Starting phenix.real_space_refine on Tue Apr 16 01:31:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wnr_21855/04_2024/6wnr_21855_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wnr_21855/04_2024/6wnr_21855.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/6wnr_21855/04_2024/6wnr_21855.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wnr_21855/04_2024/6wnr_21855.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wnr_21855/04_2024/6wnr_21855_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wnr_21855/04_2024/6wnr_21855_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 23468 2.51 5 N 6312 2.21 5 O 6953 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "W PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 26": "NH1" <-> "NH2" Residue "W ASP 29": "OD1" <-> "OD2" Residue "W GLU 41": "OE1" <-> "OE2" Residue "W GLU 45": "OE1" <-> "OE2" Residue "W PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 70": "OE1" <-> "OE2" Residue "W ARG 77": "NH1" <-> "NH2" Residue "W PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 103": "OE1" <-> "OE2" Residue "W ASP 156": "OD1" <-> "OD2" Residue "W ARG 164": "NH1" <-> "NH2" Residue "W GLU 168": "OE1" <-> "OE2" Residue "C PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C ARG 93": "NH1" <-> "NH2" Residue "C PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 161": "NH1" <-> "NH2" Residue "C ASP 170": "OD1" <-> "OD2" Residue "C ASP 181": "OD1" <-> "OD2" Residue "C TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 252": "NH1" <-> "NH2" Residue "C ASP 261": "OD1" <-> "OD2" Residue "C ASP 289": "OD1" <-> "OD2" Residue "C PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "C TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 356": "OE1" <-> "OE2" Residue "C PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 376": "NH1" <-> "NH2" Residue "C PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 422": "OD1" <-> "OD2" Residue "C PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B GLU 24": "OE1" <-> "OE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 284": "OE1" <-> "OE2" Residue "B PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 316": "OE1" <-> "OE2" Residue "B GLU 331": "OE1" <-> "OE2" Residue "B ASP 336": "OD1" <-> "OD2" Residue "B ASP 350": "OD1" <-> "OD2" Residue "B ARG 376": "NH1" <-> "NH2" Residue "B ASP 415": "OD1" <-> "OD2" Residue "B ARG 418": "NH1" <-> "NH2" Residue "B ASP 422": "OD1" <-> "OD2" Residue "B GLU 429": "OE1" <-> "OE2" Residue "B GLU 452": "OE1" <-> "OE2" Residue "B ARG 453": "NH1" <-> "NH2" Residue "B TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 460": "OE1" <-> "OE2" Residue "B TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 476": "OD1" <-> "OD2" Residue "B ARG 477": "NH1" <-> "NH2" Residue "B TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 494": "OD1" <-> "OD2" Residue "A GLU 10": "OE1" <-> "OE2" Residue "A ASP 69": "OD1" <-> "OD2" Residue "A ASP 116": "OD1" <-> "OD2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A ASP 170": "OD1" <-> "OD2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 262": "OD1" <-> "OD2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 336": "OD1" <-> "OD2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 422": "OD1" <-> "OD2" Residue "A PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 452": "OE1" <-> "OE2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 476": "OD1" <-> "OD2" Residue "A TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 494": "OD1" <-> "OD2" Residue "A PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 39": "OE1" <-> "OE2" Residue "X ASP 53": "OD1" <-> "OD2" Residue "X ASP 63": "OD1" <-> "OD2" Residue "X GLU 71": "OE1" <-> "OE2" Residue "X ARG 83": "NH1" <-> "NH2" Residue "X GLU 89": "OE1" <-> "OE2" Residue "X ARG 98": "NH1" <-> "NH2" Residue "X ARG 113": "NH1" <-> "NH2" Residue "X ARG 115": "NH1" <-> "NH2" Residue "X ARG 117": "NH1" <-> "NH2" Residue "X ARG 121": "NH1" <-> "NH2" Residue "X GLU 133": "OE1" <-> "OE2" Residue "X GLU 137": "OE1" <-> "OE2" Residue "X ASP 141": "OD1" <-> "OD2" Residue "H TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 29": "OE1" <-> "OE2" Residue "H ASP 81": "OD1" <-> "OD2" Residue "H GLU 96": "OE1" <-> "OE2" Residue "H GLU 102": "OE1" <-> "OE2" Residue "H ASP 111": "OD1" <-> "OD2" Residue "H ARG 129": "NH1" <-> "NH2" Residue "G TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 49": "NH1" <-> "NH2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G GLU 68": "OE1" <-> "OE2" Residue "G TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 84": "NH1" <-> "NH2" Residue "G GLU 101": "OE1" <-> "OE2" Residue "G PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 197": "OD1" <-> "OD2" Residue "G TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 210": "OD1" <-> "OD2" Residue "G ARG 221": "NH1" <-> "NH2" Residue "G GLU 233": "OE1" <-> "OE2" Residue "G GLU 275": "OE1" <-> "OE2" Residue "F ASP 20": "OD1" <-> "OD2" Residue "F GLU 36": "OE1" <-> "OE2" Residue "F GLU 76": "OE1" <-> "OE2" Residue "F TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 169": "OE1" <-> "OE2" Residue "F PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 200": "OD1" <-> "OD2" Residue "F ASP 242": "OD1" <-> "OD2" Residue "F TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 253": "OE1" <-> "OE2" Residue "F TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 280": "OE1" <-> "OE2" Residue "F TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 305": "OD1" <-> "OD2" Residue "F ASP 338": "OD1" <-> "OD2" Residue "F ASP 372": "OD1" <-> "OD2" Residue "F ASP 380": "OD1" <-> "OD2" Residue "F ASP 386": "OD1" <-> "OD2" Residue "F PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 422": "OD1" <-> "OD2" Residue "F TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 440": "OE1" <-> "OE2" Residue "F PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 454": "OE1" <-> "OE2" Residue "E GLU 36": "OE1" <-> "OE2" Residue "E ASP 60": "OD1" <-> "OD2" Residue "E ASP 134": "OD1" <-> "OD2" Residue "E ASP 188": "OD1" <-> "OD2" Residue "E ASP 195": "OD1" <-> "OD2" Residue "E ASP 242": "OD1" <-> "OD2" Residue "E GLU 273": "OE1" <-> "OE2" Residue "E ASP 301": "OD1" <-> "OD2" Residue "E ASP 305": "OD1" <-> "OD2" Residue "E ASP 338": "OD1" <-> "OD2" Residue "E ASP 345": "OD1" <-> "OD2" Residue "E ASP 355": "OD1" <-> "OD2" Residue "E ASP 372": "OD1" <-> "OD2" Residue "E ASP 380": "OD1" <-> "OD2" Residue "E GLU 384": "OE1" <-> "OE2" Residue "E TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 440": "OE1" <-> "OE2" Residue "E PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 104": "OE1" <-> "OE2" Residue "D GLU 118": "OE1" <-> "OE2" Residue "D ARG 164": "NH1" <-> "NH2" Residue "D TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 188": "OD1" <-> "OD2" Residue "D GLU 192": "OE1" <-> "OE2" Residue "D GLU 211": "OE1" <-> "OE2" Residue "D GLU 228": "OE1" <-> "OE2" Residue "D PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 233": "OE1" <-> "OE2" Residue "D ASP 242": "OD1" <-> "OD2" Residue "D GLU 273": "OE1" <-> "OE2" Residue "D GLU 280": "OE1" <-> "OE2" Residue "D ASP 301": "OD1" <-> "OD2" Residue "D ASP 316": "OD1" <-> "OD2" Residue "D ASP 345": "OD1" <-> "OD2" Residue "D ASP 355": "OD1" <-> "OD2" Residue "D ASP 372": "OD1" <-> "OD2" Residue "D ASP 380": "OD1" <-> "OD2" Residue "D GLU 384": "OE1" <-> "OE2" Residue "D GLU 385": "OE1" <-> "OE2" Residue "D PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 440": "OE1" <-> "OE2" Residue "I ASP 7": "OD1" <-> "OD2" Residue "I ARG 50": "NH1" <-> "NH2" Residue "J TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 37": "OE1" <-> "OE2" Residue "J ARG 50": "NH1" <-> "NH2" Residue "J ASP 61": "OD1" <-> "OD2" Residue "J TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 7": "OD1" <-> "OD2" Residue "L ASP 44": "OD1" <-> "OD2" Residue "L ARG 50": "NH1" <-> "NH2" 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 TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 7": "OD1" <-> "OD2" Residue "N TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 37": "OE1" <-> "OE2" Residue "N ASP 44": "OD1" <-> "OD2" Residue "N ARG 50": "NH1" <-> "NH2" Residue "N ASP 61": "OD1" <-> "OD2" Residue "N TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 7": "OD1" <-> "OD2" Residue "O TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 37": "OE1" <-> "OE2" Residue "O ARG 50": "NH1" <-> "NH2" Residue "O TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 7": "OD1" <-> "OD2" Residue "P TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 37": "OE1" <-> "OE2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "Q 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 "R TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 50": "NH1" <-> "NH2" Residue "Y GLU 39": "OE1" <-> "OE2" Residue "Y ASP 42": "OD1" <-> "OD2" Residue "Y GLU 48": "OE1" <-> "OE2" Residue "Y ARG 83": "NH1" <-> "NH2" Residue "Y ARG 98": "NH1" <-> "NH2" Residue "Y GLU 108": "OE1" <-> "OE2" Residue "Y ARG 113": "NH1" <-> "NH2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Y ARG 117": "NH1" <-> "NH2" Residue "Y ARG 121": "NH1" <-> "NH2" Residue "Y ARG 138": "NH1" <-> "NH2" Residue "Y ASP 150": "OD1" <-> "OD2" Residue "a PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 44": "OD1" <-> "OD2" Residue "a PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 80": "OE1" <-> "OE2" Residue "a PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 219": "OE1" <-> "OE2" Residue "a PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 269": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 36934 Number of models: 1 Model: "" Number of chains: 28 Chain: "W" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1317 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3869 Classifications: {'peptide': 512} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Chain: "B" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3869 Classifications: {'peptide': 512} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Chain: "A" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3869 Classifications: {'peptide': 512} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Chain: "X" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1179 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 150} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1034 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "G" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2186 Classifications: {'peptide': 284} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 274} Chain: "F" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "E" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "D" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "I" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "J" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "L" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "M" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "N" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "O" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 554 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Q" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "R" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "S" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Y" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1157 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 150} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "a" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2104 Classifications: {'peptide': 266} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 250} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 18.65, per 1000 atoms: 0.50 Number of scatterers: 36934 At special positions: 0 Unit cell: (181.272, 214.721, 131.638, 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 6953 8.00 N 6312 7.00 C 23468 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: 12.97 Conformation dependent library (CDL) restraints added in 6.6 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: 178 helices and 26 sheets defined 55.5% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.05 Creating SS restraints... Processing helix chain 'W' and resid 4 through 18 Proline residue: W 9 - end of helix Processing helix chain 'W' and resid 24 through 39 removed outlier: 3.661A pdb=" N ASP W 29 " --> pdb=" O GLU W 25 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS W 39 " --> pdb=" O ALA W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 41 through 48 removed outlier: 3.581A pdb=" N SER W 48 " --> pdb=" O ALA W 44 " (cutoff:3.500A) Processing helix chain 'W' and resid 53 through 61 Processing helix chain 'W' and resid 72 through 81 removed outlier: 4.583A pdb=" N ARG W 77 " --> pdb=" O GLN W 73 " (cutoff:3.500A) Processing helix chain 'W' and resid 85 through 102 Proline residue: W 89 - end of helix removed outlier: 3.917A pdb=" N LEU W 92 " --> pdb=" O PRO W 89 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN W 94 " --> pdb=" O VAL W 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 120 through 131 Processing helix chain 'W' and resid 144 through 146 No H-bonds generated for 'chain 'W' and resid 144 through 146' Processing helix chain 'W' and resid 163 through 173 Processing helix chain 'C' and resid 9 through 17 Processing helix chain 'C' and resid 21 through 23 No H-bonds generated for 'chain 'C' and resid 21 through 23' Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 175 through 186 Processing helix chain 'C' and resid 202 through 214 Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 232 through 251 Proline residue: C 239 - end of helix removed outlier: 3.569A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 276 removed outlier: 3.579A 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 298 removed outlier: 4.234A pdb=" N PHE C 291 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG C 296 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 312 Processing helix chain 'C' and resid 333 through 335 No H-bonds generated for 'chain 'C' and resid 333 through 335' Processing helix chain 'C' and resid 340 through 346 Processing helix chain 'C' and resid 357 through 362 Processing helix chain 'C' and resid 378 through 381 Processing helix chain 'C' and resid 384 through 390 Processing helix chain 'C' and resid 393 through 406 Processing helix chain 'C' and resid 417 through 431 Processing helix chain 'C' and resid 441 through 452 Processing helix chain 'C' and resid 464 through 477 removed outlier: 3.550A pdb=" N ALA C 473 " --> pdb=" O ALA C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 489 removed outlier: 3.772A pdb=" N ILE C 486 " --> pdb=" O MET C 483 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN C 487 " --> pdb=" O GLN C 484 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR C 489 " --> pdb=" O ILE C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 510 Processing helix chain 'B' and resid 5 through 18 Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 186 Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 232 through 236 Processing helix chain 'B' and resid 238 through 252 removed outlier: 3.931A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 277 removed outlier: 3.508A pdb=" N LEU B 277 " --> pdb=" O ILE B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 300 removed outlier: 4.543A pdb=" N PHE B 291 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER B 295 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG B 296 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLU B 299 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 312 Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 378 through 380 No H-bonds generated for 'chain 'B' and resid 378 through 380' Processing helix chain 'B' and resid 384 through 389 Processing helix chain 'B' and resid 393 through 409 removed outlier: 3.947A pdb=" N GLN B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N PHE B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 430 removed outlier: 3.642A pdb=" N GLN B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 452 Processing helix chain 'B' and resid 464 through 478 Processing helix chain 'B' and resid 480 through 489 Processing helix chain 'B' and resid 494 through 510 Processing helix chain 'A' and resid 5 through 19 Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 151 through 156 removed outlier: 3.824A pdb=" N MET A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 186 removed outlier: 3.954A pdb=" N GLN A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 232 through 252 Proline residue: A 239 - end of helix removed outlier: 3.651A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 276 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: 4.450A pdb=" N PHE A 291 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER A 295 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG A 296 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLU A 299 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 Processing helix chain 'A' and resid 340 through 348 Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 384 through 412 removed outlier: 4.145A pdb=" N GLY A 391 " --> pdb=" O LYS A 387 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLY A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N PHE A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLN A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N PHE A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N SER A 411 " --> pdb=" O SER A 407 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ASP A 412 " --> pdb=" O GLN A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 431 removed outlier: 3.651A pdb=" N GLN A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A 426 " --> pdb=" O ASP A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 452 Processing helix chain 'A' and resid 455 through 458 removed outlier: 3.926A pdb=" N ASP A 458 " --> pdb=" O TYR A 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 455 through 458' Processing helix chain 'A' and resid 461 through 478 removed outlier: 4.154A pdb=" N GLY A 465 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU A 468 " --> pdb=" O GLY A 465 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU A 472 " --> pdb=" O ALA A 469 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 475 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP A 478 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 489 removed outlier: 3.656A pdb=" N GLN A 488 " --> pdb=" O GLN A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 510 Processing helix chain 'X' and resid 5 through 24 removed outlier: 3.726A pdb=" N GLN X 10 " --> pdb=" O ILE X 7 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU X 16 " --> pdb=" O ALA X 13 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE X 20 " --> pdb=" O PHE X 17 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS X 23 " --> pdb=" O PHE X 20 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR X 24 " --> pdb=" O ALA X 21 " (cutoff:3.500A) Processing helix chain 'X' and resid 26 through 133 removed outlier: 3.630A pdb=" N ILE X 75 " --> pdb=" O GLU X 71 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU X 118 " --> pdb=" O LYS X 114 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU X 119 " --> pdb=" O ARG X 115 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS X 122 " --> pdb=" O GLU X 118 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE X 126 " --> pdb=" O LYS X 122 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL X 129 " --> pdb=" O ALA X 125 " (cutoff:3.500A) Processing helix chain 'X' and resid 145 through 152 Processing helix chain 'H' and resid 87 through 102 removed outlier: 3.575A pdb=" N ALA H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 125 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 57 removed outlier: 3.918A pdb=" N ARG G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA G 39 " --> pdb=" O GLN G 35 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER G 41 " --> pdb=" O ARG G 37 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Proline residue: G 43 - end of helix Processing helix chain 'G' and resid 65 through 67 No H-bonds generated for 'chain 'G' and resid 65 through 67' Processing helix chain 'G' and resid 90 through 107 Processing helix chain 'G' and resid 119 through 128 Processing helix chain 'G' and resid 145 through 160 removed outlier: 5.490A 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 197 through 202 removed outlier: 4.195A pdb=" N SER G 202 " --> pdb=" O LYS G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 282 removed outlier: 3.654A pdb=" N LYS G 258 " --> pdb=" O GLY G 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 83 No H-bonds generated for 'chain 'F' and resid 81 through 83' Processing helix chain 'F' and resid 116 through 118 No H-bonds generated for 'chain 'F' and resid 116 through 118' Processing helix chain 'F' and resid 131 through 136 Processing helix chain 'F' and resid 155 through 167 Processing helix chain 'F' and resid 183 through 196 Processing helix chain 'F' and resid 199 through 201 No H-bonds generated for 'chain 'F' and resid 199 through 201' Processing helix chain 'F' and resid 213 through 232 removed outlier: 4.412A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET F 226 " --> pdb=" O THR F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 255 removed outlier: 3.537A pdb=" N VAL F 254 " --> pdb=" O GLY F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 281 removed outlier: 3.644A pdb=" N LEU F 278 " --> pdb=" O GLU F 274 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG F 281 " --> pdb=" O VAL F 277 " (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: 4.393A pdb=" N ALA F 313 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N HIS F 314 " --> pdb=" O THR F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 327 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 376 removed outlier: 4.361A pdb=" N ASP F 372 " --> pdb=" O GLN F 368 " (cutoff:3.500A) removed outlier: 4.859A 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 Processing helix chain 'F' and resid 420 through 431 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: 3.606A pdb=" N GLU F 454 " --> pdb=" O GLU F 450 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS F 457 " --> pdb=" O VAL F 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 49 No H-bonds generated for 'chain 'E' and resid 47 through 49' Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 116 through 118 No H-bonds generated for 'chain 'E' and resid 116 through 118' Processing helix chain 'E' and resid 131 through 136 Processing helix chain 'E' and resid 155 through 168 removed outlier: 3.572A pdb=" N ALA E 167 " --> pdb=" O ILE E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 196 removed outlier: 3.549A pdb=" N SER E 196 " --> pdb=" O GLU E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 201 No H-bonds generated for 'chain 'E' and resid 199 through 201' Processing helix chain 'E' and resid 213 through 232 removed outlier: 5.137A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 258 Processing helix chain 'E' and resid 271 through 279 removed outlier: 3.581A 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: 3.890A pdb=" N GLU E 369 " --> pdb=" O GLN E 365 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE E 376 " --> pdb=" O ASP E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 381 No H-bonds generated for 'chain 'E' and resid 379 through 381' Processing helix chain 'E' and resid 386 through 399 removed outlier: 3.708A pdb=" N LYS E 395 " --> pdb=" O ALA E 391 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG E 398 " --> pdb=" O ARG E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 411 No H-bonds generated for 'chain 'E' and resid 408 through 411' Processing helix chain 'E' and resid 420 through 431 Processing helix chain 'E' and resid 440 through 442 No H-bonds generated for 'chain 'E' and resid 440 through 442' Processing helix chain 'E' and resid 449 through 458 Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 131 through 136 Processing helix chain 'D' and resid 155 through 168 Processing helix chain 'D' and resid 183 through 195 Processing helix chain 'D' and resid 198 through 201 Processing helix chain 'D' and resid 213 through 232 removed outlier: 3.888A pdb=" N VAL D 219 " --> pdb=" O ASN D 215 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 257 Processing helix chain 'D' and resid 271 through 279 Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 306 through 311 Processing helix chain 'D' and resid 323 through 327 Processing helix chain 'D' and resid 346 through 349 No H-bonds generated for 'chain 'D' and resid 346 through 349' Processing helix chain 'D' and resid 351 through 377 removed outlier: 4.747A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 381 No H-bonds generated for 'chain 'D' and resid 379 through 381' Processing helix chain 'D' and resid 386 through 399 removed outlier: 3.846A pdb=" N ALA D 391 " --> pdb=" O LYS D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 411 removed outlier: 3.974A pdb=" N VAL D 409 " --> pdb=" O VAL D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 431 Processing helix chain 'D' and resid 449 through 458 Processing helix chain 'I' and resid 4 through 7 No H-bonds generated for 'chain 'I' and resid 4 through 7' Processing helix chain 'I' and resid 9 through 41 Processing helix chain 'I' and resid 43 through 76 removed outlier: 3.827A pdb=" N ILE I 46 " --> pdb=" O PRO I 43 " (cutoff:3.500A) Proline residue: I 47 - end of helix removed outlier: 3.505A pdb=" N PHE I 53 " --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL I 56 " --> pdb=" O PHE I 53 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY I 58 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE I 63 " --> pdb=" O VAL I 60 " (cutoff:3.500A) Proline residue: I 64 - end of helix removed outlier: 3.611A pdb=" N VAL I 68 " --> pdb=" O MET I 65 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU I 70 " --> pdb=" O ALA I 67 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL I 74 " --> pdb=" O GLY I 71 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE I 76 " --> pdb=" O TYR I 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 41 Processing helix chain 'J' and resid 43 through 76 Proline residue: J 47 - end of helix removed outlier: 4.010A pdb=" N PHE J 54 " --> pdb=" O THR J 51 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY J 58 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP J 61 " --> pdb=" O GLY J 58 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE J 63 " --> pdb=" O VAL J 60 " (cutoff:3.500A) Proline residue: J 64 - end of helix removed outlier: 3.561A pdb=" N LEU J 70 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE J 76 " --> pdb=" O TYR J 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 41 removed outlier: 3.922A pdb=" N LEU L 9 " --> pdb=" O ASN L 5 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TYR L 10 " --> pdb=" O MET L 6 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET L 11 " --> pdb=" O ASP L 7 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 76 Proline residue: L 47 - end of helix removed outlier: 3.604A pdb=" N ASP L 61 " --> pdb=" O GLY L 58 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE L 63 " --> pdb=" O VAL L 60 " (cutoff:3.500A) Proline residue: L 64 - end of helix removed outlier: 3.559A pdb=" N VAL L 68 " --> pdb=" O MET L 65 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU L 70 " --> pdb=" O ALA L 67 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU L 72 " --> pdb=" O GLY L 69 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE L 76 " --> pdb=" O TYR L 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 41 removed outlier: 3.624A pdb=" N LEU M 8 " --> pdb=" O LEU M 4 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS M 34 " --> pdb=" O ILE M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 76 Proline residue: M 47 - end of helix removed outlier: 3.575A pdb=" N VAL M 56 " --> pdb=" O PHE M 53 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY M 58 " --> pdb=" O ILE M 55 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP M 61 " --> pdb=" O GLY M 58 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE M 63 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Proline residue: M 64 - end of helix removed outlier: 3.510A pdb=" N VAL M 74 " --> pdb=" O GLY M 71 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE M 76 " --> pdb=" O TYR M 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 41 removed outlier: 3.744A pdb=" N LEU N 9 " --> pdb=" O ASN N 5 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N TYR N 10 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N MET N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 76 Proline residue: N 47 - end of helix removed outlier: 3.622A pdb=" N MET N 57 " --> pdb=" O PHE N 54 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE N 63 " --> pdb=" O VAL N 60 " (cutoff:3.500A) Proline residue: N 64 - end of helix removed outlier: 3.516A pdb=" N VAL N 68 " --> pdb=" O MET N 65 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU N 70 " --> pdb=" O ALA N 67 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE N 76 " --> pdb=" O TYR N 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 41 removed outlier: 4.489A pdb=" N LEU O 8 " --> pdb=" O ASN O 5 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET O 17 " --> pdb=" O ALA O 14 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA O 24 " --> pdb=" O ALA O 21 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE O 26 " --> pdb=" O GLY O 23 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE O 28 " --> pdb=" O ALA O 25 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY O 32 " --> pdb=" O GLY O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 60 Proline residue: O 47 - end of helix removed outlier: 3.780A pdb=" N GLY O 58 " --> pdb=" O ILE O 55 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL O 60 " --> pdb=" O MET O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 76 Processing helix chain 'P' and resid 6 through 41 Processing helix chain 'P' and resid 46 through 76 removed outlier: 3.820A pdb=" N GLN P 52 " --> pdb=" O LEU P 48 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) Proline residue: P 64 - end of helix Processing helix chain 'Q' and resid 4 through 41 removed outlier: 3.865A pdb=" N LEU Q 9 " --> pdb=" O ASN Q 5 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR Q 10 " --> pdb=" O MET Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 76 Proline residue: Q 47 - end of helix removed outlier: 3.625A pdb=" N MET Q 57 " --> pdb=" O PHE Q 54 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP Q 61 " --> pdb=" O GLY Q 58 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA Q 62 " --> pdb=" O LEU Q 59 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE Q 63 " --> pdb=" O VAL Q 60 " (cutoff:3.500A) Proline residue: Q 64 - end of helix removed outlier: 3.673A pdb=" N PHE Q 76 " --> pdb=" O TYR Q 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 39 Processing helix chain 'R' and resid 43 through 76 Proline residue: R 47 - end of helix removed outlier: 3.689A pdb=" N ASP R 61 " --> pdb=" O GLY R 58 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE R 63 " --> pdb=" O VAL R 60 " (cutoff:3.500A) Proline residue: R 64 - end of helix removed outlier: 3.895A pdb=" N PHE R 76 " --> pdb=" O TYR R 73 " (cutoff:3.500A) Processing helix chain 'S' and resid 7 through 41 removed outlier: 4.011A pdb=" N MET S 11 " --> pdb=" O ASP S 7 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 60 Proline residue: S 47 - end of helix removed outlier: 3.616A pdb=" N ARG S 50 " --> pdb=" O PRO S 47 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET S 57 " --> pdb=" O PHE S 54 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 76 Processing helix chain 'Y' and resid 3 through 138 removed outlier: 3.623A pdb=" N TRP Y 26 " --> pdb=" O MET Y 22 " (cutoff:3.500A) Proline residue: Y 27 - end of helix removed outlier: 3.606A pdb=" N LYS Y 52 " --> pdb=" O GLU Y 48 " (cutoff:3.500A) Processing helix chain 'Y' and resid 142 through 152 Processing helix chain 'a' and resid 8 through 16 Processing helix chain 'a' and resid 43 through 66 Processing helix chain 'a' and resid 74 through 93 Processing helix chain 'a' and resid 100 through 120 removed outlier: 4.052A pdb=" N ASP a 119 " --> pdb=" O MET a 115 " (cutoff:3.500A) removed outlier: 4.273A 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: 3.794A pdb=" N LYS a 169 " --> pdb=" O SER a 165 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ILE a 171 " --> pdb=" O LYS a 167 " (cutoff:3.500A) removed outlier: 9.654A pdb=" N GLY a 172 " --> pdb=" O MET a 168 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY a 173 " --> pdb=" O LYS a 169 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 228 Proline residue: a 190 - end of helix removed outlier: 3.594A pdb=" N ILE a 194 " --> pdb=" O PRO a 190 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 3.713A pdb=" N LEU a 211 " --> pdb=" O LEU a 207 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN a 214 " --> pdb=" O ARG a 210 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE a 222 " --> pdb=" O GLY a 218 " (cutoff:3.500A) Processing helix chain 'a' and resid 231 through 268 removed outlier: 3.922A pdb=" N TRP a 235 " --> pdb=" O TRP a 231 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ILE a 236 " --> pdb=" O TRP a 232 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU a 237 " --> pdb=" O SER a 233 " (cutoff:3.500A) Proline residue: a 240 - end of helix removed outlier: 3.779A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'W' and resid 139 through 142 removed outlier: 4.216A pdb=" N MET W 157 " --> pdb=" O ALA W 154 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.649A pdb=" N ARG C 40 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL C 34 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 96 through 99 Processing sheet with id= D, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.842A pdb=" N LEU C 166 " --> pdb=" O GLY C 351 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 323 through 326 removed outlier: 6.478A pdb=" N LYS C 192 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ILE C 259 " --> pdb=" O LYS C 192 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE C 194 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.481A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N MET B 76 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ALA B 61 " --> pdb=" O MET B 76 " (cutoff:3.500A) removed outlier: 3.991A 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: 8.195A pdb=" N VAL B 108 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VAL B 223 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N VAL B 224 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N SER B 323 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ILE B 258 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N THR B 325 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 7.525A 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: 6.749A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.910A 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: 6.448A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 96 through 98 Processing sheet with id= L, first strand: chain 'A' and resid 107 through 109 removed outlier: 6.170A pdb=" N VAL A 223 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N SER A 323 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ILE A 258 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N THR A 325 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N TYR A 260 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU A 327 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 351 through 355 Processing sheet with id= N, first strand: chain 'H' and resid 5 through 10 removed outlier: 3.713A pdb=" N GLY H 67 " --> pdb=" O ILE H 45 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 30 through 35 removed outlier: 7.417A pdb=" N VAL H 53 " --> pdb=" O GLU H 21 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ILE H 23 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ARG H 51 " --> pdb=" O ILE H 23 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N VAL H 25 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 8.794A 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: 6.801A pdb=" N LEU G 167 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS G 166 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ASN G 172 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLN G 111 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N TYR G 77 " --> pdb=" O GLN G 111 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASP G 113 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL G 79 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA G 115 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N MET G 116 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLN G 135 " --> pdb=" O MET G 116 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 4 through 9 removed outlier: 6.566A pdb=" N ASP F 14 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE F 54 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N VAL F 42 " --> pdb=" O ILE F 54 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 76 through 78 Processing sheet with id= S, first strand: chain 'F' and resid 317 through 320 removed outlier: 7.851A pdb=" N VAL F 145 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N SER F 292 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU F 147 " --> pdb=" O SER F 292 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLN F 294 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N GLY F 149 " --> pdb=" O GLN F 294 " (cutoff:3.500A) removed outlier: 6.264A 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: 6.519A pdb=" N ASP E 14 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL E 8 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL E 12 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ILE E 54 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N VAL E 42 " --> pdb=" O ILE E 54 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU E 36 " --> pdb=" O ASN E 33 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 76 through 78 Processing sheet with id= V, first strand: chain 'E' and resid 317 through 319 removed outlier: 8.677A pdb=" N VAL E 145 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N SER E 292 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU E 147 " --> pdb=" O SER E 292 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLN E 294 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TYR E 173 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N PHE E 240 " --> pdb=" O TYR E 173 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL E 175 " --> pdb=" O PHE E 240 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 4 through 9 removed outlier: 6.421A pdb=" N ASP D 14 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL D 8 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE D 54 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL D 42 " --> pdb=" O ILE D 54 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU D 36 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASP D 27 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N HIS D 73 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLU D 30 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU D 71 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N GLN D 32 " --> pdb=" O LYS D 69 " (cutoff:3.500A) removed outlier: 9.594A pdb=" N LYS D 69 " --> pdb=" O GLN D 32 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 76 through 78 Processing sheet with id= Y, first strand: chain 'D' and resid 317 through 320 removed outlier: 8.753A pdb=" N VAL D 145 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N SER D 292 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N LEU D 147 " --> pdb=" O SER D 292 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLN D 294 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N GLY D 149 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL D 296 " --> pdb=" O GLY D 149 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'a' and resid 20 through 22 2022 hydrogen bonds defined for protein. 5253 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.23 Time building geometry restraints manager: 14.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7576 1.33 - 1.45: 7761 1.45 - 1.57: 21772 1.57 - 1.69: 25 1.69 - 1.81: 360 Bond restraints: 37494 Sorted by residual: bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.48e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.28e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.13e+01 bond pdb=" C5 ATP C 600 " pdb=" C6 ATP C 600 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.70e+01 bond pdb=" C5 ATP B 600 " pdb=" C6 ATP B 600 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.68e+01 ... (remaining 37489 not shown) Histogram of bond angle deviations from ideal: 98.22 - 105.81: 898 105.81 - 113.40: 20641 113.40 - 120.98: 18700 120.98 - 128.57: 10351 128.57 - 136.16: 170 Bond angle restraints: 50760 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 139.87 119.72 20.15 1.00e+00 1.00e+00 4.06e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 122.80 17.07 1.00e+00 1.00e+00 2.91e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 122.94 16.93 1.00e+00 1.00e+00 2.86e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 122.66 14.17 1.00e+00 1.00e+00 2.01e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 122.72 14.11 1.00e+00 1.00e+00 1.99e+02 ... (remaining 50755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.31: 22280 35.31 - 70.61: 419 70.61 - 105.92: 51 105.92 - 141.23: 3 141.23 - 176.53: 1 Dihedral angle restraints: 22754 sinusoidal: 8970 harmonic: 13784 Sorted by residual: dihedral pdb=" O1B ADP F 500 " pdb=" O3A ADP F 500 " pdb=" PB ADP F 500 " pdb=" PA ADP F 500 " ideal model delta sinusoidal sigma weight residual -60.00 116.53 -176.53 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PA ADP E 500 " pdb=" PB ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 71.63 -131.63 1 2.00e+01 2.50e-03 3.99e+01 dihedral pdb=" O2A ADP F 500 " pdb=" O3A ADP F 500 " pdb=" PA ADP F 500 " pdb=" PB ADP F 500 " ideal model delta sinusoidal sigma weight residual -60.00 63.82 -123.82 1 2.00e+01 2.50e-03 3.74e+01 ... (remaining 22751 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 5261 0.087 - 0.173: 603 0.173 - 0.260: 45 0.260 - 0.346: 4 0.346 - 0.433: 6 Chirality restraints: 5919 Sorted by residual: chirality pdb=" CB ILE P 63 " pdb=" CA ILE P 63 " pdb=" CG1 ILE P 63 " pdb=" CG2 ILE P 63 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" CA TYR X 24 " pdb=" N TYR X 24 " pdb=" C TYR X 24 " pdb=" CB TYR X 24 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.17e+00 chirality pdb=" CA PHE S 76 " pdb=" N PHE S 76 " pdb=" C PHE S 76 " pdb=" CB PHE S 76 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.08e+00 ... (remaining 5916 not shown) Planarity restraints: 6543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG P 41 " -0.146 9.50e-02 1.11e+02 8.11e-02 3.12e+01 pdb=" NE ARG P 41 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG P 41 " -0.091 2.00e-02 2.50e+03 pdb=" NH1 ARG P 41 " 0.032 2.00e-02 2.50e+03 pdb=" NH2 ARG P 41 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE J 46 " -0.024 2.00e-02 2.50e+03 4.62e-02 2.13e+01 pdb=" C ILE J 46 " 0.080 2.00e-02 2.50e+03 pdb=" O ILE J 46 " -0.028 2.00e-02 2.50e+03 pdb=" N PRO J 47 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 139 " -0.122 9.50e-02 1.11e+02 6.68e-02 2.01e+01 pdb=" NE ARG C 139 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG C 139 " -0.073 2.00e-02 2.50e+03 pdb=" NH1 ARG C 139 " 0.026 2.00e-02 2.50e+03 pdb=" NH2 ARG C 139 " 0.020 2.00e-02 2.50e+03 ... (remaining 6540 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 53 2.48 - 3.08: 26307 3.08 - 3.69: 55036 3.69 - 4.29: 82216 4.29 - 4.90: 138007 Nonbonded interactions: 301619 Sorted by model distance: nonbonded pdb=" O1G ATP C 600 " pdb="MG MG C 601 " model vdw 1.869 2.170 nonbonded pdb=" O2B ATP C 600 " pdb="MG MG C 601 " model vdw 1.883 2.170 nonbonded pdb=" O3G ATP B 600 " pdb="MG MG B 601 " model vdw 1.884 2.170 nonbonded pdb=" O2B ATP B 600 " pdb="MG MG B 601 " model vdw 1.896 2.170 nonbonded pdb=" O2G ATP A 600 " pdb="MG MG A 601 " model vdw 1.943 2.170 ... (remaining 301614 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 0 through 459 or resid 500)) selection = chain 'E' selection = (chain 'F' and (resid 0 through 459 or resid 500)) } ncs_group { reference = (chain 'I' and (resid 3 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 79)) selection = (chain 'J' and (resid 3 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 79)) selection = (chain 'L' and (resid 3 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 79)) selection = (chain 'M' and (resid 3 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 79)) selection = (chain 'N' and (resid 3 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 79)) selection = chain 'O' selection = (chain 'P' and (resid 3 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 79)) selection = (chain 'Q' and (resid 3 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 79)) selection = (chain 'R' and (resid 3 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 79)) selection = (chain 'S' and (resid 3 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 79)) } ncs_group { reference = (chain 'X' and (resid 1 through 54 or (resid 55 and (name N or name CA or name C \ or name O or name CB )) or resid 56 through 57 or (resid 58 through 59 and (nam \ e N or name CA or name C or name O or name CB )) or resid 60 through 62 or (resi \ d 63 and (name N or name CA or name C or name O or name CB )) or resid 64 throug \ h 65 or (resid 66 through 70 and (name N or name CA or name C or name O or name \ CB )) or resid 71 through 72 or (resid 73 and (name N or name CA or name C or na \ me O or name CB )) or resid 74 through 76 or (resid 77 and (name N or name CA or \ name C or name O or name CB )) or resid 78 through 153)) selection = (chain 'Y' and (resid 1 through 90 or (resid 91 through 92 and (name N or name C \ A or name C or name O or name CB )) or resid 93 through 153)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 11.150 Check model and map are aligned: 0.540 Set scattering table: 0.340 Process input model: 90.580 Find NCS groups from input model: 2.300 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 37494 Z= 0.325 Angle : 0.960 20.147 50760 Z= 0.614 Chirality : 0.056 0.433 5919 Planarity : 0.008 0.123 6543 Dihedral : 14.569 176.532 13936 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.81 % Favored : 97.17 % Rotamer: Outliers : 1.44 % Allowed : 5.86 % Favored : 92.71 % 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: -1.29 (0.11), residues: 4807 helix: -0.48 (0.09), residues: 2611 sheet: -0.65 (0.21), residues: 502 loop : -1.30 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP a 186 HIS 0.009 0.002 HIS C 423 PHE 0.039 0.003 PHE A 19 TYR 0.040 0.005 TYR N 10 ARG 0.093 0.007 ARG P 41 *********************** 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 961 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 906 time to evaluate : 4.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 76 ILE cc_start: 0.9216 (mm) cc_final: 0.9003 (mm) REVERT: W 151 ILE cc_start: 0.9163 (mm) cc_final: 0.8920 (mm) REVERT: C 484 GLN cc_start: 0.8273 (tm-30) cc_final: 0.8069 (mp10) REVERT: B 236 TYR cc_start: 0.8890 (OUTLIER) cc_final: 0.7715 (t80) REVERT: B 359 LEU cc_start: 0.9304 (mp) cc_final: 0.9090 (mt) REVERT: B 386 MET cc_start: 0.8736 (mmm) cc_final: 0.8388 (mmt) REVERT: B 422 ASP cc_start: 0.8466 (t0) cc_final: 0.8086 (t0) REVERT: X 22 MET cc_start: 0.8284 (ttm) cc_final: 0.7938 (ttp) REVERT: X 42 ASP cc_start: 0.8344 (m-30) cc_final: 0.8079 (m-30) REVERT: X 83 ARG cc_start: 0.8915 (ttt-90) cc_final: 0.8629 (ttm-80) REVERT: X 145 ASN cc_start: 0.7287 (m110) cc_final: 0.6794 (p0) REVERT: H 13 GLN cc_start: 0.8956 (pm20) cc_final: 0.8661 (pp30) REVERT: H 31 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7482 (tt0) REVERT: H 118 SER cc_start: 0.9241 (t) cc_final: 0.8904 (p) REVERT: G 177 THR cc_start: 0.9162 (OUTLIER) cc_final: 0.8952 (t) REVERT: G 200 HIS cc_start: 0.6964 (m170) cc_final: 0.6745 (m170) REVERT: G 206 LEU cc_start: 0.8812 (mt) cc_final: 0.8609 (mp) REVERT: F 228 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7649 (mt-10) REVERT: E 325 ILE cc_start: 0.8989 (mm) cc_final: 0.8445 (mm) REVERT: D 428 LYS cc_start: 0.8415 (tttt) cc_final: 0.7276 (ttpp) REVERT: D 445 MET cc_start: 0.8445 (mmt) cc_final: 0.8183 (mmm) REVERT: D 457 LYS cc_start: 0.7919 (ttpp) cc_final: 0.7654 (ttpp) REVERT: I 6 MET cc_start: 0.5741 (mtm) cc_final: 0.5248 (mmm) REVERT: I 73 TYR cc_start: 0.7933 (OUTLIER) cc_final: 0.7571 (t80) REVERT: I 75 MET cc_start: 0.8429 (ttp) cc_final: 0.8149 (tmm) REVERT: J 11 MET cc_start: 0.7451 (tpp) cc_final: 0.6692 (tmm) REVERT: J 51 THR cc_start: 0.8794 (m) cc_final: 0.8455 (p) REVERT: L 10 TYR cc_start: 0.8106 (m-80) cc_final: 0.7658 (m-10) REVERT: L 11 MET cc_start: 0.8074 (tpt) cc_final: 0.7575 (mmt) REVERT: M 42 GLN cc_start: 0.7952 (pt0) cc_final: 0.7658 (pt0) REVERT: M 55 ILE cc_start: 0.8553 (mm) cc_final: 0.8307 (mt) REVERT: N 42 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7161 (mt0) REVERT: N 68 VAL cc_start: 0.8975 (p) cc_final: 0.8554 (m) REVERT: N 76 PHE cc_start: 0.7856 (m-80) cc_final: 0.7590 (t80) REVERT: O 46 ILE cc_start: 0.9075 (pt) cc_final: 0.8727 (mt) REVERT: P 6 MET cc_start: 0.6316 (mmt) cc_final: 0.5666 (ptp) REVERT: P 73 TYR cc_start: 0.8578 (t80) cc_final: 0.8346 (t80) REVERT: P 78 VAL cc_start: 0.6734 (t) cc_final: 0.6139 (t) REVERT: Q 6 MET cc_start: 0.6491 (mtp) cc_final: 0.5437 (ppp) REVERT: Q 7 ASP cc_start: 0.6286 (t70) cc_final: 0.5744 (t0) REVERT: Q 17 MET cc_start: 0.7032 (mtm) cc_final: 0.6787 (mtt) REVERT: R 10 TYR cc_start: 0.8669 (m-80) cc_final: 0.8222 (m-80) REVERT: R 26 ILE cc_start: 0.9437 (mm) cc_final: 0.9108 (mt) REVERT: R 37 GLU cc_start: 0.8129 (pp20) cc_final: 0.7087 (tm-30) REVERT: R 57 MET cc_start: 0.8395 (ttp) cc_final: 0.7924 (ttp) REVERT: S 11 MET cc_start: 0.8670 (tpp) cc_final: 0.8360 (tpt) REVERT: S 76 PHE cc_start: 0.7681 (m-80) cc_final: 0.6951 (m-80) REVERT: Y 22 MET cc_start: 0.5786 (mmt) cc_final: 0.5177 (mmt) REVERT: Y 35 LYS cc_start: 0.8693 (tttt) cc_final: 0.8343 (ttmm) REVERT: Y 51 HIS cc_start: 0.7395 (m170) cc_final: 0.7127 (m90) REVERT: a 63 VAL cc_start: 0.6445 (t) cc_final: 0.6195 (p) REVERT: a 168 MET cc_start: 0.8479 (mmt) cc_final: 0.8224 (mmm) REVERT: a 203 LYS cc_start: 0.8896 (mttp) cc_final: 0.8689 (mtpt) REVERT: a 215 MET cc_start: 0.8490 (mmp) cc_final: 0.8253 (mmm) outliers start: 55 outliers final: 22 residues processed: 949 average time/residue: 0.5406 time to fit residues: 804.1759 Evaluate side-chains 590 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 565 time to evaluate : 4.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 168 GLU Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain I residue 73 TYR Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 44 ASP Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain a residue 149 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 401 optimal weight: 0.9990 chunk 360 optimal weight: 6.9990 chunk 199 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 242 optimal weight: 0.9990 chunk 192 optimal weight: 1.9990 chunk 372 optimal weight: 9.9990 chunk 144 optimal weight: 4.9990 chunk 226 optimal weight: 0.5980 chunk 277 optimal weight: 2.9990 chunk 431 optimal weight: 0.0020 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 82 ASN W 86 ASN W 94 GLN ** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 GLN B 147 GLN B 435 GLN B 493 ASN A 58 ASN A 294 HIS A 333 GLN A 344 ASN A 425 GLN H 14 GLN H 116 GLN ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 ASN G 252 ASN G 265 ASN G 269 GLN F 365 GLN E 351 GLN E 441 GLN D 19 GLN D 279 GLN J 42 GLN R 52 GLN ** S 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 GLN a 15 HIS a 245 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37494 Z= 0.196 Angle : 0.616 11.061 50760 Z= 0.320 Chirality : 0.043 0.255 5919 Planarity : 0.005 0.059 6543 Dihedral : 7.786 161.727 5381 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.67 % Allowed : 11.58 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: 0.23 (0.12), residues: 4807 helix: 0.91 (0.10), residues: 2600 sheet: -0.38 (0.22), residues: 514 loop : -0.75 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP a 186 HIS 0.005 0.001 HIS F 353 PHE 0.023 0.001 PHE L 53 TYR 0.019 0.001 TYR a 11 ARG 0.020 0.001 ARG M 41 *********************** 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 709 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 607 time to evaluate : 4.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 484 GLN cc_start: 0.8362 (tm-30) cc_final: 0.8008 (mp10) REVERT: B 386 MET cc_start: 0.8676 (mmm) cc_final: 0.8373 (mmt) REVERT: B 422 ASP cc_start: 0.8392 (t0) cc_final: 0.7902 (t0) REVERT: X 14 PHE cc_start: 0.6870 (t80) cc_final: 0.6658 (t80) REVERT: X 49 ARG cc_start: 0.8362 (tpp-160) cc_final: 0.7974 (ptp-170) REVERT: X 66 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8694 (pttm) REVERT: X 73 GLN cc_start: 0.8264 (tp40) cc_final: 0.7994 (mm110) REVERT: X 85 GLN cc_start: 0.8611 (tp-100) cc_final: 0.8407 (tp-100) REVERT: X 145 ASN cc_start: 0.7313 (m110) cc_final: 0.6367 (t0) REVERT: H 13 GLN cc_start: 0.9017 (pm20) cc_final: 0.8583 (pp30) REVERT: G 148 LEU cc_start: 0.9325 (mt) cc_final: 0.9094 (mm) REVERT: G 200 HIS cc_start: 0.7040 (m170) cc_final: 0.6813 (m170) REVERT: G 206 LEU cc_start: 0.8948 (mt) cc_final: 0.8695 (mp) REVERT: F 228 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7604 (mt-10) REVERT: E 428 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8466 (mtmt) REVERT: D 366 ARG cc_start: 0.8763 (tpt170) cc_final: 0.8558 (tpm170) REVERT: D 386 ASP cc_start: 0.7764 (m-30) cc_final: 0.7122 (m-30) REVERT: D 445 MET cc_start: 0.8590 (mmt) cc_final: 0.8297 (mmm) REVERT: D 457 LYS cc_start: 0.7825 (ttpp) cc_final: 0.7558 (ttpp) REVERT: I 6 MET cc_start: 0.5710 (mtm) cc_final: 0.5301 (mmm) REVERT: I 73 TYR cc_start: 0.7947 (OUTLIER) cc_final: 0.7440 (t80) REVERT: J 11 MET cc_start: 0.7370 (tpp) cc_final: 0.6716 (tmm) REVERT: J 42 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.7815 (mt0) REVERT: L 6 MET cc_start: 0.5766 (ptp) cc_final: 0.5215 (mpp) REVERT: L 17 MET cc_start: 0.8815 (mmm) cc_final: 0.8587 (mmp) REVERT: M 42 GLN cc_start: 0.7863 (pt0) cc_final: 0.7517 (pm20) REVERT: M 55 ILE cc_start: 0.8585 (mm) cc_final: 0.8261 (mt) REVERT: N 42 GLN cc_start: 0.7638 (mm-40) cc_final: 0.6963 (mt0) REVERT: P 65 MET cc_start: 0.7184 (mmm) cc_final: 0.6872 (mmt) REVERT: P 73 TYR cc_start: 0.8537 (t80) cc_final: 0.8297 (t80) REVERT: Q 6 MET cc_start: 0.5525 (mtp) cc_final: 0.5239 (ptt) REVERT: Q 10 TYR cc_start: 0.5789 (m-80) cc_final: 0.5176 (m-80) REVERT: R 11 MET cc_start: 0.6802 (OUTLIER) cc_final: 0.6075 (tpt) REVERT: S 8 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7730 (tt) REVERT: S 11 MET cc_start: 0.8563 (tpp) cc_final: 0.8258 (mmt) REVERT: S 76 PHE cc_start: 0.7813 (m-80) cc_final: 0.6850 (m-80) REVERT: Y 22 MET cc_start: 0.5886 (mmt) cc_final: 0.5249 (mmt) REVERT: Y 98 ARG cc_start: 0.8693 (tmm-80) cc_final: 0.8153 (tpt170) REVERT: a 11 TYR cc_start: 0.8094 (t80) cc_final: 0.7781 (t80) REVERT: a 117 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8922 (mm) REVERT: a 177 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7035 (mm-30) REVERT: a 257 MET cc_start: 0.8895 (tmm) cc_final: 0.8633 (tmm) outliers start: 102 outliers final: 45 residues processed: 674 average time/residue: 0.5149 time to fit residues: 560.2789 Evaluate side-chains 579 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 527 time to evaluate : 3.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain W residue 139 ASN Chi-restraints excluded: chain C residue 26 HIS Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain X residue 2 ASN Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 66 LYS Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 428 LYS Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain I residue 73 TYR Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 44 ASP Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 11 MET Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain Y residue 18 VAL Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 129 VAL Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 201 LEU Chi-restraints excluded: chain a residue 246 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 239 optimal weight: 0.0470 chunk 133 optimal weight: 0.0040 chunk 359 optimal weight: 0.0060 chunk 293 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 432 optimal weight: 1.9990 chunk 466 optimal weight: 7.9990 chunk 384 optimal weight: 10.0000 chunk 428 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 346 optimal weight: 8.9990 overall best weight: 1.2110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 67 GLN W 86 ASN W 94 GLN C 479 HIS C 511 GLN B 26 HIS A 425 GLN A 511 GLN X 104 GLN H 116 GLN G 126 ASN F 324 GLN I 42 GLN M 3 ASN R 52 GLN ** S 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 116 ASN a 181 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37494 Z= 0.189 Angle : 0.567 8.635 50760 Z= 0.292 Chirality : 0.041 0.162 5919 Planarity : 0.004 0.053 6543 Dihedral : 7.019 129.643 5358 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.43 % Allowed : 12.89 % Favored : 84.68 % 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: 0.57 (0.12), residues: 4807 helix: 1.17 (0.10), residues: 2666 sheet: -0.25 (0.22), residues: 532 loop : -0.63 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP a 235 HIS 0.005 0.001 HIS B 26 PHE 0.021 0.001 PHE Y 20 TYR 0.033 0.001 TYR a 11 ARG 0.008 0.000 ARG C 453 *********************** 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 651 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 558 time to evaluate : 4.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 28 GLN cc_start: 0.8532 (tt0) cc_final: 0.8021 (tt0) REVERT: C 225 VAL cc_start: 0.9350 (OUTLIER) cc_final: 0.9143 (m) REVERT: C 484 GLN cc_start: 0.8496 (tm-30) cc_final: 0.7943 (mp10) REVERT: B 236 TYR cc_start: 0.8931 (OUTLIER) cc_final: 0.7609 (t80) REVERT: B 386 MET cc_start: 0.8715 (mmm) cc_final: 0.8347 (mmt) REVERT: B 422 ASP cc_start: 0.8527 (t0) cc_final: 0.7918 (t0) REVERT: X 49 ARG cc_start: 0.8347 (tpp-160) cc_final: 0.7925 (ptp-170) REVERT: X 66 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8622 (pttm) REVERT: X 73 GLN cc_start: 0.8349 (tp40) cc_final: 0.8059 (mm110) REVERT: X 78 GLN cc_start: 0.8310 (pp30) cc_final: 0.8095 (pp30) REVERT: X 145 ASN cc_start: 0.7354 (m110) cc_final: 0.6336 (t0) REVERT: H 22 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8552 (pttp) REVERT: H 51 ARG cc_start: 0.8605 (ttt-90) cc_final: 0.8399 (ttt90) REVERT: H 54 LYS cc_start: 0.8498 (ttpt) cc_final: 0.8087 (mtmm) REVERT: H 116 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8063 (tm130) REVERT: G 148 LEU cc_start: 0.9377 (mt) cc_final: 0.9090 (mm) REVERT: G 200 HIS cc_start: 0.7068 (m170) cc_final: 0.6814 (m170) REVERT: F 228 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7630 (mt-10) REVERT: E 428 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8493 (mtmt) REVERT: I 6 MET cc_start: 0.5717 (mtm) cc_final: 0.5256 (mmm) REVERT: J 11 MET cc_start: 0.7445 (tpp) cc_final: 0.6687 (tmm) REVERT: J 16 MET cc_start: 0.7339 (ttt) cc_final: 0.7107 (tpp) REVERT: J 42 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.7876 (mt0) REVERT: J 61 ASP cc_start: 0.7799 (p0) cc_final: 0.7592 (p0) REVERT: L 35 PHE cc_start: 0.7635 (t80) cc_final: 0.7380 (t80) REVERT: M 17 MET cc_start: 0.7625 (mmm) cc_final: 0.7240 (mmm) REVERT: M 42 GLN cc_start: 0.8017 (pt0) cc_final: 0.7764 (pt0) REVERT: M 55 ILE cc_start: 0.8609 (mm) cc_final: 0.8241 (mt) REVERT: N 42 GLN cc_start: 0.7565 (mm-40) cc_final: 0.7129 (mp10) REVERT: N 73 TYR cc_start: 0.6057 (t80) cc_final: 0.5437 (m-80) REVERT: P 6 MET cc_start: 0.4483 (mpp) cc_final: 0.3693 (mtp) REVERT: P 73 TYR cc_start: 0.8556 (t80) cc_final: 0.8254 (t80) REVERT: Q 6 MET cc_start: 0.5427 (mtp) cc_final: 0.5171 (ppp) REVERT: Q 10 TYR cc_start: 0.5436 (m-80) cc_final: 0.5152 (m-80) REVERT: R 11 MET cc_start: 0.6887 (OUTLIER) cc_final: 0.6084 (tpt) REVERT: S 75 MET cc_start: 0.9094 (tmm) cc_final: 0.8693 (tmm) REVERT: S 76 PHE cc_start: 0.8004 (m-80) cc_final: 0.7128 (m-80) REVERT: Y 22 MET cc_start: 0.5878 (mmt) cc_final: 0.5241 (mmt) REVERT: Y 51 HIS cc_start: 0.7282 (m90) cc_final: 0.6929 (m90) REVERT: Y 98 ARG cc_start: 0.8700 (tmm-80) cc_final: 0.8132 (tpp80) REVERT: a 16 LEU cc_start: 0.8287 (mt) cc_final: 0.8064 (pp) REVERT: a 65 LYS cc_start: 0.4523 (mttt) cc_final: 0.4050 (mmtp) REVERT: a 76 GLN cc_start: 0.7827 (tm-30) cc_final: 0.7594 (tm-30) REVERT: a 117 LEU cc_start: 0.9133 (mm) cc_final: 0.8925 (mm) REVERT: a 177 GLU cc_start: 0.7391 (mt-10) cc_final: 0.6993 (mm-30) REVERT: a 234 GLN cc_start: 0.7576 (mp10) cc_final: 0.7236 (mp10) outliers start: 93 outliers final: 57 residues processed: 617 average time/residue: 0.5577 time to fit residues: 561.2584 Evaluate side-chains 578 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 513 time to evaluate : 4.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain C residue 26 HIS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 434 LYS Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 511 GLN Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 66 LYS Chi-restraints excluded: chain X residue 148 ILE Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 116 GLN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 428 LYS Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 44 ASP Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain R residue 11 MET Chi-restraints excluded: chain R residue 16 MET Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 15 VAL Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain Y residue 18 VAL Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 63 VAL Chi-restraints excluded: chain a residue 181 GLN Chi-restraints excluded: chain a residue 201 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 426 optimal weight: 0.8980 chunk 324 optimal weight: 8.9990 chunk 224 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 206 optimal weight: 1.9990 chunk 290 optimal weight: 8.9990 chunk 433 optimal weight: 5.9990 chunk 459 optimal weight: 2.9990 chunk 226 optimal weight: 7.9990 chunk 411 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 120 GLN W 139 ASN C 172 GLN B 484 GLN A 358 ASN A 511 GLN H 24 GLN ** M 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 GLN ** S 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 37494 Z= 0.296 Angle : 0.595 8.404 50760 Z= 0.305 Chirality : 0.042 0.171 5919 Planarity : 0.004 0.050 6543 Dihedral : 6.784 125.103 5355 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.85 % Allowed : 13.73 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.12), residues: 4807 helix: 1.26 (0.10), residues: 2661 sheet: -0.20 (0.21), residues: 543 loop : -0.65 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP a 235 HIS 0.004 0.001 HIS A 215 PHE 0.031 0.001 PHE Y 20 TYR 0.014 0.001 TYR G 44 ARG 0.007 0.000 ARG C 453 *********************** 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 641 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 532 time to evaluate : 4.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 123 LYS cc_start: 0.8379 (mtpp) cc_final: 0.8170 (mttt) REVERT: C 225 VAL cc_start: 0.9463 (OUTLIER) cc_final: 0.9247 (m) REVERT: C 321 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8177 (t) REVERT: C 484 GLN cc_start: 0.8496 (tm-30) cc_final: 0.8130 (mp10) REVERT: B 236 TYR cc_start: 0.9024 (OUTLIER) cc_final: 0.7776 (t80) REVERT: B 386 MET cc_start: 0.8847 (mmm) cc_final: 0.8387 (mmt) REVERT: B 422 ASP cc_start: 0.8580 (t0) cc_final: 0.7968 (t0) REVERT: X 22 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7503 (ttp) REVERT: X 66 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8597 (pttm) REVERT: X 73 GLN cc_start: 0.8411 (tp40) cc_final: 0.8153 (mm110) REVERT: X 145 ASN cc_start: 0.7048 (m110) cc_final: 0.6120 (t0) REVERT: H 51 ARG cc_start: 0.8685 (ttt-90) cc_final: 0.8458 (ttt90) REVERT: H 116 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8694 (tp40) REVERT: G 178 MET cc_start: 0.7834 (pmm) cc_final: 0.7448 (pmm) REVERT: G 200 HIS cc_start: 0.7143 (m170) cc_final: 0.6866 (m170) REVERT: F 228 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7747 (mt-10) REVERT: E 428 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8446 (mtmt) REVERT: D 56 MET cc_start: 0.8987 (mmm) cc_final: 0.8727 (mmm) REVERT: D 301 ASP cc_start: 0.8046 (t0) cc_final: 0.7803 (t0) REVERT: I 6 MET cc_start: 0.5817 (mtm) cc_final: 0.5328 (mmm) REVERT: J 11 MET cc_start: 0.7349 (tpp) cc_final: 0.6632 (tmm) REVERT: J 16 MET cc_start: 0.7413 (ttt) cc_final: 0.7142 (tpp) REVERT: J 61 ASP cc_start: 0.7866 (p0) cc_final: 0.7640 (p0) REVERT: L 28 ILE cc_start: 0.9038 (mm) cc_final: 0.8644 (mt) REVERT: L 35 PHE cc_start: 0.7701 (t80) cc_final: 0.7390 (t80) REVERT: M 17 MET cc_start: 0.7636 (mmm) cc_final: 0.7201 (mmm) REVERT: M 42 GLN cc_start: 0.7949 (pt0) cc_final: 0.7498 (pm20) REVERT: M 55 ILE cc_start: 0.8780 (mm) cc_final: 0.8392 (mt) REVERT: N 34 LYS cc_start: 0.8617 (mmmm) cc_final: 0.8363 (mmmm) REVERT: N 37 GLU cc_start: 0.8617 (tt0) cc_final: 0.8278 (tt0) REVERT: N 42 GLN cc_start: 0.7753 (mm-40) cc_final: 0.7375 (mp10) REVERT: N 73 TYR cc_start: 0.6275 (t80) cc_final: 0.5693 (m-80) REVERT: O 46 ILE cc_start: 0.8898 (pt) cc_final: 0.8647 (mt) REVERT: P 6 MET cc_start: 0.4410 (mpp) cc_final: 0.3593 (mtp) REVERT: P 73 TYR cc_start: 0.8545 (t80) cc_final: 0.8273 (t80) REVERT: Q 6 MET cc_start: 0.5399 (mtp) cc_final: 0.5107 (ppp) REVERT: Q 10 TYR cc_start: 0.5325 (m-80) cc_final: 0.4891 (m-80) REVERT: Q 11 MET cc_start: 0.5271 (tpp) cc_final: 0.4150 (tmm) REVERT: S 75 MET cc_start: 0.9019 (tmm) cc_final: 0.8627 (tmm) REVERT: S 76 PHE cc_start: 0.7947 (m-80) cc_final: 0.7430 (m-80) REVERT: Y 22 MET cc_start: 0.5852 (mmt) cc_final: 0.5625 (mmt) REVERT: Y 51 HIS cc_start: 0.7186 (m90) cc_final: 0.6876 (m90) REVERT: Y 83 ARG cc_start: 0.7878 (ttp80) cc_final: 0.7661 (ttp80) REVERT: Y 98 ARG cc_start: 0.8702 (tmm-80) cc_final: 0.8149 (tpp80) REVERT: Y 104 GLN cc_start: 0.8670 (tt0) cc_final: 0.8435 (pt0) REVERT: a 16 LEU cc_start: 0.8265 (mt) cc_final: 0.8013 (pp) REVERT: a 39 TRP cc_start: 0.7294 (m100) cc_final: 0.7035 (m100) REVERT: a 177 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6815 (mm-30) REVERT: a 196 GLU cc_start: 0.7348 (tp30) cc_final: 0.7085 (tp30) REVERT: a 234 GLN cc_start: 0.7459 (mt0) cc_final: 0.7155 (mp10) outliers start: 109 outliers final: 68 residues processed: 606 average time/residue: 0.5166 time to fit residues: 505.0581 Evaluate side-chains 577 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 502 time to evaluate : 4.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain C residue 26 HIS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 434 LYS Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain X residue 2 ASN Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 66 LYS Chi-restraints excluded: chain X residue 148 ILE Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 116 GLN Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 428 LYS Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 44 ASP Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 44 ASP Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 57 MET Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain Y residue 18 VAL Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain a residue 63 VAL Chi-restraints excluded: chain a residue 201 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 382 optimal weight: 0.7980 chunk 260 optimal weight: 0.0010 chunk 6 optimal weight: 5.9990 chunk 341 optimal weight: 0.6980 chunk 189 optimal weight: 2.9990 chunk 391 optimal weight: 5.9990 chunk 317 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 234 optimal weight: 6.9990 chunk 412 optimal weight: 8.9990 chunk 115 optimal weight: 6.9990 overall best weight: 2.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 358 ASN A 511 GLN H 14 GLN H 24 GLN D 243 ASN ** M 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 GLN Y 123 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 37494 Z= 0.249 Angle : 0.568 8.274 50760 Z= 0.290 Chirality : 0.041 0.150 5919 Planarity : 0.004 0.046 6543 Dihedral : 6.471 124.937 5352 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.82 % Allowed : 14.48 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.12), residues: 4807 helix: 1.36 (0.10), residues: 2657 sheet: -0.15 (0.22), residues: 542 loop : -0.62 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP a 235 HIS 0.004 0.001 HIS a 15 PHE 0.025 0.001 PHE Y 20 TYR 0.016 0.001 TYR C 474 ARG 0.009 0.000 ARG C 453 *********************** 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 637 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 529 time to evaluate : 4.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 119 GLN cc_start: 0.8166 (tp-100) cc_final: 0.7352 (tp-100) REVERT: W 123 LYS cc_start: 0.8393 (mtpp) cc_final: 0.8064 (mttm) REVERT: C 225 VAL cc_start: 0.9465 (OUTLIER) cc_final: 0.9263 (m) REVERT: C 321 THR cc_start: 0.8479 (OUTLIER) cc_final: 0.8135 (t) REVERT: C 484 GLN cc_start: 0.8541 (tm-30) cc_final: 0.8324 (mp10) REVERT: B 236 TYR cc_start: 0.9058 (OUTLIER) cc_final: 0.7818 (t80) REVERT: B 386 MET cc_start: 0.8884 (mmm) cc_final: 0.8489 (mmt) REVERT: B 422 ASP cc_start: 0.8498 (t0) cc_final: 0.7925 (t0) REVERT: X 2 ASN cc_start: 0.7693 (OUTLIER) cc_final: 0.7162 (p0) REVERT: X 22 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7567 (ttp) REVERT: X 66 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8589 (pttm) REVERT: X 73 GLN cc_start: 0.8457 (tp40) cc_final: 0.7977 (mm110) REVERT: X 119 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7704 (tp30) REVERT: X 145 ASN cc_start: 0.7043 (m110) cc_final: 0.6137 (t0) REVERT: H 116 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8739 (tp40) REVERT: G 178 MET cc_start: 0.7925 (pmm) cc_final: 0.7519 (pmm) REVERT: G 200 HIS cc_start: 0.7191 (m170) cc_final: 0.6861 (m170) REVERT: F 228 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7744 (mt-10) REVERT: E 428 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8339 (mtmt) REVERT: D 56 MET cc_start: 0.9011 (mmm) cc_final: 0.8754 (mmm) REVERT: I 6 MET cc_start: 0.6003 (mtm) cc_final: 0.5463 (mmm) REVERT: J 11 MET cc_start: 0.7245 (tpp) cc_final: 0.6796 (tmm) REVERT: J 16 MET cc_start: 0.7388 (ttt) cc_final: 0.7072 (tpp) REVERT: J 42 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8594 (mt0) REVERT: L 11 MET cc_start: 0.7237 (mpp) cc_final: 0.5747 (tpp) REVERT: L 28 ILE cc_start: 0.9057 (mm) cc_final: 0.8608 (mt) REVERT: L 35 PHE cc_start: 0.7509 (t80) cc_final: 0.7181 (t80) REVERT: M 17 MET cc_start: 0.7678 (mmm) cc_final: 0.7273 (mmm) REVERT: M 42 GLN cc_start: 0.7852 (pt0) cc_final: 0.7472 (pm20) REVERT: M 55 ILE cc_start: 0.8783 (mm) cc_final: 0.8379 (mt) REVERT: N 37 GLU cc_start: 0.8647 (tt0) cc_final: 0.8276 (tt0) REVERT: N 42 GLN cc_start: 0.7727 (mm-40) cc_final: 0.7381 (mp10) REVERT: N 73 TYR cc_start: 0.6357 (t80) cc_final: 0.5796 (m-80) REVERT: O 46 ILE cc_start: 0.8936 (pt) cc_final: 0.8695 (mt) REVERT: P 6 MET cc_start: 0.4357 (mpp) cc_final: 0.3592 (mtp) REVERT: P 17 MET cc_start: 0.7402 (mtt) cc_final: 0.7142 (tpt) REVERT: P 73 TYR cc_start: 0.8486 (t80) cc_final: 0.8261 (t80) REVERT: Q 6 MET cc_start: 0.5303 (mtp) cc_final: 0.4865 (ptt) REVERT: Q 10 TYR cc_start: 0.5060 (m-80) cc_final: 0.4637 (m-80) REVERT: Q 75 MET cc_start: 0.6654 (ttt) cc_final: 0.6415 (ttt) REVERT: S 75 MET cc_start: 0.9016 (tmm) cc_final: 0.8531 (tmm) REVERT: S 76 PHE cc_start: 0.7934 (m-80) cc_final: 0.7373 (m-80) REVERT: Y 22 MET cc_start: 0.5879 (mmt) cc_final: 0.5223 (mmt) REVERT: Y 51 HIS cc_start: 0.7205 (m90) cc_final: 0.6836 (m90) REVERT: Y 98 ARG cc_start: 0.8726 (tmm-80) cc_final: 0.8299 (tpt170) REVERT: a 16 LEU cc_start: 0.8242 (mt) cc_final: 0.8042 (pp) REVERT: a 168 MET cc_start: 0.8614 (mmm) cc_final: 0.8353 (mmt) REVERT: a 177 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6837 (mm-30) REVERT: a 193 LEU cc_start: 0.7181 (mt) cc_final: 0.6966 (mt) REVERT: a 234 GLN cc_start: 0.7472 (mt0) cc_final: 0.7192 (mp10) outliers start: 108 outliers final: 72 residues processed: 599 average time/residue: 0.5141 time to fit residues: 498.2451 Evaluate side-chains 586 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 504 time to evaluate : 4.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain W residue 160 ASP Chi-restraints excluded: chain C residue 26 HIS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 434 LYS Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 511 GLN Chi-restraints excluded: chain X residue 2 ASN Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 66 LYS Chi-restraints excluded: chain X residue 119 GLU Chi-restraints excluded: chain X residue 148 ILE Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 116 GLN Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 428 LYS Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 44 ASP Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 44 ASP Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 57 MET Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain R residue 16 MET Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 15 VAL Chi-restraints excluded: chain S residue 17 MET Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 63 VAL Chi-restraints excluded: chain a residue 201 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 154 optimal weight: 1.9990 chunk 413 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 269 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 459 optimal weight: 0.9980 chunk 381 optimal weight: 7.9990 chunk 212 optimal weight: 0.6980 chunk 38 optimal weight: 0.0570 chunk 152 optimal weight: 3.9990 chunk 241 optimal weight: 0.6980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 139 ASN C 479 HIS A 511 GLN H 14 GLN H 24 GLN H 116 GLN D 243 ASN ** M 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 GLN ** Y 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 116 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 37494 Z= 0.157 Angle : 0.544 9.960 50760 Z= 0.276 Chirality : 0.040 0.161 5919 Planarity : 0.004 0.048 6543 Dihedral : 6.136 121.888 5352 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.27 % Allowed : 15.40 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.12), residues: 4807 helix: 1.47 (0.10), residues: 2660 sheet: -0.09 (0.21), residues: 550 loop : -0.54 (0.15), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP a 235 HIS 0.004 0.000 HIS C 479 PHE 0.027 0.001 PHE Y 20 TYR 0.013 0.001 TYR C 400 ARG 0.008 0.000 ARG Y 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 543 time to evaluate : 4.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 12 LYS cc_start: 0.9262 (tttp) cc_final: 0.8685 (ttmm) REVERT: W 119 GLN cc_start: 0.8111 (tp-100) cc_final: 0.7322 (tp-100) REVERT: W 123 LYS cc_start: 0.8339 (mtpp) cc_final: 0.8036 (mttm) REVERT: C 321 THR cc_start: 0.8371 (OUTLIER) cc_final: 0.8019 (t) REVERT: C 484 GLN cc_start: 0.8537 (tm-30) cc_final: 0.8155 (mp10) REVERT: C 488 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8173 (mp10) REVERT: B 236 TYR cc_start: 0.8987 (OUTLIER) cc_final: 0.7787 (t80) REVERT: B 386 MET cc_start: 0.8852 (mmm) cc_final: 0.8492 (mmt) REVERT: B 399 GLN cc_start: 0.8384 (mm-40) cc_final: 0.8172 (mm-40) REVERT: B 422 ASP cc_start: 0.8431 (t0) cc_final: 0.7863 (t0) REVERT: X 2 ASN cc_start: 0.7914 (OUTLIER) cc_final: 0.7296 (p0) REVERT: X 22 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.7535 (ttp) REVERT: X 73 GLN cc_start: 0.8372 (tp40) cc_final: 0.7922 (mm110) REVERT: X 119 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7750 (tp30) REVERT: X 145 ASN cc_start: 0.7037 (m110) cc_final: 0.6074 (t0) REVERT: G 178 MET cc_start: 0.7914 (pmm) cc_final: 0.7560 (pmm) REVERT: G 200 HIS cc_start: 0.7152 (m170) cc_final: 0.6816 (m170) REVERT: F 228 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7695 (mt-10) REVERT: E 249 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8890 (tp) REVERT: E 428 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8301 (mtmt) REVERT: D 56 MET cc_start: 0.8842 (mmm) cc_final: 0.8635 (mmm) REVERT: I 6 MET cc_start: 0.6002 (mtm) cc_final: 0.5479 (mmm) REVERT: I 52 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7559 (mm-40) REVERT: J 11 MET cc_start: 0.7259 (tpp) cc_final: 0.6827 (tmm) REVERT: J 42 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8543 (mt0) REVERT: J 73 TYR cc_start: 0.6274 (t80) cc_final: 0.4580 (m-80) REVERT: L 11 MET cc_start: 0.7276 (mpp) cc_final: 0.5981 (tpp) REVERT: L 28 ILE cc_start: 0.8977 (mm) cc_final: 0.8543 (mt) REVERT: L 35 PHE cc_start: 0.7419 (t80) cc_final: 0.7115 (t80) REVERT: M 17 MET cc_start: 0.7673 (mmm) cc_final: 0.7328 (mmm) REVERT: M 42 GLN cc_start: 0.7845 (pt0) cc_final: 0.7448 (pm20) REVERT: M 55 ILE cc_start: 0.8791 (mm) cc_final: 0.8376 (mt) REVERT: N 17 MET cc_start: 0.7149 (mmm) cc_final: 0.6725 (mmp) REVERT: N 37 GLU cc_start: 0.8569 (tt0) cc_final: 0.8193 (tt0) REVERT: N 42 GLN cc_start: 0.7663 (mm-40) cc_final: 0.7283 (mp10) REVERT: N 73 TYR cc_start: 0.6356 (t80) cc_final: 0.5802 (m-80) REVERT: O 46 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8649 (mt) REVERT: P 6 MET cc_start: 0.4288 (mpp) cc_final: 0.3492 (mtp) REVERT: P 17 MET cc_start: 0.7340 (mtt) cc_final: 0.7125 (tpt) REVERT: Q 6 MET cc_start: 0.5329 (mtp) cc_final: 0.4882 (ptt) REVERT: Q 10 TYR cc_start: 0.5022 (m-80) cc_final: 0.4731 (m-80) REVERT: S 5 ASN cc_start: 0.2760 (m110) cc_final: 0.2336 (t0) REVERT: S 75 MET cc_start: 0.8996 (tmm) cc_final: 0.8490 (tmm) REVERT: S 76 PHE cc_start: 0.7854 (m-80) cc_final: 0.7286 (m-80) REVERT: Y 1 MET cc_start: 0.2515 (OUTLIER) cc_final: 0.2121 (mpp) REVERT: Y 22 MET cc_start: 0.5669 (mmt) cc_final: 0.5063 (mmt) REVERT: Y 51 HIS cc_start: 0.7247 (m90) cc_final: 0.6916 (m-70) REVERT: Y 98 ARG cc_start: 0.8689 (tmm-80) cc_final: 0.8332 (tpt170) REVERT: a 168 MET cc_start: 0.8570 (mmm) cc_final: 0.8284 (mmt) REVERT: a 177 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6735 (mm-30) REVERT: a 234 GLN cc_start: 0.7435 (mt0) cc_final: 0.7138 (mp10) outliers start: 87 outliers final: 55 residues processed: 603 average time/residue: 0.5183 time to fit residues: 504.1428 Evaluate side-chains 579 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 513 time to evaluate : 4.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain C residue 26 HIS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 434 LYS Chi-restraints excluded: chain C residue 488 GLN Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain X residue 2 ASN Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 119 GLU Chi-restraints excluded: chain X residue 148 ILE Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 428 LYS Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 44 ASP Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 44 ASP Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain S residue 17 MET Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 63 VAL Chi-restraints excluded: chain a residue 169 LYS Chi-restraints excluded: chain a residue 201 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 443 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 261 optimal weight: 4.9990 chunk 335 optimal weight: 0.8980 chunk 260 optimal weight: 2.9990 chunk 386 optimal weight: 2.9990 chunk 256 optimal weight: 4.9990 chunk 457 optimal weight: 3.9990 chunk 286 optimal weight: 6.9990 chunk 279 optimal weight: 3.9990 chunk 211 optimal weight: 0.2980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 GLN D 243 ASN ** M 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 104 GLN Y 123 GLN a 252 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37494 Z= 0.220 Angle : 0.573 11.709 50760 Z= 0.289 Chirality : 0.041 0.181 5919 Planarity : 0.004 0.043 6543 Dihedral : 6.024 121.260 5352 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.04 % Allowed : 16.08 % Favored : 81.88 % 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: 0.96 (0.12), residues: 4807 helix: 1.50 (0.10), residues: 2657 sheet: -0.00 (0.22), residues: 545 loop : -0.50 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP a 235 HIS 0.004 0.001 HIS C 479 PHE 0.028 0.001 PHE Y 20 TYR 0.037 0.001 TYR C 474 ARG 0.007 0.000 ARG Y 115 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 526 time to evaluate : 4.260 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: C 321 THR cc_start: 0.8447 (OUTLIER) cc_final: 0.8102 (t) REVERT: C 484 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8357 (mp10) REVERT: B 236 TYR cc_start: 0.9018 (OUTLIER) cc_final: 0.7838 (t80) REVERT: B 386 MET cc_start: 0.8878 (mmm) cc_final: 0.8548 (mmt) REVERT: X 2 ASN cc_start: 0.8140 (OUTLIER) cc_final: 0.7542 (p0) REVERT: X 73 GLN cc_start: 0.8404 (tp40) cc_final: 0.7947 (mm110) REVERT: X 119 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7592 (tp30) REVERT: X 145 ASN cc_start: 0.7134 (m110) cc_final: 0.6137 (t0) REVERT: G 178 MET cc_start: 0.7960 (pmm) cc_final: 0.7606 (pmm) REVERT: G 200 HIS cc_start: 0.7194 (m170) cc_final: 0.6841 (m170) REVERT: F 228 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7761 (mt-10) REVERT: E 249 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8890 (tp) REVERT: E 428 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8256 (mtmt) REVERT: D 56 MET cc_start: 0.8946 (mmm) cc_final: 0.8740 (mmm) REVERT: I 6 MET cc_start: 0.6053 (mtm) cc_final: 0.5518 (mmm) REVERT: J 11 MET cc_start: 0.7201 (tpp) cc_final: 0.6665 (tmm) REVERT: J 42 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8464 (mt0) REVERT: J 73 TYR cc_start: 0.6272 (t80) cc_final: 0.4715 (m-80) REVERT: L 11 MET cc_start: 0.7139 (mpp) cc_final: 0.5801 (tpp) REVERT: L 28 ILE cc_start: 0.8946 (mm) cc_final: 0.8522 (mt) REVERT: L 35 PHE cc_start: 0.7507 (t80) cc_final: 0.7071 (t80) REVERT: M 17 MET cc_start: 0.7745 (mmm) cc_final: 0.7533 (mmm) REVERT: M 42 GLN cc_start: 0.7884 (pt0) cc_final: 0.7486 (pm20) REVERT: M 55 ILE cc_start: 0.8771 (mm) cc_final: 0.8336 (mt) REVERT: N 37 GLU cc_start: 0.8583 (tt0) cc_final: 0.8215 (tt0) REVERT: N 42 GLN cc_start: 0.7738 (mm-40) cc_final: 0.7413 (mp10) REVERT: N 73 TYR cc_start: 0.6383 (t80) cc_final: 0.5870 (m-80) REVERT: O 7 ASP cc_start: 0.5498 (p0) cc_final: 0.4970 (p0) REVERT: O 46 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8653 (mt) REVERT: P 6 MET cc_start: 0.4277 (mpp) cc_final: 0.3504 (mtp) REVERT: Q 6 MET cc_start: 0.5373 (mtp) cc_final: 0.4911 (ptt) REVERT: Q 10 TYR cc_start: 0.4974 (m-80) cc_final: 0.4692 (m-80) REVERT: S 16 MET cc_start: 0.8412 (mtm) cc_final: 0.8139 (mtp) REVERT: S 75 MET cc_start: 0.8998 (tmm) cc_final: 0.8595 (tmm) REVERT: S 76 PHE cc_start: 0.7880 (m-80) cc_final: 0.7501 (m-80) REVERT: Y 22 MET cc_start: 0.5732 (mmt) cc_final: 0.5100 (mmt) REVERT: Y 51 HIS cc_start: 0.7298 (m90) cc_final: 0.6961 (m-70) REVERT: Y 104 GLN cc_start: 0.8532 (pt0) cc_final: 0.8088 (pm20) REVERT: a 117 LEU cc_start: 0.9012 (mm) cc_final: 0.8810 (mm) REVERT: a 177 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6610 (mm-30) REVERT: a 234 GLN cc_start: 0.7329 (mt0) cc_final: 0.7049 (mp10) outliers start: 78 outliers final: 57 residues processed: 578 average time/residue: 0.5313 time to fit residues: 500.3781 Evaluate side-chains 572 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 507 time to evaluate : 4.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain W residue 160 ASP Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 434 LYS Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain X residue 2 ASN Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 119 GLU Chi-restraints excluded: chain X residue 148 ILE Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 428 LYS Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 44 ASP Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 16 MET Chi-restraints excluded: chain S residue 15 VAL Chi-restraints excluded: chain S residue 17 MET Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 63 VAL Chi-restraints excluded: chain a residue 169 LYS Chi-restraints excluded: chain a residue 201 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 283 optimal weight: 0.8980 chunk 182 optimal weight: 10.0000 chunk 273 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 291 optimal weight: 1.9990 chunk 311 optimal weight: 8.9990 chunk 226 optimal weight: 0.0040 chunk 42 optimal weight: 4.9990 chunk 359 optimal weight: 5.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 GLN H 24 GLN H 56 HIS D 7 GLN D 243 ASN ** M 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 GLN S 5 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37494 Z= 0.170 Angle : 0.572 11.780 50760 Z= 0.285 Chirality : 0.040 0.169 5919 Planarity : 0.004 0.047 6543 Dihedral : 5.734 118.696 5348 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.96 % Allowed : 16.65 % Favored : 81.39 % 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: 1.02 (0.12), residues: 4807 helix: 1.53 (0.10), residues: 2668 sheet: 0.05 (0.22), residues: 550 loop : -0.46 (0.15), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP a 235 HIS 0.004 0.000 HIS C 479 PHE 0.028 0.001 PHE Y 20 TYR 0.028 0.001 TYR C 474 ARG 0.008 0.000 ARG Q 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 534 time to evaluate : 4.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 12 LYS cc_start: 0.9225 (tttp) cc_final: 0.8665 (ttmm) REVERT: C 321 THR cc_start: 0.8382 (OUTLIER) cc_final: 0.8037 (t) REVERT: C 484 GLN cc_start: 0.8560 (tm-30) cc_final: 0.8111 (mp10) REVERT: B 236 TYR cc_start: 0.8984 (OUTLIER) cc_final: 0.7819 (t80) REVERT: B 386 MET cc_start: 0.8866 (mmm) cc_final: 0.8540 (mmt) REVERT: A 463 LYS cc_start: 0.9281 (mtmt) cc_final: 0.8984 (mtmm) REVERT: X 2 ASN cc_start: 0.8023 (OUTLIER) cc_final: 0.7443 (p0) REVERT: X 73 GLN cc_start: 0.8410 (tp40) cc_final: 0.7955 (mm110) REVERT: X 119 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7510 (tp30) REVERT: X 145 ASN cc_start: 0.6895 (m110) cc_final: 0.5870 (t0) REVERT: G 178 MET cc_start: 0.7987 (pmm) cc_final: 0.7610 (pmm) REVERT: G 200 HIS cc_start: 0.7164 (m170) cc_final: 0.6804 (m170) REVERT: F 228 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7797 (mt-10) REVERT: E 249 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8898 (tp) REVERT: E 428 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8248 (mtmt) REVERT: D 56 MET cc_start: 0.8861 (mmm) cc_final: 0.8658 (mmm) REVERT: J 11 MET cc_start: 0.7379 (tpp) cc_final: 0.6786 (tmm) REVERT: J 42 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8447 (mt0) REVERT: J 73 TYR cc_start: 0.6442 (t80) cc_final: 0.4722 (m-80) REVERT: L 11 MET cc_start: 0.7169 (mpp) cc_final: 0.5897 (tpp) REVERT: L 28 ILE cc_start: 0.8910 (mm) cc_final: 0.8465 (mt) REVERT: L 35 PHE cc_start: 0.7353 (t80) cc_final: 0.7058 (t80) REVERT: M 17 MET cc_start: 0.7672 (mmm) cc_final: 0.7411 (mmm) REVERT: M 42 GLN cc_start: 0.7886 (pt0) cc_final: 0.7622 (pm20) REVERT: M 55 ILE cc_start: 0.8756 (mm) cc_final: 0.8340 (mt) REVERT: M 57 MET cc_start: 0.8120 (tmm) cc_final: 0.7901 (tmm) REVERT: N 16 MET cc_start: 0.7971 (ptp) cc_final: 0.7624 (ptp) REVERT: N 37 GLU cc_start: 0.8602 (tt0) cc_final: 0.8201 (tt0) REVERT: N 42 GLN cc_start: 0.7743 (mm-40) cc_final: 0.7393 (mp10) REVERT: N 73 TYR cc_start: 0.6395 (t80) cc_final: 0.5839 (m-80) REVERT: O 7 ASP cc_start: 0.5467 (p0) cc_final: 0.4988 (p0) REVERT: O 46 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8631 (mt) REVERT: P 6 MET cc_start: 0.4273 (mpp) cc_final: 0.3486 (mtp) REVERT: Q 6 MET cc_start: 0.5187 (mtp) cc_final: 0.4802 (ptt) REVERT: Q 10 TYR cc_start: 0.4938 (m-80) cc_final: 0.4712 (m-80) REVERT: R 16 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7982 (ttp) REVERT: S 16 MET cc_start: 0.8379 (mtm) cc_final: 0.8124 (mtp) REVERT: S 75 MET cc_start: 0.8973 (tmm) cc_final: 0.8581 (tmm) REVERT: S 76 PHE cc_start: 0.7903 (m-80) cc_final: 0.7609 (m-80) REVERT: Y 22 MET cc_start: 0.5662 (mmt) cc_final: 0.4992 (mmt) REVERT: Y 51 HIS cc_start: 0.7307 (m90) cc_final: 0.6937 (m-70) REVERT: Y 98 ARG cc_start: 0.8846 (tmm-80) cc_final: 0.8455 (tpt170) REVERT: Y 104 GLN cc_start: 0.8539 (pt0) cc_final: 0.8040 (pm20) REVERT: a 6 MET cc_start: 0.5733 (tpp) cc_final: 0.5137 (ppp) REVERT: a 117 LEU cc_start: 0.8864 (mm) cc_final: 0.8652 (mm) REVERT: a 177 GLU cc_start: 0.7068 (mt-10) cc_final: 0.6625 (mm-30) REVERT: a 234 GLN cc_start: 0.7298 (mt0) cc_final: 0.7031 (mp10) REVERT: a 259 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9037 (mt) outliers start: 75 outliers final: 56 residues processed: 587 average time/residue: 0.5153 time to fit residues: 489.4051 Evaluate side-chains 576 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 510 time to evaluate : 4.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain W residue 160 ASP Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 434 LYS Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain X residue 2 ASN Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 119 GLU Chi-restraints excluded: chain X residue 148 ILE Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 428 LYS Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 44 ASP Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 16 MET Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain S residue 17 MET Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 63 VAL Chi-restraints excluded: chain a residue 169 LYS Chi-restraints excluded: chain a residue 201 LEU Chi-restraints excluded: chain a residue 259 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 416 optimal weight: 6.9990 chunk 438 optimal weight: 6.9990 chunk 400 optimal weight: 5.9990 chunk 426 optimal weight: 4.9990 chunk 256 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 335 optimal weight: 9.9990 chunk 130 optimal weight: 0.3980 chunk 385 optimal weight: 9.9990 chunk 403 optimal weight: 0.0470 chunk 425 optimal weight: 0.5980 overall best weight: 1.0082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 GLN D 7 GLN D 243 ASN ** M 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 42 GLN Y 123 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37494 Z= 0.175 Angle : 0.572 12.720 50760 Z= 0.286 Chirality : 0.040 0.150 5919 Planarity : 0.004 0.046 6543 Dihedral : 5.625 116.228 5345 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.96 % Allowed : 16.73 % Favored : 81.31 % 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: 1.06 (0.12), residues: 4807 helix: 1.56 (0.10), residues: 2661 sheet: 0.07 (0.22), residues: 551 loop : -0.43 (0.15), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP a 235 HIS 0.004 0.000 HIS C 479 PHE 0.028 0.001 PHE Y 20 TYR 0.023 0.001 TYR C 474 ARG 0.010 0.000 ARG L 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 525 time to evaluate : 4.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 12 LYS cc_start: 0.9223 (tttp) cc_final: 0.8653 (ttmm) REVERT: W 79 MET cc_start: 0.9253 (mtm) cc_final: 0.8993 (mtp) REVERT: C 321 THR cc_start: 0.8380 (OUTLIER) cc_final: 0.8037 (t) REVERT: C 484 GLN cc_start: 0.8485 (tm-30) cc_final: 0.8210 (mp10) REVERT: B 236 TYR cc_start: 0.8972 (OUTLIER) cc_final: 0.7816 (t80) REVERT: B 386 MET cc_start: 0.8865 (mmm) cc_final: 0.8544 (mmt) REVERT: A 463 LYS cc_start: 0.9302 (mtmt) cc_final: 0.9001 (mtmm) REVERT: X 2 ASN cc_start: 0.8087 (OUTLIER) cc_final: 0.7535 (p0) REVERT: X 73 GLN cc_start: 0.8311 (tp40) cc_final: 0.7881 (mm110) REVERT: X 113 ARG cc_start: 0.8394 (ttp-110) cc_final: 0.8091 (ttp-110) REVERT: X 119 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7421 (tp30) REVERT: X 145 ASN cc_start: 0.6859 (m110) cc_final: 0.5835 (t0) REVERT: G 178 MET cc_start: 0.8086 (pmm) cc_final: 0.7729 (pmm) REVERT: G 200 HIS cc_start: 0.7171 (m170) cc_final: 0.6806 (m170) REVERT: F 228 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7814 (mt-10) REVERT: E 428 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8237 (mtmt) REVERT: I 42 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8130 (mm110) REVERT: J 11 MET cc_start: 0.7345 (tpp) cc_final: 0.6703 (tmm) REVERT: J 42 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8421 (mt0) REVERT: J 73 TYR cc_start: 0.6522 (t80) cc_final: 0.4933 (m-80) REVERT: L 11 MET cc_start: 0.7301 (mpp) cc_final: 0.6176 (tpp) REVERT: L 16 MET cc_start: 0.7962 (tpp) cc_final: 0.7237 (mmm) REVERT: L 28 ILE cc_start: 0.8897 (mm) cc_final: 0.8479 (mt) REVERT: L 35 PHE cc_start: 0.7408 (t80) cc_final: 0.7105 (t80) REVERT: M 17 MET cc_start: 0.7658 (mmm) cc_final: 0.7408 (mmm) REVERT: M 42 GLN cc_start: 0.7808 (pt0) cc_final: 0.7342 (pm20) REVERT: M 55 ILE cc_start: 0.8776 (mm) cc_final: 0.8329 (mt) REVERT: N 16 MET cc_start: 0.8042 (ptp) cc_final: 0.7739 (ptp) REVERT: N 42 GLN cc_start: 0.7724 (mm-40) cc_final: 0.7368 (mp10) REVERT: N 73 TYR cc_start: 0.6508 (t80) cc_final: 0.5784 (m-80) REVERT: O 7 ASP cc_start: 0.5412 (p0) cc_final: 0.4584 (p0) REVERT: O 11 MET cc_start: 0.7205 (mmm) cc_final: 0.6844 (tpp) REVERT: O 46 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8527 (mt) REVERT: P 6 MET cc_start: 0.4220 (mpp) cc_final: 0.3571 (mtp) REVERT: Q 6 MET cc_start: 0.5199 (mtp) cc_final: 0.4824 (ptt) REVERT: Q 10 TYR cc_start: 0.4969 (m-80) cc_final: 0.4741 (m-80) REVERT: R 6 MET cc_start: 0.7739 (pmm) cc_final: 0.7523 (pmm) REVERT: R 16 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.8011 (ttp) REVERT: S 16 MET cc_start: 0.8363 (mtm) cc_final: 0.8102 (mtp) REVERT: S 75 MET cc_start: 0.8952 (tmm) cc_final: 0.8554 (tmm) REVERT: S 76 PHE cc_start: 0.7866 (m-80) cc_final: 0.7591 (m-80) REVERT: Y 22 MET cc_start: 0.5702 (mmt) cc_final: 0.5018 (mmt) REVERT: Y 51 HIS cc_start: 0.7311 (m90) cc_final: 0.6918 (m-70) REVERT: Y 98 ARG cc_start: 0.8819 (tmm-80) cc_final: 0.8394 (tpt170) REVERT: Y 123 GLN cc_start: 0.9234 (tp40) cc_final: 0.8635 (pt0) REVERT: a 6 MET cc_start: 0.5762 (tpp) cc_final: 0.5130 (ppp) REVERT: a 177 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6667 (mm-30) REVERT: a 234 GLN cc_start: 0.7246 (mt0) cc_final: 0.7006 (mp10) REVERT: a 259 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9056 (mt) outliers start: 75 outliers final: 57 residues processed: 576 average time/residue: 0.5457 time to fit residues: 513.8608 Evaluate side-chains 579 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 513 time to evaluate : 4.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain W residue 160 ASP Chi-restraints excluded: chain C residue 26 HIS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 434 LYS Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain X residue 2 ASN Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 119 GLU Chi-restraints excluded: chain X residue 148 ILE Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 428 LYS Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 44 ASP Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 16 MET Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain S residue 17 MET Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 63 VAL Chi-restraints excluded: chain a residue 169 LYS Chi-restraints excluded: chain a residue 201 LEU Chi-restraints excluded: chain a residue 259 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 280 optimal weight: 2.9990 chunk 451 optimal weight: 2.9990 chunk 275 optimal weight: 5.9990 chunk 214 optimal weight: 4.9990 chunk 313 optimal weight: 10.0000 chunk 473 optimal weight: 7.9990 chunk 435 optimal weight: 2.9990 chunk 376 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 291 optimal weight: 0.8980 chunk 231 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 ASN ** M 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 ASN R 52 GLN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 37494 Z= 0.228 Angle : 0.599 13.179 50760 Z= 0.299 Chirality : 0.042 0.344 5919 Planarity : 0.004 0.046 6543 Dihedral : 5.652 115.377 5345 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.78 % Allowed : 17.25 % Favored : 80.97 % 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: 1.03 (0.12), residues: 4807 helix: 1.51 (0.10), residues: 2666 sheet: 0.07 (0.22), residues: 544 loop : -0.42 (0.15), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP a 235 HIS 0.003 0.001 HIS C 479 PHE 0.030 0.001 PHE Y 20 TYR 0.022 0.001 TYR C 474 ARG 0.009 0.000 ARG Y 115 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 520 time to evaluate : 4.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 12 LYS cc_start: 0.9229 (tttp) cc_final: 0.8666 (ttmm) REVERT: W 79 MET cc_start: 0.9283 (mtm) cc_final: 0.9030 (mtp) REVERT: C 321 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.8051 (t) REVERT: C 484 GLN cc_start: 0.8476 (tm-30) cc_final: 0.8221 (mp10) REVERT: B 10 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8346 (tm-30) REVERT: B 236 TYR cc_start: 0.9017 (OUTLIER) cc_final: 0.7851 (t80) REVERT: B 386 MET cc_start: 0.8890 (mmm) cc_final: 0.8553 (mmt) REVERT: A 52 MET cc_start: 0.8221 (ttm) cc_final: 0.7956 (ttm) REVERT: A 463 LYS cc_start: 0.9295 (mtmt) cc_final: 0.9061 (mtmm) REVERT: X 2 ASN cc_start: 0.8135 (OUTLIER) cc_final: 0.7637 (p0) REVERT: X 55 ASP cc_start: 0.8624 (t0) cc_final: 0.8136 (m-30) REVERT: X 73 GLN cc_start: 0.8314 (tp40) cc_final: 0.7888 (mm110) REVERT: X 113 ARG cc_start: 0.8328 (ttp-110) cc_final: 0.8023 (ttp-110) REVERT: X 119 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7353 (tp30) REVERT: X 145 ASN cc_start: 0.6785 (m110) cc_final: 0.5818 (t0) REVERT: H 13 GLN cc_start: 0.8993 (pp30) cc_final: 0.8269 (pp30) REVERT: G 178 MET cc_start: 0.8113 (pmm) cc_final: 0.7770 (pmm) REVERT: G 200 HIS cc_start: 0.7187 (m170) cc_final: 0.6803 (m170) REVERT: G 206 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8593 (mt) REVERT: F 228 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7759 (mt-10) REVERT: E 340 THR cc_start: 0.8691 (m) cc_final: 0.8381 (p) REVERT: D 226 MET cc_start: 0.9047 (mtt) cc_final: 0.8809 (mtt) REVERT: I 42 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8128 (mm110) REVERT: J 11 MET cc_start: 0.7365 (tpp) cc_final: 0.6419 (tmm) REVERT: J 42 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8434 (mt0) REVERT: L 11 MET cc_start: 0.7323 (mpp) cc_final: 0.6140 (tpp) REVERT: L 16 MET cc_start: 0.8398 (tpp) cc_final: 0.7827 (mmm) REVERT: L 28 ILE cc_start: 0.8834 (mm) cc_final: 0.8438 (mt) REVERT: L 35 PHE cc_start: 0.7465 (t80) cc_final: 0.7155 (t80) REVERT: M 17 MET cc_start: 0.7627 (mmm) cc_final: 0.7403 (mmm) REVERT: M 55 ILE cc_start: 0.8780 (mm) cc_final: 0.8328 (mt) REVERT: N 16 MET cc_start: 0.8169 (ptp) cc_final: 0.7856 (ptp) REVERT: N 42 GLN cc_start: 0.7799 (mm-40) cc_final: 0.7420 (mp10) REVERT: N 73 TYR cc_start: 0.6527 (t80) cc_final: 0.5802 (m-80) REVERT: O 11 MET cc_start: 0.7258 (mmm) cc_final: 0.6861 (tpp) REVERT: O 46 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8534 (mt) REVERT: O 65 MET cc_start: 0.8398 (tpt) cc_final: 0.7941 (mtp) REVERT: P 6 MET cc_start: 0.4278 (mpp) cc_final: 0.3671 (mtp) REVERT: P 17 MET cc_start: 0.7374 (mtt) cc_final: 0.6922 (tpt) REVERT: Q 6 MET cc_start: 0.5207 (mtp) cc_final: 0.4804 (ptt) REVERT: Q 10 TYR cc_start: 0.5002 (m-80) cc_final: 0.4793 (m-80) REVERT: S 16 MET cc_start: 0.8380 (mtm) cc_final: 0.8100 (mtp) REVERT: S 75 MET cc_start: 0.8941 (tmm) cc_final: 0.8529 (tmm) REVERT: S 76 PHE cc_start: 0.7914 (m-80) cc_final: 0.7547 (m-80) REVERT: Y 22 MET cc_start: 0.5686 (mmt) cc_final: 0.4998 (mmt) REVERT: Y 51 HIS cc_start: 0.7325 (m90) cc_final: 0.6930 (m-70) REVERT: Y 98 ARG cc_start: 0.8822 (tmm-80) cc_final: 0.8394 (tpt170) REVERT: a 6 MET cc_start: 0.5964 (tpp) cc_final: 0.5226 (ppp) REVERT: a 177 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6663 (mm-30) REVERT: a 234 GLN cc_start: 0.7164 (mt0) cc_final: 0.6962 (mp10) outliers start: 68 outliers final: 57 residues processed: 568 average time/residue: 0.5081 time to fit residues: 468.5345 Evaluate side-chains 576 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 512 time to evaluate : 4.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain W residue 128 MET Chi-restraints excluded: chain W residue 160 ASP Chi-restraints excluded: chain C residue 26 HIS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 434 LYS Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain X residue 2 ASN Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 119 GLU Chi-restraints excluded: chain X residue 148 ILE Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 44 ASP Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 44 ASP Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain S residue 17 MET Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 63 VAL Chi-restraints excluded: chain a residue 169 LYS Chi-restraints excluded: chain a residue 201 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 299 optimal weight: 1.9990 chunk 401 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 347 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 377 optimal weight: 7.9990 chunk 157 optimal weight: 3.9990 chunk 387 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 69 optimal weight: 0.4980 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN D 243 ASN ** M 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 GLN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 123 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.097250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.067936 restraints weight = 83594.052| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.15 r_work: 0.2843 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 37494 Z= 0.273 Angle : 0.614 12.376 50760 Z= 0.307 Chirality : 0.042 0.296 5919 Planarity : 0.004 0.051 6543 Dihedral : 5.746 115.688 5345 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.88 % Allowed : 17.39 % Favored : 80.73 % 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: 0.96 (0.12), residues: 4807 helix: 1.47 (0.10), residues: 2663 sheet: 0.04 (0.22), residues: 544 loop : -0.47 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP a 235 HIS 0.004 0.001 HIS W 21 PHE 0.036 0.001 PHE a 212 TYR 0.022 0.001 TYR C 474 ARG 0.009 0.000 ARG a 210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10279.86 seconds wall clock time: 191 minutes 57.74 seconds (11517.74 seconds total)