Starting phenix.real_space_refine on Tue Apr 16 02:47:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqs_20168/04_2024/6oqs_20168_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqs_20168/04_2024/6oqs_20168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqs_20168/04_2024/6oqs_20168.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqs_20168/04_2024/6oqs_20168.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqs_20168/04_2024/6oqs_20168_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqs_20168/04_2024/6oqs_20168_neut_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 5 5.21 5 S 180 5.16 5 C 23485 2.51 5 N 6317 2.21 5 O 6968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "W PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 26": "NH1" <-> "NH2" Residue "W ASP 29": "OD1" <-> "OD2" Residue "W GLU 36": "OE1" <-> "OE2" Residue "W GLU 41": "OE1" <-> "OE2" Residue "W GLU 45": "OE1" <-> "OE2" Residue "W GLU 54": "OE1" <-> "OE2" Residue "W PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 77": "NH1" <-> "NH2" Residue "W GLU 93": "OE1" <-> "OE2" Residue "W PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 103": "OE1" <-> "OE2" Residue "W GLU 118": "OE1" <-> "OE2" Residue "W ASP 143": "OD1" <-> "OD2" Residue "W ASP 160": "OD1" <-> "OD2" Residue "W ARG 164": "NH1" <-> "NH2" Residue "C GLU 24": "OE1" <-> "OE2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C ASP 116": "OD1" <-> "OD2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 262": "OD1" <-> "OD2" Residue "C GLU 284": "OE1" <-> "OE2" Residue "C GLU 299": "OE1" <-> "OE2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "C TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 350": "OD1" <-> "OD2" Residue "C GLU 402": "OE1" <-> "OE2" Residue "C ASP 412": "OD1" <-> "OD2" Residue "C ASP 415": "OD1" <-> "OD2" Residue "C ASP 422": "OD1" <-> "OD2" Residue "C GLU 429": "OE1" <-> "OE2" Residue "C PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 453": "NH1" <-> "NH2" Residue "C ASP 458": "OD1" <-> "OD2" Residue "C PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 494": "OD1" <-> "OD2" Residue "C ASP 505": "OD1" <-> "OD2" Residue "C PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B ASP 36": "OD1" <-> "OD2" Residue "B ASP 46": "OD1" <-> "OD2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B ARG 93": "NH1" <-> "NH2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "B ASP 181": "OD1" <-> "OD2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 376": "NH1" <-> "NH2" Residue "B TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 415": "OD1" <-> "OD2" Residue "B ASP 422": "OD1" <-> "OD2" Residue "B ASP 478": "OD1" <-> "OD2" Residue "B GLU 485": "OE1" <-> "OE2" Residue "B GLU 495": "OE1" <-> "OE2" Residue "B GLU 497": "OE1" <-> "OE2" Residue "B PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 10": "OE1" <-> "OE2" Residue "A GLU 24": "OE1" <-> "OE2" Residue "A ASP 36": "OD1" <-> "OD2" Residue "A ASP 69": "OD1" <-> "OD2" Residue "A ASP 170": "OD1" <-> "OD2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 336": "OD1" <-> "OD2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 376": "NH1" <-> "NH2" Residue "A ASP 412": "OD1" <-> "OD2" Residue "A ASP 415": "OD1" <-> "OD2" Residue "A ARG 418": "NH1" <-> "NH2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 460": "OE1" <-> "OE2" Residue "A PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 477": "NH1" <-> "NH2" Residue "A TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 39": "OE1" <-> "OE2" Residue "X ASP 42": "OD1" <-> "OD2" Residue "X ASP 53": "OD1" <-> "OD2" Residue "X ASP 55": "OD1" <-> "OD2" Residue "X GLU 71": "OE1" <-> "OE2" Residue "X ARG 83": "NH1" <-> "NH2" Residue "X ASP 88": "OD1" <-> "OD2" Residue "X GLU 93": "OE1" <-> "OE2" Residue "X GLU 97": "OE1" <-> "OE2" Residue "X ARG 98": "NH1" <-> "NH2" Residue "X 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 137": "OE1" <-> "OE2" Residue "X ASP 141": "OD1" <-> "OD2" Residue "X GLU 142": "OE1" <-> "OE2" Residue "X GLU 155": "OE1" <-> "OE2" Residue "H TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 88": "OD1" <-> "OD2" Residue "H GLU 96": "OE1" <-> "OE2" Residue "H ASP 111": "OD1" <-> "OD2" Residue "H GLU 120": "OE1" <-> "OE2" Residue "H ARG 129": "NH1" <-> "NH2" Residue "G GLU 24": "OE1" <-> "OE2" Residue "G ASP 36": "OD1" <-> "OD2" Residue "G TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G ARG 49": "NH1" <-> "NH2" Residue "G ASP 69": "OD1" <-> "OD2" Residue "G ASP 71": "OD1" <-> "OD2" Residue "G TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 84": "NH1" <-> "NH2" Residue "G PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 161": "OE1" <-> "OE2" Residue "G ASP 165": "OD1" <-> "OD2" Residue "G ASP 196": "OD1" <-> "OD2" Residue "G ASP 197": "OD1" <-> "OD2" Residue "G ARG 221": "NH1" <-> "NH2" Residue "G GLU 259": "OE1" <-> "OE2" Residue "G GLU 278": "OE1" <-> "OE2" Residue "F ASP 14": "OD1" <-> "OD2" Residue "F GLU 76": "OE1" <-> "OE2" Residue "F TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 134": "OD1" <-> "OD2" Residue "F GLU 169": "OE1" <-> "OE2" Residue "F PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 195": "OD1" <-> "OD2" Residue "F GLU 211": "OE1" <-> "OE2" Residue "F ASP 236": "OD1" <-> "OD2" Residue "F TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 253": "OE1" <-> "OE2" Residue "F TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 338": "OD1" <-> "OD2" Residue "F ASP 355": "OD1" <-> "OD2" Residue "F ASP 372": "OD1" <-> "OD2" Residue "F ASP 386": "OD1" <-> "OD2" Residue "F PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 422": "OD1" <-> "OD2" Residue "F TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 440": "OE1" <-> "OE2" Residue "F PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 36": "OE1" <-> "OE2" Residue "E GLU 118": "OE1" <-> "OE2" Residue "E GLU 127": "OE1" <-> "OE2" Residue "E ASP 134": "OD1" <-> "OD2" Residue "E PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 200": "OD1" <-> "OD2" Residue "E PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 242": "OD1" <-> "OD2" Residue "E GLU 273": "OE1" <-> "OE2" Residue "E ASP 302": "OD1" <-> "OD2" Residue "E ASP 305": "OD1" <-> "OD2" Residue "E ASP 338": "OD1" <-> "OD2" Residue "E ASP 345": "OD1" <-> "OD2" Residue "E ASP 372": "OD1" <-> "OD2" Residue "E ASP 386": "OD1" <-> "OD2" Residue "E GLU 408": "OE1" <-> "OE2" Residue "E TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D GLU 124": "OE1" <-> "OE2" Residue "D ASP 134": "OD1" <-> "OD2" Residue "D TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 188": "OD1" <-> "OD2" Residue "D GLU 192": "OE1" <-> "OE2" Residue "D GLU 211": "OE1" <-> "OE2" Residue "D PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 233": "OE1" <-> "OE2" Residue "D PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 242": "OD1" <-> "OD2" Residue "D GLU 280": "OE1" <-> "OE2" Residue "D ASP 301": "OD1" <-> "OD2" Residue "D ASP 302": "OD1" <-> "OD2" Residue "D ASP 316": "OD1" <-> "OD2" Residue "D TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 369": "OE1" <-> "OE2" Residue "D ASP 372": "OD1" <-> "OD2" Residue "D ASP 380": "OD1" <-> "OD2" Residue "D GLU 384": "OE1" <-> "OE2" Residue "D GLU 385": "OE1" <-> "OE2" Residue "D ASP 386": "OD1" <-> "OD2" Residue "D GLU 440": "OE1" <-> "OE2" Residue "D PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 7": "OD1" <-> "OD2" 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 "L ASP 7": "OD1" <-> "OD2" Residue "L TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 37": "OE1" <-> "OE2" Residue "L ARG 50": "NH1" <-> "NH2" Residue "M TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 37": "OE1" <-> "OE2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ASP 61": "OD1" <-> "OD2" Residue "N ASP 7": "OD1" <-> "OD2" Residue "N TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 37": "OE1" <-> "OE2" Residue "N ASP 44": "OD1" <-> "OD2" Residue "N ARG 50": "NH1" <-> "NH2" Residue "O TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 37": "OE1" <-> "OE2" Residue "O ASP 44": "OD1" <-> "OD2" Residue "O ARG 50": "NH1" <-> "NH2" 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 ASP 44": "OD1" <-> "OD2" Residue "Q ARG 50": "NH1" <-> "NH2" Residue "R ASP 7": "OD1" <-> "OD2" Residue "R TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "R ARG 41": "NH1" <-> "NH2" Residue "R ARG 50": "NH1" <-> "NH2" Residue "R TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 44": "OD1" <-> "OD2" Residue "S ARG 50": "NH1" <-> "NH2" Residue "Y GLU 39": "OE1" <-> "OE2" Residue "Y ASP 42": "OD1" <-> "OD2" Residue "Y GLU 48": "OE1" <-> "OE2" Residue "Y ASP 55": "OD1" <-> "OD2" Residue "Y GLU 71": "OE1" <-> "OE2" Residue "Y ARG 83": "NH1" <-> "NH2" Residue "Y GLU 93": "OE1" <-> "OE2" Residue "Y GLU 97": "OE1" <-> "OE2" Residue "Y ARG 98": "NH1" <-> "NH2" Residue "Y GLU 108": "OE1" <-> "OE2" Residue "Y GLU 110": "OE1" <-> "OE2" Residue "Y ARG 113": "NH1" <-> "NH2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Y ARG 117": "NH1" <-> "NH2" Residue "Y ARG 121": "NH1" <-> "NH2" Residue "Y ARG 138": "NH1" <-> "NH2" Residue "a TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 30": "OD1" <-> "OD2" Residue "a PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 80": "OE1" <-> "OE2" Residue "a PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 119": "OD1" <-> "OD2" Residue "a ASP 124": "OD1" <-> "OD2" 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: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 36971 Number of models: 1 Model: "" Number of chains: 28 Chain: "W" Number of atoms: 1320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1320 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 3, 'TRANS': 169} Chain: "C" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3869 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3871 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 494} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 3832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3832 Classifications: {'peptide': 508} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 489} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 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: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "P" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Q" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "R" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 552 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "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: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 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: 18.97, per 1000 atoms: 0.51 Number of scatterers: 36971 At special positions: 0 Unit cell: (176.956, 220.116, 139.191, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 180 16.00 P 16 15.00 Mg 5 11.99 O 6968 8.00 N 6317 7.00 C 23485 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.81 Conformation dependent library (CDL) restraints added in 7.0 seconds 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8818 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 183 helices and 26 sheets defined 56.1% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.41 Creating SS restraints... Processing helix chain 'W' and resid 8 through 20 Processing helix chain 'W' and resid 24 through 37 Processing helix chain 'W' and resid 41 through 48 removed outlier: 3.581A pdb=" N GLU W 45 " --> pdb=" O GLU W 41 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER W 48 " --> pdb=" O ALA W 44 " (cutoff:3.500A) Processing helix chain 'W' and resid 53 through 62 removed outlier: 3.632A pdb=" N GLU W 58 " --> pdb=" O GLU W 54 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 82 Processing helix chain 'W' and resid 85 through 102 Proline residue: W 89 - end of helix removed outlier: 3.963A pdb=" N LEU W 92 " --> pdb=" O PRO W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 120 through 131 removed outlier: 3.614A pdb=" N LYS W 130 " --> pdb=" O ALA W 126 " (cutoff:3.500A) Processing helix chain 'W' and resid 163 through 171 Processing helix chain 'C' and resid 9 through 17 Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 136 through 138 No H-bonds generated for 'chain 'C' and resid 136 through 138' Processing helix chain 'C' and resid 151 through 156 removed outlier: 3.586A pdb=" N MET C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 186 removed outlier: 4.082A pdb=" N GLN C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 removed outlier: 3.843A pdb=" N ASN C 207 " --> pdb=" O SER C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 232 through 252 Proline residue: C 239 - end of helix removed outlier: 3.815A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 276 removed outlier: 3.806A 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: 4.231A pdb=" N PHE C 291 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR C 292 " --> pdb=" O ASP C 289 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER C 295 " --> pdb=" O TYR C 292 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG C 296 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLU C 299 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 312 Processing helix chain 'C' and resid 333 through 335 No H-bonds generated for 'chain 'C' and resid 333 through 335' Processing helix chain 'C' and resid 340 through 348 removed outlier: 4.007A pdb=" N SER C 347 " --> pdb=" O THR C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 378 through 381 Processing helix chain 'C' and resid 384 through 412 removed outlier: 3.930A pdb=" N GLY C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ALA C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N PHE C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER C 407 " --> pdb=" O LEU C 403 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLN C 408 " --> pdb=" O ALA C 404 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N PHE C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N SER C 411 " --> pdb=" O SER C 407 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ASP C 412 " --> pdb=" O GLN C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 431 removed outlier: 4.344A pdb=" N GLN C 420 " --> pdb=" O ALA C 416 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 431 " --> pdb=" O VAL C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 452 Processing helix chain 'C' and resid 455 through 457 No H-bonds generated for 'chain 'C' and resid 455 through 457' Processing helix chain 'C' and resid 461 through 478 removed outlier: 3.506A pdb=" N ILE C 464 " --> pdb=" O LEU C 461 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N GLY C 465 " --> pdb=" O SER C 462 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP C 478 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 removed outlier: 3.631A pdb=" N GLN C 488 " --> pdb=" O GLN C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 510 Processing helix chain 'B' and resid 5 through 17 Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 188 removed outlier: 3.632A pdb=" N GLN B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ASP B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 232 through 252 removed outlier: 3.516A pdb=" N LEU B 237 " --> pdb=" O ALA B 233 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.665A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 277 removed outlier: 3.678A pdb=" N ALA B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 277 " --> pdb=" O ILE B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 288 through 300 removed outlier: 4.349A pdb=" N PHE B 291 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 293 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG B 296 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU B 299 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 312 Processing helix chain 'B' and resid 333 through 335 No H-bonds generated for 'chain 'B' and resid 333 through 335' Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 378 through 381 removed outlier: 3.625A pdb=" N ALA B 381 " --> pdb=" O GLY B 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 378 through 381' Processing helix chain 'B' and resid 384 through 390 Processing helix chain 'B' and resid 393 through 407 removed outlier: 3.678A pdb=" N ALA B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 431 Processing helix chain 'B' and resid 441 through 452 Processing helix chain 'B' and resid 464 through 477 Processing helix chain 'B' and resid 480 through 486 Processing helix chain 'B' and resid 494 through 510 Processing helix chain 'A' and resid 5 through 19 removed outlier: 3.678A pdb=" N SER A 9 " --> pdb=" O SER A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 175 through 188 removed outlier: 4.035A pdb=" N GLN A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ARG A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ASP A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 232 through 251 Proline residue: A 239 - end of helix removed outlier: 3.549A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 277 removed outlier: 3.658A pdb=" N VAL A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 290 through 300 removed outlier: 3.510A pdb=" N HIS A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ARG A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 Processing helix chain 'A' and resid 340 through 348 removed outlier: 3.522A pdb=" N SER A 347 " --> pdb=" O THR A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 393 through 407 removed outlier: 3.810A pdb=" N GLU A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 431 removed outlier: 3.634A pdb=" N GLN A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 452 Processing helix chain 'A' and resid 461 through 478 removed outlier: 4.401A pdb=" N GLY A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N SER A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 489 Processing helix chain 'A' and resid 494 through 509 removed outlier: 3.635A pdb=" N LYS A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 135 removed outlier: 4.104A pdb=" N GLN X 10 " --> pdb=" O ILE X 7 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE X 14 " --> pdb=" O ALA X 11 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU X 16 " --> pdb=" O ALA X 13 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE X 20 " --> pdb=" O PHE X 17 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS X 21 " --> pdb=" O VAL X 18 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS X 23 " --> pdb=" O PHE X 20 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N VAL X 25 " --> pdb=" O MET X 22 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N TRP X 26 " --> pdb=" O LYS X 23 " (cutoff:3.500A) Proline residue: X 27 - end of helix removed outlier: 3.515A pdb=" N MET X 30 " --> pdb=" O PRO X 27 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS X 38 " --> pdb=" O LYS X 35 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP X 42 " --> pdb=" O GLU X 39 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA X 50 " --> pdb=" O ALA X 47 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS X 51 " --> pdb=" O GLU X 48 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU X 54 " --> pdb=" O HIS X 51 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP X 88 " --> pdb=" O GLN X 85 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN X 106 " --> pdb=" O ALA X 103 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU X 110 " --> pdb=" O ALA X 107 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU X 118 " --> pdb=" O ARG X 115 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG X 121 " --> pdb=" O GLU X 118 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL X 124 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA X 125 " --> pdb=" O LYS X 122 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA X 128 " --> pdb=" O ALA X 125 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE X 135 " --> pdb=" O ALA X 132 " (cutoff:3.500A) Processing helix chain 'X' and resid 143 through 145 No H-bonds generated for 'chain 'X' and resid 143 through 145' Processing helix chain 'X' and resid 148 through 155 removed outlier: 3.703A pdb=" N LEU X 152 " --> pdb=" O ILE X 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 103 Processing helix chain 'H' and resid 112 through 124 removed outlier: 3.645A pdb=" N GLN H 116 " --> pdb=" O VAL H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 133 No H-bonds generated for 'chain 'H' and resid 130 through 133' Processing helix chain 'G' and resid 2 through 57 removed outlier: 3.751A pdb=" N MET G 25 " --> pdb=" O LYS G 21 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER G 41 " --> pdb=" O ARG G 37 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Proline residue: G 43 - end of helix removed outlier: 3.629A pdb=" N LYS G 50 " --> pdb=" O GLU G 46 " (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 88 through 107 removed outlier: 4.551A pdb=" N ASN G 91 " --> pdb=" O GLY G 88 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN G 93 " --> pdb=" O LEU G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 128 Processing helix chain 'G' and resid 145 through 160 removed outlier: 3.566A pdb=" N ILE G 149 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 5.369A 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: 4.280A 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: 3.598A pdb=" N ASP G 216 " --> pdb=" O LYS G 212 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR G 217 " --> pdb=" O ALA G 213 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL G 244 " --> pdb=" O ALA G 240 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS G 258 " --> pdb=" O GLY G 254 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU G 259 " --> pdb=" O SER G 255 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU G 262 " --> pdb=" O LYS G 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 83 No H-bonds generated for 'chain 'F' and resid 81 through 83' Processing helix chain 'F' and resid 116 through 118 No H-bonds generated for 'chain 'F' and resid 116 through 118' Processing helix chain 'F' and resid 131 through 136 Processing helix chain 'F' and resid 157 through 167 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: 4.835A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET F 226 " --> pdb=" O THR F 222 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 258 removed outlier: 3.909A pdb=" N ALA F 250 " --> pdb=" O TYR F 247 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU F 253 " --> pdb=" O ALA F 250 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER F 255 " --> pdb=" O THR F 252 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ALA F 256 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 279 removed outlier: 3.750A 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: 4.522A pdb=" N ALA F 313 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N HIS F 314 " --> pdb=" O THR F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 328 removed outlier: 4.148A 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 369 Processing helix chain 'F' and resid 371 through 377 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: 3.648A pdb=" N VAL F 390 " --> pdb=" O ASP F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 411 removed outlier: 3.791A pdb=" N GLU F 408 " --> pdb=" O PHE F 405 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL F 409 " --> pdb=" O VAL F 406 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR F 411 " --> pdb=" O GLU F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 432 removed outlier: 3.732A pdb=" N ARG F 425 " --> pdb=" O LYS F 421 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY F 426 " --> pdb=" O ASP F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 443 Processing helix chain 'F' and resid 449 through 458 removed outlier: 3.976A pdb=" N LYS F 457 " --> pdb=" O VAL F 453 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS F 458 " --> pdb=" O GLU F 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 131 through 136 Processing helix chain 'E' and resid 155 through 168 Processing helix chain 'E' and resid 183 through 196 removed outlier: 3.945A pdb=" N SER E 196 " --> pdb=" O GLU E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 201 No H-bonds generated for 'chain 'E' and resid 199 through 201' Processing helix chain 'E' and resid 213 through 233 removed outlier: 4.999A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU E 233 " --> pdb=" O LYS E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 258 removed outlier: 3.576A pdb=" N GLY E 251 " --> pdb=" O TYR E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 279 removed outlier: 3.696A 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: 4.301A pdb=" N GLU E 369 " --> pdb=" O GLN E 365 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 381 No H-bonds generated for 'chain 'E' and resid 379 through 381' Processing helix chain 'E' and resid 384 through 399 removed outlier: 3.793A pdb=" N LYS E 395 " --> pdb=" O ALA E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 411 removed outlier: 3.546A pdb=" N THR E 411 " --> pdb=" O GLU E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 432 Processing helix chain 'E' and resid 440 through 442 No H-bonds generated for 'chain 'E' and resid 440 through 442' Processing helix chain 'E' and resid 449 through 457 removed outlier: 4.060A pdb=" N GLU E 454 " --> pdb=" O GLU E 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 131 through 136 Processing helix chain 'D' and resid 155 through 170 Processing helix chain 'D' and resid 183 through 196 Processing helix chain 'D' and resid 199 through 201 No H-bonds generated for 'chain 'D' and resid 199 through 201' Processing helix chain 'D' and resid 213 through 233 removed outlier: 5.239A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 257 Processing helix chain 'D' and resid 271 through 281 removed outlier: 4.324A pdb=" N ARG D 281 " --> pdb=" O VAL D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 306 through 311 Processing helix chain 'D' and resid 323 through 328 Processing helix chain 'D' and resid 346 through 349 No H-bonds generated for 'chain 'D' and resid 346 through 349' Processing helix chain 'D' and resid 351 through 376 removed outlier: 4.402A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 381 No H-bonds generated for 'chain 'D' and resid 379 through 381' Processing helix chain 'D' and resid 386 through 399 Processing helix chain 'D' and resid 408 through 411 No H-bonds generated for 'chain 'D' and resid 408 through 411' Processing helix chain 'D' and resid 420 through 431 Processing helix chain 'D' and resid 440 through 443 Processing helix chain 'D' and resid 449 through 458 removed outlier: 3.627A pdb=" N LYS D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 41 removed outlier: 3.774A pdb=" N MET I 11 " --> pdb=" O ASP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 76 removed outlier: 3.731A pdb=" N ILE I 46 " --> pdb=" O PRO I 43 " (cutoff:3.500A) Proline residue: I 47 - end of helix removed outlier: 4.093A pdb=" N ARG I 50 " --> pdb=" O PRO I 47 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET I 57 " --> pdb=" O PHE I 54 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY I 58 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP I 61 " --> pdb=" O GLY I 58 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE I 63 " --> pdb=" O VAL I 60 " (cutoff:3.500A) Proline residue: I 64 - end of helix Processing helix chain 'J' and resid 4 through 41 removed outlier: 3.713A pdb=" N LEU J 8 " --> pdb=" O LEU J 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 60 removed outlier: 3.809A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 76 Processing helix chain 'L' and resid 4 through 41 removed outlier: 3.722A pdb=" N VAL L 15 " --> pdb=" O ALA L 12 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA L 24 " --> pdb=" O ALA L 21 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY L 27 " --> pdb=" O ALA L 24 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE L 28 " --> pdb=" O ALA L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 76 removed outlier: 3.799A pdb=" N ILE L 46 " --> pdb=" O PRO L 43 " (cutoff:3.500A) Proline residue: L 47 - end of helix removed outlier: 4.045A pdb=" N ARG L 50 " --> pdb=" O PRO L 47 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET L 57 " --> pdb=" O PHE L 54 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY L 58 " --> pdb=" O ILE L 55 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASP L 61 " --> pdb=" O GLY L 58 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE L 63 " --> pdb=" O VAL L 60 " (cutoff:3.500A) Proline residue: L 64 - end of helix removed outlier: 3.646A pdb=" N MET L 75 " --> pdb=" O LEU L 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 41 removed outlier: 3.512A pdb=" N MET M 11 " --> pdb=" O ASP M 7 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 60 Proline residue: M 47 - end of helix removed outlier: 4.160A pdb=" N ARG M 50 " --> pdb=" O PRO M 47 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE M 53 " --> pdb=" O ARG M 50 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY M 58 " --> pdb=" O ILE M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 76 Processing helix chain 'N' and resid 4 through 41 removed outlier: 4.520A pdb=" N LEU N 9 " --> pdb=" O ASN N 5 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TYR N 10 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET N 16 " --> pdb=" O ALA N 12 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA N 21 " --> pdb=" O MET N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 76 Proline residue: N 47 - end of helix removed outlier: 4.257A pdb=" N ARG N 50 " --> pdb=" O PRO N 47 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY N 58 " --> pdb=" O ILE N 55 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP N 61 " --> pdb=" O GLY N 58 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE N 63 " --> pdb=" O VAL N 60 " (cutoff:3.500A) Proline residue: N 64 - end of helix Processing helix chain 'O' and resid 4 through 41 removed outlier: 3.515A pdb=" N MET O 17 " --> pdb=" O ALA O 14 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU O 19 " --> pdb=" O MET O 16 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY O 23 " --> pdb=" O ALA O 20 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA O 24 " --> pdb=" O ALA O 21 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLY O 27 " --> pdb=" O ALA O 24 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE O 28 " --> pdb=" O ALA O 25 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA O 40 " --> pdb=" O GLU O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 76 removed outlier: 3.799A pdb=" N THR O 51 " --> pdb=" O PRO O 47 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE O 54 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU O 59 " --> pdb=" O ILE O 55 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP O 61 " --> pdb=" O MET O 57 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA O 62 " --> pdb=" O GLY O 58 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE O 63 " --> pdb=" O LEU O 59 " (cutoff:3.500A) Proline residue: O 64 - end of helix Processing helix chain 'P' and resid 4 through 41 removed outlier: 3.866A pdb=" N LEU P 8 " --> pdb=" O LEU P 4 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU P 9 " --> pdb=" O ASN P 5 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA P 21 " --> pdb=" O MET P 17 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE P 28 " --> pdb=" O ALA P 24 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 76 removed outlier: 3.517A pdb=" N LEU P 49 " --> pdb=" O ILE P 46 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY P 58 " --> pdb=" O ILE P 55 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE P 63 " --> pdb=" O VAL P 60 " (cutoff:3.500A) Proline residue: P 64 - end of helix Processing helix chain 'Q' and resid 4 through 41 removed outlier: 3.547A pdb=" N LEU Q 8 " --> pdb=" O LEU Q 4 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU Q 9 " --> pdb=" O ASN Q 5 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR Q 10 " --> pdb=" O MET Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 76 Proline residue: Q 47 - end of helix removed outlier: 4.209A pdb=" N ARG Q 50 " --> pdb=" O PRO Q 47 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE Q 54 " --> pdb=" O THR Q 51 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP Q 61 " --> pdb=" O GLY Q 58 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE Q 63 " --> pdb=" O VAL Q 60 " (cutoff:3.500A) Proline residue: Q 64 - end of helix removed outlier: 3.616A pdb=" N PHE Q 76 " --> pdb=" O TYR Q 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 41 removed outlier: 3.755A pdb=" N LEU R 8 " --> pdb=" O LEU R 4 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU R 9 " --> pdb=" O ASN R 5 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA R 21 " --> pdb=" O MET R 17 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE R 28 " --> pdb=" O ALA R 24 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS R 34 " --> pdb=" O ILE R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 76 removed outlier: 3.860A pdb=" N ARG R 50 " --> pdb=" O PRO R 47 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE R 63 " --> pdb=" O VAL R 60 " (cutoff:3.500A) Proline residue: R 64 - end of helix removed outlier: 3.504A pdb=" N VAL R 74 " --> pdb=" O GLY R 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 6 through 41 removed outlier: 4.555A pdb=" N TYR S 10 " --> pdb=" O ASP S 7 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL S 15 " --> pdb=" O ALA S 12 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA S 24 " --> pdb=" O ALA S 21 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE S 28 " --> pdb=" O ALA S 25 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG S 41 " --> pdb=" O GLY S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 60 Proline residue: S 47 - end of helix removed outlier: 3.504A 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 removed outlier: 3.829A pdb=" N LYS Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 26 through 139 removed outlier: 3.730A pdb=" N ALA Y 70 " --> pdb=" O LYS Y 66 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN Y 73 " --> pdb=" O LYS Y 69 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG Y 98 " --> pdb=" O ALA Y 94 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR Y 99 " --> pdb=" O GLU Y 95 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS Y 100 " --> pdb=" O GLN Y 96 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN Y 123 " --> pdb=" O GLU Y 119 " (cutoff:3.500A) Processing helix chain 'Y' and resid 142 through 153 Processing helix chain 'a' and resid 8 through 16 removed outlier: 3.604A pdb=" N GLY a 13 " --> pdb=" O GLN a 9 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU a 16 " --> pdb=" O ILE a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 43 through 64 removed outlier: 3.731A pdb=" N VAL a 63 " --> pdb=" O LEU a 59 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 93 removed outlier: 3.797A pdb=" N ALA a 78 " --> pdb=" O LYS a 74 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL a 82 " --> pdb=" O ALA a 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 100 through 120 removed outlier: 4.460A pdb=" N ASP a 119 " --> pdb=" O MET a 115 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU a 120 " --> pdb=" O ASN a 116 " (cutoff:3.500A) Processing helix chain 'a' and resid 123 through 132 Proline residue: a 127 - end of helix 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: 3.666A pdb=" N LYS a 169 " --> pdb=" O SER a 165 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE a 171 " --> pdb=" O LYS a 167 " (cutoff:3.500A) removed outlier: 9.460A pdb=" N GLY a 172 " --> pdb=" O MET a 168 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY a 173 " --> pdb=" O LYS a 169 " (cutoff:3.500A) Processing helix chain 'a' and resid 189 through 228 removed outlier: 3.995A pdb=" N ILE a 194 " --> pdb=" O PRO a 190 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS a 203 " --> pdb=" O SER a 199 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 3.698A pdb=" N LEU a 211 " --> pdb=" O LEU a 207 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN a 214 " --> pdb=" O ARG a 210 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE a 221 " --> pdb=" O ALA a 217 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE a 222 " --> pdb=" O GLY a 218 " (cutoff:3.500A) Processing helix chain 'a' and resid 231 through 233 No H-bonds generated for 'chain 'a' and resid 231 through 233' Processing helix chain 'a' and resid 235 through 268 Proline residue: a 240 - end of helix removed outlier: 4.035A pdb=" N PHE a 244 " --> pdb=" O PRO a 240 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR a 250 " --> pdb=" O ILE a 246 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE a 256 " --> pdb=" O GLN a 252 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER a 268 " --> pdb=" O LEU a 264 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'W' and resid 135 through 142 removed outlier: 3.723A pdb=" N ASN W 139 " --> pdb=" O VAL W 108 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL W 110 " --> pdb=" O ASN W 139 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 28 through 30 removed outlier: 4.185A pdb=" N MET C 52 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LEU C 66 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N SER C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG C 40 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER C 33 " --> pdb=" O ARG C 40 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N HIS C 42 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ILE C 31 " --> pdb=" O HIS C 42 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 96 through 98 Processing sheet with id= D, first strand: chain 'C' and resid 107 through 109 removed outlier: 8.330A pdb=" N VAL C 108 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL C 223 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N ILE C 222 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N CYS C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N VAL C 224 " --> pdb=" O CYS C 193 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASP C 255 " --> pdb=" O LYS C 192 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ILE C 194 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU C 257 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL C 196 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE C 259 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ILE C 198 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASP C 261 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N SER C 323 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE C 258 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N THR C 325 " --> pdb=" O ILE C 258 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N TYR C 260 " --> pdb=" O THR C 325 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.567A pdb=" N LEU C 166 " --> pdb=" O GLY C 351 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 87 through 90 removed outlier: 4.648A pdb=" N ASN B 27 " --> pdb=" O CYS B 90 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (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: 8.053A pdb=" N VAL B 108 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL B 223 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N CYS B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N VAL B 224 " --> pdb=" O CYS B 193 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N SER B 323 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ILE B 258 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N THR B 325 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N TYR B 260 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 352 through 355 removed outlier: 6.509A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.690A 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: 6.354A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 96 through 98 Processing sheet with id= L, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.845A pdb=" N LEU A 166 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N LEU A 355 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE A 168 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 221 through 226 removed outlier: 6.859A pdb=" N CYS A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N VAL A 224 " --> pdb=" O CYS A 193 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N SER A 323 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ILE A 258 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR A 325 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N TYR A 260 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU A 327 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 5 through 9 removed outlier: 3.611A pdb=" N ILE H 68 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY H 67 " --> pdb=" O ILE H 45 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 30 through 35 removed outlier: 7.330A pdb=" N VAL H 53 " --> pdb=" O GLU H 21 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE H 23 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG H 51 " --> pdb=" O ILE H 23 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N VAL H 25 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 8.873A 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: 6.578A pdb=" N LEU G 167 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS G 166 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ASN G 172 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLN G 111 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N TYR G 77 " --> pdb=" O GLN G 111 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASP G 113 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N VAL G 79 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ALA G 115 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N MET G 116 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLN G 135 " --> pdb=" O MET G 116 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 3 through 9 removed outlier: 6.552A pdb=" N ASP F 14 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ILE F 54 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 5.558A 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: 8.042A pdb=" N VAL F 145 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N SER F 292 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N LEU F 147 " --> pdb=" O SER F 292 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLN F 294 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLY F 149 " --> pdb=" O GLN F 294 " (cutoff:3.500A) removed outlier: 6.201A 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: 6.424A pdb=" N ASP E 14 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL E 8 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL E 12 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE E 54 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL E 42 " --> pdb=" O ILE E 54 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.840A pdb=" N GLU E 105 " --> pdb=" O VAL E 79 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 317 through 319 removed outlier: 8.452A pdb=" N VAL E 145 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N SER E 292 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU E 147 " --> pdb=" O SER E 292 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLN E 294 " --> pdb=" O LEU E 147 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 4 through 9 removed outlier: 6.606A pdb=" N ASP D 14 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL D 8 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE D 54 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N VAL D 42 " --> pdb=" O ILE D 54 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.653A pdb=" N GLU D 105 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 317 through 320 removed outlier: 8.802A pdb=" N VAL D 145 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER D 292 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N LEU D 147 " --> pdb=" O SER D 292 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLN D 294 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N GLY D 149 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL D 296 " --> pdb=" O GLY D 149 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'a' and resid 20 through 22 1959 hydrogen bonds defined for protein. 4638 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: 13.92 Time building geometry restraints manager: 15.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 6331 1.29 - 1.42: 8590 1.42 - 1.55: 22222 1.55 - 1.68: 25 1.68 - 1.81: 360 Bond restraints: 37528 Sorted by residual: bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.54e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.32e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.14e+01 bond pdb=" C5 ATP A 600 " pdb=" C6 ATP A 600 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.32e+01 bond pdb=" C ASP B 261 " pdb=" O ASP B 261 " ideal model delta sigma weight residual 1.237 1.162 0.075 1.17e-02 7.31e+03 4.12e+01 ... (remaining 37523 not shown) Histogram of bond angle deviations from ideal: 98.23 - 105.85: 858 105.85 - 113.46: 21332 113.46 - 121.08: 19409 121.08 - 128.70: 9002 128.70 - 136.31: 196 Bond angle restraints: 50797 Sorted by residual: angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 116.20 23.67 1.00e+00 1.00e+00 5.60e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 118.09 21.78 1.00e+00 1.00e+00 4.74e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 118.42 21.45 1.00e+00 1.00e+00 4.60e+02 angle pdb=" PA ATP C 600 " pdb=" O3A ATP C 600 " pdb=" PB ATP C 600 " ideal model delta sigma weight residual 136.83 116.65 20.18 1.00e+00 1.00e+00 4.07e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 116.74 20.09 1.00e+00 1.00e+00 4.04e+02 ... (remaining 50792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.54: 22086 30.54 - 61.08: 625 61.08 - 91.62: 78 91.62 - 122.16: 2 122.16 - 152.70: 3 Dihedral angle restraints: 22794 sinusoidal: 9010 harmonic: 13784 Sorted by residual: dihedral pdb=" O1B ADP D 500 " pdb=" O3A ADP D 500 " pdb=" PB ADP D 500 " pdb=" PA ADP D 500 " ideal model delta sinusoidal sigma weight residual 300.00 147.29 152.70 1 2.00e+01 2.50e-03 4.53e+01 dihedral pdb=" C5' ADP E 500 " pdb=" O5' ADP E 500 " pdb=" PA ADP E 500 " pdb=" O2A ADP E 500 " ideal model delta sinusoidal sigma weight residual 300.00 155.99 144.01 1 2.00e+01 2.50e-03 4.34e+01 dihedral pdb=" O2A ADP D 500 " pdb=" O3A ADP D 500 " pdb=" PA ADP D 500 " pdb=" PB ADP D 500 " ideal model delta sinusoidal sigma weight residual -60.00 65.65 -125.65 1 2.00e+01 2.50e-03 3.80e+01 ... (remaining 22791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 5208 0.071 - 0.141: 672 0.141 - 0.212: 32 0.212 - 0.283: 6 0.283 - 0.353: 2 Chirality restraints: 5920 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 2.16 0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CA VAL a 29 " pdb=" N VAL a 29 " pdb=" C VAL a 29 " pdb=" CB VAL a 29 " both_signs ideal model delta sigma weight residual False 2.44 2.75 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA ASP B 261 " pdb=" N ASP B 261 " pdb=" C ASP B 261 " pdb=" CB ASP B 261 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 5917 not shown) Planarity restraints: 6550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS H 100 " 0.023 2.00e-02 2.50e+03 4.66e-02 2.17e+01 pdb=" C LYS H 100 " -0.081 2.00e-02 2.50e+03 pdb=" O LYS H 100 " 0.030 2.00e-02 2.50e+03 pdb=" N ALA H 101 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 18 " -0.018 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C GLN C 18 " 0.061 2.00e-02 2.50e+03 pdb=" O GLN C 18 " -0.022 2.00e-02 2.50e+03 pdb=" N PHE C 19 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO G 191 " -0.015 2.00e-02 2.50e+03 3.12e-02 9.75e+00 pdb=" C PRO G 191 " 0.054 2.00e-02 2.50e+03 pdb=" O PRO G 191 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA G 192 " -0.018 2.00e-02 2.50e+03 ... (remaining 6547 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 138 2.46 - 3.07: 27408 3.07 - 3.68: 53704 3.68 - 4.29: 83303 4.29 - 4.90: 140189 Nonbonded interactions: 304742 Sorted by model distance: nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.849 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 601 " model vdw 1.854 2.170 nonbonded pdb=" O2B ATP A 600 " pdb="MG MG A 601 " model vdw 1.872 2.170 nonbonded pdb=" O2G ATP A 600 " pdb="MG MG A 601 " model vdw 1.890 2.170 nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 601 " model vdw 1.915 2.170 ... (remaining 304737 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 408 or (resid 409 through 410 and (name N or nam \ e CA or name C or name O or name CB )) or resid 411 through 511 or resid 600 thr \ ough 601)) selection = (chain 'B' and (resid 4 through 511 or resid 600 through 601)) selection = (chain 'C' and (resid 4 through 408 or (resid 409 through 410 and (name N or nam \ e CA or name C or name O or name CB )) or resid 411 through 511 or resid 600 thr \ ough 601)) } ncs_group { reference = (chain 'D' and (resid 2 through 459 or resid 500)) selection = (chain 'E' and (resid 2 through 459 or resid 500)) selection = (chain 'F' and (resid 2 through 459 or resid 500)) } ncs_group { reference = (chain 'I' and resid 3 through 78) selection = (chain 'J' and resid 3 through 78) selection = (chain 'L' and resid 3 through 78) selection = (chain 'M' and resid 3 through 78) selection = (chain 'N' and resid 3 through 78) selection = (chain 'O' and resid 3 through 78) selection = (chain 'P' and resid 3 through 78) selection = (chain 'Q' and resid 3 through 78) selection = chain 'R' selection = (chain 'S' and resid 3 through 78) } ncs_group { reference = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 11.390 Check model and map are aligned: 0.560 Set scattering table: 0.330 Process input model: 97.860 Find NCS groups from input model: 2.650 Set up NCS constraints: 0.240 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:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.112 37528 Z= 0.499 Angle : 0.846 23.673 50797 Z= 0.551 Chirality : 0.048 0.353 5920 Planarity : 0.004 0.049 6550 Dihedral : 14.506 152.702 13976 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.52 % Favored : 97.46 % Rotamer: Outliers : 1.80 % Allowed : 8.08 % Favored : 90.12 % 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: -2.20 (0.11), residues: 4807 helix: -1.35 (0.09), residues: 2630 sheet: -0.80 (0.20), residues: 539 loop : -1.55 (0.14), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP a 39 HIS 0.008 0.002 HIS a 132 PHE 0.015 0.002 PHE D 312 TYR 0.020 0.002 TYR B 236 ARG 0.008 0.001 ARG Q 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 935 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 866 time to evaluate : 4.382 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: W 4 ILE cc_start: 0.9239 (mt) cc_final: 0.8897 (mm) REVERT: W 156 ASP cc_start: 0.7806 (p0) cc_final: 0.7196 (p0) REVERT: C 115 ILE cc_start: 0.9243 (OUTLIER) cc_final: 0.9020 (tp) REVERT: C 236 TYR cc_start: 0.9170 (OUTLIER) cc_final: 0.8230 (t80) REVERT: B 236 TYR cc_start: 0.9507 (OUTLIER) cc_final: 0.9208 (t80) REVERT: B 295 SER cc_start: 0.9297 (t) cc_final: 0.9029 (p) REVERT: B 429 GLU cc_start: 0.8122 (tp30) cc_final: 0.7918 (tp30) REVERT: A 236 TYR cc_start: 0.9343 (OUTLIER) cc_final: 0.9092 (t80) REVERT: X 16 LEU cc_start: 0.9097 (mt) cc_final: 0.8798 (tt) REVERT: X 85 GLN cc_start: 0.8525 (mt0) cc_final: 0.7939 (mt0) REVERT: H 71 VAL cc_start: 0.9404 (p) cc_final: 0.8962 (m) REVERT: H 72 GLN cc_start: 0.7903 (mt0) cc_final: 0.7588 (pt0) REVERT: H 81 ASP cc_start: 0.8006 (p0) cc_final: 0.7790 (p0) REVERT: E 136 MET cc_start: 0.9103 (mmm) cc_final: 0.8850 (mmm) REVERT: E 323 ARG cc_start: 0.7988 (tpp80) cc_final: 0.7668 (ttm170) REVERT: E 373 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8421 (tt) REVERT: E 438 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7707 (pp) REVERT: D 253 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7742 (mt-10) REVERT: I 31 LEU cc_start: 0.8913 (tp) cc_final: 0.8613 (tp) REVERT: I 63 ILE cc_start: 0.8101 (mm) cc_final: 0.7851 (mt) REVERT: I 68 VAL cc_start: 0.8619 (t) cc_final: 0.8415 (t) REVERT: I 73 TYR cc_start: 0.8816 (t80) cc_final: 0.8492 (t80) REVERT: J 41 ARG cc_start: 0.8306 (ttt-90) cc_final: 0.7944 (tpp80) REVERT: J 42 GLN cc_start: 0.8972 (mt0) cc_final: 0.8627 (tt0) REVERT: L 11 MET cc_start: 0.8280 (tpt) cc_final: 0.7774 (tpp) REVERT: L 41 ARG cc_start: 0.8471 (mtt90) cc_final: 0.8226 (mmt90) REVERT: L 42 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8045 (mt0) REVERT: L 57 MET cc_start: 0.9073 (tmm) cc_final: 0.8769 (tmm) REVERT: L 65 MET cc_start: 0.8702 (mmt) cc_final: 0.8485 (mmt) REVERT: L 73 TYR cc_start: 0.8748 (t80) cc_final: 0.8405 (t80) REVERT: L 78 VAL cc_start: 0.7590 (t) cc_final: 0.7101 (t) REVERT: M 34 LYS cc_start: 0.8348 (mmtm) cc_final: 0.8123 (mmtt) REVERT: M 37 GLU cc_start: 0.8544 (pt0) cc_final: 0.8254 (pt0) REVERT: N 57 MET cc_start: 0.8074 (tmm) cc_final: 0.7581 (tmm) REVERT: N 61 ASP cc_start: 0.8283 (m-30) cc_final: 0.7874 (m-30) REVERT: O 73 TYR cc_start: 0.7360 (t80) cc_final: 0.6459 (m-10) REVERT: O 74 VAL cc_start: 0.8369 (t) cc_final: 0.7937 (m) REVERT: P 51 THR cc_start: 0.8879 (p) cc_final: 0.8676 (p) REVERT: P 52 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8293 (mm-40) REVERT: P 72 LEU cc_start: 0.7467 (mt) cc_final: 0.7141 (pp) REVERT: P 76 PHE cc_start: 0.6188 (m-80) cc_final: 0.5580 (m-10) REVERT: Q 41 ARG cc_start: 0.8065 (mtp-110) cc_final: 0.7348 (mtp-110) REVERT: Q 42 GLN cc_start: 0.8597 (mt0) cc_final: 0.8116 (mp10) REVERT: Q 51 THR cc_start: 0.9497 (m) cc_final: 0.9282 (p) REVERT: Q 53 PHE cc_start: 0.8845 (t80) cc_final: 0.8573 (t80) REVERT: Q 68 VAL cc_start: 0.9071 (t) cc_final: 0.8854 (t) REVERT: S 63 ILE cc_start: 0.8584 (mm) cc_final: 0.8293 (mt) REVERT: S 66 ILE cc_start: 0.7749 (mm) cc_final: 0.7510 (mt) REVERT: Y 14 PHE cc_start: 0.8800 (t80) cc_final: 0.8257 (t80) REVERT: Y 18 VAL cc_start: 0.8754 (t) cc_final: 0.8475 (p) REVERT: Y 26 TRP cc_start: 0.6604 (t60) cc_final: 0.6011 (t-100) REVERT: Y 33 ILE cc_start: 0.8537 (mt) cc_final: 0.8256 (pt) REVERT: Y 54 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.6302 (mm) REVERT: Y 96 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7763 (tm-30) REVERT: Y 98 ARG cc_start: 0.7921 (ttt90) cc_final: 0.7398 (ttt180) REVERT: Y 150 ASP cc_start: 0.8413 (m-30) cc_final: 0.8207 (m-30) REVERT: a 20 GLN cc_start: 0.7986 (mt0) cc_final: 0.7784 (mp10) REVERT: a 24 ARG cc_start: 0.5963 (mmt90) cc_final: 0.5520 (mmp-170) REVERT: a 30 ASP cc_start: 0.6384 (p0) cc_final: 0.6089 (p0) REVERT: a 80 GLU cc_start: 0.9072 (pt0) cc_final: 0.8725 (pt0) REVERT: a 117 LEU cc_start: 0.9407 (tp) cc_final: 0.9200 (mt) REVERT: a 199 SER cc_start: 0.8848 (t) cc_final: 0.8413 (p) REVERT: a 216 TYR cc_start: 0.9094 (t80) cc_final: 0.8587 (t80) REVERT: a 231 TRP cc_start: 0.7354 (p-90) cc_final: 0.6702 (p-90) REVERT: a 232 TRP cc_start: 0.7377 (p-90) cc_final: 0.6874 (p-90) outliers start: 69 outliers final: 28 residues processed: 923 average time/residue: 0.5362 time to fit residues: 780.8056 Evaluate side-chains 641 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 605 time to evaluate : 4.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 373 ILE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 81 LYS Chi-restraints excluded: chain Y residue 96 GLN Chi-restraints excluded: chain Y residue 145 ASN Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 165 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 399 optimal weight: 6.9990 chunk 358 optimal weight: 5.9990 chunk 198 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 241 optimal weight: 0.7980 chunk 191 optimal weight: 6.9990 chunk 370 optimal weight: 5.9990 chunk 143 optimal weight: 0.7980 chunk 225 optimal weight: 2.9990 chunk 275 optimal weight: 0.7980 chunk 429 optimal weight: 0.0980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 67 GLN ** W 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 GLN B 14 GLN B 26 HIS B 147 GLN B 186 GLN A 65 ASN A 147 GLN A 344 ASN A 484 GLN X 80 ASN H 5 HIS H 56 HIS G 54 HIS G 274 GLN F 32 GLN F 324 GLN F 368 GLN D 121 ASN ** D 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 GLN O 3 ASN R 5 ASN S 5 ASN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 37 GLN Y 73 GLN a 5 ASN a 116 ASN a 132 HIS a 185 HIS ** a 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 37528 Z= 0.192 Angle : 0.620 9.030 50797 Z= 0.325 Chirality : 0.043 0.267 5920 Planarity : 0.005 0.046 6550 Dihedral : 7.862 141.087 5398 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.58 % Allowed : 13.06 % Favored : 84.36 % 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: -0.56 (0.12), residues: 4807 helix: 0.00 (0.10), residues: 2656 sheet: -0.34 (0.21), residues: 538 loop : -0.78 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 111 HIS 0.009 0.001 HIS a 14 PHE 0.022 0.001 PHE E 189 TYR 0.024 0.001 TYR B 236 ARG 0.006 0.000 ARG X 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 655 time to evaluate : 4.063 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: W 4 ILE cc_start: 0.9176 (mt) cc_final: 0.8912 (mm) REVERT: W 156 ASP cc_start: 0.8023 (p0) cc_final: 0.7421 (p0) REVERT: W 160 ASP cc_start: 0.8757 (t70) cc_final: 0.8515 (t70) REVERT: C 115 ILE cc_start: 0.9176 (tp) cc_final: 0.8951 (tp) REVERT: C 236 TYR cc_start: 0.9074 (OUTLIER) cc_final: 0.8132 (t80) REVERT: C 343 THR cc_start: 0.9413 (OUTLIER) cc_final: 0.9024 (p) REVERT: B 262 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.7999 (m-30) REVERT: B 295 SER cc_start: 0.8948 (t) cc_final: 0.8714 (p) REVERT: B 429 GLU cc_start: 0.8063 (tp30) cc_final: 0.7841 (tp30) REVERT: A 460 GLU cc_start: 0.7852 (pm20) cc_final: 0.7568 (pm20) REVERT: X 10 GLN cc_start: 0.8422 (mm-40) cc_final: 0.8203 (mt0) REVERT: X 16 LEU cc_start: 0.9093 (mt) cc_final: 0.8892 (tp) REVERT: X 85 GLN cc_start: 0.8563 (mt0) cc_final: 0.8314 (mt0) REVERT: H 24 GLN cc_start: 0.8322 (tt0) cc_final: 0.7998 (tt0) REVERT: H 71 VAL cc_start: 0.9383 (OUTLIER) cc_final: 0.9127 (m) REVERT: H 72 GLN cc_start: 0.8207 (mt0) cc_final: 0.7991 (mt0) REVERT: H 81 ASP cc_start: 0.7780 (p0) cc_final: 0.7575 (p0) REVERT: G 207 TYR cc_start: 0.9169 (m-80) cc_final: 0.8895 (m-80) REVERT: E 323 ARG cc_start: 0.8014 (tpp80) cc_final: 0.7788 (ttm170) REVERT: E 438 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7751 (pp) REVERT: D 253 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7663 (mt-10) REVERT: D 445 MET cc_start: 0.8842 (mmt) cc_final: 0.8486 (mmm) REVERT: I 17 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8565 (tpp) REVERT: I 68 VAL cc_start: 0.8782 (t) cc_final: 0.8487 (t) REVERT: J 41 ARG cc_start: 0.8223 (ttt-90) cc_final: 0.7948 (ttm-80) REVERT: J 42 GLN cc_start: 0.8969 (mt0) cc_final: 0.8607 (tt0) REVERT: J 72 LEU cc_start: 0.9005 (mm) cc_final: 0.8626 (mm) REVERT: L 42 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8156 (mt0) REVERT: L 54 PHE cc_start: 0.9135 (m-10) cc_final: 0.8920 (m-80) REVERT: L 55 ILE cc_start: 0.8722 (mt) cc_final: 0.8427 (mp) REVERT: L 78 VAL cc_start: 0.7557 (t) cc_final: 0.7313 (m) REVERT: M 34 LYS cc_start: 0.8412 (mmtm) cc_final: 0.8081 (mmtt) REVERT: M 37 GLU cc_start: 0.8517 (pt0) cc_final: 0.8274 (pt0) REVERT: N 6 MET cc_start: 0.7978 (tmm) cc_final: 0.7653 (tmm) REVERT: N 10 TYR cc_start: 0.6314 (m-80) cc_final: 0.4785 (m-80) REVERT: N 16 MET cc_start: 0.6895 (tpt) cc_final: 0.6395 (mmm) REVERT: N 57 MET cc_start: 0.8114 (tmm) cc_final: 0.7520 (tmm) REVERT: N 61 ASP cc_start: 0.8572 (m-30) cc_final: 0.8303 (m-30) REVERT: N 65 MET cc_start: 0.7457 (mmm) cc_final: 0.6907 (mmm) REVERT: O 6 MET cc_start: 0.5140 (ppp) cc_final: 0.4682 (ppp) REVERT: O 7 ASP cc_start: 0.3644 (t0) cc_final: 0.3232 (t0) REVERT: O 73 TYR cc_start: 0.7081 (t80) cc_final: 0.6412 (m-10) REVERT: O 74 VAL cc_start: 0.8341 (t) cc_final: 0.7644 (p) REVERT: P 6 MET cc_start: 0.7497 (ppp) cc_final: 0.7121 (ppp) REVERT: P 11 MET cc_start: 0.8156 (tpp) cc_final: 0.7772 (tpp) REVERT: P 17 MET cc_start: 0.8416 (mtp) cc_final: 0.7928 (mmm) REVERT: P 50 ARG cc_start: 0.9233 (ttp80) cc_final: 0.9016 (ttp80) REVERT: P 54 PHE cc_start: 0.8197 (m-10) cc_final: 0.7963 (m-80) REVERT: P 76 PHE cc_start: 0.6194 (m-80) cc_final: 0.5618 (m-10) REVERT: Q 16 MET cc_start: 0.7573 (mtp) cc_final: 0.7306 (mtp) REVERT: Q 41 ARG cc_start: 0.8043 (mtp-110) cc_final: 0.7556 (mtp180) REVERT: Q 42 GLN cc_start: 0.8767 (mt0) cc_final: 0.8221 (mp10) REVERT: S 16 MET cc_start: 0.7405 (tpp) cc_final: 0.7115 (tpp) REVERT: Y 18 VAL cc_start: 0.8812 (t) cc_final: 0.8462 (p) REVERT: Y 54 LEU cc_start: 0.6790 (OUTLIER) cc_final: 0.6101 (mt) REVERT: Y 96 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8026 (tm-30) REVERT: Y 150 ASP cc_start: 0.8472 (m-30) cc_final: 0.8256 (m-30) REVERT: a 14 HIS cc_start: 0.7468 (p90) cc_final: 0.7229 (p-80) REVERT: a 24 ARG cc_start: 0.5913 (mmt90) cc_final: 0.5579 (mmp-170) REVERT: a 54 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8352 (pp) REVERT: a 80 GLU cc_start: 0.8861 (pt0) cc_final: 0.8561 (pt0) REVERT: a 115 MET cc_start: 0.9007 (mtm) cc_final: 0.8755 (mtm) REVERT: a 176 LYS cc_start: 0.8516 (tptt) cc_final: 0.8259 (tptp) REVERT: a 199 SER cc_start: 0.8660 (OUTLIER) cc_final: 0.8342 (p) REVERT: a 231 TRP cc_start: 0.7553 (p-90) cc_final: 0.7212 (p-90) REVERT: a 234 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7453 (mm-40) outliers start: 99 outliers final: 50 residues processed: 716 average time/residue: 0.5411 time to fit residues: 638.0519 Evaluate side-chains 638 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 577 time to evaluate : 4.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 109 ASP Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 146 SER Chi-restraints excluded: chain H residue 56 HIS Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain H residue 138 MET Chi-restraints excluded: chain G residue 31 MET Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 17 MET Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 11 MET Chi-restraints excluded: chain Y residue 8 LEU Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 96 GLN Chi-restraints excluded: chain a residue 23 LEU Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain a residue 75 PHE Chi-restraints excluded: chain a residue 124 ASP Chi-restraints excluded: chain a residue 199 SER Chi-restraints excluded: chain a residue 234 GLN Chi-restraints excluded: chain a residue 237 LEU Chi-restraints excluded: chain a residue 245 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 238 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 357 optimal weight: 7.9990 chunk 292 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 430 optimal weight: 10.0000 chunk 464 optimal weight: 2.9990 chunk 383 optimal weight: 8.9990 chunk 426 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 chunk 345 optimal weight: 0.0770 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 67 GLN ** W 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 GLN B 207 ASN B 511 GLN ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 ASN H 116 GLN G 64 HIS D 121 ASN J 3 ASN ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 GLN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 64 GLN Y 85 GLN Y 96 GLN a 18 ASN a 116 ASN a 185 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 37528 Z= 0.235 Angle : 0.583 8.717 50797 Z= 0.301 Chirality : 0.042 0.229 5920 Planarity : 0.005 0.044 6550 Dihedral : 7.160 112.887 5369 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.18 % Allowed : 14.31 % Favored : 82.51 % 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: -0.07 (0.12), residues: 4807 helix: 0.46 (0.10), residues: 2643 sheet: -0.22 (0.21), residues: 539 loop : -0.63 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP X 26 HIS 0.014 0.001 HIS H 56 PHE 0.024 0.001 PHE Y 14 TYR 0.022 0.001 TYR P 73 ARG 0.008 0.000 ARG Y 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 608 time to evaluate : 4.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 4 ILE cc_start: 0.9174 (mt) cc_final: 0.8928 (mm) REVERT: W 156 ASP cc_start: 0.8049 (p0) cc_final: 0.7339 (p0) REVERT: C 236 TYR cc_start: 0.9095 (OUTLIER) cc_final: 0.8210 (t80) REVERT: C 343 THR cc_start: 0.9423 (OUTLIER) cc_final: 0.9057 (p) REVERT: B 484 GLN cc_start: 0.8186 (mp10) cc_final: 0.7861 (mp10) REVERT: A 236 TYR cc_start: 0.9245 (OUTLIER) cc_final: 0.8835 (t80) REVERT: X 10 GLN cc_start: 0.8428 (mm-40) cc_final: 0.8163 (mt0) REVERT: X 85 GLN cc_start: 0.8542 (mt0) cc_final: 0.8017 (mt0) REVERT: H 24 GLN cc_start: 0.8300 (tt0) cc_final: 0.8099 (tt0) REVERT: H 49 MET cc_start: 0.7879 (tpp) cc_final: 0.7660 (tpp) REVERT: H 71 VAL cc_start: 0.9301 (OUTLIER) cc_final: 0.9070 (m) REVERT: H 72 GLN cc_start: 0.8159 (mt0) cc_final: 0.7885 (mt0) REVERT: H 81 ASP cc_start: 0.7746 (p0) cc_final: 0.7517 (p0) REVERT: G 70 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7733 (ptt180) REVERT: F 193 MET cc_start: 0.8837 (mmp) cc_final: 0.8635 (mmp) REVERT: E 323 ARG cc_start: 0.8123 (tpp80) cc_final: 0.7841 (ttm170) REVERT: E 438 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7902 (pp) REVERT: D 253 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7683 (mt-10) REVERT: I 65 MET cc_start: 0.8246 (ptm) cc_final: 0.8022 (ptm) REVERT: J 6 MET cc_start: 0.7852 (ptm) cc_final: 0.6509 (ppp) REVERT: J 42 GLN cc_start: 0.9034 (mt0) cc_final: 0.8777 (tt0) REVERT: J 52 GLN cc_start: 0.9010 (mm-40) cc_final: 0.8748 (mm-40) REVERT: J 72 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8583 (mm) REVERT: J 76 PHE cc_start: 0.7751 (m-10) cc_final: 0.6524 (m-10) REVERT: L 11 MET cc_start: 0.8067 (mmm) cc_final: 0.7502 (tpp) REVERT: L 42 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8136 (mt0) REVERT: L 55 ILE cc_start: 0.8744 (mt) cc_final: 0.8515 (mp) REVERT: M 57 MET cc_start: 0.8269 (ttp) cc_final: 0.7908 (tmm) REVERT: N 57 MET cc_start: 0.8078 (tmm) cc_final: 0.7518 (tmm) REVERT: N 61 ASP cc_start: 0.8704 (m-30) cc_final: 0.8428 (m-30) REVERT: N 65 MET cc_start: 0.7663 (mmm) cc_final: 0.7161 (mmm) REVERT: O 7 ASP cc_start: 0.3533 (t0) cc_final: 0.3291 (t0) REVERT: O 73 TYR cc_start: 0.7171 (t80) cc_final: 0.6448 (m-10) REVERT: O 74 VAL cc_start: 0.8405 (t) cc_final: 0.7778 (p) REVERT: P 6 MET cc_start: 0.7526 (ppp) cc_final: 0.7180 (ppp) REVERT: P 11 MET cc_start: 0.8174 (tpp) cc_final: 0.7911 (tpt) REVERT: P 17 MET cc_start: 0.8437 (mtp) cc_final: 0.8143 (mmm) REVERT: P 54 PHE cc_start: 0.8228 (m-10) cc_final: 0.8001 (m-80) REVERT: Q 41 ARG cc_start: 0.7874 (mtp-110) cc_final: 0.7520 (mtp-110) REVERT: R 16 MET cc_start: 0.8554 (tpp) cc_final: 0.8323 (mmt) REVERT: S 17 MET cc_start: 0.7275 (mmm) cc_final: 0.7028 (mtt) REVERT: Y 18 VAL cc_start: 0.8762 (t) cc_final: 0.8447 (p) REVERT: Y 54 LEU cc_start: 0.6724 (OUTLIER) cc_final: 0.6467 (mm) REVERT: Y 96 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7791 (tm-30) REVERT: a 14 HIS cc_start: 0.7521 (p90) cc_final: 0.7277 (p90) REVERT: a 54 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8413 (pp) REVERT: a 80 GLU cc_start: 0.8891 (pt0) cc_final: 0.8645 (pt0) REVERT: a 199 SER cc_start: 0.8776 (t) cc_final: 0.8478 (p) REVERT: a 216 TYR cc_start: 0.8564 (t80) cc_final: 0.8265 (t80) REVERT: a 219 GLU cc_start: 0.9252 (tt0) cc_final: 0.8898 (pt0) REVERT: a 231 TRP cc_start: 0.7619 (p-90) cc_final: 0.7320 (p-90) REVERT: a 234 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7552 (mm-40) outliers start: 122 outliers final: 71 residues processed: 694 average time/residue: 0.4968 time to fit residues: 563.5094 Evaluate side-chains 643 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 561 time to evaluate : 4.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 109 ASP Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 147 MET Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain X residue 54 LEU Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain H residue 138 MET Chi-restraints excluded: chain G residue 70 ARG Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 68 VAL Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Y residue 8 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 29 LEU Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 96 GLN Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 145 ASN Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 22 ASP Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain a residue 75 PHE Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 89 SER Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 234 GLN Chi-restraints excluded: chain a residue 237 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 425 optimal weight: 10.0000 chunk 323 optimal weight: 0.6980 chunk 223 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 205 optimal weight: 10.0000 chunk 288 optimal weight: 4.9990 chunk 431 optimal weight: 0.9980 chunk 457 optimal weight: 4.9990 chunk 225 optimal weight: 3.9990 chunk 409 optimal weight: 0.7980 chunk 123 optimal weight: 7.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 67 GLN ** W 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 511 GLN A 444 GLN X 2 ASN ** D 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 ASN ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 GLN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 10 GLN Y 123 GLN ** a 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 116 ASN a 185 HIS ** a 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 37528 Z= 0.222 Angle : 0.568 8.871 50797 Z= 0.292 Chirality : 0.042 0.220 5920 Planarity : 0.004 0.046 6550 Dihedral : 6.981 108.324 5366 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.21 % Allowed : 15.51 % Favored : 81.28 % 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: 0.15 (0.12), residues: 4807 helix: 0.67 (0.10), residues: 2637 sheet: -0.20 (0.22), residues: 527 loop : -0.58 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP X 26 HIS 0.005 0.001 HIS a 14 PHE 0.037 0.001 PHE Y 14 TYR 0.021 0.001 TYR a 94 ARG 0.006 0.000 ARG X 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 585 time to evaluate : 4.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 4 ILE cc_start: 0.9198 (mt) cc_final: 0.8954 (mm) REVERT: W 156 ASP cc_start: 0.8053 (p0) cc_final: 0.7312 (p0) REVERT: C 236 TYR cc_start: 0.9095 (OUTLIER) cc_final: 0.8184 (t80) REVERT: C 343 THR cc_start: 0.9393 (OUTLIER) cc_final: 0.9047 (p) REVERT: B 86 MET cc_start: 0.8673 (mtp) cc_final: 0.8465 (mtp) REVERT: B 484 GLN cc_start: 0.8154 (mp10) cc_final: 0.7767 (mp10) REVERT: A 49 GLN cc_start: 0.9373 (OUTLIER) cc_final: 0.8116 (tm-30) REVERT: X 10 GLN cc_start: 0.8328 (mm-40) cc_final: 0.8110 (mt0) REVERT: X 26 TRP cc_start: 0.8548 (t-100) cc_final: 0.8330 (t-100) REVERT: X 85 GLN cc_start: 0.8452 (mt0) cc_final: 0.7978 (mt0) REVERT: H 24 GLN cc_start: 0.8312 (tt0) cc_final: 0.8071 (tt0) REVERT: H 49 MET cc_start: 0.7899 (tpp) cc_final: 0.7675 (tpp) REVERT: H 71 VAL cc_start: 0.9324 (OUTLIER) cc_final: 0.9043 (m) REVERT: H 72 GLN cc_start: 0.8057 (mt0) cc_final: 0.7753 (mt0) REVERT: H 81 ASP cc_start: 0.7745 (p0) cc_final: 0.7508 (p0) REVERT: H 113 ASP cc_start: 0.8449 (m-30) cc_final: 0.8170 (m-30) REVERT: G 199 LYS cc_start: 0.6883 (OUTLIER) cc_final: 0.4950 (mptt) REVERT: E 323 ARG cc_start: 0.8132 (tpp80) cc_final: 0.7861 (ttm170) REVERT: E 438 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.7966 (pp) REVERT: D 253 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7664 (mt-10) REVERT: J 6 MET cc_start: 0.7783 (ptm) cc_final: 0.6873 (ppp) REVERT: J 41 ARG cc_start: 0.8158 (ttm-80) cc_final: 0.7682 (tpp80) REVERT: J 42 GLN cc_start: 0.9029 (mt0) cc_final: 0.8797 (tt0) REVERT: J 52 GLN cc_start: 0.9030 (mm-40) cc_final: 0.8743 (mm-40) REVERT: J 72 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8669 (mm) REVERT: J 76 PHE cc_start: 0.7846 (m-10) cc_final: 0.6626 (m-10) REVERT: L 8 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8462 (tt) REVERT: L 42 GLN cc_start: 0.8755 (mm-40) cc_final: 0.8179 (mt0) REVERT: M 55 ILE cc_start: 0.8681 (mp) cc_final: 0.8466 (pt) REVERT: M 57 MET cc_start: 0.8263 (ttp) cc_final: 0.7994 (tmm) REVERT: M 75 MET cc_start: 0.8349 (mmm) cc_final: 0.8126 (mmp) REVERT: N 57 MET cc_start: 0.8093 (tmm) cc_final: 0.7557 (tmm) REVERT: N 61 ASP cc_start: 0.8698 (m-30) cc_final: 0.8460 (m-30) REVERT: N 65 MET cc_start: 0.7697 (mmm) cc_final: 0.7138 (mmm) REVERT: O 17 MET cc_start: 0.7298 (ptm) cc_final: 0.6982 (ppp) REVERT: O 73 TYR cc_start: 0.7136 (t80) cc_final: 0.6438 (m-10) REVERT: P 6 MET cc_start: 0.7505 (ppp) cc_final: 0.7186 (ppp) REVERT: P 17 MET cc_start: 0.8395 (mtp) cc_final: 0.7931 (mmm) REVERT: P 50 ARG cc_start: 0.9105 (tmm-80) cc_final: 0.8839 (tmm-80) REVERT: P 54 PHE cc_start: 0.8072 (m-10) cc_final: 0.7856 (m-80) REVERT: Q 41 ARG cc_start: 0.7886 (mtp-110) cc_final: 0.7591 (mtp-110) REVERT: Y 18 VAL cc_start: 0.8727 (t) cc_final: 0.8446 (p) REVERT: Y 37 GLN cc_start: 0.7388 (tt0) cc_final: 0.7187 (tt0) REVERT: Y 54 LEU cc_start: 0.6738 (OUTLIER) cc_final: 0.6343 (mm) REVERT: a 11 TYR cc_start: 0.7695 (t80) cc_final: 0.7142 (t80) REVERT: a 54 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8351 (pp) REVERT: a 56 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.7690 (t80) REVERT: a 80 GLU cc_start: 0.8931 (pt0) cc_final: 0.8423 (pt0) REVERT: a 94 TYR cc_start: 0.7303 (t80) cc_final: 0.7068 (t80) REVERT: a 199 SER cc_start: 0.8766 (t) cc_final: 0.8470 (p) REVERT: a 216 TYR cc_start: 0.8592 (t80) cc_final: 0.8307 (t80) REVERT: a 219 GLU cc_start: 0.9288 (tt0) cc_final: 0.8972 (pt0) REVERT: a 231 TRP cc_start: 0.7575 (p-90) cc_final: 0.7293 (p-90) REVERT: a 234 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7590 (mm-40) outliers start: 123 outliers final: 77 residues processed: 672 average time/residue: 0.5002 time to fit residues: 550.3794 Evaluate side-chains 649 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 560 time to evaluate : 4.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 109 ASP Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 147 MET Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 511 GLN Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain X residue 2 ASN Chi-restraints excluded: chain X residue 54 LEU Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 138 MET Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain J residue 3 ASN Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 11 MET Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain S residue 31 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain Y residue 29 LEU Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 145 ASN Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 75 PHE Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 124 ASP Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 234 GLN Chi-restraints excluded: chain a residue 237 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 380 optimal weight: 2.9990 chunk 259 optimal weight: 6.9990 chunk 6 optimal weight: 0.4980 chunk 340 optimal weight: 4.9990 chunk 188 optimal weight: 6.9990 chunk 390 optimal weight: 0.3980 chunk 316 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 233 optimal weight: 3.9990 chunk 410 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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** B 511 GLN A 444 GLN X 2 ASN ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 ASN ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 3 ASN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 116 ASN a 185 HIS ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 37528 Z= 0.222 Angle : 0.561 8.435 50797 Z= 0.288 Chirality : 0.042 0.211 5920 Planarity : 0.004 0.043 6550 Dihedral : 6.761 105.886 5361 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.26 % Allowed : 16.37 % Favored : 80.37 % 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: 0.30 (0.12), residues: 4807 helix: 0.83 (0.10), residues: 2634 sheet: -0.11 (0.22), residues: 514 loop : -0.58 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP X 26 HIS 0.005 0.001 HIS a 185 PHE 0.031 0.001 PHE E 189 TYR 0.024 0.001 TYR R 10 ARG 0.008 0.000 ARG X 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 576 time to evaluate : 4.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 4 ILE cc_start: 0.9213 (mt) cc_final: 0.8976 (mm) REVERT: W 68 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7571 (pt) REVERT: W 156 ASP cc_start: 0.8073 (p0) cc_final: 0.7309 (p0) REVERT: C 236 TYR cc_start: 0.9114 (OUTLIER) cc_final: 0.8197 (t80) REVERT: C 343 THR cc_start: 0.9378 (OUTLIER) cc_final: 0.9036 (p) REVERT: B 262 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.7964 (m-30) REVERT: B 484 GLN cc_start: 0.8112 (mp10) cc_final: 0.7706 (mp10) REVERT: A 49 GLN cc_start: 0.9355 (OUTLIER) cc_final: 0.8172 (tm-30) REVERT: A 236 TYR cc_start: 0.9252 (OUTLIER) cc_final: 0.8917 (t80) REVERT: A 343 THR cc_start: 0.9256 (OUTLIER) cc_final: 0.8964 (p) REVERT: X 1 MET cc_start: 0.7946 (tmm) cc_final: 0.7171 (tmm) REVERT: X 26 TRP cc_start: 0.8561 (t-100) cc_final: 0.8315 (t-100) REVERT: H 24 GLN cc_start: 0.8301 (tt0) cc_final: 0.8073 (tt0) REVERT: H 71 VAL cc_start: 0.9309 (OUTLIER) cc_final: 0.9059 (m) REVERT: H 81 ASP cc_start: 0.7712 (p0) cc_final: 0.7477 (p0) REVERT: G 70 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7808 (ptt180) REVERT: G 199 LYS cc_start: 0.6896 (OUTLIER) cc_final: 0.4948 (mptt) REVERT: F 193 MET cc_start: 0.8772 (mmp) cc_final: 0.8560 (mmp) REVERT: E 323 ARG cc_start: 0.8141 (tpp80) cc_final: 0.7871 (ttm170) REVERT: E 438 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.7984 (pt) REVERT: D 253 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7697 (mt-10) REVERT: I 4 LEU cc_start: -0.1406 (OUTLIER) cc_final: -0.1730 (mt) REVERT: J 3 ASN cc_start: 0.1233 (OUTLIER) cc_final: 0.0823 (p0) REVERT: J 6 MET cc_start: 0.7738 (ptm) cc_final: 0.6998 (ppp) REVERT: J 17 MET cc_start: 0.9018 (mmm) cc_final: 0.8799 (mmt) REVERT: J 41 ARG cc_start: 0.8186 (ttm-80) cc_final: 0.7674 (tpp80) REVERT: J 52 GLN cc_start: 0.9039 (mm-40) cc_final: 0.8730 (mm-40) REVERT: J 72 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8528 (mm) REVERT: L 42 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8185 (mt0) REVERT: L 52 GLN cc_start: 0.8671 (mm110) cc_final: 0.8423 (mp10) REVERT: L 55 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8641 (mp) REVERT: M 57 MET cc_start: 0.8290 (ttp) cc_final: 0.8075 (tmm) REVERT: N 57 MET cc_start: 0.8114 (tmm) cc_final: 0.7502 (tmm) REVERT: N 61 ASP cc_start: 0.8578 (m-30) cc_final: 0.8355 (m-30) REVERT: N 65 MET cc_start: 0.7743 (mmm) cc_final: 0.7174 (mmm) REVERT: O 73 TYR cc_start: 0.7170 (t80) cc_final: 0.6488 (m-10) REVERT: P 6 MET cc_start: 0.7516 (ppp) cc_final: 0.7186 (ppp) REVERT: P 11 MET cc_start: 0.8098 (tpp) cc_final: 0.7632 (tpt) REVERT: P 54 PHE cc_start: 0.8174 (m-10) cc_final: 0.7898 (m-10) REVERT: Q 41 ARG cc_start: 0.7768 (mtp-110) cc_final: 0.7493 (mtp-110) REVERT: Y 18 VAL cc_start: 0.8807 (t) cc_final: 0.8460 (p) REVERT: Y 54 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.6465 (mm) REVERT: a 54 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8349 (pp) REVERT: a 56 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7578 (t80) REVERT: a 80 GLU cc_start: 0.8925 (pt0) cc_final: 0.8425 (pt0) REVERT: a 91 LYS cc_start: 0.9041 (ttmm) cc_final: 0.8628 (tppt) REVERT: a 199 SER cc_start: 0.8811 (t) cc_final: 0.8522 (p) REVERT: a 219 GLU cc_start: 0.9310 (tt0) cc_final: 0.8881 (pt0) REVERT: a 231 TRP cc_start: 0.7596 (p-90) cc_final: 0.7323 (p-90) REVERT: a 234 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7595 (mm-40) outliers start: 125 outliers final: 79 residues processed: 660 average time/residue: 0.5065 time to fit residues: 545.8711 Evaluate side-chains 652 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 554 time to evaluate : 4.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 68 LEU Chi-restraints excluded: chain W residue 109 ASP Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 147 MET Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 511 GLN Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain X residue 2 ASN Chi-restraints excluded: chain X residue 54 LEU Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 65 LEU Chi-restraints excluded: chain X residue 76 ILE Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 138 MET Chi-restraints excluded: chain G residue 70 ARG Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain J residue 3 ASN Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain N residue 16 MET Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 11 MET Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain S residue 31 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 145 ASN Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 22 ASP Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 75 PHE Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 131 GLU Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 234 GLN Chi-restraints excluded: chain a residue 237 LEU Chi-restraints excluded: chain a residue 266 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 153 optimal weight: 4.9990 chunk 411 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 268 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 457 optimal weight: 0.9980 chunk 379 optimal weight: 3.9990 chunk 211 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 240 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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** B 511 GLN A 493 ASN X 2 ASN ** X 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 GLN F 324 GLN D 121 ASN J 3 ASN ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 3 ASN ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 116 ASN a 185 HIS ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 37528 Z= 0.290 Angle : 0.590 9.872 50797 Z= 0.301 Chirality : 0.043 0.206 5920 Planarity : 0.004 0.049 6550 Dihedral : 6.738 108.019 5360 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.78 % Allowed : 16.45 % Favored : 79.77 % 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: 0.32 (0.12), residues: 4807 helix: 0.87 (0.10), residues: 2629 sheet: -0.20 (0.21), residues: 536 loop : -0.58 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 513 HIS 0.005 0.001 HIS a 185 PHE 0.038 0.001 PHE Y 14 TYR 0.020 0.001 TYR P 73 ARG 0.008 0.000 ARG X 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 563 time to evaluate : 4.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 4 ILE cc_start: 0.9247 (mt) cc_final: 0.8987 (mm) REVERT: W 156 ASP cc_start: 0.8107 (p0) cc_final: 0.7300 (p0) REVERT: C 236 TYR cc_start: 0.9172 (OUTLIER) cc_final: 0.8291 (t80) REVERT: C 343 THR cc_start: 0.9384 (OUTLIER) cc_final: 0.9028 (p) REVERT: A 49 GLN cc_start: 0.9394 (OUTLIER) cc_final: 0.8211 (tm-30) REVERT: A 343 THR cc_start: 0.9273 (OUTLIER) cc_final: 0.8959 (p) REVERT: A 401 ARG cc_start: 0.8325 (mtp-110) cc_final: 0.8082 (ttm-80) REVERT: X 1 MET cc_start: 0.7948 (tmm) cc_final: 0.7202 (tmm) REVERT: X 26 TRP cc_start: 0.8509 (t-100) cc_final: 0.8246 (t-100) REVERT: H 24 GLN cc_start: 0.8358 (tt0) cc_final: 0.8149 (tt0) REVERT: H 28 SER cc_start: 0.8686 (t) cc_final: 0.8369 (t) REVERT: H 71 VAL cc_start: 0.9252 (OUTLIER) cc_final: 0.9032 (m) REVERT: H 72 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7679 (tp40) REVERT: H 81 ASP cc_start: 0.7749 (p0) cc_final: 0.7500 (p0) REVERT: G 70 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7893 (ptt180) REVERT: G 199 LYS cc_start: 0.6973 (OUTLIER) cc_final: 0.5002 (mptt) REVERT: F 441 GLN cc_start: 0.8422 (mp10) cc_final: 0.8213 (mp10) REVERT: E 438 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8308 (pt) REVERT: D 253 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7735 (mt-10) REVERT: J 41 ARG cc_start: 0.8207 (ttm-80) cc_final: 0.7679 (tpp80) REVERT: J 52 GLN cc_start: 0.9061 (mm-40) cc_final: 0.8768 (mm-40) REVERT: J 72 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8534 (mm) REVERT: L 8 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8347 (mp) REVERT: L 42 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8251 (mt0) REVERT: N 57 MET cc_start: 0.8142 (tmm) cc_final: 0.7518 (tmm) REVERT: N 61 ASP cc_start: 0.8633 (m-30) cc_final: 0.8356 (m-30) REVERT: N 65 MET cc_start: 0.7783 (mmm) cc_final: 0.7293 (mmm) REVERT: O 73 TYR cc_start: 0.7203 (t80) cc_final: 0.6498 (m-10) REVERT: P 6 MET cc_start: 0.7488 (ppp) cc_final: 0.7215 (ppp) REVERT: P 11 MET cc_start: 0.8105 (tpp) cc_final: 0.7618 (tpt) REVERT: P 54 PHE cc_start: 0.8129 (m-10) cc_final: 0.7893 (m-10) REVERT: Q 41 ARG cc_start: 0.7828 (mtp-110) cc_final: 0.7517 (mtp-110) REVERT: Y 18 VAL cc_start: 0.8762 (t) cc_final: 0.8487 (p) REVERT: Y 54 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6477 (mm) REVERT: a 54 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8375 (pp) REVERT: a 56 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.7660 (t80) REVERT: a 80 GLU cc_start: 0.8902 (pt0) cc_final: 0.8520 (pt0) REVERT: a 199 SER cc_start: 0.8817 (t) cc_final: 0.8540 (p) REVERT: a 231 TRP cc_start: 0.7526 (p-90) cc_final: 0.7081 (p-90) REVERT: a 234 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7575 (mm-40) outliers start: 145 outliers final: 97 residues processed: 662 average time/residue: 0.4208 time to fit residues: 455.6665 Evaluate side-chains 659 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 548 time to evaluate : 3.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 109 ASP Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 147 MET Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 511 GLN Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain X residue 2 ASN Chi-restraints excluded: chain X residue 54 LEU Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 65 LEU Chi-restraints excluded: chain X residue 76 ILE Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 138 MET Chi-restraints excluded: chain G residue 70 ARG Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 17 MET Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain L residue 6 MET Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain N residue 16 MET Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 73 TYR Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 11 MET Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain S residue 31 LEU Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain Y residue 29 LEU Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 63 ASP Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 145 ASN Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 22 ASP Chi-restraints excluded: chain a residue 23 LEU Chi-restraints excluded: chain a residue 49 SER Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 75 PHE Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 131 GLU Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 234 GLN Chi-restraints excluded: chain a residue 237 LEU Chi-restraints excluded: chain a residue 266 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 441 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 260 optimal weight: 0.9980 chunk 334 optimal weight: 8.9990 chunk 258 optimal weight: 0.9990 chunk 385 optimal weight: 3.9990 chunk 255 optimal weight: 2.9990 chunk 455 optimal weight: 4.9990 chunk 285 optimal weight: 5.9990 chunk 277 optimal weight: 0.0010 chunk 210 optimal weight: 0.0870 overall best weight: 0.5166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 67 GLN ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN X 2 ASN ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN ** D 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 GLN J 3 ASN ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 116 ASN a 185 HIS ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 37528 Z= 0.148 Angle : 0.557 10.072 50797 Z= 0.282 Chirality : 0.041 0.201 5920 Planarity : 0.004 0.049 6550 Dihedral : 6.444 106.049 5358 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.89 % Allowed : 17.41 % Favored : 79.69 % 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: 0.55 (0.12), residues: 4807 helix: 1.05 (0.10), residues: 2622 sheet: 0.02 (0.22), residues: 509 loop : -0.49 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 513 HIS 0.006 0.001 HIS a 185 PHE 0.028 0.001 PHE E 189 TYR 0.021 0.001 TYR P 73 ARG 0.008 0.000 ARG X 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 586 time to evaluate : 4.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 4 ILE cc_start: 0.9184 (mt) cc_final: 0.8967 (mm) REVERT: W 156 ASP cc_start: 0.8095 (p0) cc_final: 0.7271 (p0) REVERT: C 236 TYR cc_start: 0.9092 (OUTLIER) cc_final: 0.8209 (t80) REVERT: B 262 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.8003 (m-30) REVERT: B 419 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.7234 (tptt) REVERT: A 49 GLN cc_start: 0.9333 (OUTLIER) cc_final: 0.8117 (tm-30) REVERT: A 76 MET cc_start: 0.8892 (mtp) cc_final: 0.8542 (mtp) REVERT: A 343 THR cc_start: 0.9261 (OUTLIER) cc_final: 0.8998 (p) REVERT: X 1 MET cc_start: 0.7742 (tmm) cc_final: 0.7042 (tmm) REVERT: X 10 GLN cc_start: 0.8165 (mt0) cc_final: 0.7463 (tm-30) REVERT: X 26 TRP cc_start: 0.8496 (t-100) cc_final: 0.8215 (t-100) REVERT: H 24 GLN cc_start: 0.8349 (tt0) cc_final: 0.8052 (tt0) REVERT: G 70 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7741 (ptt180) REVERT: G 116 MET cc_start: 0.9025 (mmm) cc_final: 0.8699 (mmm) REVERT: G 199 LYS cc_start: 0.6952 (OUTLIER) cc_final: 0.5042 (mptt) REVERT: E 438 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8005 (pp) REVERT: D 253 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7666 (mt-10) REVERT: D 345 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.8472 (p0) REVERT: J 41 ARG cc_start: 0.8152 (ttm-80) cc_final: 0.7841 (ttt90) REVERT: J 52 GLN cc_start: 0.8988 (mm-40) cc_final: 0.8677 (mm-40) REVERT: J 59 LEU cc_start: 0.9050 (mm) cc_final: 0.8729 (tt) REVERT: J 72 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8794 (mm) REVERT: L 8 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8416 (mp) REVERT: L 41 ARG cc_start: 0.8193 (mmt90) cc_final: 0.7945 (mmt90) REVERT: L 42 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8220 (mt0) REVERT: M 6 MET cc_start: 0.6031 (ppp) cc_final: 0.5769 (ppp) REVERT: N 57 MET cc_start: 0.8126 (tmm) cc_final: 0.7515 (tmm) REVERT: N 61 ASP cc_start: 0.8638 (m-30) cc_final: 0.8368 (m-30) REVERT: N 65 MET cc_start: 0.7759 (mmm) cc_final: 0.7271 (mmm) REVERT: O 6 MET cc_start: 0.5048 (ppp) cc_final: 0.4608 (ppp) REVERT: O 73 TYR cc_start: 0.7239 (t80) cc_final: 0.6538 (m-10) REVERT: P 6 MET cc_start: 0.7477 (ppp) cc_final: 0.7198 (ppp) REVERT: P 11 MET cc_start: 0.8120 (tpp) cc_final: 0.7633 (tpt) REVERT: P 42 GLN cc_start: 0.8397 (mm-40) cc_final: 0.7895 (mp10) REVERT: P 54 PHE cc_start: 0.8168 (m-10) cc_final: 0.7927 (m-10) REVERT: Q 41 ARG cc_start: 0.7795 (mtp-110) cc_final: 0.6746 (mtp-110) REVERT: Q 42 GLN cc_start: 0.8684 (mt0) cc_final: 0.7895 (mp10) REVERT: R 75 MET cc_start: 0.8538 (mmm) cc_final: 0.8197 (tmm) REVERT: S 66 ILE cc_start: 0.8463 (mt) cc_final: 0.8148 (mm) REVERT: Y 14 PHE cc_start: 0.8351 (t80) cc_final: 0.8031 (t80) REVERT: Y 18 VAL cc_start: 0.8777 (t) cc_final: 0.8476 (p) REVERT: Y 54 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6439 (mm) REVERT: a 11 TYR cc_start: 0.7206 (t80) cc_final: 0.6664 (t80) REVERT: a 54 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8344 (pp) REVERT: a 56 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7590 (t80) REVERT: a 80 GLU cc_start: 0.8935 (pt0) cc_final: 0.8548 (pt0) REVERT: a 124 ASP cc_start: 0.7502 (t0) cc_final: 0.6912 (m-30) REVERT: a 185 HIS cc_start: 0.3523 (OUTLIER) cc_final: 0.2957 (m-70) REVERT: a 199 SER cc_start: 0.8830 (t) cc_final: 0.8563 (p) REVERT: a 231 TRP cc_start: 0.7494 (p-90) cc_final: 0.7081 (p-90) REVERT: a 234 GLN cc_start: 0.7908 (mt0) cc_final: 0.7699 (mm-40) REVERT: a 255 ILE cc_start: 0.9427 (mt) cc_final: 0.9156 (tt) outliers start: 111 outliers final: 52 residues processed: 663 average time/residue: 0.4642 time to fit residues: 502.2689 Evaluate side-chains 625 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 558 time to evaluate : 3.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 109 ASP Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain X residue 2 ASN Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 76 ILE Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain G residue 70 ARG Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain J residue 3 ASN Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 6 MET Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain N residue 16 MET Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 29 LEU Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 145 ASN Chi-restraints excluded: chain a residue 22 ASP Chi-restraints excluded: chain a residue 49 SER Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 75 PHE Chi-restraints excluded: chain a residue 131 GLU Chi-restraints excluded: chain a residue 185 HIS Chi-restraints excluded: chain a residue 237 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 282 optimal weight: 10.0000 chunk 182 optimal weight: 1.9990 chunk 272 optimal weight: 3.9990 chunk 137 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 289 optimal weight: 0.8980 chunk 310 optimal weight: 6.9990 chunk 225 optimal weight: 0.0040 chunk 42 optimal weight: 5.9990 chunk 358 optimal weight: 2.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 511 GLN A 444 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 GLN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 ASN ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 116 ASN ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 37528 Z= 0.172 Angle : 0.574 10.411 50797 Z= 0.288 Chirality : 0.041 0.217 5920 Planarity : 0.004 0.050 6550 Dihedral : 6.292 106.035 5355 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.35 % Allowed : 18.33 % Favored : 79.33 % 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: 0.61 (0.12), residues: 4807 helix: 1.09 (0.10), residues: 2617 sheet: 0.12 (0.23), residues: 490 loop : -0.48 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 203 HIS 0.013 0.001 HIS a 185 PHE 0.017 0.001 PHE E 189 TYR 0.021 0.001 TYR B 236 ARG 0.010 0.000 ARG X 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 578 time to evaluate : 4.531 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: W 4 ILE cc_start: 0.9194 (mt) cc_final: 0.8975 (mm) REVERT: W 156 ASP cc_start: 0.8091 (p0) cc_final: 0.7274 (p0) REVERT: C 236 TYR cc_start: 0.9099 (OUTLIER) cc_final: 0.8203 (t80) REVERT: B 262 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.8000 (m-30) REVERT: B 419 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.7328 (tptt) REVERT: A 49 GLN cc_start: 0.9328 (OUTLIER) cc_final: 0.8091 (tm-30) REVERT: A 343 THR cc_start: 0.9265 (OUTLIER) cc_final: 0.8999 (p) REVERT: X 1 MET cc_start: 0.7515 (tmm) cc_final: 0.6844 (tmm) REVERT: X 26 TRP cc_start: 0.8461 (t-100) cc_final: 0.8192 (t-100) REVERT: H 72 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7697 (tp-100) REVERT: G 70 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7825 (ptt180) REVERT: G 199 LYS cc_start: 0.7015 (OUTLIER) cc_final: 0.5164 (mptt) REVERT: E 88 MET cc_start: 0.8585 (mtp) cc_final: 0.8276 (mtp) REVERT: E 438 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8007 (pp) REVERT: D 253 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7686 (mt-10) REVERT: D 345 ASP cc_start: 0.8626 (OUTLIER) cc_final: 0.8418 (p0) REVERT: J 6 MET cc_start: 0.7747 (ptm) cc_final: 0.7423 (ptp) REVERT: J 41 ARG cc_start: 0.8212 (ttm-80) cc_final: 0.7860 (ttt90) REVERT: J 52 GLN cc_start: 0.9004 (mm-40) cc_final: 0.8779 (mm-40) REVERT: J 59 LEU cc_start: 0.9001 (mm) cc_final: 0.8711 (tt) REVERT: J 72 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8725 (mm) REVERT: L 41 ARG cc_start: 0.8202 (mmt90) cc_final: 0.7797 (mmt90) REVERT: L 42 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8353 (mt0) REVERT: N 57 MET cc_start: 0.8123 (tmm) cc_final: 0.7501 (tmm) REVERT: N 61 ASP cc_start: 0.8595 (m-30) cc_final: 0.8303 (m-30) REVERT: N 65 MET cc_start: 0.7815 (mmm) cc_final: 0.7590 (mmm) REVERT: O 6 MET cc_start: 0.5078 (ppp) cc_final: 0.4660 (ppp) REVERT: O 37 GLU cc_start: 0.8246 (tp30) cc_final: 0.7942 (tp30) REVERT: O 73 TYR cc_start: 0.7247 (t80) cc_final: 0.6542 (m-10) REVERT: P 6 MET cc_start: 0.7476 (ppp) cc_final: 0.7206 (ppp) REVERT: P 11 MET cc_start: 0.8142 (tpp) cc_final: 0.7657 (tpt) REVERT: P 42 GLN cc_start: 0.8358 (mm-40) cc_final: 0.7901 (mp10) REVERT: P 54 PHE cc_start: 0.8109 (m-10) cc_final: 0.7849 (m-10) REVERT: Q 41 ARG cc_start: 0.7835 (mtp-110) cc_final: 0.7495 (mmm-85) REVERT: Q 42 GLN cc_start: 0.8721 (mt0) cc_final: 0.8129 (mp10) REVERT: R 75 MET cc_start: 0.8495 (mmm) cc_final: 0.8144 (tmm) REVERT: S 66 ILE cc_start: 0.8459 (mt) cc_final: 0.8147 (mm) REVERT: Y 14 PHE cc_start: 0.8427 (t80) cc_final: 0.8123 (t80) REVERT: Y 18 VAL cc_start: 0.8856 (t) cc_final: 0.8569 (p) REVERT: Y 54 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6481 (mm) REVERT: a 11 TYR cc_start: 0.7321 (t80) cc_final: 0.6748 (t80) REVERT: a 54 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8339 (pp) REVERT: a 56 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7669 (t80) REVERT: a 80 GLU cc_start: 0.8927 (pt0) cc_final: 0.8664 (pt0) REVERT: a 124 ASP cc_start: 0.7487 (t0) cc_final: 0.6911 (m-30) REVERT: a 199 SER cc_start: 0.8864 (t) cc_final: 0.8553 (p) REVERT: a 231 TRP cc_start: 0.7501 (p-90) cc_final: 0.7104 (p-90) REVERT: a 255 ILE cc_start: 0.9425 (mt) cc_final: 0.9196 (tt) outliers start: 90 outliers final: 51 residues processed: 637 average time/residue: 0.4971 time to fit residues: 517.4260 Evaluate side-chains 615 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 551 time to evaluate : 4.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 109 ASP Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 76 ILE Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 56 HIS Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain G residue 57 HIS Chi-restraints excluded: chain G residue 70 ARG Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain J residue 3 ASN Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain Y residue 29 LEU Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 145 ASN Chi-restraints excluded: chain a residue 22 ASP Chi-restraints excluded: chain a residue 49 SER Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 75 PHE Chi-restraints excluded: chain a residue 131 GLU Chi-restraints excluded: chain a residue 237 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 414 optimal weight: 6.9990 chunk 436 optimal weight: 10.0000 chunk 398 optimal weight: 0.9980 chunk 424 optimal weight: 7.9990 chunk 255 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 333 optimal weight: 8.9990 chunk 130 optimal weight: 0.5980 chunk 383 optimal weight: 7.9990 chunk 401 optimal weight: 0.6980 chunk 423 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 479 HIS B 511 GLN A 444 GLN X 10 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 ASN M 3 ASN M 5 ASN ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 2 ASN a 116 ASN ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 37528 Z= 0.190 Angle : 0.581 10.812 50797 Z= 0.291 Chirality : 0.042 0.228 5920 Planarity : 0.004 0.051 6550 Dihedral : 6.213 107.372 5355 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.09 % Allowed : 18.85 % Favored : 79.07 % 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: 0.68 (0.12), residues: 4807 helix: 1.17 (0.11), residues: 2606 sheet: 0.11 (0.22), residues: 499 loop : -0.46 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 26 HIS 0.005 0.001 HIS Y 51 PHE 0.026 0.001 PHE P 53 TYR 0.020 0.001 TYR P 73 ARG 0.011 0.000 ARG X 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 562 time to evaluate : 4.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 4 ILE cc_start: 0.9210 (mt) cc_final: 0.8987 (mm) REVERT: W 156 ASP cc_start: 0.8097 (p0) cc_final: 0.7284 (p0) REVERT: C 236 TYR cc_start: 0.9114 (OUTLIER) cc_final: 0.8189 (t80) REVERT: B 262 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.7996 (m-30) REVERT: B 419 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.7350 (tptt) REVERT: A 49 GLN cc_start: 0.9332 (OUTLIER) cc_final: 0.8090 (tm-30) REVERT: A 76 MET cc_start: 0.8909 (mtp) cc_final: 0.8576 (mtp) REVERT: A 343 THR cc_start: 0.9272 (OUTLIER) cc_final: 0.8996 (p) REVERT: X 1 MET cc_start: 0.7674 (tmm) cc_final: 0.6896 (tmm) REVERT: X 64 GLN cc_start: 0.8942 (pt0) cc_final: 0.8518 (pm20) REVERT: H 28 SER cc_start: 0.8631 (t) cc_final: 0.8331 (t) REVERT: H 72 GLN cc_start: 0.7803 (mm-40) cc_final: 0.7313 (tp40) REVERT: G 70 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7784 (ptt180) REVERT: G 116 MET cc_start: 0.8991 (mmm) cc_final: 0.8591 (mmm) REVERT: G 199 LYS cc_start: 0.7035 (OUTLIER) cc_final: 0.5177 (mptt) REVERT: E 438 LEU cc_start: 0.8478 (pp) cc_final: 0.8071 (pt) REVERT: D 253 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7714 (mt-10) REVERT: D 345 ASP cc_start: 0.8624 (OUTLIER) cc_final: 0.8423 (p0) REVERT: I 17 MET cc_start: 0.9255 (tpt) cc_final: 0.9021 (mmp) REVERT: J 3 ASN cc_start: 0.3428 (OUTLIER) cc_final: 0.3193 (p0) REVERT: J 6 MET cc_start: 0.7829 (ptm) cc_final: 0.7561 (ptp) REVERT: J 41 ARG cc_start: 0.8258 (ttm-80) cc_final: 0.7908 (ttt90) REVERT: J 52 GLN cc_start: 0.9010 (mm-40) cc_final: 0.8779 (mm-40) REVERT: J 59 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8732 (tt) REVERT: J 72 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8614 (mm) REVERT: L 41 ARG cc_start: 0.8225 (mmt90) cc_final: 0.7794 (mmt90) REVERT: L 42 GLN cc_start: 0.8869 (mm-40) cc_final: 0.8329 (mt0) REVERT: N 57 MET cc_start: 0.8133 (tmm) cc_final: 0.7505 (tmm) REVERT: N 61 ASP cc_start: 0.8561 (m-30) cc_final: 0.8265 (m-30) REVERT: N 65 MET cc_start: 0.7786 (mmm) cc_final: 0.7568 (mmm) REVERT: O 6 MET cc_start: 0.5233 (ppp) cc_final: 0.4883 (ppp) REVERT: O 37 GLU cc_start: 0.8177 (tp30) cc_final: 0.7898 (tp30) REVERT: O 73 TYR cc_start: 0.7260 (t80) cc_final: 0.6528 (m-10) REVERT: P 6 MET cc_start: 0.7487 (ppp) cc_final: 0.7229 (ppp) REVERT: P 11 MET cc_start: 0.8135 (tpp) cc_final: 0.7675 (tpt) REVERT: P 17 MET cc_start: 0.8169 (mmm) cc_final: 0.7919 (mmm) REVERT: P 42 GLN cc_start: 0.8351 (mm-40) cc_final: 0.7898 (mp10) REVERT: P 54 PHE cc_start: 0.8144 (m-10) cc_final: 0.7887 (m-10) REVERT: Q 41 ARG cc_start: 0.7759 (mtp-110) cc_final: 0.7346 (mmm-85) REVERT: Q 42 GLN cc_start: 0.8543 (mt0) cc_final: 0.7962 (mp10) REVERT: Q 46 ILE cc_start: 0.8929 (mt) cc_final: 0.8677 (mm) REVERT: S 66 ILE cc_start: 0.8475 (mt) cc_final: 0.8163 (mm) REVERT: Y 14 PHE cc_start: 0.8446 (t80) cc_final: 0.8140 (t80) REVERT: Y 18 VAL cc_start: 0.8797 (t) cc_final: 0.8513 (p) REVERT: Y 19 LEU cc_start: 0.7838 (pp) cc_final: 0.7473 (pp) REVERT: Y 54 LEU cc_start: 0.6808 (OUTLIER) cc_final: 0.6375 (mm) REVERT: a 9 GLN cc_start: 0.8652 (mp10) cc_final: 0.8433 (mp10) REVERT: a 11 TYR cc_start: 0.7362 (t80) cc_final: 0.6808 (t80) REVERT: a 54 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8339 (pp) REVERT: a 56 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7620 (t80) REVERT: a 80 GLU cc_start: 0.8947 (pt0) cc_final: 0.8681 (pt0) REVERT: a 124 ASP cc_start: 0.7501 (t0) cc_final: 0.6935 (m-30) REVERT: a 199 SER cc_start: 0.8863 (t) cc_final: 0.8546 (p) REVERT: a 231 TRP cc_start: 0.7285 (p-90) cc_final: 0.6940 (p-90) REVERT: a 234 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7764 (mm-40) REVERT: a 255 ILE cc_start: 0.9400 (mt) cc_final: 0.9193 (tt) outliers start: 80 outliers final: 53 residues processed: 617 average time/residue: 0.5102 time to fit residues: 518.4094 Evaluate side-chains 617 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 550 time to evaluate : 4.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 109 ASP Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain X residue 76 ILE Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 56 HIS Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain G residue 57 HIS Chi-restraints excluded: chain G residue 70 ARG Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain J residue 3 ASN Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain Y residue 29 LEU Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 145 ASN Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 22 ASP Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 131 GLU Chi-restraints excluded: chain a residue 237 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 278 optimal weight: 10.0000 chunk 449 optimal weight: 10.0000 chunk 274 optimal weight: 2.9990 chunk 213 optimal weight: 0.0970 chunk 312 optimal weight: 0.9980 chunk 471 optimal weight: 7.9990 chunk 433 optimal weight: 9.9990 chunk 375 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 289 optimal weight: 0.9990 chunk 230 optimal weight: 3.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 67 GLN B 511 GLN A 444 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 GLN J 3 ASN L 5 ASN ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 GLN Y 85 GLN a 116 ASN a 185 HIS ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 37528 Z= 0.231 Angle : 0.602 11.297 50797 Z= 0.300 Chirality : 0.042 0.253 5920 Planarity : 0.004 0.049 6550 Dihedral : 6.195 109.660 5353 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.06 % Allowed : 19.00 % Favored : 78.94 % 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: 0.64 (0.12), residues: 4807 helix: 1.15 (0.11), residues: 2618 sheet: 0.08 (0.22), residues: 502 loop : -0.50 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP X 26 HIS 0.007 0.001 HIS a 185 PHE 0.026 0.001 PHE P 53 TYR 0.022 0.001 TYR M 10 ARG 0.014 0.000 ARG X 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 558 time to evaluate : 4.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 4 ILE cc_start: 0.9231 (mt) cc_final: 0.9011 (mm) REVERT: W 156 ASP cc_start: 0.8158 (p0) cc_final: 0.7435 (p0) REVERT: C 236 TYR cc_start: 0.9133 (OUTLIER) cc_final: 0.8200 (t80) REVERT: B 262 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.8020 (m-30) REVERT: B 419 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.7385 (tptt) REVERT: A 49 GLN cc_start: 0.9374 (OUTLIER) cc_final: 0.8169 (tm-30) REVERT: A 343 THR cc_start: 0.9269 (OUTLIER) cc_final: 0.8972 (p) REVERT: X 1 MET cc_start: 0.7672 (tmm) cc_final: 0.6926 (tmm) REVERT: X 26 TRP cc_start: 0.8344 (t-100) cc_final: 0.8095 (t-100) REVERT: X 64 GLN cc_start: 0.8938 (pt0) cc_final: 0.8510 (pm20) REVERT: H 28 SER cc_start: 0.8651 (t) cc_final: 0.8358 (t) REVERT: H 51 ARG cc_start: 0.8720 (ttp80) cc_final: 0.8519 (ttp80) REVERT: H 72 GLN cc_start: 0.7715 (mm-40) cc_final: 0.7279 (tp40) REVERT: G 70 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7777 (ptt180) REVERT: G 116 MET cc_start: 0.9048 (mmm) cc_final: 0.8784 (mmm) REVERT: G 199 LYS cc_start: 0.7040 (OUTLIER) cc_final: 0.5177 (mptt) REVERT: E 438 LEU cc_start: 0.8514 (pp) cc_final: 0.8122 (pt) REVERT: D 253 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7709 (mt-10) REVERT: D 345 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8468 (p0) REVERT: I 17 MET cc_start: 0.9264 (tpt) cc_final: 0.9043 (mmp) REVERT: J 41 ARG cc_start: 0.8216 (ttm-80) cc_final: 0.7927 (ttp80) REVERT: J 52 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8795 (mm-40) REVERT: J 59 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8768 (tt) REVERT: J 72 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8690 (mm) REVERT: L 41 ARG cc_start: 0.8135 (mmt90) cc_final: 0.7850 (mmt90) REVERT: N 57 MET cc_start: 0.8147 (tmm) cc_final: 0.7507 (tmm) REVERT: N 61 ASP cc_start: 0.8604 (m-30) cc_final: 0.8301 (m-30) REVERT: N 65 MET cc_start: 0.7756 (mmm) cc_final: 0.7496 (mmm) REVERT: O 6 MET cc_start: 0.5204 (ppp) cc_final: 0.4944 (ppp) REVERT: O 37 GLU cc_start: 0.8194 (tp30) cc_final: 0.7949 (tp30) REVERT: O 73 TYR cc_start: 0.7274 (t80) cc_final: 0.6558 (m-10) REVERT: P 6 MET cc_start: 0.7553 (ppp) cc_final: 0.7298 (ppp) REVERT: P 11 MET cc_start: 0.8165 (tpp) cc_final: 0.7634 (tpt) REVERT: P 42 GLN cc_start: 0.8356 (mm-40) cc_final: 0.7890 (mp10) REVERT: P 54 PHE cc_start: 0.8148 (m-10) cc_final: 0.7879 (m-10) REVERT: Q 41 ARG cc_start: 0.7837 (mtp-110) cc_final: 0.6875 (mtp-110) REVERT: Q 42 GLN cc_start: 0.8550 (mt0) cc_final: 0.7859 (mp10) REVERT: Q 46 ILE cc_start: 0.8822 (mt) cc_final: 0.8519 (mm) REVERT: S 66 ILE cc_start: 0.8485 (mt) cc_final: 0.8172 (mm) REVERT: Y 18 VAL cc_start: 0.8725 (t) cc_final: 0.8425 (p) REVERT: Y 19 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7480 (pp) REVERT: Y 54 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6392 (mm) REVERT: a 11 TYR cc_start: 0.7373 (t80) cc_final: 0.6818 (t80) REVERT: a 54 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8374 (pp) REVERT: a 56 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7565 (t80) REVERT: a 80 GLU cc_start: 0.8975 (pt0) cc_final: 0.8594 (pt0) REVERT: a 124 ASP cc_start: 0.7488 (t0) cc_final: 0.6920 (m-30) REVERT: a 185 HIS cc_start: 0.3179 (OUTLIER) cc_final: 0.2678 (m-70) REVERT: a 199 SER cc_start: 0.8902 (t) cc_final: 0.8595 (p) REVERT: a 231 TRP cc_start: 0.7320 (p-90) cc_final: 0.6979 (p-90) REVERT: a 255 ILE cc_start: 0.9403 (mt) cc_final: 0.9202 (tt) outliers start: 79 outliers final: 53 residues processed: 611 average time/residue: 0.5027 time to fit residues: 502.0395 Evaluate side-chains 619 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 551 time to evaluate : 4.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 109 ASP Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain X residue 76 ILE Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 56 HIS Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain G residue 57 HIS Chi-restraints excluded: chain G residue 70 ARG Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 29 LEU Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 85 GLN Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 145 ASN Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 22 ASP Chi-restraints excluded: chain a residue 23 LEU Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 131 GLU Chi-restraints excluded: chain a residue 185 HIS Chi-restraints excluded: chain a residue 237 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 298 optimal weight: 0.9980 chunk 399 optimal weight: 0.0770 chunk 114 optimal weight: 6.9990 chunk 345 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 375 optimal weight: 8.9990 chunk 157 optimal weight: 4.9990 chunk 385 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 67 GLN B 511 GLN A 444 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 GLN a 116 ASN a 185 HIS ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.096438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.067910 restraints weight = 82906.276| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.15 r_work: 0.2812 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.3787 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: