start: 0.8445 (pp30) cc_final: 0.8223 (tm-30) REVERT: E 195 GLN cc_start: 0.7782 (mt0) cc_final: 0.7543 (mt0) REVERT: F 121 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8204 (mp10) REVERT: F 227 GLN cc_start: 0.8406 (tp-100) cc_final: 0.8176 (tp-100) REVERT: G 20 ARG cc_start: 0.7949 (ttm110) cc_final: 0.7422 (ttm110) REVERT: G 28 TYR cc_start: 0.8314 (m-80) cc_final: 0.7986 (m-80) REVERT: G 146 LYS cc_start: 0.8108 (pptt) cc_final: 0.7584 (mmtt) REVERT: H 62 TYR cc_start: 0.8241 (m-80) cc_final: 0.7780 (m-10) REVERT: H 78 GLU cc_start: 0.7801 (mp0) cc_final: 0.7006 (mm-30) REVERT: H 128 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7580 (mt) REVERT: H 138 LYS cc_start: 0.7882 (mmmm) cc_final: 0.7300 (mmmm) REVERT: I 78 MET cc_start: 0.8926 (tmm) cc_final: 0.8489 (tmm) REVERT: I 89 LYS cc_start: 0.9115 (ttmm) cc_final: 0.8868 (ttpp) REVERT: J 217 MET cc_start: 0.7187 (mtt) cc_final: 0.6500 (mmt) REVERT: L 19 ARG cc_start: 0.8955 (ttm170) cc_final: 0.8575 (ttm170) REVERT: M 64 TYR cc_start: 0.8875 (OUTLIER) cc_final: 0.7638 (m-10) REVERT: M 194 ASN cc_start: 0.8983 (OUTLIER) cc_final: 0.8657 (p0) REVERT: O 61 ILE cc_start: 0.7808 (OUTLIER) cc_final: 0.7407 (tt) REVERT: O 77 ASN cc_start: 0.8566 (OUTLIER) cc_final: 0.8129 (p0) REVERT: O 129 GLN cc_start: 0.8973 (tm-30) cc_final: 0.8372 (tm-30) REVERT: P 166 ASP cc_start: 0.7317 (t0) cc_final: 0.7099 (t0) REVERT: P 181 ASP cc_start: 0.8611 (p0) cc_final: 0.8295 (p0) REVERT: R 99 ASP cc_start: 0.8056 (t0) cc_final: 0.7846 (t0) REVERT: R 110 TYR cc_start: 0.8776 (t80) cc_final: 0.8547 (t80) REVERT: R 144 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8372 (mp) REVERT: S 195 GLN cc_start: 0.7720 (mt0) cc_final: 0.7514 (mt0) REVERT: U 129 TRP cc_start: 0.7889 (OUTLIER) cc_final: 0.7352 (m-10) REVERT: U 146 LYS cc_start: 0.7935 (pptt) cc_final: 0.7481 (mmtt) REVERT: U 209 LYS cc_start: 0.8206 (ptpt) cc_final: 0.7770 (pptt) REVERT: V 128 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7585 (mt) REVERT: W 78 MET cc_start: 0.8931 (tmm) cc_final: 0.8618 (tmm) REVERT: W 89 LYS cc_start: 0.9115 (ttmm) cc_final: 0.8876 (ttpp) REVERT: X 138 ASP cc_start: 0.8535 (p0) cc_final: 0.8325 (p0) REVERT: X 217 MET cc_start: 0.7144 (mtt) cc_final: 0.6455 (mmt) REVERT: Z 19 ARG cc_start: 0.8579 (ttm170) cc_final: 0.7808 (ttm170) REVERT: Z 167 ASP cc_start: 0.7623 (t70) cc_final: 0.7309 (t0) REVERT: a 64 TYR cc_start: 0.8873 (OUTLIER) cc_final: 0.7698 (m-10) REVERT: a 97 GLN cc_start: 0.8403 (mt0) cc_final: 0.8103 (mt0) REVERT: a 171 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8515 (mm-40) REVERT: a 194 ASN cc_start: 0.9031 (OUTLIER) cc_final: 0.8588 (p0) REVERT: b 89 GLN cc_start: 0.8512 (tm-30) cc_final: 0.8097 (tm-30) outliers start: 183 outliers final: 141 residues processed: 925 average time/residue: 0.6326 time to fit residues: 960.1827 Evaluate side-chains 910 residues out of total 5594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 756 time to evaluate : 5.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 226 TYR Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 220 CYS Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 160 PHE Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 84 ASP Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 221 ILE Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 240 GLU Chi-restraints excluded: chain I residue 10 ASN Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 174 ASP Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 148 ASP Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 126 SER Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 174 THR Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 168 SER Chi-restraints excluded: chain M residue 194 ASN Chi-restraints excluded: chain M residue 232 VAL Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 192 HIS Chi-restraints excluded: chain N residue 226 ILE Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain O residue 12 HIS Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain O residue 77 ASN Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain P residue 154 CYS Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 162 THR Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 226 TYR Chi-restraints excluded: chain R residue 2 SER Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 70 CYS Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 129 ILE Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain S residue 76 CYS Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 141 VAL Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 160 PHE Chi-restraints excluded: chain T residue 176 HIS Chi-restraints excluded: chain U residue 46 ILE Chi-restraints excluded: chain U residue 129 TRP Chi-restraints excluded: chain U residue 140 ILE Chi-restraints excluded: chain U residue 144 ASN Chi-restraints excluded: chain U residue 150 ASP Chi-restraints excluded: chain U residue 191 ASP Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain U residue 221 ILE Chi-restraints excluded: chain V residue 39 GLU Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 124 ASP Chi-restraints excluded: chain V residue 128 LEU Chi-restraints excluded: chain V residue 182 SER Chi-restraints excluded: chain V residue 234 THR Chi-restraints excluded: chain V residue 240 GLU Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 84 THR Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 174 ASP Chi-restraints excluded: chain W residue 204 ILE Chi-restraints excluded: chain X residue 8 ASN Chi-restraints excluded: chain X residue 92 MET Chi-restraints excluded: chain X residue 134 LEU Chi-restraints excluded: chain X residue 148 ASP Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain Y residue 32 ASP Chi-restraints excluded: chain Y residue 126 SER Chi-restraints excluded: chain Y residue 173 LEU Chi-restraints excluded: chain Y residue 174 THR Chi-restraints excluded: chain Z residue 121 VAL Chi-restraints excluded: chain Z residue 194 PHE Chi-restraints excluded: chain Z residue 197 HIS Chi-restraints excluded: chain a residue 64 TYR Chi-restraints excluded: chain a residue 162 THR Chi-restraints excluded: chain a residue 194 ASN Chi-restraints excluded: chain a residue 232 VAL Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 10 THR Chi-restraints excluded: chain b residue 12 VAL Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 226 ILE Chi-restraints excluded: chain b residue 242 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 202 optimal weight: 0.0870 chunk 541 optimal weight: 0.0060 chunk 118 optimal weight: 0.7980 chunk 352 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 601 optimal weight: 2.9990 chunk 499 optimal weight: 0.7980 chunk 278 optimal weight: 0.0170 chunk 50 optimal weight: 0.9990 chunk 199 optimal weight: 2.9990 chunk 315 optimal weight: 0.6980 overall best weight: 0.3212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 GLN I 54 HIS I 73 GLN J 80 GLN K 175 GLN L 197 HIS ** M 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 224 GLN ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 73 GLN ** X 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 175 GLN ** a 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 89 GLN ** b 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 51712 Z= 0.152 Angle : 0.529 12.852 69836 Z= 0.281 Chirality : 0.043 0.234 7816 Planarity : 0.003 0.061 8908 Dihedral : 5.194 52.375 7020 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.70 % Allowed : 16.71 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.11), residues: 6296 helix: 1.04 (0.12), residues: 2170 sheet: -0.82 (0.14), residues: 1480 loop : -1.76 (0.12), residues: 2646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 117 HIS 0.027 0.001 HIS Z 197 PHE 0.013 0.001 PHE F 160 TYR 0.021 0.001 TYR X 7 ARG 0.005 0.000 ARG Q 17 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12592 Ramachandran restraints generated. 6296 Oldfield, 0 Emsley, 6296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12592 Ramachandran restraints generated. 6296 Oldfield, 0 Emsley, 6296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1040 residues out of total 5594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 889 time to evaluate : 4.753 Fit side-chains REVERT: A 61 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7060 (tt) REVERT: A 129 GLN cc_start: 0.9000 (tm-30) cc_final: 0.8346 (tm-30) REVERT: A 139 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8665 (mp) REVERT: B 181 ASP cc_start: 0.8451 (p0) cc_final: 0.8179 (p0) REVERT: D 99 ASP cc_start: 0.7988 (t0) cc_final: 0.7730 (t0) REVERT: D 110 TYR cc_start: 0.8656 (t80) cc_final: 0.8455 (t80) REVERT: D 132 LEU cc_start: 0.7926 (pp) cc_final: 0.7667 (pp) REVERT: D 144 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8229 (mp) REVERT: D 187 PHE cc_start: 0.8556 (t80) cc_final: 0.8037 (t80) REVERT: E 164 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8179 (p0) REVERT: E 176 GLN cc_start: 0.8387 (pp30) cc_final: 0.8141 (tm-30) REVERT: E 201 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7760 (mt) REVERT: F 121 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8130 (mp10) REVERT: F 227 GLN cc_start: 0.8383 (tp-100) cc_final: 0.7592 (tm-30) REVERT: G 20 ARG cc_start: 0.7909 (ttm110) cc_final: 0.7452 (ttm110) REVERT: G 28 TYR cc_start: 0.8250 (m-80) cc_final: 0.7861 (m-80) REVERT: G 146 LYS cc_start: 0.8005 (pptt) cc_final: 0.7491 (mmtt) REVERT: H 62 TYR cc_start: 0.8178 (m-80) cc_final: 0.7743 (m-10) REVERT: H 78 GLU cc_start: 0.7783 (mp0) cc_final: 0.7008 (mm-30) REVERT: H 128 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7409 (mt) REVERT: H 138 LYS cc_start: 0.7670 (mmmm) cc_final: 0.7170 (mmmm) REVERT: H 197 TYR cc_start: 0.8707 (t80) cc_final: 0.8199 (t80) REVERT: H 221 ASP cc_start: 0.7788 (t0) cc_final: 0.7492 (t0) REVERT: I 78 MET cc_start: 0.8888 (tmm) cc_final: 0.8494 (tmm) REVERT: I 89 LYS cc_start: 0.9080 (ttmm) cc_final: 0.8857 (ttpp) REVERT: J 85 ASP cc_start: 0.7610 (p0) cc_final: 0.7186 (p0) REVERT: K 95 ARG cc_start: 0.7637 (mpt180) cc_final: 0.7235 (mpt180) REVERT: K 119 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.7515 (m-30) REVERT: L 206 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7397 (tptp) REVERT: M 64 TYR cc_start: 0.8841 (OUTLIER) cc_final: 0.7594 (m-10) REVERT: M 194 ASN cc_start: 0.8983 (OUTLIER) cc_final: 0.8536 (p0) REVERT: N 66 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7182 (mp0) REVERT: O 61 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7451 (pt) REVERT: O 129 GLN cc_start: 0.9007 (tm-30) cc_final: 0.8364 (tm-30) REVERT: P 166 ASP cc_start: 0.7338 (t0) cc_final: 0.7105 (t0) REVERT: R 110 TYR cc_start: 0.8687 (t80) cc_final: 0.8464 (t80) REVERT: R 132 LEU cc_start: 0.7982 (pp) cc_final: 0.7746 (pp) REVERT: R 144 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8322 (mp) REVERT: R 229 ILE cc_start: 0.8284 (mt) cc_final: 0.8034 (mt) REVERT: S 201 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7818 (mt) REVERT: T 227 GLN cc_start: 0.8291 (tp-100) cc_final: 0.8046 (tp40) REVERT: U 28 TYR cc_start: 0.8251 (m-80) cc_final: 0.7717 (m-80) REVERT: U 146 LYS cc_start: 0.7863 (pptt) cc_final: 0.7423 (mmtt) REVERT: V 62 TYR cc_start: 0.8468 (m-80) cc_final: 0.8072 (m-10) REVERT: V 128 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7440 (mt) REVERT: V 197 TYR cc_start: 0.8605 (t80) cc_final: 0.8175 (t80) REVERT: V 221 ASP cc_start: 0.7795 (t0) cc_final: 0.7446 (t0) REVERT: W 78 MET cc_start: 0.8899 (tmm) cc_final: 0.8594 (tmm) REVERT: W 89 LYS cc_start: 0.9055 (ttmm) cc_final: 0.8837 (ttpp) REVERT: X 101 ARG cc_start: 0.8920 (tpt90) cc_final: 0.8656 (tpt90) REVERT: Y 95 ARG cc_start: 0.7666 (mpt180) cc_final: 0.7202 (mpt180) REVERT: Z 167 ASP cc_start: 0.7662 (t70) cc_final: 0.7404 (t0) REVERT: a 64 TYR cc_start: 0.8849 (OUTLIER) cc_final: 0.7595 (m-10) REVERT: a 97 GLN cc_start: 0.8326 (mt0) cc_final: 0.8017 (mt0) REVERT: a 171 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8492 (mm-40) REVERT: a 194 ASN cc_start: 0.8979 (OUTLIER) cc_final: 0.8645 (p0) outliers start: 151 outliers final: 98 residues processed: 980 average time/residue: 0.6228 time to fit residues: 998.8711 Evaluate side-chains 933 residues out of total 5594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 818 time to evaluate : 5.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 220 CYS Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 160 PHE Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 174 ASP Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain J residue 80 GLN Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 148 ASP Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain L residue 206 LYS Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain M residue 194 ASN Chi-restraints excluded: chain M residue 232 VAL Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 192 HIS Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain O residue 12 HIS Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 220 LEU Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain P residue 224 GLN Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 134 PHE Chi-restraints excluded: chain Q residue 162 THR Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain R residue 2 SER Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 70 CYS Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 129 ILE Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain S residue 76 CYS Chi-restraints excluded: chain S residue 141 VAL Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 160 PHE Chi-restraints excluded: chain T residue 176 HIS Chi-restraints excluded: chain U residue 72 VAL Chi-restraints excluded: chain U residue 84 ASP Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 124 ASP Chi-restraints excluded: chain V residue 128 LEU Chi-restraints excluded: chain V residue 174 ILE Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 121 LEU Chi-restraints excluded: chain W residue 174 ASP Chi-restraints excluded: chain W residue 204 ILE Chi-restraints excluded: chain X residue 134 LEU Chi-restraints excluded: chain X residue 140 ILE Chi-restraints excluded: chain X residue 148 ASP Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain Y residue 32 ASP Chi-restraints excluded: chain Y residue 173 LEU Chi-restraints excluded: chain a residue 64 TYR Chi-restraints excluded: chain a residue 194 ASN Chi-restraints excluded: chain a residue 232 VAL Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 10 THR Chi-restraints excluded: chain b residue 12 VAL Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 242 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 580 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 342 optimal weight: 0.7980 chunk 439 optimal weight: 0.7980 chunk 340 optimal weight: 0.9990 chunk 506 optimal weight: 4.9990 chunk 336 optimal weight: 1.9990 chunk 599 optimal weight: 0.2980 chunk 375 optimal weight: 0.7980 chunk 365 optimal weight: 1.9990 chunk 276 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 69 ASN I 73 GLN ** J 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 175 GLN L 197 HIS ** M 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 163 GLN W 73 GLN ** X 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 175 GLN ** a 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 51712 Z= 0.193 Angle : 0.540 11.750 69836 Z= 0.286 Chirality : 0.044 0.218 7816 Planarity : 0.003 0.061 8908 Dihedral : 5.131 52.189 7020 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 2.90 % Allowed : 17.47 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.11), residues: 6296 helix: 1.11 (0.12), residues: 2172 sheet: -0.72 (0.14), residues: 1488 loop : -1.73 (0.12), residues: 2636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 117 HIS 0.009 0.001 HIS L 197 PHE 0.016 0.001 PHE C 73 TYR 0.019 0.001 TYR V 118 ARG 0.008 0.000 ARG J 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12592 Ramachandran restraints generated. 6296 Oldfield, 0 Emsley, 6296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12592 Ramachandran restraints generated. 6296 Oldfield, 0 Emsley, 6296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1005 residues out of total 5594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 843 time to evaluate : 6.762 Fit side-chains REVERT: A 61 ILE cc_start: 0.7848 (OUTLIER) cc_final: 0.7063 (tt) REVERT: A 139 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8694 (mp) REVERT: A 161 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7717 (t0) REVERT: B 181 ASP cc_start: 0.8453 (p0) cc_final: 0.8152 (p0) REVERT: D 99 ASP cc_start: 0.8084 (t0) cc_final: 0.7856 (t0) REVERT: D 110 TYR cc_start: 0.8699 (t80) cc_final: 0.8474 (t80) REVERT: D 132 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7703 (pp) REVERT: D 144 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8242 (mp) REVERT: D 187 PHE cc_start: 0.8556 (t80) cc_final: 0.8035 (t80) REVERT: E 176 GLN cc_start: 0.8362 (pp30) cc_final: 0.8113 (tm-30) REVERT: E 201 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7715 (mt) REVERT: F 121 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.8101 (mp10) REVERT: F 227 GLN cc_start: 0.8381 (tp-100) cc_final: 0.8077 (tm-30) REVERT: G 28 TYR cc_start: 0.8281 (m-80) cc_final: 0.7885 (m-80) REVERT: G 146 LYS cc_start: 0.8023 (pptt) cc_final: 0.7492 (mmtt) REVERT: H 78 GLU cc_start: 0.7714 (mp0) cc_final: 0.6931 (mm-30) REVERT: H 128 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7407 (mt) REVERT: H 138 LYS cc_start: 0.7734 (mmmm) cc_final: 0.7431 (mmmm) REVERT: H 221 ASP cc_start: 0.7755 (t0) cc_final: 0.7546 (t0) REVERT: I 78 MET cc_start: 0.8887 (tmm) cc_final: 0.8609 (tmm) REVERT: I 89 LYS cc_start: 0.9060 (ttmm) cc_final: 0.8822 (ttpp) REVERT: K 95 ARG cc_start: 0.7599 (mpt180) cc_final: 0.7156 (mpt180) REVERT: K 119 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7429 (m-30) REVERT: M 64 TYR cc_start: 0.8854 (OUTLIER) cc_final: 0.7601 (m-10) REVERT: M 194 ASN cc_start: 0.8974 (OUTLIER) cc_final: 0.8491 (p0) REVERT: N 66 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7181 (mp0) REVERT: O 61 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7191 (tt) REVERT: O 161 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7774 (t0) REVERT: P 166 ASP cc_start: 0.7350 (t0) cc_final: 0.7104 (t0) REVERT: R 99 ASP cc_start: 0.7945 (t0) cc_final: 0.7655 (t0) REVERT: R 110 TYR cc_start: 0.8684 (t80) cc_final: 0.8453 (t80) REVERT: R 132 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7763 (pp) REVERT: R 144 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8314 (mp) REVERT: R 187 PHE cc_start: 0.8495 (t80) cc_final: 0.7944 (t80) REVERT: S 164 ASN cc_start: 0.8369 (OUTLIER) cc_final: 0.8062 (p0) REVERT: S 201 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7676 (mt) REVERT: T 227 GLN cc_start: 0.8293 (tp-100) cc_final: 0.8014 (tp40) REVERT: U 28 TYR cc_start: 0.8283 (m-80) cc_final: 0.7812 (m-80) REVERT: U 146 LYS cc_start: 0.7867 (pptt) cc_final: 0.7419 (mmtt) REVERT: V 62 TYR cc_start: 0.8477 (m-80) cc_final: 0.8096 (m-10) REVERT: V 128 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7414 (mt) REVERT: V 221 ASP cc_start: 0.7756 (t0) cc_final: 0.7542 (t0) REVERT: W 78 MET cc_start: 0.8902 (tmm) cc_final: 0.8604 (tmm) REVERT: W 89 LYS cc_start: 0.9061 (ttmm) cc_final: 0.8834 (ttpp) REVERT: X 101 ARG cc_start: 0.8928 (tpt90) cc_final: 0.8670 (tpt90) REVERT: Y 95 ARG cc_start: 0.7641 (mpt180) cc_final: 0.7163 (mpt180) REVERT: a 64 TYR cc_start: 0.8864 (OUTLIER) cc_final: 0.7673 (m-10) REVERT: a 97 GLN cc_start: 0.8335 (mt0) cc_final: 0.8040 (mt0) REVERT: a 171 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8501 (mm-40) REVERT: a 194 ASN cc_start: 0.8970 (OUTLIER) cc_final: 0.8475 (p0) outliers start: 162 outliers final: 115 residues processed: 944 average time/residue: 0.6280 time to fit residues: 973.8844 Evaluate side-chains 923 residues out of total 5594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 788 time to evaluate : 5.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 220 CYS Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 160 PHE Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 118 TYR Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 240 GLU Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 174 ASP Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 148 ASP Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 168 SER Chi-restraints excluded: chain M residue 194 ASN Chi-restraints excluded: chain M residue 232 VAL Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 192 HIS Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain O residue 12 HIS Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 161 ASP Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 134 PHE Chi-restraints excluded: chain Q residue 162 THR Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain R residue 2 SER Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 70 CYS Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 129 ILE Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain S residue 76 CYS Chi-restraints excluded: chain S residue 141 VAL Chi-restraints excluded: chain S residue 164 ASN Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 160 PHE Chi-restraints excluded: chain T residue 176 HIS Chi-restraints excluded: chain U residue 72 VAL Chi-restraints excluded: chain U residue 84 ASP Chi-restraints excluded: chain U residue 150 ASP Chi-restraints excluded: chain U residue 191 ASP Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 124 ASP Chi-restraints excluded: chain V residue 128 LEU Chi-restraints excluded: chain V residue 240 GLU Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 121 LEU Chi-restraints excluded: chain W residue 174 ASP Chi-restraints excluded: chain W residue 204 ILE Chi-restraints excluded: chain W residue 212 ILE Chi-restraints excluded: chain X residue 134 LEU Chi-restraints excluded: chain X residue 148 ASP Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain Y residue 32 ASP Chi-restraints excluded: chain Y residue 98 PHE Chi-restraints excluded: chain Y residue 173 LEU Chi-restraints excluded: chain Z residue 194 PHE Chi-restraints excluded: chain a residue 64 TYR Chi-restraints excluded: chain a residue 148 VAL Chi-restraints excluded: chain a residue 162 THR Chi-restraints excluded: chain a residue 194 ASN Chi-restraints excluded: chain a residue 232 VAL Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 10 THR Chi-restraints excluded: chain b residue 12 VAL Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 242 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 370 optimal weight: 1.9990 chunk 239 optimal weight: 1.9990 chunk 358 optimal weight: 3.9990 chunk 180 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 381 optimal weight: 3.9990 chunk 408 optimal weight: 7.9990 chunk 296 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 471 optimal weight: 7.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 GLN ** J 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 175 GLN L 197 HIS ** L 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 171 GLN ** N 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 224 GLN ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 184 GLN ** T 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 175 GLN ** Z 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 89 GLN ** b 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 51712 Z= 0.348 Angle : 0.610 13.830 69836 Z= 0.322 Chirality : 0.046 0.242 7816 Planarity : 0.004 0.062 8908 Dihedral : 5.358 57.450 7020 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.18 % Allowed : 17.52 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.11), residues: 6296 helix: 1.01 (0.11), residues: 2172 sheet: -0.83 (0.14), residues: 1490 loop : -1.82 (0.12), residues: 2634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 220 HIS 0.008 0.001 HIS L 197 PHE 0.026 0.002 PHE N 54 TYR 0.019 0.002 TYR T 155 ARG 0.008 0.001 ARG I 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12592 Ramachandran restraints generated. 6296 Oldfield, 0 Emsley, 6296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12592 Ramachandran restraints generated. 6296 Oldfield, 0 Emsley, 6296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 955 residues out of total 5594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 777 time to evaluate : 5.635 Fit side-chains REVERT: A 61 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7168 (tt) REVERT: A 129 GLN cc_start: 0.9048 (tm-30) cc_final: 0.8470 (tm-30) REVERT: A 139 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8887 (mp) REVERT: A 161 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7675 (t0) REVERT: B 70 GLU cc_start: 0.7776 (mp0) cc_final: 0.7460 (mp0) REVERT: B 181 ASP cc_start: 0.8565 (p0) cc_final: 0.8275 (p0) REVERT: C 208 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7567 (pm20) REVERT: D 99 ASP cc_start: 0.8118 (t0) cc_final: 0.7907 (t0) REVERT: D 110 TYR cc_start: 0.8707 (t80) cc_final: 0.8490 (t80) REVERT: D 144 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8286 (mt) REVERT: E 176 GLN cc_start: 0.8386 (pp30) cc_final: 0.8141 (tm-30) REVERT: E 201 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7651 (mt) REVERT: F 121 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8142 (mp10) REVERT: F 227 GLN cc_start: 0.8418 (tp-100) cc_final: 0.8106 (tm-30) REVERT: G 28 TYR cc_start: 0.8314 (m-80) cc_final: 0.7988 (m-80) REVERT: G 146 LYS cc_start: 0.7960 (pptt) cc_final: 0.7471 (mmtt) REVERT: H 78 GLU cc_start: 0.7805 (mp0) cc_final: 0.7035 (mm-30) REVERT: H 128 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7586 (mt) REVERT: H 138 LYS cc_start: 0.7760 (mmmm) cc_final: 0.7528 (mmmm) REVERT: I 78 MET cc_start: 0.8916 (tmm) cc_final: 0.8663 (tmm) REVERT: K 33 ASN cc_start: 0.7661 (t0) cc_final: 0.7441 (t0) REVERT: K 39 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8711 (mm) REVERT: K 119 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7522 (m-30) REVERT: M 64 TYR cc_start: 0.8932 (OUTLIER) cc_final: 0.7779 (m-10) REVERT: M 194 ASN cc_start: 0.8949 (OUTLIER) cc_final: 0.8475 (p0) REVERT: O 61 ILE cc_start: 0.7782 (OUTLIER) cc_final: 0.7038 (tt) REVERT: O 161 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7711 (t0) REVERT: P 166 ASP cc_start: 0.7280 (t0) cc_final: 0.7040 (t0) REVERT: P 181 ASP cc_start: 0.8570 (p0) cc_final: 0.8287 (p0) REVERT: Q 208 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7499 (pm20) REVERT: R 99 ASP cc_start: 0.7982 (t0) cc_final: 0.7599 (t0) REVERT: R 110 TYR cc_start: 0.8719 (t80) cc_final: 0.8494 (t80) REVERT: R 144 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8344 (mp) REVERT: R 187 PHE cc_start: 0.8514 (t80) cc_final: 0.8011 (t80) REVERT: S 201 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7640 (mt) REVERT: T 227 GLN cc_start: 0.8320 (tp-100) cc_final: 0.7576 (tp40) REVERT: U 28 TYR cc_start: 0.8445 (m-80) cc_final: 0.8037 (m-80) REVERT: U 129 TRP cc_start: 0.7924 (OUTLIER) cc_final: 0.7430 (m-10) REVERT: U 146 LYS cc_start: 0.7964 (pptt) cc_final: 0.7465 (mmtt) REVERT: V 62 TYR cc_start: 0.8537 (m-80) cc_final: 0.8181 (m-80) REVERT: V 128 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7589 (mt) REVERT: W 78 MET cc_start: 0.8942 (tmm) cc_final: 0.8633 (tmm) REVERT: W 89 LYS cc_start: 0.9079 (ttmm) cc_final: 0.8837 (ttpp) REVERT: X 101 ARG cc_start: 0.9026 (tpt90) cc_final: 0.8756 (tpt90) REVERT: Y 33 ASN cc_start: 0.7622 (t0) cc_final: 0.7417 (t0) REVERT: Y 39 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8682 (mm) REVERT: Z 19 ARG cc_start: 0.8673 (ttm170) cc_final: 0.7923 (ttm170) REVERT: a 64 TYR cc_start: 0.8923 (OUTLIER) cc_final: 0.7839 (m-10) REVERT: a 171 GLN cc_start: 0.8757 (mm-40) cc_final: 0.8494 (mm110) REVERT: a 194 ASN cc_start: 0.9016 (OUTLIER) cc_final: 0.8498 (p0) REVERT: b 89 GLN cc_start: 0.8562 (tm-30) cc_final: 0.8127 (tm-30) REVERT: b 180 TYR cc_start: 0.8371 (OUTLIER) cc_final: 0.7549 (t80) REVERT: b 217 ASP cc_start: 0.8377 (t0) cc_final: 0.8160 (t0) outliers start: 178 outliers final: 131 residues processed: 890 average time/residue: 0.6231 time to fit residues: 911.5014 Evaluate side-chains 921 residues out of total 5594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 767 time to evaluate : 5.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 220 CYS Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 160 PHE Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 84 ASP Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 1 THR Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 118 TYR Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 240 GLU Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 174 ASP Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 148 ASP Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain L residue 206 LYS Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 168 SER Chi-restraints excluded: chain M residue 194 ASN Chi-restraints excluded: chain M residue 232 VAL Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 192 HIS Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain O residue 12 HIS Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 161 ASP Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain P residue 224 GLN Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 82 ASP Chi-restraints excluded: chain Q residue 134 PHE Chi-restraints excluded: chain Q residue 162 THR Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 208 GLU Chi-restraints excluded: chain R residue 2 SER Chi-restraints excluded: chain R residue 7 ILE Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 70 CYS Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 129 ILE Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain S residue 76 CYS Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 141 VAL Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain S residue 220 CYS Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 176 HIS Chi-restraints excluded: chain U residue 46 ILE Chi-restraints excluded: chain U residue 72 VAL Chi-restraints excluded: chain U residue 84 ASP Chi-restraints excluded: chain U residue 129 TRP Chi-restraints excluded: chain U residue 144 ASN Chi-restraints excluded: chain U residue 150 ASP Chi-restraints excluded: chain U residue 191 ASP Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain U residue 221 ILE Chi-restraints excluded: chain V residue 1 THR Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 124 ASP Chi-restraints excluded: chain V residue 128 LEU Chi-restraints excluded: chain V residue 174 ILE Chi-restraints excluded: chain V residue 234 THR Chi-restraints excluded: chain V residue 240 GLU Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 84 THR Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 174 ASP Chi-restraints excluded: chain W residue 204 ILE Chi-restraints excluded: chain W residue 212 ILE Chi-restraints excluded: chain X residue 134 LEU Chi-restraints excluded: chain X residue 148 ASP Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain Y residue 32 ASP Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Y residue 126 SER Chi-restraints excluded: chain Y residue 173 LEU Chi-restraints excluded: chain Z residue 194 PHE Chi-restraints excluded: chain Z residue 206 LYS Chi-restraints excluded: chain a residue 64 TYR Chi-restraints excluded: chain a residue 162 THR Chi-restraints excluded: chain a residue 194 ASN Chi-restraints excluded: chain a residue 232 VAL Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 10 THR Chi-restraints excluded: chain b residue 12 VAL Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 180 TYR Chi-restraints excluded: chain b residue 242 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 545 optimal weight: 0.9980 chunk 574 optimal weight: 0.9980 chunk 524 optimal weight: 2.9990 chunk 558 optimal weight: 0.8980 chunk 336 optimal weight: 1.9990 chunk 243 optimal weight: 5.9990 chunk 438 optimal weight: 2.9990 chunk 171 optimal weight: 0.8980 chunk 504 optimal weight: 0.6980 chunk 528 optimal weight: 1.9990 chunk 556 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN D 97 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 175 GLN L 197 HIS ** L 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 224 GLN ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 175 GLN ** Z 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 97 GLN ** a 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 51712 Z= 0.215 Angle : 0.562 14.474 69836 Z= 0.298 Chirality : 0.044 0.197 7816 Planarity : 0.003 0.059 8908 Dihedral : 5.231 53.280 7020 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.90 % Allowed : 17.95 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.11), residues: 6296 helix: 1.13 (0.12), residues: 2168 sheet: -0.78 (0.14), residues: 1500 loop : -1.78 (0.12), residues: 2628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 117 HIS 0.008 0.001 HIS L 197 PHE 0.022 0.001 PHE T 160 TYR 0.018 0.001 TYR X 7 ARG 0.008 0.000 ARG Q 17 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12592 Ramachandran restraints generated. 6296 Oldfield, 0 Emsley, 6296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12592 Ramachandran restraints generated. 6296 Oldfield, 0 Emsley, 6296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 973 residues out of total 5594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 811 time to evaluate : 6.034 Fit side-chains REVERT: A 61 ILE cc_start: 0.7722 (OUTLIER) cc_final: 0.6964 (tt) REVERT: A 161 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7655 (t0) REVERT: B 70 GLU cc_start: 0.7774 (mp0) cc_final: 0.7351 (mp0) REVERT: B 166 ASP cc_start: 0.7326 (t0) cc_final: 0.7095 (t0) REVERT: B 181 ASP cc_start: 0.8492 (p0) cc_final: 0.8216 (p0) REVERT: D 68 HIS cc_start: 0.7755 (OUTLIER) cc_final: 0.7476 (p-80) REVERT: D 132 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7516 (pp) REVERT: D 144 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8300 (mp) REVERT: D 187 PHE cc_start: 0.8561 (t80) cc_final: 0.8083 (t80) REVERT: E 176 GLN cc_start: 0.8402 (pp30) cc_final: 0.8152 (tm-30) REVERT: E 201 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7826 (mt) REVERT: F 121 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8053 (mp10) REVERT: F 227 GLN cc_start: 0.8369 (tp-100) cc_final: 0.8061 (tm-30) REVERT: G 28 TYR cc_start: 0.8235 (m-80) cc_final: 0.7888 (m-80) REVERT: G 146 LYS cc_start: 0.7915 (pptt) cc_final: 0.7414 (mmtt) REVERT: H 128 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7452 (mt) REVERT: H 138 LYS cc_start: 0.7714 (mmmm) cc_final: 0.7513 (mmmm) REVERT: H 221 ASP cc_start: 0.7692 (t0) cc_final: 0.7432 (t0) REVERT: I 78 MET cc_start: 0.8891 (tmm) cc_final: 0.8664 (tmm) REVERT: I 89 LYS cc_start: 0.9026 (ttmm) cc_final: 0.8777 (ttpp) REVERT: J 217 MET cc_start: 0.7568 (mmt) cc_final: 0.6799 (mmt) REVERT: K 119 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7523 (m-30) REVERT: M 64 TYR cc_start: 0.8878 (OUTLIER) cc_final: 0.7691 (m-10) REVERT: M 194 ASN cc_start: 0.8995 (OUTLIER) cc_final: 0.8495 (p0) REVERT: O 61 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.6909 (tt) REVERT: O 161 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7604 (t0) REVERT: O 255 TYR cc_start: 0.5869 (OUTLIER) cc_final: 0.5638 (m-80) REVERT: P 166 ASP cc_start: 0.7348 (t0) cc_final: 0.7081 (t0) REVERT: R 99 ASP cc_start: 0.7896 (t0) cc_final: 0.7657 (t0) REVERT: R 144 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8300 (mp) REVERT: R 187 PHE cc_start: 0.8547 (t80) cc_final: 0.8082 (t80) REVERT: S 201 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7720 (mt) REVERT: T 133 MET cc_start: 0.7599 (tpp) cc_final: 0.7332 (mmm) REVERT: T 227 GLN cc_start: 0.8163 (tp-100) cc_final: 0.7852 (tp40) REVERT: U 28 TYR cc_start: 0.8347 (m-80) cc_final: 0.7877 (m-80) REVERT: U 146 LYS cc_start: 0.7828 (pptt) cc_final: 0.7425 (mmtt) REVERT: V 62 TYR cc_start: 0.8505 (m-80) cc_final: 0.8171 (m-80) REVERT: V 128 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7528 (mt) REVERT: V 197 TYR cc_start: 0.8624 (t80) cc_final: 0.8076 (t80) REVERT: W 78 MET cc_start: 0.8933 (tmm) cc_final: 0.8634 (tmm) REVERT: W 89 LYS cc_start: 0.9106 (ttmm) cc_final: 0.8855 (ttpp) REVERT: X 101 ARG cc_start: 0.8993 (tpt90) cc_final: 0.8716 (tpt90) REVERT: X 217 MET cc_start: 0.7515 (mmt) cc_final: 0.6910 (mmt) REVERT: Z 19 ARG cc_start: 0.8557 (ttm170) cc_final: 0.7843 (ttm170) REVERT: a 64 TYR cc_start: 0.8868 (OUTLIER) cc_final: 0.7672 (m-10) REVERT: a 171 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8460 (mm110) REVERT: a 194 ASN cc_start: 0.8999 (OUTLIER) cc_final: 0.8513 (p0) REVERT: b 89 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8066 (tm-30) REVERT: b 180 TYR cc_start: 0.8305 (OUTLIER) cc_final: 0.7434 (t80) REVERT: b 217 ASP cc_start: 0.8363 (t0) cc_final: 0.8050 (t0) outliers start: 162 outliers final: 129 residues processed: 910 average time/residue: 0.6257 time to fit residues: 937.8842 Evaluate side-chains 918 residues out of total 5594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 769 time to evaluate : 5.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 220 CYS Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 160 PHE Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 221 ILE Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 118 TYR Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 240 GLU Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 174 ASP Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 148 ASP Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain L residue 197 HIS Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 168 SER Chi-restraints excluded: chain M residue 194 ASN Chi-restraints excluded: chain M residue 232 VAL Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain O residue 12 HIS Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 161 ASP Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 255 TYR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain P residue 224 GLN Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 134 PHE Chi-restraints excluded: chain Q residue 162 THR Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain R residue 2 SER Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 70 CYS Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 129 ILE Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain S residue 76 CYS Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 141 VAL Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain S residue 240 ILE Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 176 HIS Chi-restraints excluded: chain T residue 214 VAL Chi-restraints excluded: chain U residue 46 ILE Chi-restraints excluded: chain U residue 72 VAL Chi-restraints excluded: chain U residue 84 ASP Chi-restraints excluded: chain U residue 144 ASN Chi-restraints excluded: chain U residue 150 ASP Chi-restraints excluded: chain U residue 191 ASP Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 118 TYR Chi-restraints excluded: chain V residue 124 ASP Chi-restraints excluded: chain V residue 128 LEU Chi-restraints excluded: chain V residue 174 ILE Chi-restraints excluded: chain V residue 234 THR Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 84 THR Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 174 ASP Chi-restraints excluded: chain W residue 204 ILE Chi-restraints excluded: chain W residue 212 ILE Chi-restraints excluded: chain X residue 134 LEU Chi-restraints excluded: chain X residue 148 ASP Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain Y residue 32 ASP Chi-restraints excluded: chain Y residue 98 PHE Chi-restraints excluded: chain Y residue 173 LEU Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain Z residue 206 LYS Chi-restraints excluded: chain a residue 64 TYR Chi-restraints excluded: chain a residue 148 VAL Chi-restraints excluded: chain a residue 162 THR Chi-restraints excluded: chain a residue 194 ASN Chi-restraints excluded: chain a residue 232 VAL Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 10 THR Chi-restraints excluded: chain b residue 12 VAL Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 180 TYR Chi-restraints excluded: chain b residue 242 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 366 optimal weight: 2.9990 chunk 590 optimal weight: 1.9990 chunk 360 optimal weight: 0.6980 chunk 280 optimal weight: 0.7980 chunk 410 optimal weight: 7.9990 chunk 619 optimal weight: 4.9990 chunk 570 optimal weight: 2.9990 chunk 493 optimal weight: 0.0040 chunk 51 optimal weight: 0.9980 chunk 381 optimal weight: 3.9990 chunk 302 optimal weight: 1.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 9 GLN ** J 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 175 GLN L 197 HIS ** M 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 224 GLN ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 9 GLN W 73 GLN ** X 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 175 GLN ** Z 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 51712 Z= 0.229 Angle : 0.569 15.398 69836 Z= 0.301 Chirality : 0.044 0.209 7816 Planarity : 0.004 0.060 8908 Dihedral : 5.208 53.099 7020 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 3.00 % Allowed : 18.02 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.11), residues: 6296 helix: 1.14 (0.12), residues: 2172 sheet: -0.79 (0.14), residues: 1512 loop : -1.78 (0.12), residues: 2612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 220 HIS 0.025 0.001 HIS L 197 PHE 0.028 0.001 PHE T 160 TYR 0.018 0.001 TYR Q 223 ARG 0.008 0.000 ARG Q 17 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12592 Ramachandran restraints generated. 6296 Oldfield, 0 Emsley, 6296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12592 Ramachandran restraints generated. 6296 Oldfield, 0 Emsley, 6296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 5594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 789 time to evaluate : 6.441 Fit side-chains REVERT: A 61 ILE cc_start: 0.7727 (OUTLIER) cc_final: 0.6965 (tt) REVERT: A 161 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.7639 (t0) REVERT: A 196 ILE cc_start: 0.7466 (OUTLIER) cc_final: 0.7256 (mm) REVERT: B 70 GLU cc_start: 0.7776 (mp0) cc_final: 0.7469 (mp0) REVERT: B 166 ASP cc_start: 0.7324 (t0) cc_final: 0.7093 (t0) REVERT: B 181 ASP cc_start: 0.8483 (p0) cc_final: 0.8184 (p0) REVERT: D 68 HIS cc_start: 0.7736 (OUTLIER) cc_final: 0.7406 (p-80) REVERT: D 132 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7467 (pp) REVERT: D 144 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8278 (mp) REVERT: D 187 PHE cc_start: 0.8562 (t80) cc_final: 0.8086 (t80) REVERT: F 121 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8066 (mp10) REVERT: F 227 GLN cc_start: 0.8371 (tp-100) cc_final: 0.8060 (tm-30) REVERT: G 28 TYR cc_start: 0.8249 (m-80) cc_final: 0.7879 (m-80) REVERT: G 129 TRP cc_start: 0.7874 (OUTLIER) cc_final: 0.7339 (m-10) REVERT: G 146 LYS cc_start: 0.7920 (pptt) cc_final: 0.7414 (mmtt) REVERT: H 78 GLU cc_start: 0.7574 (mp0) cc_final: 0.6836 (mm-30) REVERT: H 128 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7500 (mt) REVERT: H 138 LYS cc_start: 0.7722 (mmmm) cc_final: 0.7517 (mmmm) REVERT: H 221 ASP cc_start: 0.7698 (t0) cc_final: 0.7438 (t0) REVERT: I 78 MET cc_start: 0.8889 (tmm) cc_final: 0.8663 (tmm) REVERT: I 89 LYS cc_start: 0.9025 (ttmm) cc_final: 0.8770 (ttpp) REVERT: J 217 MET cc_start: 0.7563 (mmt) cc_final: 0.6795 (mmt) REVERT: K 119 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7502 (m-30) REVERT: M 64 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.7696 (m-10) REVERT: M 194 ASN cc_start: 0.8998 (OUTLIER) cc_final: 0.8497 (p0) REVERT: O 11 ARG cc_start: 0.6705 (mmt90) cc_final: 0.6460 (mmt90) REVERT: O 61 ILE cc_start: 0.7736 (OUTLIER) cc_final: 0.6921 (tt) REVERT: O 161 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7594 (t0) REVERT: O 196 ILE cc_start: 0.7467 (OUTLIER) cc_final: 0.7246 (mm) REVERT: P 166 ASP cc_start: 0.7346 (t0) cc_final: 0.7076 (t0) REVERT: R 99 ASP cc_start: 0.7883 (t0) cc_final: 0.7649 (t0) REVERT: R 144 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8302 (mp) REVERT: R 187 PHE cc_start: 0.8550 (t80) cc_final: 0.8087 (t80) REVERT: S 164 ASN cc_start: 0.8498 (OUTLIER) cc_final: 0.8190 (p0) REVERT: S 201 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7742 (mt) REVERT: T 133 MET cc_start: 0.7703 (tpp) cc_final: 0.7474 (mmm) REVERT: T 227 GLN cc_start: 0.8249 (tp-100) cc_final: 0.7932 (tp40) REVERT: U 28 TYR cc_start: 0.8357 (m-80) cc_final: 0.7890 (m-80) REVERT: U 129 TRP cc_start: 0.7830 (OUTLIER) cc_final: 0.7303 (m-10) REVERT: U 146 LYS cc_start: 0.7830 (pptt) cc_final: 0.7426 (mmtt) REVERT: V 62 TYR cc_start: 0.8506 (m-80) cc_final: 0.8174 (m-80) REVERT: V 128 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7499 (mt) REVERT: V 221 ASP cc_start: 0.7706 (t0) cc_final: 0.7425 (t0) REVERT: W 78 MET cc_start: 0.8932 (tmm) cc_final: 0.8636 (tmm) REVERT: W 89 LYS cc_start: 0.9092 (ttmm) cc_final: 0.8827 (ttpp) REVERT: X 101 ARG cc_start: 0.8992 (tpt90) cc_final: 0.8713 (tpt90) REVERT: X 217 MET cc_start: 0.7507 (mmt) cc_final: 0.6913 (mmt) REVERT: Y 33 ASN cc_start: 0.7544 (t0) cc_final: 0.7342 (t0) REVERT: Z 19 ARG cc_start: 0.8572 (ttm170) cc_final: 0.7857 (ttm170) REVERT: Z 36 GLU cc_start: 0.7709 (tt0) cc_final: 0.7451 (tt0) REVERT: a 64 TYR cc_start: 0.8869 (OUTLIER) cc_final: 0.7678 (m-10) REVERT: a 171 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8452 (mm110) REVERT: a 194 ASN cc_start: 0.9000 (OUTLIER) cc_final: 0.8518 (p0) REVERT: b 89 GLN cc_start: 0.8514 (tm-30) cc_final: 0.8074 (tm-30) REVERT: b 180 TYR cc_start: 0.8295 (OUTLIER) cc_final: 0.7435 (t80) REVERT: b 217 ASP cc_start: 0.8294 (t0) cc_final: 0.8042 (t0) outliers start: 168 outliers final: 137 residues processed: 895 average time/residue: 0.6201 time to fit residues: 913.4385 Evaluate side-chains 948 residues out of total 5594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 788 time to evaluate : 5.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 220 CYS Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 84 ASP Chi-restraints excluded: chain G residue 129 TRP Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 221 ILE Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 118 TYR Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 240 GLU Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 174 ASP Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 148 ASP Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain L residue 206 LYS Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 168 SER Chi-restraints excluded: chain M residue 194 ASN Chi-restraints excluded: chain M residue 232 VAL Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain O residue 12 HIS Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 161 ASP Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 196 ILE Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 134 PHE Chi-restraints excluded: chain Q residue 162 THR Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain R residue 2 SER Chi-restraints excluded: chain R residue 7 ILE Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 70 CYS Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 129 ILE Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain S residue 76 CYS Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 141 VAL Chi-restraints excluded: chain S residue 164 ASN Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain S residue 220 CYS Chi-restraints excluded: chain S residue 240 ILE Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 176 HIS Chi-restraints excluded: chain T residue 214 VAL Chi-restraints excluded: chain U residue 46 ILE Chi-restraints excluded: chain U residue 72 VAL Chi-restraints excluded: chain U residue 84 ASP Chi-restraints excluded: chain U residue 129 TRP Chi-restraints excluded: chain U residue 144 ASN Chi-restraints excluded: chain U residue 150 ASP Chi-restraints excluded: chain U residue 191 ASP Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 118 TYR Chi-restraints excluded: chain V residue 124 ASP Chi-restraints excluded: chain V residue 128 LEU Chi-restraints excluded: chain V residue 174 ILE Chi-restraints excluded: chain V residue 234 THR Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 84 THR Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 174 ASP Chi-restraints excluded: chain W residue 204 ILE Chi-restraints excluded: chain W residue 212 ILE Chi-restraints excluded: chain X residue 134 LEU Chi-restraints excluded: chain X residue 148 ASP Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain Y residue 32 ASP Chi-restraints excluded: chain Y residue 98 PHE Chi-restraints excluded: chain Y residue 173 LEU Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain Z residue 194 PHE Chi-restraints excluded: chain Z residue 206 LYS Chi-restraints excluded: chain a residue 64 TYR Chi-restraints excluded: chain a residue 148 VAL Chi-restraints excluded: chain a residue 162 THR Chi-restraints excluded: chain a residue 194 ASN Chi-restraints excluded: chain a residue 232 VAL Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 10 THR Chi-restraints excluded: chain b residue 12 VAL Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 180 TYR Chi-restraints excluded: chain b residue 242 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 391 optimal weight: 0.6980 chunk 525 optimal weight: 0.0670 chunk 151 optimal weight: 0.8980 chunk 454 optimal weight: 3.9990 chunk 72 optimal weight: 0.0170 chunk 137 optimal weight: 0.7980 chunk 494 optimal weight: 2.9990 chunk 206 optimal weight: 0.4980 chunk 507 optimal weight: 0.0370 chunk 62 optimal weight: 0.3980 chunk 91 optimal weight: 0.9980 overall best weight: 0.2034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 168 ASN I 145 ASN ** J 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 175 GLN L 197 HIS ** M 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 119 ASN P 224 GLN ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 168 ASN W 73 GLN Y 175 GLN ** a 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 89 GLN ** b 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.132987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.113383 restraints weight = 70193.546| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.05 r_work: 0.3275 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 51712 Z= 0.148 Angle : 0.534 13.884 69836 Z= 0.284 Chirality : 0.043 0.215 7816 Planarity : 0.003 0.062 8908 Dihedral : 4.950 46.715 7020 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.34 % Allowed : 18.68 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.11), residues: 6296 helix: 1.31 (0.12), residues: 2172 sheet: -0.63 (0.14), residues: 1446 loop : -1.76 (0.12), residues: 2678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 117 HIS 0.011 0.001 HIS L 197 PHE 0.023 0.001 PHE T 160 TYR 0.017 0.001 TYR X 119 ARG 0.009 0.000 ARG Q 17 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15455.12 seconds wall clock time: 277 minutes 3.07 seconds (16623.07 seconds total)