Starting phenix.real_space_refine (version: 1.21rc1) on Mon May 15 14:22:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqw_20172/05_2023/6oqw_20172_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqw_20172/05_2023/6oqw_20172.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/6oqw_20172/05_2023/6oqw_20172.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqw_20172/05_2023/6oqw_20172.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqw_20172/05_2023/6oqw_20172_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqw_20172/05_2023/6oqw_20172_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 23445 2.51 5 N 6306 2.21 5 O 6949 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "W PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 26": "NH1" <-> "NH2" Residue "W ASP 29": "OD1" <-> "OD2" Residue "W GLU 41": "OE1" <-> "OE2" Residue "W GLU 45": "OE1" <-> "OE2" Residue "W PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 70": "OE1" <-> "OE2" Residue "W ARG 77": "NH1" <-> "NH2" Residue "W PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 103": "OE1" <-> "OE2" Residue "W ASP 156": "OD1" <-> "OD2" Residue "W ARG 164": "NH1" <-> "NH2" Residue "W GLU 168": "OE1" <-> "OE2" Residue "C PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C ARG 93": "NH1" <-> "NH2" Residue "C PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 161": "NH1" <-> "NH2" Residue "C ASP 170": "OD1" <-> "OD2" Residue "C ASP 181": "OD1" <-> "OD2" Residue "C TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 252": "NH1" <-> "NH2" Residue "C ASP 261": "OD1" <-> "OD2" Residue "C PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "C TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 356": "OE1" <-> "OE2" Residue "C PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 376": "NH1" <-> "NH2" Residue "C TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 422": "OD1" <-> "OD2" Residue "C PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 460": "OE1" <-> "OE2" Residue "C PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B GLU 24": "OE1" <-> "OE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 284": "OE1" <-> "OE2" Residue "B PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B GLU 316": "OE1" <-> "OE2" Residue "B GLU 331": "OE1" <-> "OE2" Residue "B ASP 336": "OD1" <-> "OD2" Residue "B ASP 350": "OD1" <-> "OD2" Residue "B ARG 376": "NH1" <-> "NH2" Residue "B ASP 415": "OD1" <-> "OD2" Residue "B ARG 418": "NH1" <-> "NH2" Residue "B ASP 422": "OD1" <-> "OD2" Residue "B GLU 429": "OE1" <-> "OE2" Residue "B PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 452": "OE1" <-> "OE2" Residue "B ARG 453": "NH1" <-> "NH2" Residue "B PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 476": "OD1" <-> "OD2" Residue "B ARG 477": "NH1" <-> "NH2" Residue "B TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 494": "OD1" <-> "OD2" Residue "A GLU 10": "OE1" <-> "OE2" Residue "A ASP 69": "OD1" <-> "OD2" Residue "A ASP 116": "OD1" <-> "OD2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A GLU 165": "OE1" <-> "OE2" 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 TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 262": "OD1" <-> "OD2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 336": "OD1" <-> "OD2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 422": "OD1" <-> "OD2" Residue "A PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 452": "OE1" <-> "OE2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 476": "OD1" <-> "OD2" Residue "A TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 494": "OD1" <-> "OD2" Residue "A PHE 507": "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 ASP 53": "OD1" <-> "OD2" Residue "X ASP 63": "OD1" <-> "OD2" Residue "X ARG 83": "NH1" <-> "NH2" Residue "X GLU 89": "OE1" <-> "OE2" Residue "X ARG 98": "NH1" <-> "NH2" Residue "X GLU 110": "OE1" <-> "OE2" 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 133": "OE1" <-> "OE2" Residue "X ASP 141": "OD1" <-> "OD2" Residue "H TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 29": "OE1" <-> "OE2" Residue "H ASP 81": "OD1" <-> "OD2" Residue "H GLU 96": "OE1" <-> "OE2" Residue "H GLU 102": "OE1" <-> "OE2" Residue "H ASP 111": "OD1" <-> "OD2" Residue "H ARG 129": "NH1" <-> "NH2" Residue "H GLU 132": "OE1" <-> "OE2" Residue "G TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 49": "NH1" <-> "NH2" Residue "G GLU 68": "OE1" <-> "OE2" Residue "G TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 84": "NH1" <-> "NH2" Residue "G GLU 101": "OE1" <-> "OE2" Residue "G PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 161": "OE1" <-> "OE2" Residue "G PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 196": "OD1" <-> "OD2" Residue "G ASP 197": "OD1" <-> "OD2" Residue "G TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 210": "OD1" <-> "OD2" Residue "G ARG 221": "NH1" <-> "NH2" Residue "G GLU 233": "OE1" <-> "OE2" Residue "G GLU 275": "OE1" <-> "OE2" Residue "F ASP 20": "OD1" <-> "OD2" Residue "F GLU 36": "OE1" <-> "OE2" Residue "F GLU 76": "OE1" <-> "OE2" Residue "F TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 169": "OE1" <-> "OE2" Residue "F PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 200": "OD1" <-> "OD2" Residue "F ASP 242": "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 GLU 280": "OE1" <-> "OE2" Residue "F TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 305": "OD1" <-> "OD2" Residue "F ASP 338": "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 "F PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 454": "OE1" <-> "OE2" Residue "E GLU 36": "OE1" <-> "OE2" Residue "E ASP 60": "OD1" <-> "OD2" Residue "E ASP 134": "OD1" <-> "OD2" Residue "E ASP 188": "OD1" <-> "OD2" Residue "E ASP 195": "OD1" <-> "OD2" Residue "E ASP 242": "OD1" <-> "OD2" Residue "E GLU 273": "OE1" <-> "OE2" Residue "E ASP 301": "OD1" <-> "OD2" Residue "E ASP 305": "OD1" <-> "OD2" Residue "E ASP 338": "OD1" <-> "OD2" Residue "E ASP 345": "OD1" <-> "OD2" Residue "E ASP 355": "OD1" <-> "OD2" Residue "E ASP 372": "OD1" <-> "OD2" Residue "E ASP 380": "OD1" <-> "OD2" Residue "E GLU 384": "OE1" <-> "OE2" Residue "E TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 440": "OE1" <-> "OE2" Residue "E PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D GLU 104": "OE1" <-> "OE2" Residue "D GLU 118": "OE1" <-> "OE2" Residue "D ARG 164": "NH1" <-> "NH2" 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 GLU 273": "OE1" <-> "OE2" Residue "D GLU 280": "OE1" <-> "OE2" Residue "D ASP 301": "OD1" <-> "OD2" Residue "D ASP 316": "OD1" <-> "OD2" Residue "D ASP 345": "OD1" <-> "OD2" Residue "D ASP 355": "OD1" <-> "OD2" 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 PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 440": "OE1" <-> "OE2" Residue "I ASP 7": "OD1" <-> "OD2" Residue "I TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 44": "OD1" <-> "OD2" Residue "I ARG 50": "NH1" <-> "NH2" Residue "J TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 37": "OE1" <-> "OE2" Residue "J ARG 50": "NH1" <-> "NH2" Residue "J ASP 61": "OD1" <-> "OD2" Residue "J TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 7": "OD1" <-> "OD2" Residue "L GLU 37": "OE1" <-> "OE2" Residue "L ASP 44": "OD1" <-> "OD2" Residue "L ARG 50": "NH1" <-> "NH2" Residue "L PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 50": "NH1" <-> "NH2" Residue "M PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "N ASP 61": "OD1" <-> "OD2" Residue "O TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 37": "OE1" <-> "OE2" Residue "O ARG 50": "NH1" <-> "NH2" Residue "O TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 7": "OD1" <-> "OD2" Residue "P TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 37": "OE1" <-> "OE2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "Q TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 50": "NH1" <-> "NH2" Residue "R TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 41": "NH1" <-> "NH2" Residue "R ARG 50": "NH1" <-> "NH2" Residue "S TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 50": "NH1" <-> "NH2" Residue "S TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 39": "OE1" <-> "OE2" Residue "Y ASP 42": "OD1" <-> "OD2" Residue "Y GLU 48": "OE1" <-> "OE2" Residue "Y ARG 83": "NH1" <-> "NH2" Residue "Y ASP 88": "OD1" <-> "OD2" Residue "Y ARG 98": "NH1" <-> "NH2" 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 "Y ASP 141": "OD1" <-> "OD2" Residue "Y ASP 150": "OD1" <-> "OD2" Residue "a TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 30": "OD1" <-> "OD2" Residue "a ASP 44": "OD1" <-> "OD2" Residue "a PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 219": "OE1" <-> "OE2" Residue "a PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 269": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 36901 Number of models: 1 Model: "" Number of chains: 28 Chain: "W" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1317 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3849 Classifications: {'peptide': 510} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 491} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3877 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 494} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 3852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3852 Classifications: {'peptide': 510} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 491} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1179 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 150} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 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: "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: "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: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 554 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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: "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: "Y" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1171 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 152} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 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: "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: 18.32, per 1000 atoms: 0.50 Number of scatterers: 36901 At special positions: 0 Unit cell: (178.035, 214.721, 133.796, 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 6949 8.00 N 6306 7.00 C 23445 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: 14.53 Conformation dependent library (CDL) restraints added in 5.5 seconds 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8810 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 180 helices and 25 sheets defined 54.8% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.24 Creating SS restraints... Processing helix chain 'W' and resid 4 through 18 Proline residue: W 9 - end of helix Processing helix chain 'W' and resid 24 through 39 removed outlier: 3.719A pdb=" N ASP W 29 " --> pdb=" O GLU W 25 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS W 39 " --> pdb=" O ALA W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 43 through 48 removed outlier: 3.625A pdb=" N SER W 48 " --> pdb=" O ALA W 44 " (cutoff:3.500A) Processing helix chain 'W' and resid 53 through 61 Processing helix chain 'W' and resid 72 through 81 removed outlier: 4.576A pdb=" N ARG W 77 " --> pdb=" O GLN W 73 " (cutoff:3.500A) Processing helix chain 'W' and resid 85 through 102 Proline residue: W 89 - end of helix removed outlier: 3.935A pdb=" N LEU W 92 " --> pdb=" O PRO W 89 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN W 94 " --> pdb=" O VAL W 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 120 through 131 Processing helix chain 'W' and resid 144 through 146 No H-bonds generated for 'chain 'W' and resid 144 through 146' Processing helix chain 'W' and resid 163 through 173 removed outlier: 3.596A pdb=" N ASP W 172 " --> pdb=" O GLU W 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 17 Processing helix chain 'C' and resid 21 through 23 No H-bonds generated for 'chain 'C' and resid 21 through 23' 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 153 through 156 No H-bonds generated for 'chain 'C' and resid 153 through 156' Processing helix chain 'C' and resid 175 through 188 removed outlier: 3.650A pdb=" N GLN C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ASP C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 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 251 Proline residue: C 239 - end of helix removed outlier: 3.797A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 276 removed outlier: 3.854A pdb=" N VAL C 268 " --> pdb=" O SER C 264 " (cutoff:3.500A) 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: 4.530A pdb=" N PHE C 291 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER C 295 " --> pdb=" O TYR C 292 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ARG C 296 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 4.588A 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 346 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 389 Processing helix chain 'C' and resid 393 through 406 removed outlier: 3.695A pdb=" N GLU C 402 " --> pdb=" O ALA C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 431 removed outlier: 3.855A pdb=" N ASP C 422 " --> pdb=" O ARG C 418 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N GLN C 425 " --> pdb=" O LEU C 421 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR C 428 " --> pdb=" O GLY C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 452 Processing helix chain 'C' and resid 464 through 477 removed outlier: 3.512A pdb=" N ALA C 473 " --> pdb=" O ALA C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 484 No H-bonds generated for 'chain 'C' and resid 482 through 484' Processing helix chain 'C' and resid 494 through 510 removed outlier: 3.692A pdb=" N LYS C 499 " --> pdb=" O GLU C 495 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR C 510 " --> pdb=" O SER C 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 17 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 186 removed outlier: 3.900A pdb=" N GLN B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 232 through 236 Processing helix chain 'B' and resid 238 through 252 removed outlier: 4.116A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 277 removed outlier: 4.052A pdb=" N VAL B 268 " --> pdb=" O SER B 264 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 277 " --> pdb=" O ILE B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 300 removed outlier: 4.561A pdb=" N PHE B 291 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER B 295 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG B 296 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 4.769A 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 340 through 348 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 409 removed outlier: 3.925A pdb=" N GLN B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N PHE B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 430 removed outlier: 3.705A pdb=" N ASP B 422 " --> pdb=" O ARG B 418 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 452 Processing helix chain 'B' and resid 465 through 478 Processing helix chain 'B' and resid 480 through 489 Processing helix chain 'B' and resid 494 through 508 Processing helix chain 'A' and resid 5 through 19 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 154 No H-bonds generated for 'chain 'A' and resid 151 through 154' Processing helix chain 'A' and resid 175 through 183 removed outlier: 3.565A pdb=" N ALA A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 215 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 252 Proline residue: A 239 - end of helix removed outlier: 3.793A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 276 removed outlier: 3.865A pdb=" N VAL A 268 " --> pdb=" O SER A 264 " (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 288 through 300 removed outlier: 4.482A pdb=" N PHE A 291 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER A 295 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG A 296 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLU A 299 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 Processing helix chain 'A' and resid 340 through 348 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 409 removed outlier: 4.087A pdb=" N GLY A 391 " --> pdb=" O LYS A 387 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N GLY A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N PHE A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N GLN A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N PHE A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 430 removed outlier: 3.994A pdb=" N GLN A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A 426 " --> pdb=" O ASP A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 452 Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 461 through 478 removed outlier: 4.473A pdb=" N GLY A 465 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLU A 468 " --> pdb=" O GLY A 465 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU A 472 " --> pdb=" O ALA A 469 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL A 475 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP A 478 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 489 removed outlier: 3.698A pdb=" N GLN A 488 " --> pdb=" O GLN A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 510 Processing helix chain 'X' and resid 5 through 24 removed outlier: 4.369A pdb=" N GLN X 10 " --> pdb=" O ILE X 7 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE X 12 " --> pdb=" O GLY X 9 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU X 16 " --> pdb=" O ALA X 13 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL X 18 " --> pdb=" O VAL X 15 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE X 20 " --> pdb=" O PHE X 17 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA X 21 " --> pdb=" O VAL X 18 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS X 23 " --> pdb=" O PHE X 20 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR X 24 " --> pdb=" O ALA X 21 " (cutoff:3.500A) Processing helix chain 'X' and resid 26 through 135 removed outlier: 3.721A pdb=" N ALA X 32 " --> pdb=" O PRO X 28 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLY X 43 " --> pdb=" O GLU X 39 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU X 44 " --> pdb=" O ILE X 40 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU X 54 " --> pdb=" O ALA X 50 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP X 55 " --> pdb=" O HIS X 51 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL X 74 " --> pdb=" O ALA X 70 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE X 75 " --> pdb=" O GLU X 71 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA X 107 " --> pdb=" O ALA X 103 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA X 111 " --> pdb=" O ALA X 107 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU X 118 " --> pdb=" O LYS X 114 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU X 119 " --> pdb=" O ARG X 115 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS X 122 " --> pdb=" O GLU X 118 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE X 126 " --> pdb=" O LYS X 122 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL X 129 " --> pdb=" O ALA X 125 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE X 135 " --> pdb=" O GLY X 131 " (cutoff:3.500A) Processing helix chain 'X' and resid 145 through 147 No H-bonds generated for 'chain 'X' and resid 145 through 147' Processing helix chain 'X' and resid 149 through 152 No H-bonds generated for 'chain 'X' and resid 149 through 152' Processing helix chain 'H' and resid 87 through 102 removed outlier: 3.557A pdb=" N GLU H 91 " --> pdb=" O GLN H 87 " (cutoff:3.500A) removed outlier: 3.604A 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 'G' and resid 3 through 57 removed outlier: 3.526A pdb=" N LYS G 9 " --> pdb=" O ASP G 5 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA G 39 " --> pdb=" O GLN G 35 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER G 41 " --> pdb=" O ARG G 37 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Proline residue: G 43 - end of helix removed outlier: 3.856A pdb=" N VAL G 51 " --> pdb=" O THR G 47 " (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: 3.626A pdb=" N LEU G 94 " --> pdb=" O LEU G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 128 removed outlier: 3.542A pdb=" N ASN G 126 " --> pdb=" O VAL G 122 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER G 127 " --> pdb=" O SER G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 160 removed outlier: 5.502A 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: 4.185A 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: 3.706A pdb=" N THR G 217 " --> pdb=" O ALA G 213 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS G 258 " --> pdb=" O GLY G 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' 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 155 through 166 Processing helix chain 'F' and resid 183 through 196 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: 4.974A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET F 226 " --> pdb=" O THR F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 255 removed outlier: 3.626A pdb=" N GLY F 251 " --> pdb=" O TYR F 247 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL F 254 " --> pdb=" O ALA F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 279 removed outlier: 3.968A 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: 4.516A pdb=" N ALA F 313 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N HIS F 314 " --> pdb=" O THR F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 328 removed outlier: 3.626A pdb=" N LEU F 328 " --> pdb=" O GLN F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 349 No H-bonds generated for 'chain 'F' and resid 346 through 349' Processing helix chain 'F' and resid 351 through 377 removed outlier: 4.378A pdb=" N ASP F 372 " --> pdb=" O GLN F 368 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ILE F 373 " --> pdb=" O GLU F 369 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE F 376 " --> pdb=" O ASP F 372 " (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 384 through 399 removed outlier: 3.839A pdb=" N LEU F 388 " --> pdb=" O GLU F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 431 Processing helix chain 'F' and resid 440 through 443 Processing helix chain 'F' and resid 449 through 457 removed outlier: 3.643A pdb=" N GLU F 454 " --> pdb=" O GLU F 450 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS F 457 " --> pdb=" O VAL F 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 49 No H-bonds generated for 'chain 'E' and resid 47 through 49' 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 116 through 118 No H-bonds generated for 'chain 'E' and resid 116 through 118' Processing helix chain 'E' and resid 131 through 136 Processing helix chain 'E' and resid 155 through 168 removed outlier: 3.545A pdb=" N ALA E 167 " --> pdb=" O ILE E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 196 removed outlier: 3.502A 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 232 removed outlier: 5.118A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 258 Processing helix chain 'E' and resid 271 through 279 removed outlier: 3.582A pdb=" N GLY E 276 " --> pdb=" O ALA E 272 " (cutoff:3.500A) removed outlier: 3.617A 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 311 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: 3.916A pdb=" N GLU E 369 " --> pdb=" O GLN E 365 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) removed outlier: 3.611A 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 386 through 399 removed outlier: 3.500A pdb=" N ALA E 391 " --> pdb=" O LYS E 387 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS E 395 " --> pdb=" O ALA E 391 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG E 398 " --> pdb=" O ARG E 394 " (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 458 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 168 Processing helix chain 'D' and resid 183 through 195 Processing helix chain 'D' and resid 198 through 201 Processing helix chain 'D' and resid 213 through 217 Processing helix chain 'D' and resid 219 through 232 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 314 removed outlier: 4.416A pdb=" N ALA D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N HIS D 314 " --> pdb=" O THR D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 327 Processing helix chain 'D' and resid 346 through 377 removed outlier: 7.448A pdb=" N GLN D 351 " --> pdb=" O LEU D 347 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N GLU D 352 " --> pdb=" O VAL D 348 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N HIS D 353 " --> pdb=" O VAL D 349 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.416A 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 removed outlier: 3.810A pdb=" N ALA D 391 " --> pdb=" O LYS D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 411 removed outlier: 4.033A pdb=" N VAL D 409 " --> pdb=" O VAL D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 431 Processing helix chain 'D' and resid 449 through 458 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: 3.793A pdb=" N ALA I 20 " --> pdb=" O MET I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 76 removed outlier: 3.975A pdb=" N LEU I 59 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ILE I 63 " --> pdb=" O LEU I 59 " (cutoff:3.500A) Proline residue: I 64 - end of helix Processing helix chain 'J' and resid 5 through 41 removed outlier: 3.599A pdb=" N LYS J 34 " --> pdb=" O ILE J 30 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA J 40 " --> pdb=" O LEU J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 77 removed outlier: 4.002A pdb=" N THR J 51 " --> pdb=" O PRO J 47 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 4.774A 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 4 through 39 removed outlier: 4.157A pdb=" N LEU L 8 " --> pdb=" O ASN L 5 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU L 9 " --> pdb=" O MET L 6 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA L 13 " --> pdb=" O TYR L 10 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA L 14 " --> pdb=" O MET L 11 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL L 15 " --> pdb=" O ALA L 12 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET L 17 " --> pdb=" O ALA L 14 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ALA L 20 " --> pdb=" O MET L 17 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY L 23 " --> pdb=" O ALA L 20 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA L 24 " --> pdb=" O ALA L 21 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA L 25 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY L 27 " --> pdb=" O ALA L 24 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE L 30 " --> pdb=" O GLY L 27 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY L 32 " --> pdb=" O GLY L 29 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU L 37 " --> pdb=" O LYS L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 76 removed outlier: 3.500A pdb=" N ILE L 46 " --> pdb=" O PRO L 43 " (cutoff:3.500A) Proline residue: L 47 - end of helix removed outlier: 3.976A pdb=" N MET L 57 " --> pdb=" O PHE L 54 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP L 61 " --> pdb=" O GLY L 58 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE L 63 " --> pdb=" O VAL L 60 " (cutoff:3.500A) Proline residue: L 64 - end of helix removed outlier: 3.909A pdb=" N VAL L 68 " --> pdb=" O MET L 65 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL L 74 " --> pdb=" O GLY L 71 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE L 76 " --> pdb=" O TYR L 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 39 removed outlier: 4.775A pdb=" N LEU M 9 " --> pdb=" O MET M 6 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA M 12 " --> pdb=" O LEU M 9 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET M 16 " --> pdb=" O ALA M 13 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY M 18 " --> pdb=" O VAL M 15 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU M 19 " --> pdb=" O MET M 16 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA M 20 " --> pdb=" O MET M 17 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY M 23 " --> pdb=" O ALA M 20 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA M 25 " --> pdb=" O ILE M 22 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE M 26 " --> pdb=" O GLY M 23 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY M 27 " --> pdb=" O ALA M 24 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE M 30 " --> pdb=" O GLY M 27 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY M 33 " --> pdb=" O ILE M 30 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU M 37 " --> pdb=" O LYS M 34 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY M 38 " --> pdb=" O PHE M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 75 Proline residue: M 47 - end of helix removed outlier: 3.828A pdb=" N ARG M 50 " --> pdb=" O PRO M 47 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY M 58 " --> pdb=" O ILE M 55 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP M 61 " --> pdb=" O GLY M 58 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE M 63 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Proline residue: M 64 - end of helix Processing helix chain 'N' and resid 4 through 41 removed outlier: 4.901A pdb=" N LEU N 9 " --> pdb=" O ASN N 5 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TYR N 10 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N MET N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 76 Proline residue: N 47 - end of helix removed outlier: 3.890A pdb=" N ARG N 50 " --> pdb=" O PRO N 47 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET N 57 " --> pdb=" O PHE N 54 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP N 61 " --> pdb=" O GLY N 58 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE N 63 " --> pdb=" O VAL N 60 " (cutoff:3.500A) Proline residue: N 64 - end of helix removed outlier: 4.016A pdb=" N VAL N 68 " --> pdb=" O MET N 65 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE N 76 " --> pdb=" O TYR N 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 7 through 41 removed outlier: 3.634A pdb=" N ARG O 41 " --> pdb=" O GLU O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 76 removed outlier: 3.883A pdb=" N ILE O 46 " --> pdb=" O PRO O 43 " (cutoff:3.500A) Proline residue: O 47 - end of helix removed outlier: 3.732A pdb=" N ARG O 50 " --> pdb=" O PRO O 47 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE O 53 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY O 58 " --> pdb=" O ILE O 55 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL O 60 " --> pdb=" O MET O 57 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP O 61 " --> pdb=" O GLY O 58 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE O 63 " --> pdb=" O VAL O 60 " (cutoff:3.500A) Proline residue: O 64 - end of helix removed outlier: 3.836A pdb=" N PHE O 76 " --> pdb=" O TYR O 73 " (cutoff:3.500A) Processing helix chain 'P' and resid 6 through 41 Processing helix chain 'P' and resid 46 through 76 removed outlier: 3.999A pdb=" N GLN P 52 " --> pdb=" O LEU P 48 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA P 62 " --> pdb=" O GLY P 58 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) Proline residue: P 64 - end of helix removed outlier: 3.618A pdb=" N ALA P 67 " --> pdb=" O ILE P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 41 removed outlier: 4.321A pdb=" N LEU Q 8 " --> pdb=" O ASN Q 5 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU Q 9 " --> pdb=" O MET Q 6 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA Q 12 " --> pdb=" O LEU Q 9 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL Q 15 " --> pdb=" O ALA Q 12 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N MET Q 17 " --> pdb=" O ALA Q 14 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU Q 19 " --> pdb=" O MET Q 16 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA Q 20 " --> pdb=" O MET Q 17 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY Q 23 " --> pdb=" O ALA Q 20 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE Q 26 " --> pdb=" O GLY Q 23 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY Q 27 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE Q 28 " --> pdb=" O ALA Q 25 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE Q 30 " --> pdb=" O GLY Q 27 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLY Q 32 " --> pdb=" O GLY Q 29 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY Q 38 " --> pdb=" O PHE Q 35 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG Q 41 " --> pdb=" O GLY Q 38 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 76 Proline residue: Q 47 - end of helix removed outlier: 3.888A pdb=" N PHE Q 53 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET Q 57 " --> pdb=" O PHE Q 54 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY Q 58 " --> pdb=" O ILE Q 55 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP Q 61 " --> pdb=" O GLY Q 58 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE Q 63 " --> pdb=" O VAL Q 60 " (cutoff:3.500A) Proline residue: Q 64 - end of helix removed outlier: 3.826A pdb=" N TYR Q 73 " --> pdb=" O LEU Q 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 39 removed outlier: 4.210A pdb=" N LEU R 8 " --> pdb=" O LEU R 4 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET R 16 " --> pdb=" O ALA R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 76 removed outlier: 3.749A pdb=" N ILE R 46 " --> pdb=" O PRO R 43 " (cutoff:3.500A) Proline residue: R 47 - end of helix removed outlier: 4.059A pdb=" N ARG R 50 " --> pdb=" O PRO R 47 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET R 57 " --> pdb=" O PHE R 54 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASP R 61 " --> pdb=" O GLY R 58 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE R 63 " --> pdb=" O VAL R 60 " (cutoff:3.500A) Proline residue: R 64 - end of helix removed outlier: 3.921A pdb=" N VAL R 68 " --> pdb=" O MET R 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 8 through 41 removed outlier: 3.651A pdb=" N LYS S 34 " --> pdb=" O ILE S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 60 Proline residue: S 47 - end of helix removed outlier: 3.772A pdb=" N ILE S 55 " --> pdb=" O GLN S 52 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N MET S 57 " --> pdb=" O PHE S 54 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 76 Processing helix chain 'Y' and resid 3 through 24 Processing helix chain 'Y' and resid 26 through 138 removed outlier: 3.831A pdb=" N HIS Y 51 " --> pdb=" O ALA Y 47 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS Y 52 " --> pdb=" O GLU Y 48 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA Y 59 " --> pdb=" O ASP Y 55 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU Y 95 " --> pdb=" O LYS Y 91 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG Y 98 " --> pdb=" O ALA Y 94 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN Y 106 " --> pdb=" O VAL Y 102 " (cutoff:3.500A) Processing helix chain 'Y' and resid 142 through 152 removed outlier: 3.791A pdb=" N ASP Y 147 " --> pdb=" O ALA Y 143 " (cutoff:3.500A) Processing helix chain 'a' and resid 8 through 15 removed outlier: 3.521A pdb=" N GLY a 13 " --> pdb=" O GLN a 9 " (cutoff:3.500A) Processing helix chain 'a' and resid 43 through 64 removed outlier: 3.787A pdb=" N VAL a 63 " --> pdb=" O LEU a 59 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 93 removed outlier: 3.807A pdb=" N ALA a 78 " --> pdb=" O LYS a 74 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE a 79 " --> pdb=" O PHE a 75 " (cutoff:3.500A) Processing helix chain 'a' and resid 100 through 120 removed outlier: 3.587A pdb=" N MET a 118 " --> pdb=" O LEU a 114 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP a 119 " --> pdb=" O MET a 115 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LEU a 120 " --> pdb=" O ASN a 116 " (cutoff:3.500A) Processing helix chain 'a' and resid 125 through 132 removed outlier: 3.517A 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: 3.787A pdb=" N LYS a 169 " --> pdb=" O SER a 165 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE a 171 " --> pdb=" O LYS a 167 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N GLY a 172 " --> pdb=" O MET a 168 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY a 173 " --> pdb=" O LYS a 169 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS a 176 " --> pdb=" O GLY a 172 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 227 Proline residue: a 190 - end of helix removed outlier: 3.723A pdb=" N LEU a 193 " --> pdb=" O PRO a 190 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLU a 196 " --> pdb=" O LEU a 193 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER a 199 " --> pdb=" O GLU a 196 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS a 203 " --> pdb=" O LEU a 200 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 3.892A pdb=" N ARG a 210 " --> pdb=" O LEU a 207 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY a 213 " --> pdb=" O ARG a 210 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN a 214 " --> pdb=" O LEU a 211 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR a 216 " --> pdb=" O GLY a 213 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA a 217 " --> pdb=" O ASN a 214 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE a 221 " --> pdb=" O GLY a 218 " (cutoff:3.500A) Processing helix chain 'a' and resid 231 through 268 removed outlier: 4.547A pdb=" N TRP a 235 " --> pdb=" O TRP a 231 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ILE a 236 " --> pdb=" O TRP a 232 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU a 237 " --> pdb=" O SER a 233 " (cutoff:3.500A) Proline residue: a 240 - end of helix removed outlier: 4.008A pdb=" N PHE a 244 " --> pdb=" O PRO a 240 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR a 250 " --> pdb=" O ILE a 246 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU a 251 " --> pdb=" O LEU a 247 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE a 256 " --> pdb=" O GLN a 252 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR a 260 " --> pdb=" O PHE a 256 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'W' and resid 139 through 142 removed outlier: 4.167A pdb=" N MET W 157 " --> pdb=" O ALA W 154 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.696A pdb=" N ARG C 40 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL C 34 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.021A 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 99 Processing sheet with id= D, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.681A pdb=" N LEU C 166 " --> pdb=" O GLY C 351 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 221 through 226 removed outlier: 6.867A pdb=" N CYS C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N VAL C 224 " --> pdb=" O CYS C 193 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N SER C 323 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE C 258 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N THR C 325 " --> pdb=" O ILE C 258 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N TYR C 260 " --> pdb=" O THR C 325 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.515A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N MET B 76 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA B 61 " --> pdb=" O MET B 76 " (cutoff:3.500A) removed outlier: 4.049A 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 107 through 109 removed outlier: 8.286A pdb=" N VAL B 108 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL B 223 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 9.077A pdb=" N ILE B 222 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N CYS B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N VAL B 224 " --> pdb=" O CYS B 193 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ASP B 255 " --> pdb=" O LYS B 192 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ILE B 194 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU B 257 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N VAL B 196 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE B 259 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ILE B 198 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ASP B 261 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLN B 200 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N SER B 323 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ILE B 258 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N THR B 325 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N TYR B 260 " --> pdb=" O THR B 325 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 352 through 355 removed outlier: 6.813A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE B 168 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.501A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 4.053A 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 107 through 109 removed outlier: 8.441A pdb=" N VAL A 108 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL A 223 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N CYS A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N VAL A 224 " --> pdb=" O CYS A 193 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N SER A 323 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ILE A 258 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N THR A 325 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N TYR A 260 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU A 327 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 351 through 355 Processing sheet with id= N, first strand: chain 'H' and resid 5 through 9 Processing sheet with id= O, first strand: chain 'H' and resid 30 through 35 removed outlier: 7.291A pdb=" N VAL H 53 " --> pdb=" O GLU H 21 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE H 23 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ARG H 51 " --> pdb=" O ILE H 23 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL H 25 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N MET H 49 " --> pdb=" O VAL H 25 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 180 through 188 removed outlier: 3.803A pdb=" N LEU G 187 " --> pdb=" O LEU G 167 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N LEU G 167 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ASN G 172 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLN G 111 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N TYR G 77 " --> pdb=" O GLN G 111 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASP G 113 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N VAL G 79 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ALA G 115 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N MET G 116 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLN G 135 " --> pdb=" O MET G 116 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 4 through 9 removed outlier: 6.556A pdb=" N ASP F 14 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE F 54 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 5.484A 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 78 Processing sheet with id= S, first strand: chain 'F' and resid 317 through 320 removed outlier: 7.798A pdb=" N VAL F 145 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N SER F 292 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU F 147 " --> pdb=" O SER F 292 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLN F 294 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N GLY F 149 " --> pdb=" O GLN F 294 " (cutoff:3.500A) removed outlier: 6.320A 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: 6.606A pdb=" N ASP E 14 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL E 8 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL E 12 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ILE E 54 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N VAL E 42 " --> pdb=" O ILE E 54 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU E 36 " --> pdb=" O ASN E 33 " (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: 8.731A pdb=" N VAL E 145 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER E 292 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N LEU E 147 " --> pdb=" O SER E 292 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLN E 294 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TYR E 173 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N PHE E 240 " --> pdb=" O TYR E 173 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL E 175 " --> pdb=" O PHE E 240 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 3 through 9 removed outlier: 6.490A pdb=" N ASP D 14 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL D 8 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE D 54 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N VAL D 42 " --> pdb=" O ILE D 54 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU D 36 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASP D 27 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N HIS D 73 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLU D 30 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU D 71 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N GLN D 32 " --> pdb=" O LYS D 69 " (cutoff:3.500A) removed outlier: 9.610A pdb=" N LYS D 69 " --> pdb=" O GLN D 32 " (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: 8.855A pdb=" N VAL D 145 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N SER D 292 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N LEU D 147 " --> pdb=" O SER D 292 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLN D 294 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N GLY D 149 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL D 296 " --> pdb=" O GLY D 149 " (cutoff:3.500A) 1875 hydrogen bonds defined for protein. 4800 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: 12.09 Time building geometry restraints manager: 15.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 6312 1.30 - 1.43: 8660 1.43 - 1.56: 22103 1.56 - 1.68: 24 1.68 - 1.81: 360 Bond restraints: 37459 Sorted by residual: bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.64e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.17e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.15e+01 bond pdb=" C5 ATP A 600 " pdb=" C6 ATP A 600 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 5.01e+01 bond pdb=" C5 ATP C 600 " pdb=" C6 ATP C 600 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.88e+01 ... (remaining 37454 not shown) Histogram of bond angle deviations from ideal: 95.24 - 103.48: 533 103.48 - 111.71: 17650 111.71 - 119.94: 16601 119.94 - 128.18: 15707 128.18 - 136.41: 220 Bond angle restraints: 50711 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 139.87 119.86 20.01 1.00e+00 1.00e+00 4.00e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 120.46 19.41 1.00e+00 1.00e+00 3.77e+02 angle pdb=" N VAL A 377 " pdb=" CA VAL A 377 " pdb=" C VAL A 377 " ideal model delta sigma weight residual 111.81 95.24 16.57 8.60e-01 1.35e+00 3.71e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 121.06 18.81 1.00e+00 1.00e+00 3.54e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 119.14 17.69 1.00e+00 1.00e+00 3.13e+02 ... (remaining 50706 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.90: 21740 27.90 - 55.79: 798 55.79 - 83.69: 91 83.69 - 111.58: 12 111.58 - 139.48: 3 Dihedral angle restraints: 22644 sinusoidal: 8872 harmonic: 13772 Sorted by residual: 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 79.48 -139.48 1 2.00e+01 2.50e-03 4.22e+01 dihedral pdb=" O1B ADP F 500 " pdb=" O3A ADP F 500 " pdb=" PB ADP F 500 " pdb=" PA ADP F 500 " ideal model delta sinusoidal sigma weight residual 300.00 162.22 137.78 1 2.00e+01 2.50e-03 4.18e+01 dihedral pdb=" O2A ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PA ADP E 500 " pdb=" PB ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 71.62 -131.62 1 2.00e+01 2.50e-03 3.99e+01 ... (remaining 22641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 5438 0.086 - 0.172: 434 0.172 - 0.258: 28 0.258 - 0.345: 10 0.345 - 0.431: 4 Chirality restraints: 5914 Sorted by residual: 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 ILE A 222 " pdb=" N ILE A 222 " pdb=" C ILE A 222 " pdb=" CB ILE A 222 " both_signs ideal model delta sigma weight residual False 2.43 2.81 -0.38 2.00e-01 2.50e+01 3.64e+00 chirality pdb=" CA GLU G 208 " pdb=" N GLU G 208 " pdb=" C GLU G 208 " pdb=" CB GLU G 208 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 5911 not shown) Planarity restraints: 6538 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU J 36 " -0.026 2.00e-02 2.50e+03 5.18e-02 2.69e+01 pdb=" C LEU J 36 " 0.090 2.00e-02 2.50e+03 pdb=" O LEU J 36 " -0.033 2.00e-02 2.50e+03 pdb=" N GLU J 37 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 209 " 0.025 2.00e-02 2.50e+03 4.87e-02 2.37e+01 pdb=" C VAL A 209 " -0.084 2.00e-02 2.50e+03 pdb=" O VAL A 209 " 0.031 2.00e-02 2.50e+03 pdb=" N ARG A 210 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER a 27 " -0.020 2.00e-02 2.50e+03 4.02e-02 1.61e+01 pdb=" C SER a 27 " 0.069 2.00e-02 2.50e+03 pdb=" O SER a 27 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU a 28 " -0.024 2.00e-02 2.50e+03 ... (remaining 6535 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 145 2.52 - 3.11: 29955 3.11 - 3.71: 55260 3.71 - 4.30: 81233 4.30 - 4.90: 136685 Nonbonded interactions: 303278 Sorted by model distance: nonbonded pdb=" O1 PO4 D 501 " pdb="MG MG D 502 " model vdw 1.924 2.170 nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 601 " model vdw 1.926 2.170 nonbonded pdb=" O1G ATP C 600 " pdb="MG MG C 601 " model vdw 1.941 2.170 nonbonded pdb=" O2B ATP C 600 " pdb="MG MG C 601 " model vdw 1.945 2.170 nonbonded pdb=" O2G ATP A 600 " pdb="MG MG A 601 " model vdw 1.946 2.170 ... (remaining 303273 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 511 or resid 600 through 601)) selection = (chain 'B' and (resid 4 through 511 or resid 600 through 601)) selection = (chain 'C' and (resid 4 through 511 or resid 600 through 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 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 78)) selection = (chain 'J' and (resid 3 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 78)) selection = (chain 'L' and (resid 3 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 78)) selection = (chain 'M' and (resid 3 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 78)) selection = (chain 'N' and (resid 3 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 78)) selection = (chain 'O' and resid 3 through 78) selection = (chain 'P' and (resid 3 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 78)) selection = (chain 'Q' and (resid 3 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 78)) selection = (chain 'R' and (resid 3 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 78)) selection = (chain 'S' and (resid 3 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 78)) } ncs_group { reference = (chain 'X' and (resid 1 through 54 or (resid 55 and (name N or name CA or name C \ or name O or name CB )) or resid 56 through 57 or (resid 58 through 59 and (nam \ e N or name CA or name C or name O or name CB )) or resid 60 through 62 or (resi \ d 63 and (name N or name CA or name C or name O or name CB )) or resid 64 throug \ h 65 or (resid 66 through 70 and (name N or name CA or name C or name O or name \ CB )) or resid 71 through 72 or (resid 73 and (name N or name CA or name C or na \ me O or name CB )) or resid 74 through 76 or (resid 77 and (name N or name CA or \ name C or name O or name CB )) or resid 78 through 153)) selection = (chain 'Y' and (resid 1 through 90 or (resid 91 through 92 and (name N or name C \ A or name C or name O or name CB )) or resid 93 through 153)) } 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: 2.040 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: 0.020 Extract box with map and model: 12.410 Check model and map are aligned: 0.520 Set scattering table: 0.290 Process input model: 86.210 Find NCS groups from input model: 2.510 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 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 : 0.005 0.113 37459 Z= 0.307 Angle : 0.818 20.009 50711 Z= 0.542 Chirality : 0.049 0.431 5914 Planarity : 0.004 0.059 6538 Dihedral : 14.421 139.481 13834 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.31 % Favored : 96.63 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.11 % 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: -2.30 (0.11), residues: 4803 helix: -1.48 (0.09), residues: 2604 sheet: -0.59 (0.20), residues: 515 loop : -1.59 (0.14), residues: 1684 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 945 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 878 time to evaluate : 4.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 31 residues processed: 938 average time/residue: 0.5263 time to fit residues: 782.0453 Evaluate side-chains 628 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 597 time to evaluate : 4.256 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.3438 time to fit residues: 25.9588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 400 optimal weight: 10.0000 chunk 359 optimal weight: 6.9990 chunk 199 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 242 optimal weight: 0.4980 chunk 191 optimal weight: 0.8980 chunk 371 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 225 optimal weight: 0.9990 chunk 276 optimal weight: 0.9990 chunk 430 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 21 HIS ** W 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 82 ASN ** W 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN C 186 GLN C 443 GLN B 186 GLN B 399 GLN B 493 ASN ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 ASN A 333 GLN A 344 ASN A 488 GLN X 37 GLN G 54 HIS G 91 ASN G 252 ASN G 265 ASN G 269 GLN E 351 GLN E 441 GLN D 19 GLN D 279 GLN J 42 GLN O 3 ASN R 42 GLN S 3 ASN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 37 GLN a 234 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 37459 Z= 0.205 Angle : 0.642 12.475 50711 Z= 0.325 Chirality : 0.043 0.259 5914 Planarity : 0.004 0.051 6538 Dihedral : 6.161 123.853 5242 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer Outliers : 1.99 % Cbeta Deviations : 0.00 % 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: -0.74 (0.12), residues: 4803 helix: -0.13 (0.10), residues: 2597 sheet: -0.26 (0.21), residues: 530 loop : -0.91 (0.15), residues: 1676 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 657 time to evaluate : 4.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 29 residues processed: 704 average time/residue: 0.5116 time to fit residues: 583.4626 Evaluate side-chains 595 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 566 time to evaluate : 4.070 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.3306 time to fit residues: 23.6128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 239 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 358 optimal weight: 0.9980 chunk 293 optimal weight: 0.6980 chunk 118 optimal weight: 6.9990 chunk 431 optimal weight: 0.8980 chunk 465 optimal weight: 7.9990 chunk 384 optimal weight: 0.9980 chunk 427 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 345 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 HIS ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 73 GLN X 123 GLN G 64 HIS F 343 GLN N 5 ASN O 42 GLN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 37 GLN Y 106 GLN Y 123 GLN ** a 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 181 GLN ** a 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 37459 Z= 0.179 Angle : 0.599 11.044 50711 Z= 0.298 Chirality : 0.042 0.240 5914 Planarity : 0.004 0.056 6538 Dihedral : 5.650 123.265 5242 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 1.91 % Cbeta Deviations : 0.00 % 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: -0.04 (0.12), residues: 4803 helix: 0.47 (0.10), residues: 2600 sheet: 0.06 (0.21), residues: 550 loop : -0.70 (0.15), residues: 1653 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 613 time to evaluate : 4.620 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 outliers start: 73 outliers final: 25 residues processed: 660 average time/residue: 0.5112 time to fit residues: 548.4769 Evaluate side-chains 575 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 550 time to evaluate : 4.235 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.3414 time to fit residues: 21.9886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 426 optimal weight: 10.0000 chunk 324 optimal weight: 8.9990 chunk 223 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 205 optimal weight: 0.7980 chunk 289 optimal weight: 1.9990 chunk 432 optimal weight: 3.9990 chunk 458 optimal weight: 0.9990 chunk 226 optimal weight: 4.9990 chunk 410 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 120 GLN C 423 HIS ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 37 GLN H 14 GLN G 126 ASN E 361 GLN ** J 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 33 ASN ** a 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 37459 Z= 0.236 Angle : 0.599 10.840 50711 Z= 0.298 Chirality : 0.043 0.272 5914 Planarity : 0.004 0.054 6538 Dihedral : 5.493 119.573 5242 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % 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: 0.19 (0.12), residues: 4803 helix: 0.68 (0.10), residues: 2619 sheet: 0.13 (0.21), residues: 561 loop : -0.61 (0.15), residues: 1623 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 579 time to evaluate : 4.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 32 residues processed: 622 average time/residue: 0.5249 time to fit residues: 528.7573 Evaluate side-chains 566 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 534 time to evaluate : 4.281 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.3504 time to fit residues: 26.4798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 381 optimal weight: 4.9990 chunk 260 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 341 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 390 optimal weight: 0.8980 chunk 316 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 233 optimal weight: 3.9990 chunk 411 optimal weight: 5.9990 chunk 115 optimal weight: 0.6980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN C 423 HIS ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 37 GLN X 123 GLN H 116 GLN ** J 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN a 20 GLN ** a 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 37459 Z= 0.331 Angle : 0.642 9.875 50711 Z= 0.322 Chirality : 0.044 0.299 5914 Planarity : 0.004 0.059 6538 Dihedral : 5.607 117.965 5242 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % 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: 0.20 (0.12), residues: 4803 helix: 0.75 (0.10), residues: 2602 sheet: 0.08 (0.21), residues: 547 loop : -0.69 (0.15), residues: 1654 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 590 time to evaluate : 4.445 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 35 residues processed: 633 average time/residue: 0.5182 time to fit residues: 531.3293 Evaluate side-chains 582 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 547 time to evaluate : 4.267 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.3558 time to fit residues: 28.8481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 154 optimal weight: 1.9990 chunk 412 optimal weight: 9.9990 chunk 90 optimal weight: 0.7980 chunk 269 optimal weight: 3.9990 chunk 113 optimal weight: 0.0770 chunk 458 optimal weight: 2.9990 chunk 380 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 chunk 151 optimal weight: 0.9990 chunk 240 optimal weight: 3.9990 overall best weight: 0.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 HIS ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 511 GLN X 37 GLN H 72 GLN D 243 ASN ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN S 52 GLN ** a 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4360 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: