Starting phenix.real_space_refine on Tue Apr 16 02:49:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqv_20171/04_2024/6oqv_20171_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqv_20171/04_2024/6oqv_20171.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/6oqv_20171/04_2024/6oqv_20171.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqv_20171/04_2024/6oqv_20171.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqv_20171/04_2024/6oqv_20171_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqv_20171/04_2024/6oqv_20171_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 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 26": "NH1" <-> "NH2" Residue "W ASP 29": "OD1" <-> "OD2" Residue "W GLU 45": "OE1" <-> "OE2" Residue "W GLU 54": "OE1" <-> "OE2" Residue "W PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 69": "OD1" <-> "OD2" Residue "W ARG 77": "NH1" <-> "NH2" Residue "W GLU 93": "OE1" <-> "OE2" 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 ARG 15": "NH1" <-> "NH2" Residue "C GLU 24": "OE1" <-> "OE2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C ASP 116": "OD1" <-> "OD2" Residue "C ASP 170": "OD1" <-> "OD2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C 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 PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 402": "OE1" <-> "OE2" Residue "C ASP 414": "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 ARG 477": "NH1" <-> "NH2" Residue "C TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 505": "OD1" <-> "OD2" Residue "C PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B ASP 36": "OD1" <-> "OD2" Residue "B ASP 46": "OD1" <-> "OD2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B ARG 93": "NH1" <-> "NH2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "B ASP 181": "OD1" <-> "OD2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B ASP 262": "OD1" <-> "OD2" 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 412": "OD1" <-> "OD2" Residue "B ASP 415": "OD1" <-> "OD2" Residue "B ASP 478": "OD1" <-> "OD2" Residue "B GLU 485": "OE1" <-> "OE2" Residue "B GLU 495": "OE1" <-> "OE2" Residue "B GLU 497": "OE1" <-> "OE2" Residue "A PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 36": "OD1" <-> "OD2" Residue "A ASP 69": "OD1" <-> "OD2" Residue "A GLU 84": "OE1" <-> "OE2" Residue "A ASP 170": "OD1" <-> "OD2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 262": "OD1" <-> "OD2" 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 ASP 422": "OD1" <-> "OD2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 460": "OE1" <-> "OE2" Residue "A PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 477": "NH1" <-> "NH2" Residue "A GLU 485": "OE1" <-> "OE2" 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 63": "OD1" <-> "OD2" Residue "X GLU 77": "OE1" <-> "OE2" Residue "X ARG 83": "NH1" <-> "NH2" Residue "X ASP 88": "OD1" <-> "OD2" Residue "X GLU 89": "OE1" <-> "OE2" Residue "X ARG 98": "NH1" <-> "NH2" Residue "X GLU 110": "OE1" <-> "OE2" Residue "X ARG 113": "NH1" <-> "NH2" Residue "X ARG 115": "NH1" <-> "NH2" Residue "X ARG 117": "NH1" <-> "NH2" Residue "X GLU 137": "OE1" <-> "OE2" Residue "X ARG 138": "NH1" <-> "NH2" Residue "X GLU 155": "OE1" <-> "OE2" Residue "H TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 29": "OE1" <-> "OE2" 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 GLU 103": "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 ARG 84": "NH1" <-> "NH2" Residue "G PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 147": "OE1" <-> "OE2" Residue "G TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 165": "OD1" <-> "OD2" Residue "G TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 196": "OD1" <-> "OD2" Residue "G ASP 197": "OD1" <-> "OD2" Residue "G ARG 221": "NH1" <-> "NH2" Residue "G GLU 259": "OE1" <-> "OE2" Residue "G GLU 275": "OE1" <-> "OE2" Residue "G GLU 278": "OE1" <-> "OE2" Residue "F ASP 14": "OD1" <-> "OD2" Residue "F GLU 76": "OE1" <-> "OE2" Residue "F GLU 100": "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 "E GLU 36": "OE1" <-> "OE2" Residue "E GLU 127": "OE1" <-> "OE2" Residue "E ASP 134": "OD1" <-> "OD2" Residue "E ASP 200": "OD1" <-> "OD2" Residue "E ASP 242": "OD1" <-> "OD2" Residue "E GLU 273": "OE1" <-> "OE2" Residue "E ASP 302": "OD1" <-> "OD2" Residue "E ASP 305": "OD1" <-> "OD2" Residue "E ASP 345": "OD1" <-> "OD2" Residue "E ASP 380": "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 "E TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 16": "OE1" <-> "OE2" 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 PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 301": "OD1" <-> "OD2" Residue "D ASP 316": "OD1" <-> "OD2" Residue "D ASP 338": "OD1" <-> "OD2" Residue "D ASP 345": "OD1" <-> "OD2" Residue "D GLU 369": "OE1" <-> "OE2" Residue "D ASP 372": "OD1" <-> "OD2" Residue "D GLU 384": "OE1" <-> "OE2" Residue "D GLU 385": "OE1" <-> "OE2" Residue "D ASP 386": "OD1" <-> "OD2" Residue "D GLU 408": "OE1" <-> "OE2" Residue "D GLU 440": "OE1" <-> "OE2" Residue "I ASP 7": "OD1" <-> "OD2" Residue "I TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 50": "NH1" <-> "NH2" Residue "J TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 37": "OE1" <-> "OE2" Residue "J ARG 50": "NH1" <-> "NH2" Residue "J PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 7": "OD1" <-> "OD2" Residue "L GLU 37": "OE1" <-> "OE2" Residue "L ASP 44": "OD1" <-> "OD2" Residue "L ARG 50": "NH1" <-> "NH2" Residue "L TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 7": "OD1" <-> "OD2" Residue "M TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 37": "OE1" <-> "OE2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 7": "OD1" <-> "OD2" Residue "N GLU 37": "OE1" <-> "OE2" Residue "N ARG 50": "NH1" <-> "NH2" Residue "N TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 37": "OE1" <-> "OE2" Residue "O ARG 50": "NH1" <-> "NH2" Residue "O PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 7": "OD1" <-> "OD2" Residue "P GLU 37": "OE1" <-> "OE2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "P TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 7": "OD1" <-> "OD2" Residue "Q ASP 44": "OD1" <-> "OD2" Residue "Q ARG 50": "NH1" <-> "NH2" 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 "S ARG 50": "NH1" <-> "NH2" Residue "S PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 42": "OD1" <-> "OD2" Residue "Y GLU 48": "OE1" <-> "OE2" Residue "Y ARG 83": "NH1" <-> "NH2" Residue "Y ASP 88": "OD1" <-> "OD2" Residue "Y ARG 98": "NH1" <-> "NH2" Residue "Y ARG 113": "NH1" <-> "NH2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Y ARG 117": "NH1" <-> "NH2" Residue "Y ARG 121": "NH1" <-> "NH2" Residue "Y GLU 133": "OE1" <-> "OE2" Residue "Y ARG 138": "NH1" <-> "NH2" Residue "Y ASP 150": "OD1" <-> "OD2" Residue "a TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 30": "OD1" <-> "OD2" Residue "a PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 80": "OE1" <-> "OE2" Residue "a PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 216": "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: 0.15s 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: 3877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3877 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 494} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3846 Classifications: {'peptide': 510} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 491} 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: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3849 Classifications: {'peptide': 510} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 491} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "H" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1034 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "G" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2186 Classifications: {'peptide': 284} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 274} Chain: "F" Number of atoms: 3520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3520 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 437} Chain: "E" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "D" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "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} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "a" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2104 Classifications: {'peptide': 266} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 250} Chain: "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: 18.92, per 1000 atoms: 0.51 Number of scatterers: 36971 At special positions: 0 Unit cell: (184.509, 214.721, 132.717, 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: 15.85 Conformation dependent library (CDL) restraints added in 7.2 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: 185 helices and 25 sheets defined 55.9% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.13 Creating SS restraints... Processing helix chain 'W' and resid 4 through 20 Proline residue: W 9 - end of helix Processing helix chain 'W' and resid 24 through 39 removed outlier: 3.924A pdb=" N ASP W 29 " --> pdb=" O GLU W 25 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR W 38 " --> pdb=" O ALA W 34 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS W 39 " --> pdb=" O ALA W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 41 through 48 removed outlier: 3.705A pdb=" N GLU W 45 " --> pdb=" O GLU W 41 " (cutoff:3.500A) Processing helix chain 'W' and resid 53 through 63 removed outlier: 3.850A pdb=" N VAL W 63 " --> pdb=" O SER W 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 81 Processing helix chain 'W' and resid 85 through 103 Proline residue: W 89 - end of helix removed outlier: 3.937A pdb=" N LEU W 92 " --> pdb=" O PRO W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 120 through 131 Processing helix chain 'W' and resid 164 through 171 removed outlier: 3.708A pdb=" N ARG W 169 " --> pdb=" O GLY W 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 17 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: 3.515A pdb=" N SER C 155 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N MET C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 151 through 156' Processing helix chain 'C' and resid 175 through 188 removed outlier: 3.814A pdb=" N GLN C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ASP C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 removed outlier: 3.903A pdb=" N ASN C 207 " --> pdb=" O SER C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 220 removed outlier: 3.768A pdb=" N ALA C 219 " --> pdb=" O GLY C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 252 Proline residue: C 239 - end of helix removed outlier: 3.656A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 276 removed outlier: 4.090A 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: 4.213A pdb=" N PHE C 291 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR C 292 " --> pdb=" O ASP C 289 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU C 293 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER C 295 " --> pdb=" O TYR C 292 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ARG C 296 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU C 299 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 312 Processing helix chain 'C' and resid 333 through 335 No H-bonds generated for 'chain 'C' and resid 333 through 335' Processing helix chain 'C' and resid 340 through 348 removed outlier: 3.742A pdb=" N SER C 347 " --> pdb=" O THR C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 362 Processing helix chain 'C' and resid 378 through 381 Processing helix chain 'C' and resid 384 through 412 removed outlier: 4.033A pdb=" N GLY C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ALA C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N PHE C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER C 407 " --> pdb=" O LEU C 403 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N GLN C 408 " --> pdb=" O ALA C 404 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N PHE C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N SER C 411 " --> pdb=" O SER C 407 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ASP C 412 " --> pdb=" O GLN C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 430 removed outlier: 4.777A pdb=" N GLN C 420 " --> pdb=" O ALA C 416 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN C 425 " --> pdb=" O LEU C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 452 removed outlier: 3.590A pdb=" N ALA C 451 " --> pdb=" O VAL C 447 " (cutoff:3.500A) 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: 4.993A pdb=" N GLY C 465 " --> pdb=" O SER C 462 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL C 475 " --> pdb=" O LEU C 472 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP C 478 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 Processing helix chain 'C' and resid 494 through 510 removed outlier: 3.513A pdb=" N ALA C 509 " --> pdb=" O ASP C 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 18 removed outlier: 3.506A pdb=" N SER B 9 " --> pdb=" O SER B 5 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS B 13 " --> pdb=" O SER B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 188 removed outlier: 3.870A pdb=" N GLN B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.312A 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 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 232 through 252 Proline residue: B 239 - end of helix removed outlier: 3.745A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 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 290 through 300 removed outlier: 3.873A pdb=" N HIS B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ARG B 300 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 313 Processing helix chain 'B' and resid 333 through 335 No H-bonds generated for 'chain 'B' and resid 333 through 335' Processing helix chain 'B' and resid 340 through 346 Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 378 through 381 Processing helix chain 'B' and resid 384 through 390 Processing helix chain 'B' and resid 393 through 406 removed outlier: 3.736A pdb=" N ALA B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 430 Processing helix chain 'B' and resid 443 through 452 removed outlier: 3.880A pdb=" N ALA B 451 " --> pdb=" O VAL B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 477 Processing helix chain 'B' and resid 480 through 488 removed outlier: 4.146A pdb=" N GLN B 488 " --> pdb=" O GLN B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 509 Processing helix chain 'A' and resid 9 through 17 Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 151 through 156 removed outlier: 3.537A pdb=" N MET A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 188 removed outlier: 3.757A pdb=" N ALA A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.500A 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 252 Proline residue: A 239 - end of helix removed outlier: 4.083A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 277 removed outlier: 3.753A pdb=" N VAL A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) removed outlier: 4.129A 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 288 through 300 removed outlier: 4.608A pdb=" N PHE A 291 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR A 292 " --> pdb=" O ASP A 289 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER A 295 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG A 296 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU A 299 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 Processing helix chain 'A' and resid 340 through 347 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 409 removed outlier: 3.918A pdb=" N GLU A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLN A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N PHE A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 431 removed outlier: 4.211A pdb=" N GLN A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 452 Processing helix chain 'A' and resid 461 through 478 removed outlier: 4.403A pdb=" N GLY A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N SER A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 489 removed outlier: 3.658A pdb=" N GLU A 485 " --> pdb=" O PRO A 481 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN A 488 " --> pdb=" O GLN A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 509 Processing helix chain 'X' and resid 6 through 22 Processing helix chain 'X' and resid 26 through 136 removed outlier: 3.750A pdb=" N ALA X 32 " --> pdb=" O PRO X 28 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY X 43 " --> pdb=" O GLU X 39 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU X 44 " --> pdb=" O ILE X 40 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA X 45 " --> pdb=" O ALA X 41 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER X 46 " --> pdb=" O ASP X 42 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA X 47 " --> pdb=" O GLY X 43 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N HIS X 51 " --> pdb=" O ALA X 47 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LYS X 52 " --> pdb=" O GLU X 48 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASP X 55 " --> pdb=" O HIS X 51 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU X 56 " --> pdb=" O LYS X 52 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU X 77 " --> pdb=" O GLN X 73 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN X 78 " --> pdb=" O VAL X 74 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA X 79 " --> pdb=" O ILE X 75 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU X 97 " --> pdb=" O GLU X 93 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS X 100 " --> pdb=" O GLN X 96 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA X 103 " --> pdb=" O THR X 99 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU X 110 " --> pdb=" O GLN X 106 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA X 111 " --> pdb=" O ALA X 107 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS X 114 " --> pdb=" O GLU X 110 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG X 121 " --> pdb=" O ARG X 117 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LYS X 122 " --> pdb=" O GLU X 118 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN X 123 " --> pdb=" O GLU X 119 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE X 126 " --> pdb=" O LYS X 122 " (cutoff:3.500A) Processing helix chain 'X' and resid 145 through 154 removed outlier: 3.533A pdb=" N ALA X 154 " --> pdb=" O ASP X 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 103 removed outlier: 3.658A pdb=" N GLU H 91 " --> pdb=" O GLN H 87 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA H 92 " --> pdb=" O ASP H 88 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU H 102 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 124 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 3 through 39 removed outlier: 3.887A pdb=" N SER G 8 " --> pdb=" O LYS G 4 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 55 Processing helix chain 'G' and resid 65 through 67 No H-bonds generated for 'chain 'G' and resid 65 through 67' Processing helix chain 'G' and resid 90 through 108 removed outlier: 3.948A pdb=" N LYS G 108 " --> pdb=" O THR G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 127 Processing helix chain 'G' and resid 145 through 160 removed outlier: 4.746A 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: 4.041A 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 280 removed outlier: 3.679A pdb=" N THR G 217 " --> pdb=" O ALA G 213 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS G 258 " --> pdb=" O GLY G 254 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU G 262 " --> pdb=" O LYS G 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 21 No H-bonds generated for 'chain 'F' and resid 19 through 21' 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: 5.207A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR F 222 " --> pdb=" O ARG F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 258 removed outlier: 3.645A pdb=" N GLU F 253 " --> pdb=" O ALA F 250 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ALA F 256 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 279 removed outlier: 4.029A 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: 4.610A pdb=" N ALA F 313 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N HIS F 314 " --> pdb=" O THR F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 328 removed outlier: 4.299A pdb=" N LEU F 328 " --> pdb=" O GLN F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 349 No H-bonds generated for 'chain 'F' and resid 346 through 349' Processing helix chain 'F' and resid 351 through 377 removed outlier: 3.537A pdb=" N LEU F 370 " --> pdb=" O ARG F 366 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS F 371 " --> pdb=" O TYR F 367 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ASP F 372 " --> pdb=" O GLN F 368 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ILE F 373 " --> pdb=" O GLU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 381 No H-bonds generated for 'chain 'F' and resid 379 through 381' Processing helix chain 'F' and resid 386 through 399 removed outlier: 3.717A pdb=" N LYS F 395 " --> pdb=" O ALA F 391 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG F 398 " --> pdb=" O ARG F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 411 removed outlier: 3.737A pdb=" N GLU F 408 " --> pdb=" O PHE F 405 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL F 409 " --> pdb=" O VAL F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 432 removed outlier: 3.651A pdb=" N ARG F 425 " --> pdb=" O LYS F 421 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY F 426 " --> pdb=" O ASP F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 442 No H-bonds generated for 'chain 'F' and resid 440 through 442' Processing helix chain 'F' and resid 449 through 457 removed outlier: 3.949A pdb=" N LYS F 457 " --> pdb=" O VAL F 453 " (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 116 through 118 No H-bonds generated for 'chain 'E' and resid 116 through 118' Processing helix chain 'E' and resid 131 through 136 Processing helix chain 'E' and resid 155 through 168 removed outlier: 3.504A pdb=" N ALA E 167 " --> pdb=" O ILE E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 194 Processing helix chain 'E' and resid 199 through 201 No H-bonds generated for 'chain 'E' and resid 199 through 201' Processing helix chain 'E' and resid 213 through 233 removed outlier: 5.111A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU E 233 " --> pdb=" O LYS E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 258 Processing helix chain 'E' and resid 271 through 279 removed outlier: 3.591A pdb=" N GLY E 276 " --> pdb=" O ALA E 272 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU E 278 " --> pdb=" O GLU E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 301 No H-bonds generated for 'chain 'E' and resid 299 through 301' Processing helix chain 'E' and resid 306 through 312 Processing helix chain 'E' and resid 323 through 327 Processing helix chain 'E' and resid 346 through 349 No H-bonds generated for 'chain 'E' and resid 346 through 349' Processing helix chain 'E' and resid 351 through 377 removed outlier: 4.323A pdb=" N GLU E 369 " --> pdb=" O GLN E 365 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA E 375 " --> pdb=" O LYS E 371 " (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: 3.731A pdb=" N VAL E 389 " --> pdb=" O GLU E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 411 No H-bonds generated for 'chain 'E' and resid 408 through 411' Processing helix chain 'E' and resid 420 through 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: 4.245A pdb=" N GLU E 454 " --> pdb=" O GLU E 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 131 through 136 Processing helix chain 'D' and resid 155 through 169 Processing helix chain 'D' and resid 183 through 195 Processing helix chain 'D' and resid 199 through 201 No H-bonds generated for 'chain 'D' and resid 199 through 201' Processing helix chain 'D' and resid 213 through 232 removed outlier: 5.023A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 258 Processing helix chain 'D' and resid 271 through 279 removed outlier: 3.569A pdb=" N GLY D 276 " --> pdb=" O ALA D 272 " (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 314 removed outlier: 3.517A pdb=" N THR D 311 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE D 312 " --> pdb=" O PRO D 308 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ALA D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N HIS D 314 " --> pdb=" O THR D 310 " (cutoff:3.500A) 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 377 removed outlier: 3.698A pdb=" N GLU D 369 " --> pdb=" O GLN D 365 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE D 376 " --> pdb=" O ASP D 372 " (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 384 through 399 Processing helix chain 'D' and resid 407 through 411 removed outlier: 4.055A pdb=" N THR D 411 " --> pdb=" O GLU D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 432 Processing helix chain 'D' and resid 440 through 443 Processing helix chain 'D' and resid 449 through 458 removed outlier: 4.125A pdb=" N LYS D 457 " --> pdb=" O VAL D 453 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 41 removed outlier: 5.442A pdb=" N LEU I 9 " --> pdb=" O ASN I 5 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TYR I 10 " --> pdb=" O MET I 6 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N MET I 11 " --> pdb=" O ASP I 7 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA I 12 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE I 22 " --> pdb=" O GLY I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 76 removed outlier: 4.108A pdb=" N LEU I 59 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL I 60 " --> pdb=" O VAL I 56 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP I 61 " --> pdb=" O MET I 57 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA I 62 " --> pdb=" O GLY I 58 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ILE I 63 " --> pdb=" O LEU I 59 " (cutoff:3.500A) Proline residue: I 64 - end of helix removed outlier: 4.079A pdb=" N MET I 75 " --> pdb=" O GLY I 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 41 removed outlier: 3.661A pdb=" N LEU J 8 " --> pdb=" O LEU J 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 76 removed outlier: 4.148A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA J 62 " --> pdb=" O GLY J 58 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ILE J 63 " --> pdb=" O LEU J 59 " (cutoff:3.500A) Proline residue: J 64 - end of helix removed outlier: 3.614A pdb=" N LEU J 72 " --> pdb=" O VAL J 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 41 removed outlier: 4.026A pdb=" N LEU L 9 " --> pdb=" O ASN L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 76 Proline residue: L 47 - end of helix removed outlier: 4.094A pdb=" N ASP L 61 " --> pdb=" O GLY L 58 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE L 63 " --> pdb=" O VAL L 60 " (cutoff:3.500A) Proline residue: L 64 - end of helix Processing helix chain 'M' and resid 4 through 41 removed outlier: 3.665A pdb=" N LEU M 8 " --> pdb=" O ASN M 5 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU M 19 " --> pdb=" O MET M 16 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA M 20 " --> pdb=" O MET M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 77 Proline residue: M 47 - end of helix removed outlier: 4.416A pdb=" N GLY M 58 " --> pdb=" O ILE M 55 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP M 61 " --> pdb=" O GLY M 58 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ILE M 63 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Proline residue: M 64 - end of helix removed outlier: 3.628A pdb=" N ALA M 77 " --> pdb=" O VAL M 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 6 No H-bonds generated for 'chain 'N' and resid 4 through 6' Processing helix chain 'N' and resid 8 through 42 Processing helix chain 'N' and resid 45 through 60 removed outlier: 4.069A pdb=" N MET N 57 " --> pdb=" O PHE N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 76 Processing helix chain 'O' and resid 4 through 41 removed outlier: 3.778A pdb=" N LEU O 8 " --> pdb=" O ASN O 5 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE O 28 " --> pdb=" O ALA O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 60 removed outlier: 3.755A pdb=" N PHE O 54 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE O 55 " --> pdb=" O THR O 51 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL O 56 " --> pdb=" O GLN O 52 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU O 59 " --> pdb=" O ILE O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 75 removed outlier: 3.724A pdb=" N GLY O 69 " --> pdb=" O MET O 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 41 Processing helix chain 'P' and resid 46 through 76 removed outlier: 3.737A pdb=" N GLY P 58 " --> pdb=" O PHE P 54 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEU P 59 " --> pdb=" O ILE P 55 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL P 60 " --> pdb=" O VAL P 56 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP P 61 " --> pdb=" O MET P 57 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) Proline residue: P 64 - end of helix removed outlier: 3.552A pdb=" N ALA P 67 " --> pdb=" O ILE P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 41 removed outlier: 4.027A pdb=" N LEU Q 8 " --> pdb=" O ASN Q 5 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LEU Q 9 " --> pdb=" O MET Q 6 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL Q 15 " --> pdb=" O ALA Q 12 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 76 Proline residue: Q 47 - end of helix removed outlier: 3.562A pdb=" N GLY Q 58 " --> pdb=" O ILE Q 55 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA Q 62 " --> pdb=" O LEU Q 59 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE Q 63 " --> pdb=" O VAL Q 60 " (cutoff:3.500A) Proline residue: Q 64 - end of helix removed outlier: 3.513A pdb=" N GLY Q 69 " --> pdb=" O ILE Q 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 41 removed outlier: 3.875A pdb=" N LEU R 8 " --> pdb=" O LEU R 4 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS R 34 " --> pdb=" O ILE R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 77 removed outlier: 4.320A pdb=" N LEU R 59 " --> pdb=" O ILE R 55 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA R 62 " --> pdb=" O GLY R 58 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ILE R 63 " --> pdb=" O LEU R 59 " (cutoff:3.500A) Proline residue: R 64 - end of helix Processing helix chain 'S' and resid 7 through 41 removed outlier: 4.080A pdb=" N MET S 11 " --> pdb=" O ASP S 7 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA S 21 " --> pdb=" O MET S 17 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU S 31 " --> pdb=" O GLY S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 60 Proline residue: S 47 - end of helix removed outlier: 3.766A pdb=" N PHE S 54 " --> pdb=" O THR S 51 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET S 57 " --> pdb=" O PHE S 54 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL S 60 " --> pdb=" O MET S 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 75 Processing helix chain 'Y' and resid 3 through 24 removed outlier: 3.844A pdb=" N LYS Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 26 through 139 removed outlier: 3.800A pdb=" N ALA Y 47 " --> pdb=" O GLY Y 43 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP Y 55 " --> pdb=" O HIS Y 51 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER Y 60 " --> pdb=" O LEU Y 56 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU Y 65 " --> pdb=" O ALA Y 61 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LYS Y 66 " --> pdb=" O THR Y 62 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE Y 76 " --> pdb=" O ALA Y 72 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS Y 81 " --> pdb=" O GLU Y 77 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS Y 91 " --> pdb=" O LEU Y 87 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG Y 98 " --> pdb=" O ALA Y 94 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN Y 123 " --> pdb=" O GLU Y 119 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG Y 138 " --> pdb=" O LYS Y 134 " (cutoff:3.500A) Processing helix chain 'Y' and resid 142 through 155 Processing helix chain 'a' and resid 8 through 16 removed outlier: 5.144A pdb=" N GLY a 13 " --> pdb=" O GLN a 9 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU a 16 " --> pdb=" O ILE a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 43 through 64 removed outlier: 3.722A pdb=" N LEU a 55 " --> pdb=" O VAL a 51 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL a 63 " --> pdb=" O LEU a 59 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 91 removed outlier: 4.031A pdb=" N ALA a 78 " --> pdb=" O LYS a 74 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE a 79 " --> pdb=" O PHE a 75 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER a 89 " --> pdb=" O PHE a 85 " (cutoff:3.500A) Processing helix chain 'a' and resid 100 through 120 removed outlier: 3.638A pdb=" N LEU a 104 " --> pdb=" O LEU a 100 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ASP a 119 " --> pdb=" O MET a 115 " (cutoff:3.500A) removed outlier: 4.650A 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: 3.592A pdb=" N SER a 152 " --> pdb=" O ASN a 148 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE a 166 " --> pdb=" O LEU a 162 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ILE a 171 " --> pdb=" O LYS a 167 " (cutoff:3.500A) removed outlier: 9.412A pdb=" N GLY a 172 " --> pdb=" O MET a 168 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 228 Proline residue: a 190 - end of helix removed outlier: 4.118A pdb=" N GLU a 196 " --> pdb=" O LEU a 193 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER a 199 " --> pdb=" O GLU a 196 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 3.728A pdb=" N ARG a 210 " --> pdb=" O LEU a 207 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE a 221 " --> pdb=" O GLY a 218 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU a 228 " --> pdb=" O ILE a 225 " (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: 3.503A pdb=" N ILE a 246 " --> pdb=" O ALA a 242 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE a 248 " --> pdb=" O PHE a 244 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA a 253 " --> pdb=" O ILE a 249 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'W' and resid 135 through 142 removed outlier: 3.856A pdb=" N VAL W 110 " --> pdb=" O ASN W 139 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 87 through 90 removed outlier: 4.278A pdb=" N ASN C 27 " --> pdb=" O CYS C 90 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ARG C 40 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL C 34 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 96 through 98 Processing sheet with id= D, first strand: chain 'C' and resid 107 through 109 removed outlier: 8.449A pdb=" N VAL C 108 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL C 223 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N CYS C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N VAL C 224 " --> pdb=" O CYS C 193 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE C 198 " --> pdb=" O ASP C 261 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N SER C 323 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ILE C 258 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N THR C 325 " --> pdb=" O ILE C 258 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TYR C 260 " --> pdb=" O THR C 325 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 351 through 355 Processing sheet with id= F, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.606A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 96 through 98 Processing sheet with id= H, first strand: chain 'B' and resid 107 through 109 removed outlier: 8.321A pdb=" N VAL B 108 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL B 223 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N VAL B 224 " --> pdb=" O CYS B 193 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER B 323 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ILE B 258 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N THR B 325 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 7.638A 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: 6.806A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.616A 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: 6.122A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.790A 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: 6.690A pdb=" N LEU A 166 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU A 355 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.763A 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: 6.811A pdb=" N CYS A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N VAL A 224 " --> pdb=" O CYS A 193 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 198 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N SER A 323 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ILE A 258 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N THR A 325 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N TYR A 260 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 5 through 9 removed outlier: 3.549A pdb=" N ILE H 68 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY H 67 " --> pdb=" O ILE H 45 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 32 through 35 removed outlier: 7.218A pdb=" N VAL H 53 " --> pdb=" O GLU H 21 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE H 23 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ARG H 51 " --> pdb=" O ILE H 23 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL H 25 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 9.378A 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: 6.586A pdb=" N LEU G 167 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS G 166 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ASN G 172 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN G 111 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N TYR G 77 " --> pdb=" O GLN G 111 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASP G 113 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N VAL G 79 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA G 115 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N MET G 116 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 4.343A 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: 6.508A pdb=" N ASP F 14 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE F 54 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N VAL F 42 " --> pdb=" O ILE F 54 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 76 through 79 removed outlier: 4.677A pdb=" N GLU F 105 " --> pdb=" O VAL F 79 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 317 through 320 removed outlier: 7.934A pdb=" N VAL F 145 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N SER F 292 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N LEU F 147 " --> pdb=" O SER F 292 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLN F 294 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N GLY F 149 " --> pdb=" O GLN F 294 " (cutoff:3.500A) removed outlier: 6.404A 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: 6.600A pdb=" N ASP E 14 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL E 8 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL E 12 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE E 54 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N VAL E 42 " --> pdb=" O ILE E 54 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 76 through 78 Processing sheet with id= V, first strand: chain 'E' and resid 317 through 319 removed outlier: 8.640A pdb=" N VAL E 145 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N SER E 292 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU E 147 " --> pdb=" O SER E 292 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLN E 294 " --> pdb=" O LEU E 147 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 3 through 9 removed outlier: 6.481A pdb=" N ASP D 14 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL D 8 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE D 54 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 5.626A 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: 4.673A 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: 8.901A pdb=" N VAL D 145 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N SER D 292 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LEU D 147 " --> pdb=" O SER D 292 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLN D 294 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N GLY D 149 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL D 296 " --> pdb=" O GLY D 149 " (cutoff:3.500A) 1942 hydrogen bonds defined for protein. 4986 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: 13.44 Time building geometry restraints manager: 17.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 6336 1.30 - 1.43: 8776 1.43 - 1.56: 22032 1.56 - 1.69: 24 1.69 - 1.81: 360 Bond restraints: 37528 Sorted by residual: bond pdb=" C MET Y 30 " pdb=" N ALA Y 31 " ideal model delta sigma weight residual 1.334 1.464 -0.130 1.43e-02 4.89e+03 8.21e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.71e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.456 -0.068 1.00e-02 1.00e+04 4.65e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.454 -0.066 1.00e-02 1.00e+04 4.40e+01 bond pdb=" C5 ATP B 600 " pdb=" C6 ATP B 600 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.99e+01 ... (remaining 37523 not shown) Histogram of bond angle deviations from ideal: 98.41 - 106.00: 888 106.00 - 113.59: 21530 113.59 - 121.17: 19621 121.17 - 128.76: 8559 128.76 - 136.35: 199 Bond angle restraints: 50797 Sorted by residual: angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 113.42 26.45 1.00e+00 1.00e+00 7.00e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 114.55 25.32 1.00e+00 1.00e+00 6.41e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 115.68 24.19 1.00e+00 1.00e+00 5.85e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 116.13 20.70 1.00e+00 1.00e+00 4.29e+02 angle pdb=" PA ATP C 600 " pdb=" O3A ATP C 600 " pdb=" PB ATP C 600 " ideal model delta sigma weight residual 136.83 117.54 19.29 1.00e+00 1.00e+00 3.72e+02 ... (remaining 50792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.84: 22278 34.84 - 69.68: 459 69.68 - 104.52: 52 104.52 - 139.36: 2 139.36 - 174.20: 3 Dihedral angle restraints: 22794 sinusoidal: 9010 harmonic: 13784 Sorted by residual: dihedral pdb=" O2A ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PA ADP E 500 " pdb=" PB ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 114.20 -174.20 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP F 500 " pdb=" O5' ADP F 500 " pdb=" PA ADP F 500 " pdb=" O2A ADP F 500 " ideal model delta sinusoidal sigma weight residual 300.00 152.32 147.69 1 2.00e+01 2.50e-03 4.43e+01 dihedral pdb=" O1B ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PB ADP E 500 " pdb=" PA ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 82.47 -142.47 1 2.00e+01 2.50e-03 4.30e+01 ... (remaining 22791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 5462 0.092 - 0.184: 427 0.184 - 0.276: 23 0.276 - 0.369: 5 0.369 - 0.461: 3 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 2.05 0.46 2.00e-01 2.50e+01 5.31e+00 chirality pdb=" CA GLU X 48 " pdb=" N GLU X 48 " pdb=" C GLU X 48 " pdb=" CB GLU X 48 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.84e+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 2.13 0.38 2.00e-01 2.50e+01 3.63e+00 ... (remaining 5917 not shown) Planarity restraints: 6550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET Y 30 " -0.025 2.00e-02 2.50e+03 4.78e-02 2.28e+01 pdb=" C MET Y 30 " 0.083 2.00e-02 2.50e+03 pdb=" O MET Y 30 " -0.031 2.00e-02 2.50e+03 pdb=" N ALA Y 31 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 207 " -0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C GLY F 207 " 0.070 2.00e-02 2.50e+03 pdb=" O GLY F 207 " -0.026 2.00e-02 2.50e+03 pdb=" N GLN F 208 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 264 " 0.018 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C ALA D 264 " -0.065 2.00e-02 2.50e+03 pdb=" O ALA D 264 " 0.024 2.00e-02 2.50e+03 pdb=" N VAL D 265 " 0.023 2.00e-02 2.50e+03 ... (remaining 6547 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 49 2.37 - 3.00: 23814 3.00 - 3.64: 53479 3.64 - 4.27: 84834 4.27 - 4.90: 141912 Nonbonded interactions: 304088 Sorted by model distance: nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.740 2.170 nonbonded pdb=" O2B ATP B 600 " pdb="MG MG B 601 " model vdw 1.793 2.170 nonbonded pdb=" OG1 THR D 156 " pdb="MG MG D 502 " model vdw 1.817 2.170 nonbonded pdb=" O2B ATP A 600 " pdb="MG MG A 601 " model vdw 1.821 2.170 nonbonded pdb=" O1 PO4 D 501 " pdb="MG MG D 502 " model vdw 1.850 2.170 ... (remaining 304083 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: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 11.290 Check model and map are aligned: 0.520 Set scattering table: 0.330 Process input model: 99.720 Find NCS groups from input model: 2.820 Set up NCS constraints: 0.310 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 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 : 0.010 0.130 37528 Z= 0.636 Angle : 0.937 26.453 50797 Z= 0.610 Chirality : 0.053 0.461 5920 Planarity : 0.005 0.048 6550 Dihedral : 14.887 174.200 13976 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.95 % Allowed : 8.32 % Favored : 88.74 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.10), residues: 4807 helix: -1.86 (0.08), residues: 2588 sheet: -1.04 (0.20), residues: 516 loop : -1.74 (0.14), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP Y 26 HIS 0.007 0.002 HIS a 95 PHE 0.023 0.002 PHE Y 20 TYR 0.022 0.002 TYR Y 24 ARG 0.010 0.001 ARG X 117 *********************** 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 876 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 763 time to evaluate : 4.900 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: W 70 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7671 (mt-10) REVERT: W 90 ASP cc_start: 0.9275 (m-30) cc_final: 0.8994 (m-30) REVERT: W 143 ASP cc_start: 0.8289 (t0) cc_final: 0.8035 (t0) REVERT: W 156 ASP cc_start: 0.8563 (p0) cc_final: 0.8091 (p0) REVERT: C 86 MET cc_start: 0.8721 (mtt) cc_final: 0.8488 (mtt) REVERT: C 161 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8561 (mtt-85) REVERT: C 187 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.7778 (ptt90) REVERT: B 7 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7903 (mp0) REVERT: A 236 TYR cc_start: 0.9150 (OUTLIER) cc_final: 0.8576 (t80) REVERT: A 426 LYS cc_start: 0.8599 (mmtt) cc_final: 0.8333 (mmtp) REVERT: A 429 GLU cc_start: 0.8967 (tp30) cc_final: 0.8688 (tp30) REVERT: A 463 LYS cc_start: 0.7877 (tttt) cc_final: 0.7512 (ttpp) REVERT: X 106 GLN cc_start: 0.9192 (tm-30) cc_final: 0.8985 (tm-30) REVERT: X 123 GLN cc_start: 0.8206 (mm110) cc_final: 0.7804 (mm-40) REVERT: H 13 GLN cc_start: 0.7791 (pt0) cc_final: 0.7579 (pm20) REVERT: H 22 LYS cc_start: 0.8408 (ptpp) cc_final: 0.8064 (pttt) REVERT: H 49 MET cc_start: 0.8837 (mmt) cc_final: 0.8587 (mmm) REVERT: H 51 ARG cc_start: 0.8322 (mtp-110) cc_final: 0.7940 (ttp80) REVERT: H 65 SER cc_start: 0.9139 (m) cc_final: 0.8407 (t) REVERT: G 116 MET cc_start: 0.9238 (mmm) cc_final: 0.8582 (mmm) REVERT: F 226 MET cc_start: 0.8793 (mtt) cc_final: 0.8546 (mtt) REVERT: E 136 MET cc_start: 0.9115 (mmm) cc_final: 0.8798 (mmm) REVERT: E 242 ASP cc_start: 0.7988 (t70) cc_final: 0.7731 (t0) REVERT: E 249 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8384 (mp) REVERT: E 381 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8481 (tm-30) REVERT: D 88 MET cc_start: 0.8987 (mtm) cc_final: 0.8547 (mtm) REVERT: D 301 ASP cc_start: 0.8538 (t0) cc_final: 0.8216 (t0) REVERT: D 386 ASP cc_start: 0.8443 (m-30) cc_final: 0.8049 (m-30) REVERT: I 10 TYR cc_start: 0.8807 (m-80) cc_final: 0.8586 (m-80) REVERT: I 57 MET cc_start: 0.9238 (tmm) cc_final: 0.8820 (tmm) REVERT: I 63 ILE cc_start: 0.9400 (mm) cc_final: 0.9171 (mt) REVERT: I 73 TYR cc_start: 0.8656 (t80) cc_final: 0.8265 (t80) REVERT: J 68 VAL cc_start: 0.9029 (t) cc_final: 0.8736 (p) REVERT: J 75 MET cc_start: 0.9067 (ttp) cc_final: 0.8862 (ttm) REVERT: L 10 TYR cc_start: 0.9002 (m-80) cc_final: 0.8567 (m-80) REVERT: L 11 MET cc_start: 0.8883 (tpt) cc_final: 0.8476 (tpt) REVERT: L 37 GLU cc_start: 0.8576 (pt0) cc_final: 0.8282 (mm-30) REVERT: L 57 MET cc_start: 0.8508 (tmm) cc_final: 0.8212 (tmm) REVERT: L 61 ASP cc_start: 0.8991 (m-30) cc_final: 0.8693 (m-30) REVERT: M 30 ILE cc_start: 0.8918 (mt) cc_final: 0.8620 (mt) REVERT: M 34 LYS cc_start: 0.9323 (mmtm) cc_final: 0.9050 (mmmt) REVERT: M 73 TYR cc_start: 0.8751 (t80) cc_final: 0.8475 (t80) REVERT: N 10 TYR cc_start: 0.8677 (m-80) cc_final: 0.8326 (m-10) REVERT: N 42 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8633 (mm-40) REVERT: N 55 ILE cc_start: 0.8974 (mm) cc_final: 0.8740 (mt) REVERT: N 65 MET cc_start: 0.9285 (mtt) cc_final: 0.9066 (mtm) REVERT: O 6 MET cc_start: 0.7516 (ttm) cc_final: 0.7202 (tmm) REVERT: P 8 LEU cc_start: 0.9081 (mt) cc_final: 0.8819 (tp) REVERT: P 17 MET cc_start: 0.8923 (mtm) cc_final: 0.8703 (mtp) REVERT: P 53 PHE cc_start: 0.9303 (t80) cc_final: 0.9061 (t80) REVERT: P 73 TYR cc_start: 0.8437 (t80) cc_final: 0.8090 (t80) REVERT: Q 17 MET cc_start: 0.8317 (mtm) cc_final: 0.7578 (mtm) REVERT: R 44 ASP cc_start: 0.7892 (m-30) cc_final: 0.7625 (m-30) REVERT: S 11 MET cc_start: 0.9116 (tpp) cc_final: 0.8722 (tpt) REVERT: S 17 MET cc_start: 0.8495 (mtp) cc_final: 0.8186 (mmm) REVERT: S 73 TYR cc_start: 0.8551 (t80) cc_final: 0.8051 (t80) REVERT: Y 37 GLN cc_start: 0.8548 (mt0) cc_final: 0.8284 (mm-40) REVERT: Y 83 ARG cc_start: 0.7442 (ttm110) cc_final: 0.7203 (ttp80) REVERT: Y 98 ARG cc_start: 0.8754 (ttp80) cc_final: 0.8547 (ttp80) REVERT: a 24 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6786 (mmt180) REVERT: a 26 PHE cc_start: 0.6216 (OUTLIER) cc_final: 0.5075 (m-80) REVERT: a 94 TYR cc_start: 0.6962 (t80) cc_final: 0.6404 (t80) REVERT: a 115 MET cc_start: 0.8096 (mtm) cc_final: 0.7873 (mtp) REVERT: a 119 ASP cc_start: 0.8261 (t0) cc_final: 0.7891 (t0) REVERT: a 155 LEU cc_start: 0.9245 (mt) cc_final: 0.8920 (mt) REVERT: a 167 LYS cc_start: 0.8969 (tttt) cc_final: 0.8333 (mtpp) REVERT: a 231 TRP cc_start: 0.7521 (p-90) cc_final: 0.7040 (p-90) REVERT: a 263 TYR cc_start: 0.9094 (m-10) cc_final: 0.8848 (m-10) outliers start: 113 outliers final: 57 residues processed: 850 average time/residue: 0.5415 time to fit residues: 725.4409 Evaluate side-chains 641 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 576 time to evaluate : 4.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 150 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain A residue 20 ASN Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 511 GLN Chi-restraints excluded: chain X residue 66 LYS Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 78 GLN Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 147 ASP Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 210 ASP Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 58 SER Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain Y residue 88 ASP Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain a residue 24 ARG Chi-restraints excluded: chain a residue 26 PHE Chi-restraints excluded: chain a residue 147 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 400 optimal weight: 8.9990 chunk 359 optimal weight: 0.9980 chunk 199 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 242 optimal weight: 0.9990 chunk 191 optimal weight: 7.9990 chunk 371 optimal weight: 9.9990 chunk 143 optimal weight: 0.8980 chunk 225 optimal weight: 1.9990 chunk 276 optimal weight: 2.9990 chunk 430 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 W 82 ASN ** W 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 369 ASN C 479 HIS C 488 GLN C 511 GLN B 4 ASN B 58 ASN B 147 GLN B 186 GLN A 65 ASN A 147 GLN A 344 ASN A 479 HIS A 484 GLN X 80 ASN G 59 ASN G 111 GLN E 441 GLN D 170 HIS D 279 GLN D 294 GLN I 42 GLN L 5 ASN L 52 GLN Q 3 ASN R 5 ASN R 52 GLN S 52 GLN Y 10 GLN Y 64 GLN Y 85 GLN a 14 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1966 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= 0.210 Angle : 0.630 9.451 50797 Z= 0.330 Chirality : 0.044 0.217 5920 Planarity : 0.005 0.043 6550 Dihedral : 8.893 174.788 5455 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.23 % Allowed : 12.77 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.11), residues: 4807 helix: -0.13 (0.10), residues: 2581 sheet: -0.63 (0.22), residues: 492 loop : -0.93 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 186 HIS 0.006 0.001 HIS G 64 PHE 0.024 0.001 PHE Q 53 TYR 0.018 0.001 TYR A 236 ARG 0.011 0.001 ARG X 117 *********************** 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 787 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 663 time to evaluate : 4.426 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: W 90 ASP cc_start: 0.9039 (m-30) cc_final: 0.8691 (m-30) REVERT: W 109 ASP cc_start: 0.7905 (m-30) cc_final: 0.7463 (t0) REVERT: W 156 ASP cc_start: 0.8501 (p0) cc_final: 0.7953 (p0) REVERT: B 7 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7892 (mp0) REVERT: B 488 GLN cc_start: 0.9087 (mm-40) cc_final: 0.8841 (mm110) REVERT: A 484 GLN cc_start: 0.8710 (tp40) cc_final: 0.8184 (tp-100) REVERT: A 488 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8393 (mt0) REVERT: X 73 GLN cc_start: 0.8621 (tp-100) cc_final: 0.8278 (tp-100) REVERT: X 83 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8282 (tmm-80) REVERT: X 106 GLN cc_start: 0.9068 (tm-30) cc_final: 0.8600 (pp30) REVERT: X 123 GLN cc_start: 0.8167 (mm110) cc_final: 0.7369 (mm-40) REVERT: X 145 ASN cc_start: 0.7714 (t0) cc_final: 0.7260 (m-40) REVERT: H 22 LYS cc_start: 0.8605 (ptpp) cc_final: 0.8395 (pttt) REVERT: H 49 MET cc_start: 0.8875 (mmt) cc_final: 0.8638 (mmm) REVERT: H 51 ARG cc_start: 0.8444 (mtp-110) cc_final: 0.8062 (ttp80) REVERT: H 65 SER cc_start: 0.9081 (m) cc_final: 0.8426 (t) REVERT: H 127 GLN cc_start: 0.7563 (tm-30) cc_final: 0.7302 (tm-30) REVERT: H 132 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8010 (pt0) REVERT: G 23 MET cc_start: 0.8666 (mtm) cc_final: 0.8406 (mtp) REVERT: G 101 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8126 (mp0) REVERT: G 233 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7910 (tt0) REVERT: F 193 MET cc_start: 0.8633 (mmp) cc_final: 0.8312 (mmp) REVERT: E 125 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9135 (mp) REVERT: E 192 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7704 (tp30) REVERT: E 249 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8381 (mp) REVERT: E 365 GLN cc_start: 0.8987 (pt0) cc_final: 0.8775 (tt0) REVERT: E 381 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8496 (tm-30) REVERT: D 338 ASP cc_start: 0.8275 (m-30) cc_final: 0.8053 (m-30) REVERT: I 16 MET cc_start: 0.8431 (tpt) cc_final: 0.8126 (tpt) REVERT: I 42 GLN cc_start: 0.8244 (mm110) cc_final: 0.7906 (mm110) REVERT: I 54 PHE cc_start: 0.8771 (m-80) cc_final: 0.8545 (m-80) REVERT: I 57 MET cc_start: 0.9278 (tmm) cc_final: 0.8963 (tmm) REVERT: I 73 TYR cc_start: 0.8780 (t80) cc_final: 0.8363 (t80) REVERT: J 6 MET cc_start: 0.7563 (mtm) cc_final: 0.7318 (ptt) REVERT: J 10 TYR cc_start: 0.8842 (m-80) cc_final: 0.8207 (m-80) REVERT: L 11 MET cc_start: 0.8902 (tpt) cc_final: 0.8501 (tpt) REVERT: L 61 ASP cc_start: 0.9028 (m-30) cc_final: 0.8795 (m-30) REVERT: L 75 MET cc_start: 0.8644 (tpt) cc_final: 0.8344 (tpp) REVERT: L 76 PHE cc_start: 0.7953 (m-80) cc_final: 0.7551 (m-10) REVERT: M 30 ILE cc_start: 0.8848 (mt) cc_final: 0.8616 (mt) REVERT: M 35 PHE cc_start: 0.8820 (t80) cc_final: 0.8477 (t80) REVERT: M 57 MET cc_start: 0.8810 (tmm) cc_final: 0.8508 (tmm) REVERT: M 73 TYR cc_start: 0.8724 (t80) cc_final: 0.8491 (t80) REVERT: N 16 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.8219 (ttm) REVERT: N 55 ILE cc_start: 0.9010 (mm) cc_final: 0.8756 (mt) REVERT: N 57 MET cc_start: 0.9023 (tmm) cc_final: 0.8798 (ppp) REVERT: N 63 ILE cc_start: 0.8869 (mm) cc_final: 0.8301 (mt) REVERT: O 6 MET cc_start: 0.7295 (OUTLIER) cc_final: 0.7005 (tmm) REVERT: O 10 TYR cc_start: 0.7189 (m-80) cc_final: 0.6833 (m-80) REVERT: O 57 MET cc_start: 0.9001 (tmm) cc_final: 0.8706 (tmm) REVERT: O 75 MET cc_start: 0.8587 (mtp) cc_final: 0.8148 (tpt) REVERT: P 17 MET cc_start: 0.8762 (mtm) cc_final: 0.8468 (mtp) REVERT: P 73 TYR cc_start: 0.8353 (t80) cc_final: 0.7920 (t80) REVERT: Q 7 ASP cc_start: 0.8400 (t0) cc_final: 0.7326 (m-30) REVERT: Q 16 MET cc_start: 0.8629 (mtp) cc_final: 0.8312 (tpp) REVERT: Q 52 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8693 (mm110) REVERT: R 44 ASP cc_start: 0.7912 (m-30) cc_final: 0.7621 (m-30) REVERT: S 11 MET cc_start: 0.8852 (tpp) cc_final: 0.8363 (tpt) REVERT: S 17 MET cc_start: 0.8511 (mtp) cc_final: 0.8094 (mmm) REVERT: S 73 TYR cc_start: 0.8416 (t80) cc_final: 0.7927 (t80) REVERT: Y 64 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7349 (mm-40) REVERT: Y 65 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6789 (tp) REVERT: Y 83 ARG cc_start: 0.7606 (ttm110) cc_final: 0.7285 (ttp80) REVERT: Y 91 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8884 (mmtm) REVERT: Y 98 ARG cc_start: 0.8779 (ttp80) cc_final: 0.8351 (ttt90) REVERT: a 24 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.6562 (mmt180) REVERT: a 91 LYS cc_start: 0.8969 (mmmt) cc_final: 0.8739 (mmmt) REVERT: a 119 ASP cc_start: 0.8195 (t0) cc_final: 0.7949 (t0) REVERT: a 155 LEU cc_start: 0.9107 (mt) cc_final: 0.8872 (mt) REVERT: a 167 LYS cc_start: 0.8797 (tttt) cc_final: 0.8398 (mtpp) REVERT: a 216 TYR cc_start: 0.8831 (t80) cc_final: 0.8597 (t80) REVERT: a 231 TRP cc_start: 0.7462 (p-90) cc_final: 0.7199 (p-90) outliers start: 124 outliers final: 56 residues processed: 740 average time/residue: 0.5127 time to fit residues: 616.7079 Evaluate side-chains 649 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 581 time to evaluate : 4.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 150 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 20 ASN Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 511 GLN Chi-restraints excluded: chain X residue 83 ARG Chi-restraints excluded: chain X residue 147 ASP Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 372 ASP Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 360 VAL 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 453 VAL Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain N residue 11 MET Chi-restraints excluded: chain N residue 16 MET Chi-restraints excluded: chain O residue 6 MET Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 52 GLN Chi-restraints excluded: chain S residue 5 ASN Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain Y residue 65 LEU Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 91 LYS Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain a residue 24 ARG Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 114 LEU Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 200 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 239 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 358 optimal weight: 7.9990 chunk 293 optimal weight: 4.9990 chunk 118 optimal weight: 10.0000 chunk 431 optimal weight: 0.4980 chunk 465 optimal weight: 50.0000 chunk 384 optimal weight: 5.9990 chunk 427 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 345 optimal weight: 0.0060 overall best weight: 2.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 GLN B 4 ASN X 64 GLN X 78 GLN X 80 ASN H 104 HIS G 64 HIS D 243 ASN J 3 ASN ** P 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 42 GLN R 52 GLN Y 85 GLN a 76 GLN a 132 HIS a 252 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 37528 Z= 0.268 Angle : 0.601 8.385 50797 Z= 0.312 Chirality : 0.043 0.184 5920 Planarity : 0.004 0.042 6550 Dihedral : 7.886 158.877 5394 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.55 % Allowed : 14.18 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.12), residues: 4807 helix: 0.43 (0.10), residues: 2595 sheet: -0.52 (0.22), residues: 523 loop : -0.70 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 186 HIS 0.013 0.001 HIS a 132 PHE 0.030 0.001 PHE L 54 TYR 0.022 0.001 TYR L 73 ARG 0.006 0.000 ARG X 113 *********************** 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 745 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 609 time to evaluate : 4.498 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: W 39 LYS cc_start: 0.9234 (mttt) cc_final: 0.8985 (mtpt) REVERT: W 90 ASP cc_start: 0.8992 (m-30) cc_final: 0.8698 (m-30) REVERT: W 109 ASP cc_start: 0.7832 (m-30) cc_final: 0.7436 (t0) REVERT: W 128 MET cc_start: 0.9374 (mmm) cc_final: 0.9031 (mmm) REVERT: W 143 ASP cc_start: 0.8013 (t0) cc_final: 0.7802 (t0) REVERT: W 156 ASP cc_start: 0.8535 (p0) cc_final: 0.8106 (p0) REVERT: C 1 MET cc_start: 0.7177 (tmm) cc_final: 0.6728 (tmm) REVERT: B 7 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7875 (mp0) REVERT: B 513 TRP cc_start: 0.6161 (OUTLIER) cc_final: 0.5191 (m100) REVERT: A 262 ASP cc_start: 0.7810 (p0) cc_final: 0.7383 (p0) REVERT: X 73 GLN cc_start: 0.8641 (tp-100) cc_final: 0.8226 (tp-100) REVERT: X 106 GLN cc_start: 0.9019 (tm-30) cc_final: 0.8777 (pp30) REVERT: X 123 GLN cc_start: 0.8227 (mm110) cc_final: 0.7377 (mm-40) REVERT: X 145 ASN cc_start: 0.7695 (t0) cc_final: 0.7212 (m110) REVERT: H 49 MET cc_start: 0.8850 (mmt) cc_final: 0.8641 (tpp) REVERT: H 51 ARG cc_start: 0.8569 (mtp-110) cc_final: 0.8345 (ttp80) REVERT: H 65 SER cc_start: 0.9165 (m) cc_final: 0.8417 (t) REVERT: H 98 LYS cc_start: 0.8927 (mtmt) cc_final: 0.8389 (mtmm) REVERT: G 101 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8096 (mp0) REVERT: E 125 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9103 (mp) REVERT: E 232 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.8288 (m-30) REVERT: E 249 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8388 (mp) REVERT: E 365 GLN cc_start: 0.8965 (pt0) cc_final: 0.8427 (tp-100) REVERT: D 301 ASP cc_start: 0.8470 (t0) cc_final: 0.8040 (t0) REVERT: D 338 ASP cc_start: 0.8286 (m-30) cc_final: 0.8065 (m-30) REVERT: D 366 ARG cc_start: 0.8254 (tpt170) cc_final: 0.7660 (tpt170) REVERT: D 370 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8266 (mp) REVERT: I 17 MET cc_start: 0.8511 (mtm) cc_final: 0.8200 (mmm) REVERT: I 42 GLN cc_start: 0.8072 (mm110) cc_final: 0.7789 (mm-40) REVERT: I 57 MET cc_start: 0.9221 (tmm) cc_final: 0.8896 (tmm) REVERT: I 73 TYR cc_start: 0.8781 (t80) cc_final: 0.8393 (t80) REVERT: J 10 TYR cc_start: 0.8930 (m-80) cc_final: 0.8692 (m-80) REVERT: L 10 TYR cc_start: 0.8789 (m-80) cc_final: 0.8375 (m-80) REVERT: L 11 MET cc_start: 0.8905 (tpt) cc_final: 0.8503 (tpt) REVERT: L 50 ARG cc_start: 0.8770 (mtm110) cc_final: 0.8362 (mtp180) REVERT: L 61 ASP cc_start: 0.8874 (m-30) cc_final: 0.8624 (m-30) REVERT: M 17 MET cc_start: 0.8978 (mmt) cc_final: 0.8589 (mmt) REVERT: M 30 ILE cc_start: 0.8816 (mt) cc_final: 0.8599 (mt) REVERT: M 35 PHE cc_start: 0.8837 (t80) cc_final: 0.8500 (t80) REVERT: M 57 MET cc_start: 0.8789 (tmm) cc_final: 0.8487 (tmm) REVERT: M 73 TYR cc_start: 0.8664 (t80) cc_final: 0.8401 (t80) REVERT: N 16 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8234 (ttm) REVERT: N 55 ILE cc_start: 0.9041 (mm) cc_final: 0.8749 (mt) REVERT: N 63 ILE cc_start: 0.8747 (mm) cc_final: 0.8434 (mt) REVERT: N 66 ILE cc_start: 0.8914 (tt) cc_final: 0.8489 (tp) REVERT: O 6 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.7146 (tmm) REVERT: O 57 MET cc_start: 0.8972 (tmm) cc_final: 0.8717 (tmm) REVERT: O 75 MET cc_start: 0.8597 (mtp) cc_final: 0.8016 (tpp) REVERT: P 10 TYR cc_start: 0.8670 (m-80) cc_final: 0.8347 (m-80) REVERT: P 17 MET cc_start: 0.8786 (mtm) cc_final: 0.8502 (mtp) REVERT: P 65 MET cc_start: 0.9136 (mmm) cc_final: 0.8896 (mmm) REVERT: P 73 TYR cc_start: 0.8273 (t80) cc_final: 0.7893 (t80) REVERT: Q 16 MET cc_start: 0.8485 (mtp) cc_final: 0.8179 (tpp) REVERT: Q 52 GLN cc_start: 0.8971 (mm-40) cc_final: 0.8569 (mm110) REVERT: S 11 MET cc_start: 0.8751 (tpp) cc_final: 0.8258 (tpt) REVERT: S 17 MET cc_start: 0.8515 (mtp) cc_final: 0.8117 (mmm) REVERT: S 73 TYR cc_start: 0.8377 (t80) cc_final: 0.7944 (t80) REVERT: Y 64 GLN cc_start: 0.7955 (mp10) cc_final: 0.7709 (mm-40) REVERT: Y 98 ARG cc_start: 0.8812 (ttp80) cc_final: 0.8430 (ttt90) REVERT: a 24 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6405 (mmt180) REVERT: a 91 LYS cc_start: 0.8940 (mmmt) cc_final: 0.8444 (mmmt) REVERT: a 119 ASP cc_start: 0.8076 (t0) cc_final: 0.7875 (t0) REVERT: a 146 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.8037 (p0) REVERT: a 169 LYS cc_start: 0.6232 (mmtt) cc_final: 0.5765 (mmtp) REVERT: a 231 TRP cc_start: 0.7481 (p-90) cc_final: 0.7186 (p-90) outliers start: 136 outliers final: 79 residues processed: 702 average time/residue: 0.5028 time to fit residues: 577.5090 Evaluate side-chains 660 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 570 time to evaluate : 4.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 48 SER Chi-restraints excluded: chain W residue 150 VAL Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 511 GLN Chi-restraints excluded: chain X residue 15 VAL Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain X residue 83 ARG Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 147 ASP Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 372 ASP Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 232 ASP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain D residue 54 ILE 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 243 ASN Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 61 ASP Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain N residue 16 MET Chi-restraints excluded: chain O residue 6 MET Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 5 ASN Chi-restraints excluded: chain R residue 52 GLN Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain S residue 5 ASN Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain Y residue 15 VAL Chi-restraints excluded: chain Y residue 51 HIS Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain a residue 24 ARG Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 146 ASP Chi-restraints excluded: chain a residue 147 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 426 optimal weight: 9.9990 chunk 324 optimal weight: 3.9990 chunk 223 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 205 optimal weight: 9.9990 chunk 289 optimal weight: 5.9990 chunk 432 optimal weight: 5.9990 chunk 458 optimal weight: 0.9990 chunk 226 optimal weight: 3.9990 chunk 410 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 GLN X 80 ASN F 43 GLN ** P 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 52 GLN Q 42 GLN R 52 GLN Y 64 GLN ** Y 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 20 GLN a 76 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 37528 Z= 0.270 Angle : 0.591 8.943 50797 Z= 0.304 Chirality : 0.043 0.186 5920 Planarity : 0.004 0.043 6550 Dihedral : 7.592 141.999 5390 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.52 % Allowed : 15.02 % Favored : 81.47 % 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: 0.06 (0.12), residues: 4807 helix: 0.65 (0.10), residues: 2604 sheet: -0.43 (0.22), residues: 516 loop : -0.60 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 186 HIS 0.003 0.001 HIS F 170 PHE 0.019 0.001 PHE L 54 TYR 0.016 0.001 TYR A 236 ARG 0.011 0.000 ARG X 117 *********************** 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 732 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 597 time to evaluate : 4.443 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: W 39 LYS cc_start: 0.9191 (mttt) cc_final: 0.8976 (mtpt) REVERT: W 90 ASP cc_start: 0.8964 (m-30) cc_final: 0.8649 (m-30) REVERT: W 128 MET cc_start: 0.9340 (mmm) cc_final: 0.9083 (mmp) REVERT: W 143 ASP cc_start: 0.8075 (t0) cc_final: 0.7814 (t0) REVERT: W 156 ASP cc_start: 0.8548 (p0) cc_final: 0.8086 (p0) REVERT: C 1 MET cc_start: 0.7200 (tmm) cc_final: 0.6730 (tmm) REVERT: C 343 THR cc_start: 0.9258 (OUTLIER) cc_final: 0.9000 (p) REVERT: B 7 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7818 (mp0) REVERT: B 513 TRP cc_start: 0.6160 (OUTLIER) cc_final: 0.5107 (m100) REVERT: A 49 GLN cc_start: 0.9488 (OUTLIER) cc_final: 0.9134 (tp40) REVERT: A 262 ASP cc_start: 0.7791 (p0) cc_final: 0.7327 (p0) REVERT: A 356 GLU cc_start: 0.8047 (tp30) cc_final: 0.7581 (tt0) REVERT: A 484 GLN cc_start: 0.8725 (tp40) cc_final: 0.8447 (tp-100) REVERT: X 73 GLN cc_start: 0.8558 (tp-100) cc_final: 0.8209 (tp-100) REVERT: X 117 ARG cc_start: 0.7952 (ttp80) cc_final: 0.7529 (ttp80) REVERT: X 123 GLN cc_start: 0.8207 (mm110) cc_final: 0.7353 (mm-40) REVERT: X 145 ASN cc_start: 0.7761 (t0) cc_final: 0.7259 (m-40) REVERT: H 65 SER cc_start: 0.9156 (m) cc_final: 0.8398 (t) REVERT: H 98 LYS cc_start: 0.8966 (mtmt) cc_final: 0.8415 (mtmm) REVERT: G 101 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8022 (mp0) REVERT: E 161 GLU cc_start: 0.8650 (tp30) cc_final: 0.8380 (tp30) REVERT: E 232 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8271 (m-30) REVERT: E 249 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8388 (mp) REVERT: E 365 GLN cc_start: 0.8933 (pt0) cc_final: 0.8433 (tp-100) REVERT: D 301 ASP cc_start: 0.8538 (t0) cc_final: 0.8111 (t0) REVERT: D 338 ASP cc_start: 0.8274 (m-30) cc_final: 0.8064 (m-30) REVERT: D 366 ARG cc_start: 0.8278 (tpt170) cc_final: 0.7667 (tpt170) REVERT: D 370 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8269 (mp) REVERT: I 42 GLN cc_start: 0.7978 (mm110) cc_final: 0.7645 (mm-40) REVERT: I 57 MET cc_start: 0.9172 (tmm) cc_final: 0.8855 (tmm) REVERT: I 73 TYR cc_start: 0.8731 (t80) cc_final: 0.8378 (t80) REVERT: L 5 ASN cc_start: 0.7339 (p0) cc_final: 0.6953 (m110) REVERT: L 11 MET cc_start: 0.8964 (tpt) cc_final: 0.8687 (tpp) REVERT: L 37 GLU cc_start: 0.8863 (tt0) cc_final: 0.8415 (tp30) REVERT: L 50 ARG cc_start: 0.8708 (mtm110) cc_final: 0.8169 (mtp180) REVERT: M 30 ILE cc_start: 0.8806 (mt) cc_final: 0.8600 (mt) REVERT: M 35 PHE cc_start: 0.8888 (t80) cc_final: 0.8574 (t80) REVERT: M 73 TYR cc_start: 0.8616 (t80) cc_final: 0.8371 (t80) REVERT: N 16 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8193 (ttm) REVERT: N 17 MET cc_start: 0.9067 (mmt) cc_final: 0.8859 (mmp) REVERT: N 37 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7657 (tm-30) REVERT: N 55 ILE cc_start: 0.9077 (mm) cc_final: 0.8792 (mt) REVERT: N 63 ILE cc_start: 0.8743 (mm) cc_final: 0.8391 (mt) REVERT: O 6 MET cc_start: 0.7285 (OUTLIER) cc_final: 0.6992 (tmm) REVERT: O 53 PHE cc_start: 0.9440 (t80) cc_final: 0.9240 (t80) REVERT: O 57 MET cc_start: 0.9028 (tmm) cc_final: 0.8749 (tmm) REVERT: P 10 TYR cc_start: 0.8791 (m-80) cc_final: 0.8250 (m-80) REVERT: P 11 MET cc_start: 0.9047 (tpp) cc_final: 0.8840 (tpp) REVERT: P 17 MET cc_start: 0.8738 (mtm) cc_final: 0.8456 (mtp) REVERT: P 65 MET cc_start: 0.9121 (mmm) cc_final: 0.8849 (mmm) REVERT: P 73 TYR cc_start: 0.8208 (t80) cc_final: 0.7926 (t80) REVERT: Q 52 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8543 (mm110) REVERT: R 44 ASP cc_start: 0.8034 (m-30) cc_final: 0.7750 (m-30) REVERT: S 11 MET cc_start: 0.8749 (tpp) cc_final: 0.8221 (tpt) REVERT: S 17 MET cc_start: 0.8550 (mtp) cc_final: 0.8118 (mmm) REVERT: S 73 TYR cc_start: 0.8420 (t80) cc_final: 0.8060 (t80) REVERT: Y 64 GLN cc_start: 0.7736 (mp-120) cc_final: 0.7431 (mm-40) REVERT: Y 98 ARG cc_start: 0.8816 (ttp80) cc_final: 0.8392 (tpt90) REVERT: a 24 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6408 (mmt180) REVERT: a 56 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7545 (t80) REVERT: a 91 LYS cc_start: 0.8953 (mmmt) cc_final: 0.8427 (mmmt) REVERT: a 119 ASP cc_start: 0.8020 (t0) cc_final: 0.7795 (t0) REVERT: a 146 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.8071 (p0) REVERT: a 169 LYS cc_start: 0.6182 (mmtt) cc_final: 0.5741 (mmtt) REVERT: a 231 TRP cc_start: 0.7490 (p-90) cc_final: 0.7215 (p-90) outliers start: 135 outliers final: 90 residues processed: 690 average time/residue: 0.5394 time to fit residues: 611.2381 Evaluate side-chains 672 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 569 time to evaluate : 4.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 141 LYS Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 150 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 511 GLN Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 42 ASP Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain X residue 83 ARG Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 147 ASP Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 138 MET Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 232 ASP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 366 ARG Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain D residue 54 ILE 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 277 VAL Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain N residue 16 MET Chi-restraints excluded: chain O residue 6 MET Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 46 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 52 GLN Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain S residue 5 ASN Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 15 VAL Chi-restraints excluded: chain Y residue 15 VAL Chi-restraints excluded: chain Y residue 51 HIS Chi-restraints excluded: chain Y residue 55 ASP Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain a residue 24 ARG Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 114 LEU Chi-restraints excluded: chain a residue 146 ASP Chi-restraints excluded: chain a residue 147 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 381 optimal weight: 6.9990 chunk 260 optimal weight: 0.0060 chunk 6 optimal weight: 2.9990 chunk 341 optimal weight: 0.9990 chunk 189 optimal weight: 2.9990 chunk 390 optimal weight: 3.9990 chunk 316 optimal weight: 0.4980 chunk 0 optimal weight: 8.9990 chunk 233 optimal weight: 5.9990 chunk 411 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 80 ASN O 52 GLN ** P 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 5 ASN ** P 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 42 GLN R 52 GLN ** Y 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 76 GLN a 252 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 37528 Z= 0.182 Angle : 0.556 10.871 50797 Z= 0.284 Chirality : 0.042 0.217 5920 Planarity : 0.004 0.045 6550 Dihedral : 7.158 127.092 5390 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.31 % Allowed : 15.59 % Favored : 81.10 % 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: 0.34 (0.12), residues: 4807 helix: 0.87 (0.10), residues: 2615 sheet: -0.26 (0.22), residues: 509 loop : -0.49 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP a 186 HIS 0.002 0.000 HIS W 21 PHE 0.031 0.001 PHE L 54 TYR 0.016 0.001 TYR L 73 ARG 0.007 0.000 ARG X 113 *********************** 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 747 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 620 time to evaluate : 4.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 39 LYS cc_start: 0.9195 (mttt) cc_final: 0.8995 (mtpt) REVERT: W 128 MET cc_start: 0.9331 (mmm) cc_final: 0.9070 (mmp) REVERT: W 143 ASP cc_start: 0.8033 (t0) cc_final: 0.7739 (t0) REVERT: W 156 ASP cc_start: 0.8484 (p0) cc_final: 0.8050 (p0) REVERT: C 1 MET cc_start: 0.7349 (tmm) cc_final: 0.6933 (tmm) REVERT: C 132 ILE cc_start: 0.9337 (pt) cc_final: 0.9004 (mm) REVERT: C 343 THR cc_start: 0.9239 (OUTLIER) cc_final: 0.9027 (p) REVERT: B 67 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8170 (mm-30) REVERT: A 49 GLN cc_start: 0.9449 (OUTLIER) cc_final: 0.9089 (tp40) REVERT: A 262 ASP cc_start: 0.7670 (p0) cc_final: 0.7185 (p0) REVERT: A 356 GLU cc_start: 0.7927 (tp30) cc_final: 0.7527 (tt0) REVERT: A 484 GLN cc_start: 0.8731 (tp40) cc_final: 0.8455 (tp-100) REVERT: X 73 GLN cc_start: 0.8538 (tp-100) cc_final: 0.8191 (tp-100) REVERT: X 117 ARG cc_start: 0.7930 (ttp80) cc_final: 0.7465 (ttp80) REVERT: X 123 GLN cc_start: 0.8201 (mm110) cc_final: 0.7248 (mm-40) REVERT: X 145 ASN cc_start: 0.7694 (t0) cc_final: 0.7216 (m-40) REVERT: H 46 LYS cc_start: 0.9414 (mtmm) cc_final: 0.9193 (mtmm) REVERT: H 65 SER cc_start: 0.9098 (OUTLIER) cc_final: 0.8273 (t) REVERT: H 98 LYS cc_start: 0.8995 (mtmt) cc_final: 0.8445 (mtmm) REVERT: G 38 MET cc_start: 0.8127 (ttp) cc_final: 0.7852 (ttp) REVERT: G 101 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8039 (mp0) REVERT: F 88 MET cc_start: 0.8913 (mtp) cc_final: 0.8704 (mtp) REVERT: F 193 MET cc_start: 0.8520 (mmp) cc_final: 0.8166 (mmp) REVERT: E 232 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.8237 (m-30) REVERT: E 249 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8402 (mp) REVERT: E 365 GLN cc_start: 0.8846 (pt0) cc_final: 0.8445 (tp40) REVERT: D 301 ASP cc_start: 0.8588 (t0) cc_final: 0.8178 (t0) REVERT: D 370 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8297 (mp) REVERT: I 42 GLN cc_start: 0.7859 (mm110) cc_final: 0.7658 (mm110) REVERT: I 57 MET cc_start: 0.9086 (tmm) cc_final: 0.8769 (tmm) REVERT: I 65 MET cc_start: 0.9034 (mmp) cc_final: 0.8670 (mmp) REVERT: J 17 MET cc_start: 0.9353 (mmp) cc_final: 0.8980 (mmt) REVERT: L 5 ASN cc_start: 0.7211 (p0) cc_final: 0.6688 (m110) REVERT: L 11 MET cc_start: 0.8800 (tpt) cc_final: 0.8495 (tpp) REVERT: L 37 GLU cc_start: 0.8802 (tt0) cc_final: 0.8524 (tp30) REVERT: L 42 GLN cc_start: 0.8313 (mt0) cc_final: 0.8045 (tm-30) REVERT: M 26 ILE cc_start: 0.8903 (mm) cc_final: 0.8681 (mm) REVERT: M 30 ILE cc_start: 0.8796 (mt) cc_final: 0.8594 (mt) REVERT: M 35 PHE cc_start: 0.8893 (t80) cc_final: 0.8493 (t80) REVERT: M 73 TYR cc_start: 0.8576 (t80) cc_final: 0.8326 (t80) REVERT: N 16 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8208 (ttm) REVERT: N 55 ILE cc_start: 0.9075 (mm) cc_final: 0.8781 (mt) REVERT: N 63 ILE cc_start: 0.8657 (mm) cc_final: 0.8396 (mt) REVERT: O 9 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8213 (mt) REVERT: O 53 PHE cc_start: 0.9392 (t80) cc_final: 0.9096 (t80) REVERT: O 57 MET cc_start: 0.9030 (tmm) cc_final: 0.8804 (tmm) REVERT: O 75 MET cc_start: 0.8407 (mtp) cc_final: 0.8070 (tpp) REVERT: P 10 TYR cc_start: 0.8769 (m-80) cc_final: 0.8410 (m-80) REVERT: P 11 MET cc_start: 0.8899 (tpp) cc_final: 0.8646 (tpp) REVERT: P 65 MET cc_start: 0.9088 (mmm) cc_final: 0.8790 (mmm) REVERT: P 73 TYR cc_start: 0.8195 (t80) cc_final: 0.7900 (t80) REVERT: Q 52 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8603 (mm110) REVERT: R 44 ASP cc_start: 0.8066 (m-30) cc_final: 0.7771 (m-30) REVERT: R 52 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8531 (mm110) REVERT: S 17 MET cc_start: 0.8638 (mtp) cc_final: 0.8067 (mmm) REVERT: S 73 TYR cc_start: 0.8370 (t80) cc_final: 0.8027 (t80) REVERT: Y 64 GLN cc_start: 0.7789 (mp-120) cc_final: 0.7487 (mm-40) REVERT: Y 98 ARG cc_start: 0.8789 (ttp80) cc_final: 0.8381 (tpt90) REVERT: a 24 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.6432 (mmt180) REVERT: a 56 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.7575 (t80) REVERT: a 91 LYS cc_start: 0.8945 (mmmt) cc_final: 0.8471 (mmmt) REVERT: a 94 TYR cc_start: 0.6928 (t80) cc_final: 0.6316 (t80) REVERT: a 106 LEU cc_start: 0.9066 (tp) cc_final: 0.8830 (pp) REVERT: a 119 ASP cc_start: 0.8069 (t0) cc_final: 0.7804 (t0) REVERT: a 146 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.7885 (p0) REVERT: a 169 LYS cc_start: 0.6311 (mmtt) cc_final: 0.5692 (mmtt) REVERT: a 231 TRP cc_start: 0.7530 (p-90) cc_final: 0.7293 (p-90) outliers start: 127 outliers final: 83 residues processed: 700 average time/residue: 0.5093 time to fit residues: 584.2468 Evaluate side-chains 670 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 574 time to evaluate : 6.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 48 SER Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 20 ASN Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 511 GLN Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 147 ASP Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 232 ASP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 366 ARG Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 446 VAL 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 348 VAL Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain N residue 16 MET Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 5 ASN Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 52 GLN Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain S residue 5 ASN Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 15 VAL Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain Y residue 15 VAL Chi-restraints excluded: chain Y residue 51 HIS Chi-restraints excluded: chain Y residue 55 ASP Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 127 LEU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain a residue 24 ARG Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 114 LEU Chi-restraints excluded: chain a residue 146 ASP Chi-restraints excluded: chain a residue 221 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 154 optimal weight: 4.9990 chunk 412 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 269 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 458 optimal weight: 2.9990 chunk 380 optimal weight: 7.9990 chunk 212 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 151 optimal weight: 0.0570 chunk 240 optimal weight: 7.9990 overall best weight: 3.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 80 ASN X 104 GLN G 57 HIS D 437 HIS ** P 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 42 GLN R 52 GLN ** S 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 76 GLN ** a 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2857 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: