Starting phenix.real_space_refine (version: 1.21rc1) on Mon May 15 16:10:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqt_20169/05_2023/6oqt_20169_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqt_20169/05_2023/6oqt_20169.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/6oqt_20169/05_2023/6oqt_20169.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqt_20169/05_2023/6oqt_20169.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqt_20169/05_2023/6oqt_20169_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqt_20169/05_2023/6oqt_20169_neut_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.003 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 5 5.21 5 S 180 5.16 5 C 23485 2.51 5 N 6317 2.21 5 O 6968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "W PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 26": "NH1" <-> "NH2" Residue "W ASP 29": "OD1" <-> "OD2" Residue "W GLU 36": "OE1" <-> "OE2" Residue "W GLU 41": "OE1" <-> "OE2" Residue "W GLU 45": "OE1" <-> "OE2" Residue "W GLU 54": "OE1" <-> "OE2" Residue "W PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 69": "OD1" <-> "OD2" Residue "W GLU 70": "OE1" <-> "OE2" Residue "W ARG 77": "NH1" <-> "NH2" Residue "W GLU 93": "OE1" <-> "OE2" Residue "W PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 103": "OE1" <-> "OE2" Residue "W ASP 109": "OD1" <-> "OD2" Residue "W GLU 118": "OE1" <-> "OE2" Residue "W ASP 143": "OD1" <-> "OD2" Residue "W ASP 160": "OD1" <-> "OD2" Residue "W ARG 164": "NH1" <-> "NH2" Residue "W GLU 168": "OE1" <-> "OE2" Residue "C GLU 24": "OE1" <-> "OE2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C ASP 116": "OD1" <-> "OD2" Residue "C ASP 170": "OD1" <-> "OD2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 262": "OD1" <-> "OD2" Residue "C GLU 284": "OE1" <-> "OE2" Residue "C GLU 299": "OE1" <-> "OE2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "C PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 336": "OD1" <-> "OD2" Residue "C GLU 402": "OE1" <-> "OE2" Residue "C ASP 412": "OD1" <-> "OD2" Residue "C GLU 429": "OE1" <-> "OE2" Residue "C PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 453": "NH1" <-> "NH2" Residue "C ASP 458": "OD1" <-> "OD2" Residue "C PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 494": "OD1" <-> "OD2" Residue "C ASP 505": "OD1" <-> "OD2" Residue "C PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B GLU 24": "OE1" <-> "OE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B ASP 36": "OD1" <-> "OD2" Residue "B ASP 46": "OD1" <-> "OD2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B ARG 93": "NH1" <-> "NH2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "B ASP 181": "OD1" <-> "OD2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 376": "NH1" <-> "NH2" Residue "B TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 412": "OD1" <-> "OD2" Residue "B ASP 415": "OD1" <-> "OD2" Residue "B ASP 422": "OD1" <-> "OD2" Residue "B ASP 478": "OD1" <-> "OD2" Residue "B GLU 485": "OE1" <-> "OE2" Residue "B GLU 495": "OE1" <-> "OE2" Residue "B GLU 497": "OE1" <-> "OE2" Residue "A GLU 10": "OE1" <-> "OE2" Residue "A GLU 24": "OE1" <-> "OE2" Residue "A ASP 36": "OD1" <-> "OD2" Residue "A ASP 69": "OD1" <-> "OD2" Residue "A ASP 170": "OD1" <-> "OD2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 261": "OD1" <-> "OD2" Residue "A ASP 262": "OD1" <-> "OD2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 336": "OD1" <-> "OD2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 376": "NH1" <-> "NH2" Residue "A ASP 412": "OD1" <-> "OD2" Residue "A ASP 415": "OD1" <-> "OD2" Residue "A ARG 418": "NH1" <-> "NH2" Residue "A ASP 422": "OD1" <-> "OD2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 460": "OE1" <-> "OE2" Residue "A PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 476": "OD1" <-> "OD2" Residue "A ARG 477": "NH1" <-> "NH2" Residue "A TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 39": "OE1" <-> "OE2" Residue "X ASP 42": "OD1" <-> "OD2" Residue "X GLU 48": "OE1" <-> "OE2" Residue "X ASP 53": "OD1" <-> "OD2" Residue "X GLU 71": "OE1" <-> "OE2" Residue "X ARG 83": "NH1" <-> "NH2" Residue "X ASP 88": "OD1" <-> "OD2" Residue "X GLU 93": "OE1" <-> "OE2" Residue "X GLU 97": "OE1" <-> "OE2" Residue "X ARG 98": "NH1" <-> "NH2" Residue "X ARG 113": "NH1" <-> "NH2" Residue "X ARG 115": "NH1" <-> "NH2" Residue "X ARG 117": "NH1" <-> "NH2" Residue "X ARG 121": "NH1" <-> "NH2" Residue "X GLU 137": "OE1" <-> "OE2" Residue "X ASP 141": "OD1" <-> "OD2" Residue "X GLU 142": "OE1" <-> "OE2" Residue "X GLU 155": "OE1" <-> "OE2" Residue "H TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 31": "OE1" <-> "OE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H GLU 96": "OE1" <-> "OE2" Residue "H ASP 111": "OD1" <-> "OD2" Residue "H TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 120": "OE1" <-> "OE2" Residue "H ARG 129": "NH1" <-> "NH2" Residue "G GLU 24": "OE1" <-> "OE2" Residue "G ASP 36": "OD1" <-> "OD2" Residue "G TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G ARG 49": "NH1" <-> "NH2" Residue "G ASP 71": "OD1" <-> "OD2" Residue "G TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 84": "NH1" <-> "NH2" Residue "G PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 161": "OE1" <-> "OE2" Residue "G ASP 165": "OD1" <-> "OD2" Residue "G ASP 194": "OD1" <-> "OD2" Residue "G ASP 196": "OD1" <-> "OD2" Residue "G ASP 197": "OD1" <-> "OD2" Residue "G ARG 221": "NH1" <-> "NH2" Residue "G GLU 259": "OE1" <-> "OE2" Residue "G GLU 275": "OE1" <-> "OE2" Residue "G GLU 278": "OE1" <-> "OE2" Residue "F ASP 14": "OD1" <-> "OD2" Residue "F GLU 76": "OE1" <-> "OE2" Residue "F TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 134": "OD1" <-> "OD2" Residue "F GLU 169": "OE1" <-> "OE2" Residue "F PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 195": "OD1" <-> "OD2" Residue "F GLU 211": "OE1" <-> "OE2" Residue "F GLU 228": "OE1" <-> "OE2" Residue "F ASP 236": "OD1" <-> "OD2" Residue "F TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 253": "OE1" <-> "OE2" Residue "F TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 338": "OD1" <-> "OD2" Residue "F ASP 355": "OD1" <-> "OD2" Residue "F ASP 372": "OD1" <-> "OD2" Residue "F ASP 386": "OD1" <-> "OD2" Residue "F PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 422": "OD1" <-> "OD2" Residue "F TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 440": "OE1" <-> "OE2" Residue "E GLU 36": "OE1" <-> "OE2" Residue "E GLU 118": "OE1" <-> "OE2" Residue "E GLU 127": "OE1" <-> "OE2" Residue "E ASP 134": "OD1" <-> "OD2" Residue "E ASP 200": "OD1" <-> "OD2" Residue "E ASP 242": "OD1" <-> "OD2" Residue "E GLU 273": "OE1" <-> "OE2" Residue "E ASP 302": "OD1" <-> "OD2" Residue "E ASP 305": "OD1" <-> "OD2" Residue "E ASP 345": "OD1" <-> "OD2" Residue "E GLU 384": "OE1" <-> "OE2" Residue "E ASP 386": "OD1" <-> "OD2" Residue "E PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 408": "OE1" <-> "OE2" Residue "E PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 20": "OD1" <-> "OD2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D GLU 124": "OE1" <-> "OE2" Residue "D ASP 134": "OD1" <-> "OD2" Residue "D TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 188": "OD1" <-> "OD2" Residue "D GLU 192": "OE1" <-> "OE2" Residue "D GLU 211": "OE1" <-> "OE2" Residue "D PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 233": "OE1" <-> "OE2" Residue "D ASP 242": "OD1" <-> "OD2" Residue "D TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 316": "OD1" <-> "OD2" Residue "D ASP 345": "OD1" <-> "OD2" Residue "D GLU 369": "OE1" <-> "OE2" Residue "D ASP 372": "OD1" <-> "OD2" Residue "D ASP 380": "OD1" <-> "OD2" Residue "D GLU 384": "OE1" <-> "OE2" Residue "D GLU 385": "OE1" <-> "OE2" Residue "D ASP 386": "OD1" <-> "OD2" Residue "D GLU 440": "OE1" <-> "OE2" Residue "D PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 50": "NH1" <-> "NH2" Residue "J TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 37": "OE1" <-> "OE2" Residue "L ASP 44": "OD1" <-> "OD2" Residue "L ARG 50": "NH1" <-> "NH2" Residue "L TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 7": "OD1" <-> "OD2" Residue "M TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 37": "OE1" <-> "OE2" Residue "M ASP 44": "OD1" <-> "OD2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "N ASP 7": "OD1" <-> "OD2" Residue "N TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 44": "OD1" <-> "OD2" Residue "N ARG 50": "NH1" <-> "NH2" Residue "O ASP 7": "OD1" <-> "OD2" Residue "O GLU 37": "OE1" <-> "OE2" Residue "O ARG 50": "NH1" <-> "NH2" Residue "P ASP 7": "OD1" <-> "OD2" Residue "P GLU 37": "OE1" <-> "OE2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "P PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 50": "NH1" <-> "NH2" Residue "R ASP 7": "OD1" <-> "OD2" Residue "R TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "R ARG 41": "NH1" <-> "NH2" Residue "R ARG 50": "NH1" <-> "NH2" Residue "Y GLU 39": "OE1" <-> "OE2" Residue "Y ASP 42": "OD1" <-> "OD2" Residue "Y GLU 48": "OE1" <-> "OE2" Residue "Y GLU 71": "OE1" <-> "OE2" Residue "Y ARG 83": "NH1" <-> "NH2" Residue "Y ASP 88": "OD1" <-> "OD2" Residue "Y GLU 97": "OE1" <-> "OE2" Residue "Y ARG 98": "NH1" <-> "NH2" Residue "Y GLU 110": "OE1" <-> "OE2" Residue "Y ARG 113": "NH1" <-> "NH2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Y ARG 117": "NH1" <-> "NH2" Residue "Y ARG 121": "NH1" <-> "NH2" Residue "Y ARG 138": "NH1" <-> "NH2" Residue "a TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 30": "OD1" <-> "OD2" Residue "a PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 80": "OE1" <-> "OE2" Residue "a PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 219": "OE1" <-> "OE2" Residue "a PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 269": "OE1" <-> "OE2" Residue "I ASP 7": "OD1" <-> "OD2" Residue "I TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 50": "NH1" <-> "NH2" Residue "I PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 44": "OD1" <-> "OD2" Residue "S ARG 50": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 36971 Number of models: 1 Model: "" Number of chains: 28 Chain: "W" Number of atoms: 1320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1320 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 3, 'TRANS': 169} Chain: "C" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3869 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3871 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 494} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 3832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3832 Classifications: {'peptide': 508} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 489} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "H" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1034 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "G" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2186 Classifications: {'peptide': 284} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 274} Chain: "F" Number of atoms: 3520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3520 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 437} Chain: "E" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "D" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "J" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "L" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "M" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "N" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "O" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "P" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Q" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "R" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 552 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "Y" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "a" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2104 Classifications: {'peptide': 266} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 250} Chain: "I" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "S" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 18.05, per 1000 atoms: 0.49 Number of scatterers: 36971 At special positions: 0 Unit cell: (176.956, 219.037, 138.112, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 180 16.00 P 16 15.00 Mg 5 11.99 O 6968 8.00 N 6317 7.00 C 23485 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.47 Conformation dependent library (CDL) restraints added in 4.4 seconds 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8818 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 183 helices and 26 sheets defined 55.6% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 815.85 Creating SS restraints... Processing helix chain 'W' and resid 8 through 20 Processing helix chain 'W' and resid 24 through 39 removed outlier: 3.971A pdb=" N LYS W 39 " --> pdb=" O ALA W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 41 through 46 removed outlier: 3.563A pdb=" N GLU W 45 " --> pdb=" O GLU W 41 " (cutoff:3.500A) Processing helix chain 'W' and resid 53 through 63 removed outlier: 3.901A pdb=" N GLU W 58 " --> pdb=" O GLU W 54 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL W 63 " --> pdb=" O SER W 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 81 Processing helix chain 'W' and resid 85 through 102 Proline residue: W 89 - end of helix removed outlier: 4.061A pdb=" N LEU W 92 " --> pdb=" O PRO W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 120 through 131 removed outlier: 3.683A pdb=" N LYS W 130 " --> pdb=" O ALA W 126 " (cutoff:3.500A) Processing helix chain 'W' and resid 163 through 171 Processing helix chain 'C' and resid 9 through 17 Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 136 through 138 No H-bonds generated for 'chain 'C' and resid 136 through 138' Processing helix chain 'C' and resid 151 through 156 removed outlier: 3.671A pdb=" N MET C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 188 removed outlier: 4.091A pdb=" N GLN C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ASP C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 removed outlier: 3.821A pdb=" N ASN C 207 " --> pdb=" O SER C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 232 through 236 Processing helix chain 'C' and resid 238 through 252 removed outlier: 3.669A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 276 Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 288 through 300 removed outlier: 4.287A pdb=" N PHE C 291 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 293 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER C 295 " --> pdb=" O TYR C 292 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG C 296 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU C 299 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 312 Processing helix chain 'C' and resid 333 through 335 No H-bonds generated for 'chain 'C' and resid 333 through 335' Processing helix chain 'C' and resid 340 through 348 removed outlier: 3.608A pdb=" N ASN C 344 " --> pdb=" O PHE C 340 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER C 347 " --> pdb=" O THR C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 378 through 381 Processing helix chain 'C' and resid 384 through 412 removed outlier: 3.773A pdb=" N GLY C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR C 395 " --> pdb=" O GLY C 391 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ALA C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N PHE C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER C 407 " --> pdb=" O LEU C 403 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLN C 408 " --> pdb=" O ALA C 404 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N PHE C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N SER C 411 " --> pdb=" O SER C 407 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ASP C 412 " --> pdb=" O GLN C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 431 removed outlier: 4.354A pdb=" N GLN C 420 " --> pdb=" O ALA C 416 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS C 426 " --> pdb=" O ASP C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 452 Processing helix chain 'C' and resid 455 through 457 No H-bonds generated for 'chain 'C' and resid 455 through 457' Processing helix chain 'C' and resid 461 through 478 removed outlier: 3.665A pdb=" N ILE C 464 " --> pdb=" O LEU C 461 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLY C 465 " --> pdb=" O SER C 462 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP C 478 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 removed outlier: 3.653A pdb=" N GLN C 488 " --> pdb=" O GLN C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 510 Processing helix chain 'B' and resid 5 through 17 removed outlier: 3.643A pdb=" N ILE B 12 " --> pdb=" O ILE B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 188 removed outlier: 3.752A pdb=" N ALA B 182 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ASP B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 232 through 252 Proline residue: B 239 - end of helix removed outlier: 3.670A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 277 removed outlier: 3.501A pdb=" N LEU B 277 " --> pdb=" O ILE B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 288 through 300 removed outlier: 4.404A pdb=" N PHE B 291 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 293 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG B 296 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU B 299 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 312 Processing helix chain 'B' and resid 333 through 335 No H-bonds generated for 'chain 'B' and resid 333 through 335' Processing helix chain 'B' and resid 340 through 346 Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 378 through 381 Processing helix chain 'B' and resid 384 through 390 Processing helix chain 'B' and resid 393 through 406 removed outlier: 3.712A pdb=" N GLU B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 431 Processing helix chain 'B' and resid 441 through 452 Processing helix chain 'B' and resid 461 through 477 removed outlier: 3.695A pdb=" N ILE B 464 " --> pdb=" O LEU B 461 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLY B 465 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL B 475 " --> pdb=" O LEU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 486 Processing helix chain 'B' and resid 494 through 510 Processing helix chain 'A' and resid 7 through 19 Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 151 through 156 removed outlier: 3.573A pdb=" N SER A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 151 through 156' Processing helix chain 'A' and resid 175 through 188 removed outlier: 3.997A pdb=" N GLN A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARG A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ASP A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 232 through 251 Proline residue: A 239 - end of helix removed outlier: 3.715A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 277 removed outlier: 4.045A pdb=" N LEU A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 290 through 300 removed outlier: 3.605A pdb=" N HIS A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ARG A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 Processing helix chain 'A' and resid 333 through 335 No H-bonds generated for 'chain 'A' and resid 333 through 335' Processing helix chain 'A' and resid 340 through 347 removed outlier: 3.662A pdb=" N SER A 347 " --> pdb=" O THR A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 393 through 406 removed outlier: 3.760A pdb=" N GLU A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 430 removed outlier: 3.667A pdb=" N GLN A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 452 Processing helix chain 'A' and resid 461 through 478 removed outlier: 4.436A pdb=" N GLY A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N SER A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 489 Processing helix chain 'A' and resid 494 through 509 removed outlier: 3.566A pdb=" N LYS A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 24 removed outlier: 3.719A pdb=" N GLN X 10 " --> pdb=" O ILE X 7 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL X 15 " --> pdb=" O ILE X 12 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU X 16 " --> pdb=" O ALA X 13 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE X 20 " --> pdb=" O PHE X 17 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS X 23 " --> pdb=" O PHE X 20 " (cutoff:3.500A) Processing helix chain 'X' and resid 26 through 135 removed outlier: 3.541A pdb=" N ALA X 32 " --> pdb=" O PRO X 28 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE X 33 " --> pdb=" O LEU X 29 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG X 36 " --> pdb=" O ALA X 32 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS X 51 " --> pdb=" O ALA X 47 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU X 54 " --> pdb=" O ALA X 50 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER X 60 " --> pdb=" O LEU X 56 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE X 76 " --> pdb=" O ALA X 72 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN X 96 " --> pdb=" O ALA X 92 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS X 114 " --> pdb=" O GLU X 110 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU X 119 " --> pdb=" O ARG X 115 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N LYS X 122 " --> pdb=" O GLU X 118 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN X 123 " --> pdb=" O GLU X 119 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE X 126 " --> pdb=" O LYS X 122 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL X 129 " --> pdb=" O ALA X 125 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA X 132 " --> pdb=" O ALA X 128 " (cutoff:3.500A) Processing helix chain 'X' and resid 143 through 145 No H-bonds generated for 'chain 'X' and resid 143 through 145' Processing helix chain 'X' and resid 148 through 155 Processing helix chain 'H' and resid 88 through 102 removed outlier: 3.694A pdb=" N ALA H 92 " --> pdb=" O ASP H 88 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 124 Processing helix chain 'H' and resid 130 through 132 No H-bonds generated for 'chain 'H' and resid 130 through 132' Processing helix chain 'G' and resid 2 through 57 removed outlier: 3.658A pdb=" N ALA G 39 " --> pdb=" O GLN G 35 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER G 41 " --> pdb=" O ARG G 37 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Proline residue: G 43 - end of helix removed outlier: 3.755A pdb=" N HIS G 57 " --> pdb=" O GLY G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 67 No H-bonds generated for 'chain 'G' and resid 65 through 67' Processing helix chain 'G' and resid 90 through 107 removed outlier: 3.566A pdb=" N THR G 104 " --> pdb=" O ALA G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 128 Processing helix chain 'G' and resid 145 through 160 removed outlier: 5.285A pdb=" N GLY G 150 " --> pdb=" O SER G 146 " (cutoff:3.500A) Proline residue: G 151 - end of helix Processing helix chain 'G' and resid 199 through 202 removed outlier: 3.890A pdb=" N SER G 202 " --> pdb=" O LYS G 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 199 through 202' Processing helix chain 'G' and resid 211 through 282 removed outlier: 3.590A pdb=" N ASP G 216 " --> pdb=" O LYS G 212 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR G 217 " --> pdb=" O ALA G 213 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL G 244 " --> pdb=" O ALA G 240 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS G 258 " --> pdb=" O GLY G 254 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU G 259 " --> pdb=" O SER G 255 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU G 262 " --> pdb=" O LYS G 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 83 No H-bonds generated for 'chain 'F' and resid 81 through 83' Processing helix chain 'F' and resid 116 through 118 No H-bonds generated for 'chain 'F' and resid 116 through 118' Processing helix chain 'F' and resid 131 through 136 Processing helix chain 'F' and resid 157 through 166 Processing helix chain 'F' and resid 183 through 195 Processing helix chain 'F' and resid 199 through 201 No H-bonds generated for 'chain 'F' and resid 199 through 201' Processing helix chain 'F' and resid 213 through 232 removed outlier: 4.919A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET F 226 " --> pdb=" O THR F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 258 removed outlier: 3.991A pdb=" N ALA F 250 " --> pdb=" O TYR F 247 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU F 253 " --> pdb=" O ALA F 250 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER F 255 " --> pdb=" O THR F 252 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ALA F 256 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 279 removed outlier: 3.965A pdb=" N LEU F 278 " --> pdb=" O GLU F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 301 No H-bonds generated for 'chain 'F' and resid 299 through 301' Processing helix chain 'F' and resid 306 through 314 removed outlier: 4.525A pdb=" N ALA F 313 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N HIS F 314 " --> pdb=" O THR F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 328 removed outlier: 4.320A pdb=" N LEU F 328 " --> pdb=" O GLN F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 377 removed outlier: 7.340A pdb=" N GLN F 351 " --> pdb=" O LEU F 347 " (cutoff:3.500A) removed outlier: 9.341A pdb=" N GLU F 352 " --> pdb=" O VAL F 348 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N HIS F 353 " --> pdb=" O VAL F 349 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS F 371 " --> pdb=" O TYR F 367 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ASP F 372 " --> pdb=" O GLN F 368 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ILE F 373 " --> pdb=" O GLU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 381 No H-bonds generated for 'chain 'F' and resid 379 through 381' Processing helix chain 'F' and resid 386 through 400 Processing helix chain 'F' and resid 408 through 411 No H-bonds generated for 'chain 'F' and resid 408 through 411' Processing helix chain 'F' and resid 420 through 432 removed outlier: 3.727A pdb=" N ARG F 425 " --> pdb=" O LYS F 421 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY F 426 " --> pdb=" O ASP F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 442 No H-bonds generated for 'chain 'F' and resid 440 through 442' Processing helix chain 'F' and resid 449 through 458 removed outlier: 4.015A pdb=" N LYS F 457 " --> pdb=" O VAL F 453 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LYS F 458 " --> pdb=" O GLU F 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 131 through 136 Processing helix chain 'E' and resid 155 through 168 Processing helix chain 'E' and resid 183 through 196 removed outlier: 3.788A pdb=" N SER E 196 " --> pdb=" O GLU E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 201 No H-bonds generated for 'chain 'E' and resid 199 through 201' Processing helix chain 'E' and resid 213 through 233 removed outlier: 5.066A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU E 233 " --> pdb=" O LYS E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 258 removed outlier: 3.582A pdb=" N GLY E 251 " --> pdb=" O TYR E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 279 removed outlier: 3.756A pdb=" N LEU E 278 " --> pdb=" O GLU E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 301 No H-bonds generated for 'chain 'E' and resid 299 through 301' Processing helix chain 'E' and resid 306 through 312 Processing helix chain 'E' and resid 323 through 327 Processing helix chain 'E' and resid 346 through 349 No H-bonds generated for 'chain 'E' and resid 346 through 349' Processing helix chain 'E' and resid 351 through 377 removed outlier: 4.391A pdb=" N GLU E 369 " --> pdb=" O GLN E 365 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE E 376 " --> pdb=" O ASP E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 381 No H-bonds generated for 'chain 'E' and resid 379 through 381' Processing helix chain 'E' and resid 384 through 399 removed outlier: 3.627A pdb=" N LEU E 388 " --> pdb=" O GLU E 384 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL E 389 " --> pdb=" O GLU E 385 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA E 391 " --> pdb=" O LYS E 387 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS E 395 " --> pdb=" O ALA E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 411 No H-bonds generated for 'chain 'E' and resid 408 through 411' Processing helix chain 'E' and resid 420 through 431 Processing helix chain 'E' and resid 440 through 442 No H-bonds generated for 'chain 'E' and resid 440 through 442' Processing helix chain 'E' and resid 449 through 457 removed outlier: 3.925A pdb=" N GLU E 454 " --> pdb=" O GLU E 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 131 through 136 Processing helix chain 'D' and resid 155 through 169 Processing helix chain 'D' and resid 183 through 195 Processing helix chain 'D' and resid 199 through 201 No H-bonds generated for 'chain 'D' and resid 199 through 201' Processing helix chain 'D' and resid 213 through 233 removed outlier: 5.024A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 257 Processing helix chain 'D' and resid 271 through 279 Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 306 through 311 Processing helix chain 'D' and resid 323 through 327 Processing helix chain 'D' and resid 346 through 377 removed outlier: 7.368A pdb=" N GLN D 351 " --> pdb=" O LEU D 347 " (cutoff:3.500A) removed outlier: 9.075A pdb=" N GLU D 352 " --> pdb=" O VAL D 348 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N HIS D 353 " --> pdb=" O VAL D 349 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 381 No H-bonds generated for 'chain 'D' and resid 379 through 381' Processing helix chain 'D' and resid 386 through 399 Processing helix chain 'D' and resid 407 through 411 removed outlier: 3.743A pdb=" N THR D 411 " --> pdb=" O GLU D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 431 Processing helix chain 'D' and resid 440 through 443 Processing helix chain 'D' and resid 449 through 456 Processing helix chain 'J' and resid 4 through 41 removed outlier: 5.074A pdb=" N LEU J 9 " --> pdb=" O MET J 6 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR J 10 " --> pdb=" O ASP J 7 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE J 28 " --> pdb=" O ALA J 25 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA J 40 " --> pdb=" O GLU J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 76 removed outlier: 4.123A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA J 62 " --> pdb=" O GLY J 58 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE J 63 " --> pdb=" O LEU J 59 " (cutoff:3.500A) Proline residue: J 64 - end of helix Processing helix chain 'L' and resid 7 through 41 Processing helix chain 'L' and resid 43 through 76 removed outlier: 3.518A pdb=" N ILE L 46 " --> pdb=" O PRO L 43 " (cutoff:3.500A) Proline residue: L 47 - end of helix removed outlier: 3.875A pdb=" N ASP L 61 " --> pdb=" O GLY L 58 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE L 63 " --> pdb=" O VAL L 60 " (cutoff:3.500A) Proline residue: L 64 - end of helix Processing helix chain 'M' and resid 4 through 41 removed outlier: 3.976A pdb=" N LEU M 8 " --> pdb=" O LEU M 4 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS M 34 " --> pdb=" O ILE M 30 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG M 41 " --> pdb=" O GLU M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 76 Proline residue: M 47 - end of helix removed outlier: 4.014A pdb=" N MET M 57 " --> pdb=" O PHE M 54 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILE M 63 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Proline residue: M 64 - end of helix removed outlier: 3.544A pdb=" N PHE M 76 " --> pdb=" O TYR M 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 41 removed outlier: 4.318A pdb=" N LEU N 8 " --> pdb=" O ASN N 5 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LEU N 9 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA N 12 " --> pdb=" O LEU N 9 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU N 37 " --> pdb=" O LYS N 34 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA N 40 " --> pdb=" O GLU N 37 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 76 Proline residue: N 47 - end of helix removed outlier: 3.642A pdb=" N GLY N 58 " --> pdb=" O ILE N 55 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP N 61 " --> pdb=" O GLY N 58 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA N 62 " --> pdb=" O LEU N 59 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE N 63 " --> pdb=" O VAL N 60 " (cutoff:3.500A) Proline residue: N 64 - end of helix removed outlier: 3.505A pdb=" N VAL N 68 " --> pdb=" O MET N 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 41 removed outlier: 4.664A pdb=" N LEU O 9 " --> pdb=" O MET O 6 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU O 19 " --> pdb=" O MET O 16 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE O 28 " --> pdb=" O ALA O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 60 removed outlier: 3.582A pdb=" N LEU O 59 " --> pdb=" O ILE O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 76 Processing helix chain 'P' and resid 6 through 41 removed outlier: 3.514A pdb=" N TYR P 10 " --> pdb=" O MET P 6 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 76 removed outlier: 3.751A pdb=" N LEU P 59 " --> pdb=" O ILE P 55 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA P 62 " --> pdb=" O GLY P 58 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ILE P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) Proline residue: P 64 - end of helix removed outlier: 3.673A pdb=" N LEU P 70 " --> pdb=" O ILE P 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 6 No H-bonds generated for 'chain 'Q' and resid 4 through 6' Processing helix chain 'Q' and resid 8 through 41 Processing helix chain 'Q' and resid 43 through 76 Proline residue: Q 47 - end of helix removed outlier: 3.937A pdb=" N MET Q 57 " --> pdb=" O PHE Q 54 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY Q 58 " --> pdb=" O ILE Q 55 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE Q 63 " --> pdb=" O VAL Q 60 " (cutoff:3.500A) Proline residue: Q 64 - end of helix Processing helix chain 'R' and resid 6 through 41 Processing helix chain 'R' and resid 46 through 76 removed outlier: 3.631A pdb=" N LEU R 59 " --> pdb=" O ILE R 55 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA R 62 " --> pdb=" O GLY R 58 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ILE R 63 " --> pdb=" O LEU R 59 " (cutoff:3.500A) Proline residue: R 64 - end of helix Processing helix chain 'Y' and resid 3 through 24 removed outlier: 3.764A pdb=" N ILE Y 12 " --> pdb=" O LEU Y 8 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA Y 13 " --> pdb=" O GLY Y 9 " (cutoff:3.500A) Processing helix chain 'Y' and resid 26 through 139 removed outlier: 3.593A pdb=" N THR Y 62 " --> pdb=" O LYS Y 58 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP Y 63 " --> pdb=" O ALA Y 59 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP Y 88 " --> pdb=" O SER Y 84 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS Y 91 " --> pdb=" O LEU Y 87 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN Y 96 " --> pdb=" O ALA Y 92 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN Y 106 " --> pdb=" O VAL Y 102 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA Y 107 " --> pdb=" O ALA Y 103 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU Y 108 " --> pdb=" O GLN Y 104 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU Y 110 " --> pdb=" O GLN Y 106 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL Y 129 " --> pdb=" O ALA Y 125 " (cutoff:3.500A) Processing helix chain 'Y' and resid 142 through 155 removed outlier: 3.606A pdb=" N ASP Y 147 " --> pdb=" O ALA Y 143 " (cutoff:3.500A) Processing helix chain 'a' and resid 8 through 16 removed outlier: 3.699A pdb=" N LEU a 16 " --> pdb=" O ILE a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 43 through 64 removed outlier: 3.840A pdb=" N VAL a 63 " --> pdb=" O LEU a 59 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 93 removed outlier: 3.727A pdb=" N ALA a 78 " --> pdb=" O LYS a 74 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE a 79 " --> pdb=" O PHE a 75 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET a 93 " --> pdb=" O SER a 89 " (cutoff:3.500A) Processing helix chain 'a' and resid 100 through 120 removed outlier: 4.136A pdb=" N ASP a 119 " --> pdb=" O MET a 115 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU a 120 " --> pdb=" O ASN a 116 " (cutoff:3.500A) Processing helix chain 'a' and resid 123 through 132 Proline residue: a 127 - end of helix removed outlier: 3.587A pdb=" N GLU a 131 " --> pdb=" O PRO a 127 " (cutoff:3.500A) Processing helix chain 'a' and resid 143 through 145 No H-bonds generated for 'chain 'a' and resid 143 through 145' Processing helix chain 'a' and resid 147 through 180 removed outlier: 3.516A pdb=" N ILE a 159 " --> pdb=" O LEU a 155 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS a 169 " --> pdb=" O SER a 165 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ILE a 171 " --> pdb=" O LYS a 167 " (cutoff:3.500A) removed outlier: 9.202A pdb=" N GLY a 172 " --> pdb=" O MET a 168 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 227 Proline residue: a 190 - end of helix removed outlier: 3.958A pdb=" N LEU a 193 " --> pdb=" O PRO a 190 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU a 196 " --> pdb=" O LEU a 193 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER a 202 " --> pdb=" O SER a 199 " (cutoff:3.500A) Proline residue: a 204 - end of helix Processing helix chain 'a' and resid 234 through 268 Proline residue: a 240 - end of helix removed outlier: 4.167A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE a 248 " --> pdb=" O PHE a 244 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA a 253 " --> pdb=" O ILE a 249 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE a 256 " --> pdb=" O GLN a 252 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 7 No H-bonds generated for 'chain 'I' and resid 4 through 7' Processing helix chain 'I' and resid 9 through 41 removed outlier: 3.508A pdb=" N ARG I 41 " --> pdb=" O GLU I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 76 Proline residue: I 47 - end of helix removed outlier: 3.734A pdb=" N ARG I 50 " --> pdb=" O PRO I 47 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE I 53 " --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL I 56 " --> pdb=" O PHE I 53 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY I 58 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP I 61 " --> pdb=" O GLY I 58 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE I 63 " --> pdb=" O VAL I 60 " (cutoff:3.500A) Proline residue: I 64 - end of helix removed outlier: 3.518A pdb=" N GLY I 69 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU I 70 " --> pdb=" O ALA I 67 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR I 73 " --> pdb=" O LEU I 70 " (cutoff:3.500A) Processing helix chain 'S' and resid 6 through 41 removed outlier: 3.698A pdb=" N TYR S 10 " --> pdb=" O MET S 6 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET S 11 " --> pdb=" O ASP S 7 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS S 34 " --> pdb=" O ILE S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 60 removed outlier: 3.628A pdb=" N ILE S 46 " --> pdb=" O PRO S 43 " (cutoff:3.500A) Proline residue: S 47 - end of helix removed outlier: 4.051A pdb=" N ARG S 50 " --> pdb=" O PRO S 47 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE S 55 " --> pdb=" O GLN S 52 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY S 58 " --> pdb=" O ILE S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 76 Processing sheet with id= A, first strand: chain 'W' and resid 135 through 142 Processing sheet with id= B, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.402A pdb=" N ARG C 40 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL C 34 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER C 70 " --> pdb=" O GLU C 67 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ARG C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 96 through 98 Processing sheet with id= D, first strand: chain 'C' and resid 107 through 109 removed outlier: 8.378A pdb=" N VAL C 108 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL C 223 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 8.871A pdb=" N ILE C 222 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N CYS C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N VAL C 224 " --> pdb=" O CYS C 193 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASP C 255 " --> pdb=" O LYS C 192 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ILE C 194 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU C 257 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N VAL C 196 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE C 259 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ILE C 198 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASP C 261 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N SER C 323 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE C 258 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N THR C 325 " --> pdb=" O ILE C 258 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N TYR C 260 " --> pdb=" O THR C 325 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 352 through 355 removed outlier: 6.576A pdb=" N LEU C 166 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N LEU C 355 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE C 168 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 87 through 90 removed outlier: 4.595A pdb=" N ASN B 27 " --> pdb=" O CYS B 90 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ARG B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 96 through 98 Processing sheet with id= H, first strand: chain 'B' and resid 352 through 355 removed outlier: 6.509A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE B 168 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 221 through 226 removed outlier: 6.858A pdb=" N CYS B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N VAL B 224 " --> pdb=" O CYS B 193 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N SER B 323 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ILE B 258 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N THR B 325 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N TYR B 260 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.350A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 96 through 98 Processing sheet with id= L, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.608A pdb=" N LEU A 166 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LEU A 355 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE A 168 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 221 through 226 removed outlier: 6.825A pdb=" N CYS A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N VAL A 224 " --> pdb=" O CYS A 193 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N SER A 323 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ILE A 258 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N THR A 325 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N TYR A 260 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU A 327 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 41 through 45 removed outlier: 3.618A pdb=" N GLY H 67 " --> pdb=" O ILE H 45 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE H 68 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N HIS H 5 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N VAL H 78 " --> pdb=" O HIS H 5 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASP H 7 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL H 53 " --> pdb=" O GLU H 21 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE H 23 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG H 51 " --> pdb=" O ILE H 23 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 22 through 27 Processing sheet with id= P, first strand: chain 'G' and resid 180 through 188 removed outlier: 6.558A pdb=" N LEU G 167 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS G 166 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ASN G 172 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN G 111 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N TYR G 77 " --> pdb=" O GLN G 111 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ASP G 113 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL G 79 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA G 115 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N MET G 116 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLN G 135 " --> pdb=" O MET G 116 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 3 through 9 removed outlier: 6.558A pdb=" N ASP F 14 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE F 54 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL F 42 " --> pdb=" O ILE F 54 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 76 through 79 removed outlier: 4.804A pdb=" N GLU F 105 " --> pdb=" O VAL F 79 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 317 through 320 removed outlier: 7.911A pdb=" N VAL F 145 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER F 292 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LEU F 147 " --> pdb=" O SER F 292 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLN F 294 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N GLY F 149 " --> pdb=" O GLN F 294 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL F 296 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 4 through 9 removed outlier: 6.474A pdb=" N ASP E 14 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL E 8 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL E 12 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE E 54 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N VAL E 42 " --> pdb=" O ILE E 54 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 76 through 78 Processing sheet with id= V, first strand: chain 'E' and resid 317 through 319 removed outlier: 8.546A pdb=" N VAL E 145 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N SER E 292 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LEU E 147 " --> pdb=" O SER E 292 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLN E 294 " --> pdb=" O LEU E 147 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 3 through 9 removed outlier: 6.486A pdb=" N ASP D 14 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL D 8 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE D 54 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N VAL D 42 " --> pdb=" O ILE D 54 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU D 36 " --> pdb=" O ASN D 33 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 76 through 78 Processing sheet with id= Y, first strand: chain 'D' and resid 317 through 320 removed outlier: 8.765A pdb=" N VAL D 145 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER D 292 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N LEU D 147 " --> pdb=" O SER D 292 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN D 294 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N GLY D 149 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL D 296 " --> pdb=" O GLY D 149 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'a' and resid 20 through 22 1941 hydrogen bonds defined for protein. 4869 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: 10.83 Time building geometry restraints manager: 14.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 6333 1.30 - 1.42: 8611 1.42 - 1.55: 22200 1.55 - 1.68: 24 1.68 - 1.81: 360 Bond restraints: 37528 Sorted by residual: bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.21e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.09e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.01e+01 bond pdb=" C5 ATP B 600 " pdb=" C6 ATP B 600 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.85e+01 bond pdb=" C VAL F 205 " pdb=" O VAL F 205 " ideal model delta sigma weight residual 1.237 1.170 0.066 1.07e-02 8.73e+03 3.84e+01 ... (remaining 37523 not shown) Histogram of bond angle deviations from ideal: 97.88 - 105.57: 843 105.57 - 113.26: 21099 113.26 - 120.95: 19048 120.95 - 128.65: 9611 128.65 - 136.34: 196 Bond angle restraints: 50797 Sorted by residual: angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 118.69 21.18 1.00e+00 1.00e+00 4.49e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 118.75 21.12 1.00e+00 1.00e+00 4.46e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 119.39 20.48 1.00e+00 1.00e+00 4.19e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 117.42 19.41 1.00e+00 1.00e+00 3.77e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 120.69 16.14 1.00e+00 1.00e+00 2.61e+02 ... (remaining 50792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.39: 21943 29.39 - 58.77: 669 58.77 - 88.16: 80 88.16 - 117.54: 4 117.54 - 146.93: 5 Dihedral angle restraints: 22701 sinusoidal: 8917 harmonic: 13784 Sorted by residual: dihedral pdb=" O1B ADP D 500 " pdb=" O3A ADP D 500 " pdb=" PB ADP D 500 " pdb=" PA ADP D 500 " ideal model delta sinusoidal sigma weight residual 300.00 153.07 146.93 1 2.00e+01 2.50e-03 4.41e+01 dihedral pdb=" O2A ADP F 500 " pdb=" O3A ADP F 500 " pdb=" PA ADP F 500 " pdb=" PB ADP F 500 " ideal model delta sinusoidal sigma weight residual -60.00 85.51 -145.51 1 2.00e+01 2.50e-03 4.38e+01 dihedral pdb=" C5' ADP D 500 " pdb=" O5' ADP D 500 " pdb=" PA ADP D 500 " pdb=" O2A ADP D 500 " ideal model delta sinusoidal sigma weight residual 300.00 166.99 133.02 1 2.00e+01 2.50e-03 4.04e+01 ... (remaining 22698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 5534 0.094 - 0.188: 362 0.188 - 0.282: 18 0.282 - 0.376: 4 0.376 - 0.469: 2 Chirality restraints: 5920 Sorted by residual: chirality pdb=" CA GLN B 511 " pdb=" N GLN B 511 " pdb=" C GLN B 511 " pdb=" CB GLN B 511 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.51e+00 chirality pdb=" CA LEU a 178 " pdb=" N LEU a 178 " pdb=" C LEU a 178 " pdb=" CB LEU a 178 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" CA ASP C 261 " pdb=" N ASP C 261 " pdb=" C ASP C 261 " pdb=" CB ASP C 261 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 ... (remaining 5917 not shown) Planarity restraints: 6550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 264 " 0.024 2.00e-02 2.50e+03 4.86e-02 2.36e+01 pdb=" C ALA D 264 " -0.084 2.00e-02 2.50e+03 pdb=" O ALA D 264 " 0.030 2.00e-02 2.50e+03 pdb=" N VAL D 265 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 261 " -0.022 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C ASP A 261 " 0.075 2.00e-02 2.50e+03 pdb=" O ASP A 261 " -0.027 2.00e-02 2.50e+03 pdb=" N ASP A 262 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 264 " 0.021 2.00e-02 2.50e+03 4.25e-02 1.81e+01 pdb=" C ALA E 264 " -0.074 2.00e-02 2.50e+03 pdb=" O ALA E 264 " 0.027 2.00e-02 2.50e+03 pdb=" N VAL E 265 " 0.026 2.00e-02 2.50e+03 ... (remaining 6547 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 46 2.41 - 3.03: 24595 3.03 - 3.65: 53379 3.65 - 4.28: 84573 4.28 - 4.90: 142032 Nonbonded interactions: 304625 Sorted by model distance: nonbonded pdb=" O2G ATP C 600 " pdb="MG MG C 601 " model vdw 1.781 2.170 nonbonded pdb=" O2B ATP A 600 " pdb="MG MG A 601 " model vdw 1.852 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 601 " model vdw 1.860 2.170 nonbonded pdb=" O3 PO4 D 501 " pdb="MG MG D 502 " model vdw 1.870 2.170 nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.888 2.170 ... (remaining 304620 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' and (resid 4 through 408 or (resid 409 through 410 and (name N or nam \ e CA or name C or name O or name CB )) or resid 411 through 511 or resid 600 thr \ ough 601)) selection = (chain 'B' and (resid 4 through 511 or resid 600 through 601)) selection = (chain 'C' and (resid 4 through 408 or (resid 409 through 410 and (name N or nam \ e CA or name C or name O or name CB )) or resid 411 through 511 or resid 600 thr \ ough 601)) } ncs_group { reference = (chain 'D' and (resid 2 through 459 or resid 500)) selection = (chain 'E' and (resid 2 through 459 or resid 500)) selection = (chain 'F' and (resid 2 through 459 or resid 500)) } ncs_group { reference = (chain 'I' and resid 3 through 78) selection = (chain 'J' and resid 3 through 78) selection = (chain 'L' and resid 3 through 78) selection = (chain 'M' and resid 3 through 78) selection = (chain 'N' and resid 3 through 78) selection = (chain 'O' and resid 3 through 78) selection = (chain 'P' and resid 3 through 78) selection = (chain 'Q' and resid 3 through 78) selection = chain 'R' selection = (chain 'S' and resid 3 through 78) } ncs_group { reference = chain 'X' selection = chain 'Y' } 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: 0.010 Normalize map: mean=0, sd=1: 2.340 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: 0.030 Extract box with map and model: 12.520 Check model and map are aligned: 0.560 Set scattering table: 0.310 Process input model: 80.840 Find NCS groups from input model: 3.260 Set up NCS constraints: 0.210 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 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 : 0.008 0.114 37528 Z= 0.510 Angle : 0.855 21.180 50797 Z= 0.552 Chirality : 0.050 0.469 5920 Planarity : 0.004 0.049 6550 Dihedral : 14.363 146.931 13883 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.11), residues: 4807 helix: -1.46 (0.09), residues: 2654 sheet: -0.52 (0.20), residues: 538 loop : -1.26 (0.14), residues: 1615 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 750 time to evaluate : 4.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 32 residues processed: 813 average time/residue: 0.5089 time to fit residues: 652.6380 Evaluate side-chains 634 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 602 time to evaluate : 3.497 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.2667 time to fit residues: 20.7445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 399 optimal weight: 0.7980 chunk 358 optimal weight: 0.9980 chunk 198 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 241 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 370 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 225 optimal weight: 0.8980 chunk 275 optimal weight: 0.9990 chunk 429 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: