Starting phenix.real_space_refine on Wed Jun 11 13:08:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bu7_44902/06_2025/9bu7_44902.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bu7_44902/06_2025/9bu7_44902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bu7_44902/06_2025/9bu7_44902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bu7_44902/06_2025/9bu7_44902.map" model { file = "/net/cci-nas-00/data/ceres_data/9bu7_44902/06_2025/9bu7_44902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bu7_44902/06_2025/9bu7_44902.cif" } resolution = 3.64 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= 0.002 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 37 5.49 5 Mg 2 5.21 5 S 35 5.16 5 C 7900 2.51 5 N 2348 2.21 5 O 2509 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12831 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 1501 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 201} Link IDs: {'PTRANS': 9, 'TRANS': 267} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 747 Unresolved non-hydrogen angles: 952 Unresolved non-hydrogen dihedrals: 643 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 12, 'TRP:plan': 6, 'ASP:plan': 14, 'PHE:plan': 13, 'GLU:plan': 14, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 407 Chain: "B" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 1492 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 205} Link IDs: {'PTRANS': 10, 'TRANS': 267} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 761 Unresolved non-hydrogen angles: 972 Unresolved non-hydrogen dihedrals: 651 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 12, 'TRP:plan': 6, 'ASP:plan': 15, 'PHE:plan': 13, 'GLU:plan': 16, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 423 Chain: "C" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 1453 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 212} Link IDs: {'PTRANS': 9, 'TRANS': 266} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 788 Unresolved non-hydrogen angles: 1006 Unresolved non-hydrogen dihedrals: 674 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 5, 'TYR:plan': 6, 'ASN:plan1': 11, 'TRP:plan': 6, 'ASP:plan': 14, 'PHE:plan': 13, 'GLU:plan': 15, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 428 Chain: "D" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 1503 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 198} Link IDs: {'PTRANS': 9, 'TRANS': 267} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 745 Unresolved non-hydrogen angles: 952 Unresolved non-hydrogen dihedrals: 639 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 11, 'TRP:plan': 6, 'ASP:plan': 14, 'PHE:plan': 13, 'GLU:plan': 16, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 412 Chain: "E" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2060 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 9, 'TRANS': 267} Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 6, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 90 Chain: "F" Number of atoms: 2106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2106 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 10, 'TRANS': 260} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 47 Chain: "G" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2047 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 10, 'TRANS': 266} Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 106 Chain: "H" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 289 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "I" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 285 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.45, per 1000 atoms: 0.97 Number of scatterers: 12831 At special positions: 0 Unit cell: (87.648, 137.28, 137.808, 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 35 16.00 P 37 15.00 Mg 2 11.99 O 2509 8.00 N 2348 7.00 C 7900 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 - 3.00 Amino acid : True - 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: 3.54 Conformation dependent library (CDL) restraints added in 1.9 seconds 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3634 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 20 sheets defined 47.6% alpha, 8.7% beta 12 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 4.53 Creating SS restraints... Processing helix chain 'A' and resid 218 through 235 Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 246 through 254 removed outlier: 3.655A pdb=" N TYR A 250 " --> pdb=" O ASP A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 278 Processing helix chain 'A' and resid 279 through 285 removed outlier: 3.998A pdb=" N TYR A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 304 Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.545A pdb=" N SER A 314 " --> pdb=" O GLN A 310 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 350 removed outlier: 3.599A pdb=" N ALA A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 removed outlier: 3.982A pdb=" N VAL A 370 " --> pdb=" O ASN A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 395 removed outlier: 4.704A pdb=" N GLU A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N SER A 389 " --> pdb=" O LYS A 385 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 443 Processing helix chain 'A' and resid 462 through 475 removed outlier: 3.947A pdb=" N PHE A 469 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP A 475 " --> pdb=" O ARG A 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 235 Processing helix chain 'B' and resid 238 through 246 Processing helix chain 'B' and resid 246 through 254 removed outlier: 3.688A pdb=" N TYR B 250 " --> pdb=" O ASP B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 276 Processing helix chain 'B' and resid 279 through 284 Processing helix chain 'B' and resid 296 through 305 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 339 through 349 Processing helix chain 'B' and resid 366 through 370 removed outlier: 4.200A pdb=" N VAL B 370 " --> pdb=" O ASN B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 395 Processing helix chain 'B' and resid 437 through 443 Processing helix chain 'B' and resid 462 through 476 Processing helix chain 'C' and resid 218 through 235 Processing helix chain 'C' and resid 238 through 246 Processing helix chain 'C' and resid 246 through 254 removed outlier: 3.895A pdb=" N TYR C 250 " --> pdb=" O ASP C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 278 removed outlier: 3.850A pdb=" N GLN C 262 " --> pdb=" O ASN C 258 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS C 278 " --> pdb=" O MET C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 281 No H-bonds generated for 'chain 'C' and resid 280 through 281' 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 296 through 305 Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.572A pdb=" N SER C 314 " --> pdb=" O GLN C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 349 Processing helix chain 'C' and resid 383 through 394 removed outlier: 4.399A pdb=" N GLU C 388 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N SER C 389 " --> pdb=" O LYS C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 443 Processing helix chain 'C' and resid 455 through 459 removed outlier: 4.430A pdb=" N GLY C 459 " --> pdb=" O HIS C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 476 Processing helix chain 'D' and resid 218 through 235 Processing helix chain 'D' and resid 238 through 246 Processing helix chain 'D' and resid 246 through 253 removed outlier: 4.163A pdb=" N TYR D 250 " --> pdb=" O ASP D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 278 removed outlier: 4.625A pdb=" N LYS D 264 " --> pdb=" O ARG D 260 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA D 265 " --> pdb=" O SER D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 285 Processing helix chain 'D' and resid 296 through 304 Processing helix chain 'D' and resid 308 through 322 Processing helix chain 'D' and resid 339 through 348 removed outlier: 3.760A pdb=" N ALA D 346 " --> pdb=" O ASN D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 395 Processing helix chain 'D' and resid 437 through 443 Processing helix chain 'D' and resid 462 through 476 removed outlier: 4.173A pdb=" N LYS D 474 " --> pdb=" O PHE D 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 235 Processing helix chain 'E' and resid 238 through 246 Processing helix chain 'E' and resid 246 through 256 removed outlier: 3.623A pdb=" N TYR E 250 " --> pdb=" O ASP E 246 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA E 256 " --> pdb=" O SER E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 278 Processing helix chain 'E' and resid 279 through 285 removed outlier: 3.581A pdb=" N TYR E 283 " --> pdb=" O THR E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 295 removed outlier: 4.031A pdb=" N SER E 295 " --> pdb=" O ASP E 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 292 through 295' Processing helix chain 'E' and resid 296 through 306 removed outlier: 3.543A pdb=" N LYS E 300 " --> pdb=" O ASN E 296 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN E 305 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY E 306 " --> pdb=" O LEU E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 339 through 351 removed outlier: 3.647A pdb=" N VAL E 351 " --> pdb=" O ILE E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 385 No H-bonds generated for 'chain 'E' and resid 383 through 385' Processing helix chain 'E' and resid 386 through 394 Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 462 through 475 Processing helix chain 'F' and resid 218 through 234 removed outlier: 3.502A pdb=" N ALA F 222 " --> pdb=" O SER F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 246 Processing helix chain 'F' and resid 246 through 254 removed outlier: 3.931A pdb=" N TYR F 250 " --> pdb=" O ASP F 246 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN F 254 " --> pdb=" O TYR F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 276 removed outlier: 4.148A pdb=" N LYS F 264 " --> pdb=" O ARG F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 285 removed outlier: 3.890A pdb=" N VAL F 285 " --> pdb=" O PRO F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 305 removed outlier: 3.632A pdb=" N LYS F 300 " --> pdb=" O ASN F 296 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN F 305 " --> pdb=" O ILE F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 322 Processing helix chain 'F' and resid 339 through 351 removed outlier: 3.882A pdb=" N ILE F 343 " --> pdb=" O GLY F 339 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL F 351 " --> pdb=" O ILE F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 394 removed outlier: 4.427A pdb=" N ALA F 392 " --> pdb=" O GLU F 388 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE F 393 " --> pdb=" O SER F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 464 through 475 removed outlier: 3.921A pdb=" N ASP F 475 " --> pdb=" O ARG F 471 " (cutoff:3.500A) Processing helix chain 'G' and resid 218 through 234 Processing helix chain 'G' and resid 238 through 246 Processing helix chain 'G' and resid 246 through 254 removed outlier: 3.753A pdb=" N TYR G 250 " --> pdb=" O ASP G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 276 removed outlier: 4.303A pdb=" N SER G 261 " --> pdb=" O SER G 257 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS G 264 " --> pdb=" O ARG G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 285 removed outlier: 4.314A pdb=" N TYR G 283 " --> pdb=" O THR G 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 305 Processing helix chain 'G' and resid 308 through 321 Processing helix chain 'G' and resid 339 through 350 Processing helix chain 'G' and resid 386 through 394 removed outlier: 3.782A pdb=" N ALA G 392 " --> pdb=" O GLU G 388 " (cutoff:3.500A) Processing helix chain 'G' and resid 437 through 443 removed outlier: 3.828A pdb=" N LEU G 441 " --> pdb=" O HIS G 437 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 476 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 356 removed outlier: 6.619A pdb=" N GLY A 355 " --> pdb=" O TRP A 376 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N GLU A 378 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE A 375 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N THR A 419 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TRP A 377 " --> pdb=" O THR A 419 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 382 through 383 removed outlier: 6.554A pdb=" N MET A 382 " --> pdb=" O ILE A 428 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 399 through 403 removed outlier: 4.389A pdb=" N GLN A 403 " --> pdb=" O SER A 407 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N SER A 407 " --> pdb=" O GLN A 403 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 356 removed outlier: 6.322A pdb=" N GLY B 355 " --> pdb=" O TRP B 376 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLU B 378 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE B 330 " --> pdb=" O VAL B 418 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N SER B 420 " --> pdb=" O ILE B 330 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU B 332 " --> pdb=" O SER B 420 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TRP B 331 " --> pdb=" O PHE B 448 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 399 through 403 removed outlier: 3.574A pdb=" N VAL B 399 " --> pdb=" O ILE B 411 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLN B 403 " --> pdb=" O SER B 407 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N SER B 407 " --> pdb=" O GLN B 403 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 427 through 429 Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 356 removed outlier: 6.241A pdb=" N GLY C 355 " --> pdb=" O TRP C 376 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLU C 378 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR C 419 " --> pdb=" O TRP C 377 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 399 through 403 removed outlier: 3.506A pdb=" N VAL C 399 " --> pdb=" O ILE C 411 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLN C 403 " --> pdb=" O SER C 407 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N SER C 407 " --> pdb=" O GLN C 403 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 427 through 429 Processing sheet with id=AB1, first strand: chain 'D' and resid 355 through 356 removed outlier: 6.382A pdb=" N GLY D 355 " --> pdb=" O TRP D 376 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 382 through 383 removed outlier: 6.571A pdb=" N MET D 382 " --> pdb=" O ILE D 428 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 399 through 403 removed outlier: 4.383A pdb=" N GLN D 403 " --> pdb=" O SER D 407 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N SER D 407 " --> pdb=" O GLN D 403 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 354 through 356 removed outlier: 6.928A pdb=" N ILE E 375 " --> pdb=" O ILE E 417 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR E 329 " --> pdb=" O PHE E 446 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N PHE E 448 " --> pdb=" O THR E 329 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TRP E 331 " --> pdb=" O PHE E 448 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 399 through 400 removed outlier: 3.846A pdb=" N VAL E 399 " --> pdb=" O ILE E 411 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 427 through 429 removed outlier: 3.589A pdb=" N VAL E 427 " --> pdb=" O THR E 434 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 354 through 355 removed outlier: 3.510A pdb=" N GLY F 355 " --> pdb=" O VAL F 374 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N THR F 329 " --> pdb=" O PHE F 446 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N PHE F 448 " --> pdb=" O THR F 329 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TRP F 331 " --> pdb=" O PHE F 448 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 399 through 401 removed outlier: 3.986A pdb=" N VAL F 399 " --> pdb=" O ILE F 411 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 355 through 356 removed outlier: 6.325A pdb=" N GLY G 355 " --> pdb=" O TRP G 376 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE G 375 " --> pdb=" O ILE G 417 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N THR G 419 " --> pdb=" O ILE G 375 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TRP G 377 " --> pdb=" O THR G 419 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 399 through 401 removed outlier: 3.810A pdb=" N VAL G 399 " --> pdb=" O ILE G 411 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA G 409 " --> pdb=" O VAL G 401 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 428 through 429 636 hydrogen bonds defined for protein. 1839 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 68 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 4.25 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 4450 1.36 - 1.50: 3615 1.50 - 1.65: 4969 1.65 - 1.80: 31 1.80 - 1.95: 24 Bond restraints: 13089 Sorted by residual: bond pdb=" N ILE A 236 " pdb=" CA ILE A 236 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.24e-02 6.50e+03 8.72e+00 bond pdb=" N ILE B 347 " pdb=" CA ILE B 347 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.23e-02 6.61e+03 8.68e+00 bond pdb=" N VAL F 215 " pdb=" CA VAL F 215 " ideal model delta sigma weight residual 1.459 1.493 -0.035 1.19e-02 7.06e+03 8.53e+00 bond pdb=" N THR B 462 " pdb=" CA THR B 462 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.17e-02 7.31e+03 8.15e+00 bond pdb=" N PHE D 333 " pdb=" CA PHE D 333 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.15e-02 7.56e+03 7.79e+00 ... (remaining 13084 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.94: 16514 0.94 - 1.89: 1163 1.89 - 2.83: 285 2.83 - 3.77: 112 3.77 - 4.71: 30 Bond angle restraints: 18104 Sorted by residual: angle pdb=" N LYS B 463 " pdb=" CA LYS B 463 " pdb=" C LYS B 463 " ideal model delta sigma weight residual 111.71 107.04 4.67 1.15e+00 7.56e-01 1.65e+01 angle pdb=" CA ALA G 313 " pdb=" C ALA G 313 " pdb=" O ALA G 313 " ideal model delta sigma weight residual 120.24 116.04 4.20 1.11e+00 8.12e-01 1.43e+01 angle pdb=" N ILE A 347 " pdb=" CA ILE A 347 " pdb=" C ILE A 347 " ideal model delta sigma weight residual 111.91 108.57 3.34 8.90e-01 1.26e+00 1.41e+01 angle pdb=" N LYS C 391 " pdb=" CA LYS C 391 " pdb=" C LYS C 391 " ideal model delta sigma weight residual 111.82 107.50 4.32 1.16e+00 7.43e-01 1.39e+01 angle pdb=" N ALA F 390 " pdb=" CA ALA F 390 " pdb=" C ALA F 390 " ideal model delta sigma weight residual 112.54 108.06 4.48 1.22e+00 6.72e-01 1.35e+01 ... (remaining 18099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.55: 7342 34.55 - 69.10: 186 69.10 - 103.65: 5 103.65 - 138.20: 2 138.20 - 172.75: 4 Dihedral angle restraints: 7539 sinusoidal: 1948 harmonic: 5591 Sorted by residual: dihedral pdb=" CA LEU F 276 " pdb=" C LEU F 276 " pdb=" N THR F 277 " pdb=" CA THR F 277 " ideal model delta harmonic sigma weight residual 180.00 160.01 19.99 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ILE G 293 " pdb=" C ILE G 293 " pdb=" N SER G 294 " pdb=" CA SER G 294 " ideal model delta harmonic sigma weight residual 180.00 160.02 19.98 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" O1B AGS E 501 " pdb=" O3B AGS E 501 " pdb=" PB AGS E 501 " pdb=" PG AGS E 501 " ideal model delta sinusoidal sigma weight residual 68.91 -50.06 118.97 1 3.00e+01 1.11e-03 1.58e+01 ... (remaining 7536 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1498 0.039 - 0.078: 411 0.078 - 0.117: 251 0.117 - 0.156: 29 0.156 - 0.195: 9 Chirality restraints: 2198 Sorted by residual: chirality pdb=" CA ILE C 393 " pdb=" N ILE C 393 " pdb=" C ILE C 393 " pdb=" CB ILE C 393 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.48e-01 chirality pdb=" CA VAL C 315 " pdb=" N VAL C 315 " pdb=" C VAL C 315 " pdb=" CB VAL C 315 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.09e-01 chirality pdb=" CA ILE A 236 " pdb=" N ILE A 236 " pdb=" C ILE A 236 " pdb=" CB ILE A 236 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.89e-01 ... (remaining 2195 not shown) Planarity restraints: 2294 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN G 310 " -0.016 2.00e-02 2.50e+03 3.11e-02 9.67e+00 pdb=" C GLN G 310 " 0.054 2.00e-02 2.50e+03 pdb=" O GLN G 310 " -0.020 2.00e-02 2.50e+03 pdb=" N TYR G 311 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 389 " 0.015 2.00e-02 2.50e+03 2.91e-02 8.49e+00 pdb=" C SER F 389 " -0.050 2.00e-02 2.50e+03 pdb=" O SER F 389 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA F 390 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 443 " 0.013 2.00e-02 2.50e+03 2.70e-02 7.30e+00 pdb=" C ASP A 443 " -0.047 2.00e-02 2.50e+03 pdb=" O ASP A 443 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG A 444 " 0.016 2.00e-02 2.50e+03 ... (remaining 2291 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 28 2.41 - 3.03: 8477 3.03 - 3.65: 18449 3.65 - 4.28: 25540 4.28 - 4.90: 42460 Nonbonded interactions: 94954 Sorted by model distance: nonbonded pdb=" OG1 THR E 341 " pdb="MG MG E 502 " model vdw 1.785 2.170 nonbonded pdb=" OG1 THR F 341 " pdb="MG MG F 502 " model vdw 1.837 2.170 nonbonded pdb=" S1G AGS F 501 " pdb="MG MG F 502 " model vdw 2.149 2.530 nonbonded pdb=" O GLU B 239 " pdb=" N TRP B 242 " model vdw 2.197 3.120 nonbonded pdb=" O ALA G 336 " pdb=" OG1 THR G 337 " model vdw 2.199 3.040 ... (remaining 94949 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 214 or (resid 215 through 217 and (name N or name CA or na \ me C or name O or name CB )) or resid 218 through 220 or (resid 221 through 223 \ and (name N or name CA or name C or name O or name CB )) or resid 224 through 22 \ 5 or (resid 226 and (name N or name CA or name C or name O or name CB )) or resi \ d 227 through 231 or (resid 232 through 234 and (name N or name CA or name C or \ name O or name CB )) or resid 235 through 236 or (resid 237 through 240 and (nam \ e N or name CA or name C or name O or name CB )) or resid 241 through 242 or (re \ sid 243 through 249 and (name N or name CA or name C or name O or name CB )) or \ resid 250 or (resid 251 through 252 and (name N or name CA or name C or name O o \ r name CB )) or resid 253 through 274 or (resid 275 through 280 and (name N or n \ ame CA or name C or name O or name CB )) or resid 281 or (resid 283 through 285 \ and (name N or name CA or name C or name O or name CB )) or resid 286 through 42 \ 8 or resid 435 through 489)) selection = (chain 'B' and (resid 214 through 215 or (resid 216 through 217 and (name N or n \ ame CA or name C or name O or name CB )) or resid 218 through 224 or (resid 225 \ through 226 and (name N or name CA or name C or name O or name CB )) or resid 22 \ 7 through 232 or (resid 233 through 234 and (name N or name CA or name C or name \ O or name CB )) or resid 235 through 242 or (resid 243 through 249 and (name N \ or name CA or name C or name O or name CB )) or resid 250 or (resid 251 through \ 252 and (name N or name CA or name C or name O or name CB )) or resid 253 throug \ h 260 or (resid 261 and (name N or name CA or name C or name O or name CB )) or \ resid 262 through 266 or (resid 267 through 268 and (name N or name CA or name C \ or name O or name CB )) or resid 269 through 272 or (resid 273 through 280 and \ (name N or name CA or name C or name O or name CB )) or resid 281 or (resid 283 \ through 285 and (name N or name CA or name C or name O or name CB )) or resid 28 \ 6 through 428 or resid 435 through 489)) selection = (chain 'C' and (resid 214 through 220 or (resid 221 through 223 and (name N or n \ ame CA or name C or name O or name CB )) or resid 224 through 238 or (resid 239 \ through 240 and (name N or name CA or name C or name O or name CB )) or resid 24 \ 1 through 245 or (resid 246 through 249 and (name N or name CA or name C or name \ O or name CB )) or resid 250 through 251 or (resid 252 and (name N or name CA o \ r name C or name O or name CB )) or resid 253 through 257 or (resid 258 and (nam \ e N or name CA or name C or name O or name CB )) or resid 259 through 266 or (re \ sid 267 through 268 and (name N or name CA or name C or name O or name CB )) or \ resid 269 through 428 or resid 435 through 489)) selection = (chain 'D' and (resid 214 or (resid 215 through 217 and (name N or name CA or na \ me C or name O or name CB )) or resid 218 through 220 or (resid 221 through 223 \ and (name N or name CA or name C or name O or name CB )) or resid 224 or (resid \ 225 through 226 and (name N or name CA or name C or name O or name CB )) or resi \ d 227 through 231 or (resid 232 through 234 and (name N or name CA or name C or \ name O or name CB )) or resid 235 through 237 or (resid 238 through 240 and (nam \ e N or name CA or name C or name O or name CB )) or resid 241 through 242 or (re \ sid 243 through 249 and (name N or name CA or name C or name O or name CB )) or \ resid 250 or (resid 251 through 252 and (name N or name CA or name C or name O o \ r name CB )) or resid 253 through 256 or (resid 257 through 258 and (name N or n \ ame CA or name C or name O or name CB )) or resid 259 through 260 or (resid 261 \ and (name N or name CA or name C or name O or name CB )) or resid 262 through 27 \ 2 or (resid 273 through 280 and (name N or name CA or name C or name O or name C \ B )) or resid 281 or (resid 283 through 285 and (name N or name CA or name C or \ name O or name CB )) or resid 286 through 428 or resid 435 through 489)) selection = (chain 'E' and (resid 214 or (resid 215 through 217 and (name N or name CA or na \ me C or name O or name CB )) or resid 218 or (resid 219 and (name N or name CA o \ r name C or name O or name CB )) or resid 220 or (resid 221 through 223 and (nam \ e N or name CA or name C or name O or name CB )) or resid 224 or (resid 225 thro \ ugh 226 and (name N or name CA or name C or name O or name CB )) or resid 227 th \ rough 231 or (resid 232 through 234 and (name N or name CA or name C or name O o \ r name CB )) or resid 235 through 236 or (resid 237 through 240 and (name N or n \ ame CA or name C or name O or name CB )) or resid 241 through 242 or (resid 243 \ through 249 and (name N or name CA or name C or name O or name CB )) or resid 25 \ 0 or (resid 251 through 252 and (name N or name CA or name C or name O or name C \ B )) or resid 253 through 256 or (resid 257 through 258 and (name N or name CA o \ r name C or name O or name CB )) or resid 259 through 260 or (resid 261 and (nam \ e N or name CA or name C or name O or name CB )) or resid 262 through 266 or (re \ sid 267 through 268 and (name N or name CA or name C or name O or name CB )) or \ resid 269 through 271 or (resid 272 through 280 and (name N or name CA or name C \ or name O or name CB )) or resid 281 or (resid 283 through 285 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 286 through 305 and (name N o \ r name CA or name C or name O or name CB )) or resid 306 or (resid 307 through 3 \ 17 and (name N or name CA or name C or name O or name CB )) or resid 318 or (res \ id 319 through 324 and (name N or name CA or name C or name O or name CB )) or r \ esid 325 or (resid 326 through 333 and (name N or name CA or name C or name O or \ name CB )) or resid 334 or (resid 335 through 338 and (name N or name CA or nam \ e C or name O or name CB )) or resid 339 or (resid 340 through 354 and (name N o \ r name CA or name C or name O or name CB )) or resid 355 or (resid 356 through 3 \ 79 and (name N or name CA or name C or name O or name CB )) or (resid 380 throug \ h 394 and (name N or name CA or name C or name O or name CB )) or (resid 395 thr \ ough 428 and (name N or name CA or name C or name O or name CB )) or (resid 435 \ through 458 and (name N or name CA or name C or name O or name CB )) or resid 45 \ 9 or (resid 460 through 488 and (name N or name CA or name C or name O or name C \ B )) or resid 489)) selection = (chain 'F' and (resid 214 or (resid 215 through 217 and (name N or name CA or na \ me C or name O or name CB )) or resid 218 or (resid 219 and (name N or name CA o \ r name C or name O or name CB )) or resid 220 or (resid 221 through 223 and (nam \ e N or name CA or name C or name O or name CB )) or resid 224 or (resid 225 thro \ ugh 226 and (name N or name CA or name C or name O or name CB )) or resid 227 th \ rough 231 or (resid 232 through 234 and (name N or name CA or name C or name O o \ r name CB )) or resid 235 through 236 or (resid 237 through 240 and (name N or n \ ame CA or name C or name O or name CB )) or resid 241 through 242 or (resid 243 \ through 249 and (name N or name CA or name C or name O or name CB )) or resid 25 \ 0 or (resid 251 through 252 and (name N or name CA or name C or name O or name C \ B )) or resid 253 through 256 or (resid 257 through 258 and (name N or name CA o \ r name C or name O or name CB )) or resid 259 or (resid 260 through 261 and (nam \ e N or name CA or name C or name O or name CB )) or resid 262 through 263 or (re \ sid 264 through 268 and (name N or name CA or name C or name O or name CB )) or \ resid 269 through 271 or (resid 272 through 280 and (name N or name CA or name C \ or name O or name CB )) or resid 281 or (resid 283 through 285 and (name N or n \ ame CA or name C or name O or name CB )) or resid 286 or (resid 287 through 305 \ and (name N or name CA or name C or name O or name CB )) or resid 306 or (resid \ 307 through 317 and (name N or name CA or name C or name O or name CB )) or resi \ d 318 or (resid 319 through 324 and (name N or name CA or name C or name O or na \ me CB )) or resid 325 or (resid 326 through 333 and (name N or name CA or name C \ or name O or name CB )) or resid 334 or (resid 335 through 338 and (name N or n \ ame CA or name C or name O or name CB )) or resid 339 or (resid 340 through 354 \ and (name N or name CA or name C or name O or name CB )) or resid 355 or (resid \ 356 through 379 and (name N or name CA or name C or name O or name CB )) or resi \ d 380 or (resid 381 through 394 and (name N or name CA or name C or name O or na \ me CB )) or resid 395 through 396 or (resid 397 through 458 and (name N or name \ CA or name C or name O or name CB )) or resid 459 or (resid 460 through 488 and \ (name N or name CA or name C or name O or name CB )) or resid 489)) selection = (chain 'G' and (resid 214 or (resid 215 through 217 and (name N or name CA or na \ me C or name O or name CB )) or resid 218 through 220 or (resid 221 through 223 \ and (name N or name CA or name C or name O or name CB )) or resid 224 or (resid \ 225 through 226 and (name N or name CA or name C or name O or name CB )) or resi \ d 227 through 231 or (resid 232 through 234 and (name N or name CA or name C or \ name O or name CB )) or resid 235 through 236 or (resid 237 through 240 and (nam \ e N or name CA or name C or name O or name CB )) or resid 241 through 242 or (re \ sid 243 through 249 and (name N or name CA or name C or name O or name CB )) or \ resid 250 or (resid 251 through 252 and (name N or name CA or name C or name O o \ r name CB )) or resid 253 through 256 or (resid 257 through 258 and (name N or n \ ame CA or name C or name O or name CB )) or resid 259 through 260 or (resid 261 \ and (name N or name CA or name C or name O or name CB )) or resid 262 through 26 \ 6 or (resid 267 through 268 and (name N or name CA or name C or name O or name C \ B )) or resid 269 through 271 or (resid 272 through 280 and (name N or name CA o \ r name C or name O or name CB )) or resid 281 or (resid 283 through 285 and (nam \ e N or name CA or name C or name O or name CB )) or resid 286 or (resid 287 thro \ ugh 305 and (name N or name CA or name C or name O or name CB )) or resid 306 or \ (resid 307 through 317 and (name N or name CA or name C or name O or name CB )) \ or resid 318 or (resid 319 through 324 and (name N or name CA or name C or name \ O or name CB )) or resid 325 or (resid 326 through 333 and (name N or name CA o \ r name C or name O or name CB )) or resid 334 or (resid 335 through 338 and (nam \ e N or name CA or name C or name O or name CB )) or (resid 339 through 354 and ( \ name N or name CA or name C or name O or name CB )) or resid 355 or (resid 356 t \ hrough 379 and (name N or name CA or name C or name O or name CB )) or (resid 38 \ 0 through 394 and (name N or name CA or name C or name O or name CB )) or resid \ 395 through 396 or (resid 397 through 428 and (name N or name CA or name C or na \ me O or name CB )) or (resid 435 through 458 and (name N or name CA or name C or \ name O or name CB )) or (resid 459 through 488 and (name N or name CA or name C \ or name O or name CB )) or resid 489)) } 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 group one per residue 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: 16.320 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: 0.730 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 40.470 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.070 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 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 0.037 13089 Z= 0.276 Angle : 0.628 4.714 18104 Z= 0.422 Chirality : 0.048 0.195 2198 Planarity : 0.003 0.035 2294 Dihedral : 14.960 172.750 3905 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.13 % Allowed : 6.67 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.87 (0.19), residues: 1915 helix: -0.43 (0.18), residues: 832 sheet: -2.29 (0.30), residues: 240 loop : -1.66 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 230 HIS 0.003 0.001 HIS G 482 PHE 0.014 0.001 PHE G 446 TYR 0.019 0.002 TYR G 311 ARG 0.003 0.000 ARG E 453 Details of bonding type rmsd hydrogen bonds : bond 0.19325 ( 670) hydrogen bonds : angle 7.32441 ( 1907) covalent geometry : bond 0.00472 (13089) covalent geometry : angle 0.62767 (18104) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 224 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 SER cc_start: 0.7964 (p) cc_final: 0.7680 (p) REVERT: E 323 LYS cc_start: 0.7431 (ttmt) cc_final: 0.7007 (ttpp) REVERT: E 480 VAL cc_start: 0.8510 (OUTLIER) cc_final: 0.8278 (p) REVERT: F 216 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.7442 (mt) REVERT: F 282 ASP cc_start: 0.7574 (t70) cc_final: 0.7286 (t0) REVERT: G 238 SER cc_start: 0.7658 (p) cc_final: 0.7451 (t) REVERT: G 241 GLN cc_start: 0.8063 (mt0) cc_final: 0.7641 (tp-100) REVERT: G 439 GLN cc_start: 0.8315 (tp40) cc_final: 0.7863 (mm-40) outliers start: 16 outliers final: 5 residues processed: 237 average time/residue: 0.2301 time to fit residues: 80.4621 Evaluate side-chains 161 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 154 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain E residue 480 VAL Chi-restraints excluded: chain F residue 216 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 0.0570 chunk 144 optimal weight: 0.8980 chunk 80 optimal weight: 50.0000 chunk 49 optimal weight: 20.0000 chunk 97 optimal weight: 40.0000 chunk 77 optimal weight: 50.0000 chunk 149 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 111 optimal weight: 0.8980 chunk 173 optimal weight: 0.7980 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 244 GLN E 247 GLN E 254 ASN F 247 GLN F 254 ASN F 305 ASN F 410 GLN G 269 ASN G 476 HIS G 482 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.184003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.137998 restraints weight = 18107.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.133679 restraints weight = 15953.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.135402 restraints weight = 13406.463| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13089 Z= 0.166 Angle : 0.536 5.981 18104 Z= 0.303 Chirality : 0.045 0.146 2198 Planarity : 0.003 0.032 2294 Dihedral : 14.425 174.534 2337 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.87 % Allowed : 13.87 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.88 (0.19), residues: 1915 helix: 0.51 (0.18), residues: 862 sheet: -2.10 (0.28), residues: 264 loop : -1.16 (0.23), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 230 HIS 0.005 0.001 HIS G 482 PHE 0.014 0.001 PHE C 253 TYR 0.016 0.002 TYR D 250 ARG 0.003 0.001 ARG G 297 Details of bonding type rmsd hydrogen bonds : bond 0.04626 ( 670) hydrogen bonds : angle 4.55914 ( 1907) covalent geometry : bond 0.00374 (13089) covalent geometry : angle 0.53598 (18104) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 240 LYS cc_start: 0.8623 (mttm) cc_final: 0.8353 (mtpp) REVERT: F 282 ASP cc_start: 0.7705 (t70) cc_final: 0.7479 (t0) REVERT: F 411 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8352 (pt) REVERT: G 424 MET cc_start: 0.8028 (mmm) cc_final: 0.7730 (mtt) REVERT: G 439 GLN cc_start: 0.8260 (tp40) cc_final: 0.7996 (mm-40) outliers start: 29 outliers final: 17 residues processed: 184 average time/residue: 0.2007 time to fit residues: 57.3490 Evaluate side-chains 169 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 435 PHE Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 411 ILE Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 261 SER Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 369 CYS Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 466 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 67 optimal weight: 20.0000 chunk 71 optimal weight: 40.0000 chunk 135 optimal weight: 0.0570 chunk 185 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 181 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.8704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.181448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.136516 restraints weight = 18412.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.132081 restraints weight = 20056.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.133281 restraints weight = 18590.053| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13089 Z= 0.144 Angle : 0.492 6.663 18104 Z= 0.272 Chirality : 0.044 0.158 2198 Planarity : 0.003 0.029 2294 Dihedral : 14.487 175.652 2329 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 5.33 % Allowed : 14.13 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.37 (0.19), residues: 1915 helix: 0.97 (0.18), residues: 868 sheet: -1.65 (0.29), residues: 265 loop : -1.04 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 230 HIS 0.003 0.001 HIS G 482 PHE 0.014 0.001 PHE G 364 TYR 0.017 0.002 TYR D 250 ARG 0.004 0.000 ARG F 327 Details of bonding type rmsd hydrogen bonds : bond 0.03658 ( 670) hydrogen bonds : angle 3.92365 ( 1907) covalent geometry : bond 0.00335 (13089) covalent geometry : angle 0.49225 (18104) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 168 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 253 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.7699 (t80) REVERT: F 282 ASP cc_start: 0.7710 (t70) cc_final: 0.7499 (t0) REVERT: G 378 GLU cc_start: 0.7310 (pm20) cc_final: 0.7103 (pm20) outliers start: 40 outliers final: 25 residues processed: 192 average time/residue: 0.1931 time to fit residues: 57.9305 Evaluate side-chains 177 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 435 PHE Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 254 ASN Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 369 CYS Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 353 PHE Chi-restraints excluded: chain G residue 369 CYS Chi-restraints excluded: chain G residue 412 ASP Chi-restraints excluded: chain G residue 451 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 99 optimal weight: 50.0000 chunk 31 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 20 optimal weight: 20.0000 chunk 172 optimal weight: 0.6980 chunk 89 optimal weight: 50.0000 chunk 69 optimal weight: 30.0000 chunk 23 optimal weight: 0.0570 chunk 72 optimal weight: 50.0000 chunk 106 optimal weight: 10.0000 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 241 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.182570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.137218 restraints weight = 18267.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.133238 restraints weight = 17244.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.134751 restraints weight = 15672.378| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13089 Z= 0.132 Angle : 0.472 6.708 18104 Z= 0.260 Chirality : 0.043 0.185 2198 Planarity : 0.002 0.032 2294 Dihedral : 14.481 175.584 2327 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.80 % Allowed : 16.40 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.10 (0.19), residues: 1915 helix: 1.20 (0.18), residues: 868 sheet: -1.46 (0.29), residues: 263 loop : -0.94 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 230 HIS 0.002 0.000 HIS G 482 PHE 0.017 0.001 PHE G 364 TYR 0.014 0.001 TYR G 311 ARG 0.002 0.000 ARG F 327 Details of bonding type rmsd hydrogen bonds : bond 0.03279 ( 670) hydrogen bonds : angle 3.70920 ( 1907) covalent geometry : bond 0.00309 (13089) covalent geometry : angle 0.47152 (18104) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 1.396 Fit side-chains revert: symmetry clash REVERT: C 253 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.7748 (t80) REVERT: F 282 ASP cc_start: 0.7790 (t70) cc_final: 0.7562 (t0) REVERT: G 310 GLN cc_start: 0.7662 (mm-40) cc_final: 0.7405 (mm-40) REVERT: G 378 GLU cc_start: 0.7361 (pm20) cc_final: 0.7152 (pm20) outliers start: 36 outliers final: 25 residues processed: 170 average time/residue: 0.1990 time to fit residues: 53.7202 Evaluate side-chains 172 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 254 ASN Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 254 ASN Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 369 CYS Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 353 PHE Chi-restraints excluded: chain G residue 369 CYS Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 466 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 97 optimal weight: 50.0000 chunk 188 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 138 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 27 optimal weight: 0.0050 chunk 156 optimal weight: 0.0670 chunk 165 optimal weight: 2.9990 chunk 78 optimal weight: 20.0000 chunk 9 optimal weight: 0.0030 chunk 71 optimal weight: 50.0000 overall best weight: 0.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 296 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.179592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.132074 restraints weight = 18181.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.128324 restraints weight = 15442.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.128508 restraints weight = 13576.159| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13089 Z= 0.111 Angle : 0.455 6.901 18104 Z= 0.250 Chirality : 0.043 0.135 2198 Planarity : 0.002 0.032 2294 Dihedral : 14.477 176.389 2327 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.13 % Allowed : 17.47 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.09 (0.19), residues: 1915 helix: 1.34 (0.18), residues: 873 sheet: -1.26 (0.30), residues: 263 loop : -0.88 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 230 HIS 0.001 0.000 HIS G 482 PHE 0.020 0.001 PHE G 364 TYR 0.011 0.001 TYR G 311 ARG 0.002 0.000 ARG G 297 Details of bonding type rmsd hydrogen bonds : bond 0.02972 ( 670) hydrogen bonds : angle 3.54222 ( 1907) covalent geometry : bond 0.00254 (13089) covalent geometry : angle 0.45458 (18104) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 1.428 Fit side-chains revert: symmetry clash REVERT: C 253 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.7760 (t80) outliers start: 31 outliers final: 20 residues processed: 172 average time/residue: 0.1948 time to fit residues: 53.8742 Evaluate side-chains 167 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 435 PHE Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 369 CYS Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 296 ASN Chi-restraints excluded: chain G residue 369 CYS Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 466 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 25 optimal weight: 10.0000 chunk 151 optimal weight: 3.9990 chunk 37 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 17 optimal weight: 50.0000 chunk 6 optimal weight: 9.9990 chunk 50 optimal weight: 0.0980 chunk 186 optimal weight: 1.9990 chunk 70 optimal weight: 50.0000 chunk 5 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 254 ASN F 269 ASN F 349 HIS G 241 GLN G 269 ASN G 296 ASN G 310 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.179201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.133416 restraints weight = 18385.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.129394 restraints weight = 17902.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.129721 restraints weight = 17707.967| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 13089 Z= 0.255 Angle : 0.583 7.817 18104 Z= 0.315 Chirality : 0.046 0.154 2198 Planarity : 0.003 0.035 2294 Dihedral : 14.589 176.495 2327 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 6.27 % Allowed : 16.53 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.11 (0.19), residues: 1915 helix: 1.15 (0.18), residues: 867 sheet: -1.39 (0.30), residues: 253 loop : -0.93 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 242 HIS 0.004 0.001 HIS G 482 PHE 0.018 0.002 PHE G 446 TYR 0.020 0.002 TYR E 311 ARG 0.007 0.001 ARG G 297 Details of bonding type rmsd hydrogen bonds : bond 0.03997 ( 670) hydrogen bonds : angle 3.91381 ( 1907) covalent geometry : bond 0.00619 (13089) covalent geometry : angle 0.58348 (18104) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 151 time to evaluate : 1.455 Fit side-chains REVERT: C 253 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.7685 (t80) REVERT: E 378 GLU cc_start: 0.7546 (tm-30) cc_final: 0.7222 (tm-30) outliers start: 47 outliers final: 34 residues processed: 181 average time/residue: 0.2037 time to fit residues: 57.1319 Evaluate side-chains 182 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 254 ASN Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 435 PHE Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 369 CYS Chi-restraints excluded: chain F residue 462 THR Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 461 VAL Chi-restraints excluded: chain G residue 466 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 23 optimal weight: 30.0000 chunk 154 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 126 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 310 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.176750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.130063 restraints weight = 18531.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.124404 restraints weight = 20583.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.125058 restraints weight = 21412.361| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13089 Z= 0.171 Angle : 0.510 7.192 18104 Z= 0.276 Chirality : 0.045 0.389 2198 Planarity : 0.002 0.033 2294 Dihedral : 14.518 176.171 2327 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.67 % Allowed : 18.80 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.09 (0.19), residues: 1915 helix: 1.36 (0.18), residues: 867 sheet: -1.23 (0.31), residues: 248 loop : -0.90 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 230 HIS 0.003 0.001 HIS G 482 PHE 0.012 0.001 PHE F 446 TYR 0.013 0.001 TYR E 311 ARG 0.002 0.000 ARG F 327 Details of bonding type rmsd hydrogen bonds : bond 0.03370 ( 670) hydrogen bonds : angle 3.67216 ( 1907) covalent geometry : bond 0.00409 (13089) covalent geometry : angle 0.50974 (18104) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 1.281 Fit side-chains REVERT: C 253 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.7668 (t80) REVERT: E 274 MET cc_start: 0.7280 (mtm) cc_final: 0.7034 (mtm) REVERT: E 378 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7219 (tm-30) outliers start: 35 outliers final: 24 residues processed: 174 average time/residue: 0.1898 time to fit residues: 51.5482 Evaluate side-chains 173 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 369 CYS Chi-restraints excluded: chain F residue 462 THR Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 369 CYS Chi-restraints excluded: chain G residue 466 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 58 optimal weight: 0.6980 chunk 79 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 120 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 92 optimal weight: 40.0000 chunk 141 optimal weight: 0.6980 chunk 150 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 269 ASN G 241 GLN ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 310 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.176639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.129087 restraints weight = 18529.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.122745 restraints weight = 17554.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.123789 restraints weight = 17291.509| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13089 Z= 0.127 Angle : 0.478 7.157 18104 Z= 0.261 Chirality : 0.043 0.314 2198 Planarity : 0.002 0.034 2294 Dihedral : 14.444 176.737 2327 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.27 % Allowed : 20.40 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.19), residues: 1915 helix: 1.52 (0.18), residues: 876 sheet: -1.07 (0.32), residues: 238 loop : -0.84 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 230 HIS 0.002 0.000 HIS G 482 PHE 0.009 0.001 PHE C 253 TYR 0.011 0.001 TYR E 311 ARG 0.004 0.000 ARG F 260 Details of bonding type rmsd hydrogen bonds : bond 0.03030 ( 670) hydrogen bonds : angle 3.49582 ( 1907) covalent geometry : bond 0.00300 (13089) covalent geometry : angle 0.47762 (18104) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 1.257 Fit side-chains REVERT: C 253 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.7756 (t80) REVERT: E 274 MET cc_start: 0.7309 (mtm) cc_final: 0.7038 (mtm) REVERT: E 378 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7237 (tm-30) outliers start: 32 outliers final: 25 residues processed: 171 average time/residue: 0.1912 time to fit residues: 50.9774 Evaluate side-chains 174 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 254 ASN Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 369 CYS Chi-restraints excluded: chain F residue 462 THR Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 466 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 54 optimal weight: 0.2980 chunk 59 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 50.0000 chunk 170 optimal weight: 0.0060 chunk 111 optimal weight: 0.7980 chunk 105 optimal weight: 40.0000 chunk 17 optimal weight: 30.0000 chunk 94 optimal weight: 7.9990 chunk 49 optimal weight: 50.0000 chunk 171 optimal weight: 0.9980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN E 421 ASN G 241 GLN ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 310 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.179900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.131638 restraints weight = 18343.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.127084 restraints weight = 14362.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.128311 restraints weight = 12501.449| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13089 Z= 0.117 Angle : 0.474 7.121 18104 Z= 0.257 Chirality : 0.043 0.358 2198 Planarity : 0.002 0.033 2294 Dihedral : 14.399 177.715 2327 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.87 % Allowed : 21.73 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.46 (0.19), residues: 1915 helix: 1.65 (0.18), residues: 878 sheet: -0.97 (0.32), residues: 238 loop : -0.77 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 230 HIS 0.002 0.000 HIS G 482 PHE 0.021 0.001 PHE E 364 TYR 0.010 0.001 TYR E 311 ARG 0.006 0.000 ARG F 260 Details of bonding type rmsd hydrogen bonds : bond 0.02828 ( 670) hydrogen bonds : angle 3.39510 ( 1907) covalent geometry : bond 0.00275 (13089) covalent geometry : angle 0.47352 (18104) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 1.280 Fit side-chains REVERT: C 253 PHE cc_start: 0.8620 (OUTLIER) cc_final: 0.7767 (t80) REVERT: E 274 MET cc_start: 0.7309 (mtm) cc_final: 0.7081 (mtm) REVERT: E 378 GLU cc_start: 0.7561 (tm-30) cc_final: 0.7151 (tm-30) REVERT: F 419 THR cc_start: 0.9047 (p) cc_final: 0.8818 (p) outliers start: 29 outliers final: 22 residues processed: 164 average time/residue: 0.1811 time to fit residues: 47.2911 Evaluate side-chains 166 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain E residue 254 ASN Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 421 ASN Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 369 CYS Chi-restraints excluded: chain F residue 462 THR Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 466 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 168 optimal weight: 0.0980 chunk 187 optimal weight: 0.6980 chunk 49 optimal weight: 50.0000 chunk 111 optimal weight: 0.4980 chunk 8 optimal weight: 40.0000 chunk 4 optimal weight: 0.4980 chunk 163 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 144 optimal weight: 0.6980 chunk 135 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 241 GLN ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 310 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.180168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.132637 restraints weight = 18400.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.128074 restraints weight = 15469.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.128970 restraints weight = 13207.080| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13089 Z= 0.113 Angle : 0.474 7.243 18104 Z= 0.258 Chirality : 0.043 0.344 2198 Planarity : 0.002 0.034 2294 Dihedral : 14.392 177.856 2327 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.47 % Allowed : 22.80 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.49 (0.19), residues: 1915 helix: 1.67 (0.18), residues: 878 sheet: -0.94 (0.32), residues: 238 loop : -0.76 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 230 HIS 0.001 0.000 HIS G 482 PHE 0.011 0.001 PHE G 353 TYR 0.017 0.001 TYR C 250 ARG 0.004 0.000 ARG F 260 Details of bonding type rmsd hydrogen bonds : bond 0.02784 ( 670) hydrogen bonds : angle 3.37120 ( 1907) covalent geometry : bond 0.00261 (13089) covalent geometry : angle 0.47387 (18104) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 1.268 Fit side-chains REVERT: C 253 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.7769 (t80) REVERT: E 274 MET cc_start: 0.7381 (mtm) cc_final: 0.7115 (mtm) REVERT: E 378 GLU cc_start: 0.7614 (tm-30) cc_final: 0.7189 (tm-30) REVERT: F 240 LYS cc_start: 0.8640 (mtpp) cc_final: 0.8382 (mmmt) REVERT: F 419 THR cc_start: 0.9024 (p) cc_final: 0.8797 (p) outliers start: 26 outliers final: 21 residues processed: 163 average time/residue: 0.1809 time to fit residues: 47.2090 Evaluate side-chains 165 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain E residue 254 ASN Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 369 CYS Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 466 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 47 optimal weight: 50.0000 chunk 39 optimal weight: 50.0000 chunk 150 optimal weight: 0.7980 chunk 43 optimal weight: 30.0000 chunk 108 optimal weight: 0.4980 chunk 100 optimal weight: 7.9990 chunk 105 optimal weight: 0.0980 chunk 73 optimal weight: 6.9990 chunk 12 optimal weight: 50.0000 chunk 53 optimal weight: 0.6980 chunk 119 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 305 ASN G 310 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.180156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.133425 restraints weight = 18487.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.127571 restraints weight = 18845.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.129034 restraints weight = 17819.649| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13089 Z= 0.117 Angle : 0.471 7.311 18104 Z= 0.256 Chirality : 0.043 0.379 2198 Planarity : 0.002 0.033 2294 Dihedral : 14.377 178.628 2327 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.07 % Allowed : 23.20 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.51 (0.19), residues: 1915 helix: 1.69 (0.18), residues: 881 sheet: -0.85 (0.32), residues: 236 loop : -0.80 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 230 HIS 0.002 0.000 HIS G 482 PHE 0.009 0.001 PHE C 253 TYR 0.015 0.001 TYR A 283 ARG 0.004 0.000 ARG F 260 Details of bonding type rmsd hydrogen bonds : bond 0.02758 ( 670) hydrogen bonds : angle 3.33628 ( 1907) covalent geometry : bond 0.00275 (13089) covalent geometry : angle 0.47073 (18104) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4513.30 seconds wall clock time: 78 minutes 38.94 seconds (4718.94 seconds total)