Starting phenix.real_space_refine on Thu May 15 06:57:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bu7_44902/05_2025/9bu7_44902.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bu7_44902/05_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_44902/05_2025/9bu7_44902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bu7_44902/05_2025/9bu7_44902.map" model { file = "/net/cci-nas-00/data/ceres_data/9bu7_44902/05_2025/9bu7_44902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bu7_44902/05_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-5687/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: 11.62, per 1000 atoms: 0.91 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: 3.60 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: 4.01 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: 3.69 Time building geometry restraints manager: 4.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 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: 14.310 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: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 36.880 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.610 ------------------------------------------------------------------------------- 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 : 1.298 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: 0.2190 time to fit residues: 76.4091 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 : 1.302 ------------------------------------------------------------------------------- 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 = 0.137997 restraints weight = 18107.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.133679 restraints weight = 15953.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.135404 restraints weight = 13406.369| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 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 : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 240 LYS cc_start: 0.8644 (mttm) cc_final: 0.8364 (mtpp) REVERT: F 282 ASP cc_start: 0.7752 (t70) cc_final: 0.7508 (t0) REVERT: F 411 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8348 (pt) REVERT: G 424 MET cc_start: 0.8042 (mmm) cc_final: 0.7753 (mtt) REVERT: G 439 GLN cc_start: 0.8270 (tp40) cc_final: 0.7985 (mm-40) outliers start: 29 outliers final: 17 residues processed: 184 average time/residue: 0.2050 time to fit residues: 58.9052 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 : 1.475 ------------------------------------------------------------------------------- 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: 1.9990 chunk 185 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 181 optimal weight: 0.2980 chunk 58 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.178660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.132523 restraints weight = 18313.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.126765 restraints weight = 18255.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.127528 restraints weight = 17866.661| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13089 Z= 0.158 Angle : 0.501 6.661 18104 Z= 0.276 Chirality : 0.044 0.176 2198 Planarity : 0.003 0.032 2294 Dihedral : 14.485 175.440 2329 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 5.47 % Allowed : 14.00 % 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: -0.39 (0.19), residues: 1915 helix: 0.97 (0.18), residues: 862 sheet: -1.69 (0.29), residues: 265 loop : -1.05 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 230 HIS 0.004 0.001 HIS G 482 PHE 0.015 0.001 PHE D 253 TYR 0.016 0.002 TYR D 250 ARG 0.004 0.000 ARG F 327 Details of bonding type rmsd hydrogen bonds : bond 0.03801 ( 670) hydrogen bonds : angle 3.97979 ( 1907) covalent geometry : bond 0.00373 (13089) covalent geometry : angle 0.50083 (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 205 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 164 time to evaluate : 1.525 Fit side-chains revert: symmetry clash REVERT: C 253 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.7744 (t80) REVERT: E 378 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7151 (tm-30) REVERT: F 282 ASP cc_start: 0.7870 (t70) cc_final: 0.7590 (t0) REVERT: G 239 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7589 (mt-10) REVERT: G 378 GLU cc_start: 0.7457 (pm20) cc_final: 0.7215 (pm20) outliers start: 41 outliers final: 28 residues processed: 187 average time/residue: 0.1903 time to fit residues: 55.6154 Evaluate side-chains 181 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 1.289 ------------------------------------------------------------------------------- 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 254 ASN 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 296 ASN 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 Chi-restraints excluded: chain G residue 466 VAL 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: 0.9990 chunk 87 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 20 optimal weight: 9.9990 chunk 172 optimal weight: 0.5980 chunk 89 optimal weight: 40.0000 chunk 69 optimal weight: 40.0000 chunk 23 optimal weight: 20.0000 chunk 72 optimal weight: 40.0000 chunk 106 optimal weight: 9.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 254 ASN G 241 GLN G 269 ASN ** G 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.174725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.127013 restraints weight = 18441.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.121883 restraints weight = 19757.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.122858 restraints weight = 17287.749| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.067 13089 Z= 0.376 Angle : 0.696 8.155 18104 Z= 0.376 Chirality : 0.049 0.176 2198 Planarity : 0.004 0.041 2294 Dihedral : 14.704 174.892 2327 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 6.80 % Allowed : 16.13 % Favored : 77.07 % 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: -0.79 (0.19), residues: 1915 helix: 0.57 (0.18), residues: 865 sheet: -1.86 (0.29), residues: 254 loop : -1.20 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 230 HIS 0.006 0.001 HIS G 482 PHE 0.023 0.003 PHE F 446 TYR 0.025 0.002 TYR E 311 ARG 0.004 0.001 ARG F 327 Details of bonding type rmsd hydrogen bonds : bond 0.04999 ( 670) hydrogen bonds : angle 4.45240 ( 1907) covalent geometry : bond 0.00907 (13089) covalent geometry : angle 0.69614 (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 208 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 157 time to evaluate : 1.339 Fit side-chains REVERT: C 253 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.7834 (t80) REVERT: E 378 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7382 (tm-30) REVERT: F 282 ASP cc_start: 0.7835 (t70) cc_final: 0.7401 (t0) outliers start: 51 outliers final: 35 residues processed: 190 average time/residue: 0.1910 time to fit residues: 57.3758 Evaluate side-chains 181 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 1.410 ------------------------------------------------------------------------------- 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 B residue 241 GLN 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 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 435 PHE Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 369 CYS Chi-restraints excluded: chain F residue 386 VAL Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 218 SER Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 330 ILE 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 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: 8.9990 chunk 188 optimal weight: 0.7980 chunk 100 optimal weight: 30.0000 chunk 138 optimal weight: 0.4980 chunk 57 optimal weight: 0.8980 chunk 27 optimal weight: 0.3980 chunk 156 optimal weight: 0.9980 chunk 165 optimal weight: 0.9980 chunk 78 optimal weight: 20.0000 chunk 9 optimal weight: 40.0000 chunk 71 optimal weight: 50.0000 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 254 ASN F 269 ASN G 269 ASN ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.179732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.131268 restraints weight = 18271.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.127213 restraints weight = 17910.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.128205 restraints weight = 15616.536| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3217 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= 0.126 Angle : 0.492 7.693 18104 Z= 0.271 Chirality : 0.044 0.406 2198 Planarity : 0.003 0.038 2294 Dihedral : 14.510 174.906 2327 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.40 % Allowed : 18.80 % Favored : 76.80 % 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: -0.23 (0.19), residues: 1915 helix: 1.11 (0.18), residues: 860 sheet: -1.63 (0.30), residues: 254 loop : -0.98 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 230 HIS 0.002 0.001 HIS G 349 PHE 0.018 0.001 PHE G 364 TYR 0.014 0.001 TYR G 311 ARG 0.003 0.000 ARG F 444 Details of bonding type rmsd hydrogen bonds : bond 0.03511 ( 670) hydrogen bonds : angle 3.79995 ( 1907) covalent geometry : bond 0.00290 (13089) covalent geometry : angle 0.49200 (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 195 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 1.479 Fit side-chains REVERT: C 253 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.7650 (t80) REVERT: E 274 MET cc_start: 0.7540 (mtm) cc_final: 0.7324 (mtm) REVERT: E 378 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7270 (tm-30) REVERT: F 282 ASP cc_start: 0.7863 (t70) cc_final: 0.7483 (t0) REVERT: F 411 ILE cc_start: 0.8628 (tt) cc_final: 0.8404 (pt) outliers start: 33 outliers final: 22 residues processed: 179 average time/residue: 0.1870 time to fit residues: 53.3160 Evaluate side-chains 173 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 1.309 ------------------------------------------------------------------------------- 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 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 401 VAL Chi-restraints excluded: chain E residue 445 MET 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 369 CYS Chi-restraints excluded: chain G residue 451 THR 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: 0.9990 chunk 37 optimal weight: 30.0000 chunk 13 optimal weight: 8.9990 chunk 17 optimal weight: 50.0000 chunk 6 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 186 optimal weight: 3.9990 chunk 70 optimal weight: 30.0000 chunk 5 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 310 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.173301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.127174 restraints weight = 18875.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.120364 restraints weight = 21268.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.122107 restraints weight = 19304.282| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.101 13089 Z= 0.368 Angle : 0.685 8.283 18104 Z= 0.368 Chirality : 0.050 0.328 2198 Planarity : 0.004 0.038 2294 Dihedral : 14.690 175.413 2327 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 6.40 % Allowed : 18.93 % Favored : 74.67 % 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: -0.62 (0.19), residues: 1915 helix: 0.69 (0.18), residues: 868 sheet: -1.78 (0.30), residues: 254 loop : -1.08 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 230 HIS 0.006 0.001 HIS G 482 PHE 0.024 0.003 PHE F 446 TYR 0.021 0.002 TYR E 311 ARG 0.005 0.001 ARG F 260 Details of bonding type rmsd hydrogen bonds : bond 0.04875 ( 670) hydrogen bonds : angle 4.32574 ( 1907) covalent geometry : bond 0.00894 (13089) covalent geometry : angle 0.68537 (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 201 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 153 time to evaluate : 1.446 Fit side-chains revert: symmetry clash REVERT: C 253 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.7806 (t80) REVERT: E 378 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7450 (tm-30) REVERT: F 282 ASP cc_start: 0.7904 (t70) cc_final: 0.7444 (t0) outliers start: 48 outliers final: 40 residues processed: 179 average time/residue: 0.1924 time to fit residues: 54.1324 Evaluate side-chains 190 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 149 time to evaluate : 1.324 ------------------------------------------------------------------------------- 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 276 LEU 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 218 SER 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 304 LEU Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 221 SER 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 G residue 215 VAL Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain G residue 263 ILE 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 369 CYS Chi-restraints excluded: chain G residue 412 ASP Chi-restraints excluded: chain G residue 451 THR 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: 20.0000 chunk 154 optimal weight: 2.9990 chunk 185 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 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 = 0.4161 r_free = 0.4161 target = 0.174189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.126668 restraints weight = 18591.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.119305 restraints weight = 19419.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.120483 restraints weight = 19153.370| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3659 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= 0.143 Angle : 0.496 7.218 18104 Z= 0.272 Chirality : 0.044 0.341 2198 Planarity : 0.003 0.040 2294 Dihedral : 14.506 175.252 2327 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.93 % Allowed : 21.33 % 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: -0.14 (0.19), residues: 1915 helix: 1.21 (0.18), residues: 861 sheet: -1.58 (0.31), residues: 244 loop : -0.99 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 230 HIS 0.002 0.001 HIS G 482 PHE 0.015 0.001 PHE F 435 TYR 0.016 0.002 TYR G 311 ARG 0.004 0.000 ARG G 444 Details of bonding type rmsd hydrogen bonds : bond 0.03488 ( 670) hydrogen bonds : angle 3.74500 ( 1907) covalent geometry : bond 0.00336 (13089) covalent geometry : angle 0.49644 (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 197 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 1.331 Fit side-chains revert: symmetry clash REVERT: A 253 PHE cc_start: 0.7821 (OUTLIER) cc_final: 0.7413 (t80) REVERT: C 253 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.7701 (t80) REVERT: E 274 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.7125 (mtm) REVERT: E 378 GLU cc_start: 0.7546 (tm-30) cc_final: 0.7282 (tm-30) REVERT: F 282 ASP cc_start: 0.7924 (t70) cc_final: 0.7481 (t0) REVERT: F 471 ARG cc_start: 0.8164 (tpt90) cc_final: 0.7921 (tpt90) outliers start: 37 outliers final: 29 residues processed: 178 average time/residue: 0.1882 time to fit residues: 52.7026 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 : 1.417 ------------------------------------------------------------------------------- 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 253 PHE 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 252 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 274 MET Chi-restraints excluded: chain E residue 435 PHE Chi-restraints excluded: chain F residue 232 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 387 VAL Chi-restraints excluded: chain F residue 411 ILE Chi-restraints excluded: chain F residue 412 ASP Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain G residue 369 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 58 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 26 optimal weight: 0.0010 chunk 54 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 92 optimal weight: 40.0000 chunk 141 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 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 = 0.4200 r_free = 0.4200 target = 0.177684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.133034 restraints weight = 18539.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.128582 restraints weight = 20683.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.128742 restraints weight = 19839.039| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3790 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= 0.134 Angle : 0.489 7.150 18104 Z= 0.266 Chirality : 0.044 0.317 2198 Planarity : 0.002 0.040 2294 Dihedral : 14.453 176.123 2327 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.93 % Allowed : 22.00 % Favored : 73.07 % 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: 0.07 (0.19), residues: 1915 helix: 1.40 (0.18), residues: 863 sheet: -1.42 (0.31), residues: 249 loop : -0.92 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 230 HIS 0.002 0.000 HIS G 482 PHE 0.011 0.001 PHE C 253 TYR 0.013 0.001 TYR G 311 ARG 0.006 0.000 ARG F 260 Details of bonding type rmsd hydrogen bonds : bond 0.03245 ( 670) hydrogen bonds : angle 3.60929 ( 1907) covalent geometry : bond 0.00316 (13089) covalent geometry : angle 0.48934 (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 192 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 1.475 Fit side-chains revert: symmetry clash REVERT: A 253 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.7316 (t80) REVERT: C 253 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.7721 (t80) REVERT: E 274 MET cc_start: 0.7236 (OUTLIER) cc_final: 0.7024 (mtm) REVERT: F 282 ASP cc_start: 0.7863 (t70) cc_final: 0.7474 (t0) REVERT: F 471 ARG cc_start: 0.8108 (tpt90) cc_final: 0.7830 (tpt90) outliers start: 37 outliers final: 28 residues processed: 174 average time/residue: 0.1972 time to fit residues: 53.5723 Evaluate side-chains 182 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 1.448 ------------------------------------------------------------------------------- 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 253 PHE 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 251 ILE Chi-restraints excluded: chain D residue 252 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 274 MET Chi-restraints excluded: chain E residue 401 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 387 VAL Chi-restraints excluded: chain F residue 411 ILE Chi-restraints excluded: chain F residue 412 ASP 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 276 LEU Chi-restraints excluded: chain G residue 369 CYS 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: 10.0000 chunk 59 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 50.0000 chunk 170 optimal weight: 0.0070 chunk 111 optimal weight: 0.6980 chunk 105 optimal weight: 40.0000 chunk 17 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 49 optimal weight: 0.1980 chunk 171 optimal weight: 0.9980 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 = 0.4247 r_free = 0.4247 target = 0.182146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.135337 restraints weight = 18530.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.129657 restraints weight = 18887.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.130540 restraints weight = 18310.540| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3925 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= 0.114 Angle : 0.481 7.432 18104 Z= 0.261 Chirality : 0.043 0.351 2198 Planarity : 0.002 0.039 2294 Dihedral : 14.414 176.923 2327 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.80 % Allowed : 21.87 % Favored : 73.33 % 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: 0.28 (0.20), residues: 1915 helix: 1.56 (0.18), residues: 867 sheet: -1.25 (0.31), residues: 247 loop : -0.83 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 230 HIS 0.002 0.000 HIS E 437 PHE 0.010 0.001 PHE C 253 TYR 0.012 0.001 TYR G 311 ARG 0.005 0.000 ARG F 260 Details of bonding type rmsd hydrogen bonds : bond 0.02939 ( 670) hydrogen bonds : angle 3.44664 ( 1907) covalent geometry : bond 0.00264 (13089) covalent geometry : angle 0.48063 (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 198 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 1.410 Fit side-chains revert: symmetry clash REVERT: A 253 PHE cc_start: 0.7664 (OUTLIER) cc_final: 0.7250 (t80) REVERT: C 253 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.7716 (t80) REVERT: E 274 MET cc_start: 0.7284 (OUTLIER) cc_final: 0.7048 (mtm) REVERT: F 240 LYS cc_start: 0.8529 (mtpp) cc_final: 0.8292 (mmmt) REVERT: F 282 ASP cc_start: 0.7807 (t70) cc_final: 0.7475 (t0) REVERT: F 471 ARG cc_start: 0.8092 (tpt90) cc_final: 0.7819 (tpt90) REVERT: G 378 GLU cc_start: 0.7285 (pm20) cc_final: 0.6947 (pm20) outliers start: 36 outliers final: 28 residues processed: 180 average time/residue: 0.1940 time to fit residues: 54.8795 Evaluate side-chains 185 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 VAL 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 253 PHE Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 252 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 274 MET Chi-restraints excluded: chain E residue 401 VAL 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 F residue 387 VAL Chi-restraints excluded: chain F residue 411 ILE Chi-restraints excluded: chain F residue 412 ASP Chi-restraints excluded: chain F residue 462 THR Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 218 SER Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain G residue 369 CYS 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: 1.9990 chunk 187 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 8 optimal weight: 30.0000 chunk 4 optimal weight: 1.9990 chunk 163 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4206 r_free = 0.4206 target = 0.178192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.133150 restraints weight = 18524.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.128903 restraints weight = 20765.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.129991 restraints weight = 19619.030| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.4040 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= 0.132 Angle : 0.487 7.390 18104 Z= 0.263 Chirality : 0.044 0.320 2198 Planarity : 0.002 0.039 2294 Dihedral : 14.425 177.535 2327 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.40 % Allowed : 22.40 % Favored : 73.20 % 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: 0.34 (0.20), residues: 1915 helix: 1.60 (0.18), residues: 868 sheet: -1.19 (0.31), residues: 247 loop : -0.80 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 230 HIS 0.002 0.000 HIS G 482 PHE 0.011 0.001 PHE C 253 TYR 0.012 0.001 TYR C 250 ARG 0.004 0.000 ARG F 260 Details of bonding type rmsd hydrogen bonds : bond 0.03014 ( 670) hydrogen bonds : angle 3.45459 ( 1907) covalent geometry : bond 0.00313 (13089) covalent geometry : angle 0.48699 (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 187 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 1.524 Fit side-chains REVERT: A 253 PHE cc_start: 0.7646 (OUTLIER) cc_final: 0.7230 (t80) REVERT: C 253 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.7686 (t80) REVERT: E 368 ASP cc_start: 0.8484 (t70) cc_final: 0.8044 (p0) REVERT: F 240 LYS cc_start: 0.8518 (mtpp) cc_final: 0.8271 (mmmt) REVERT: F 282 ASP cc_start: 0.7782 (t70) cc_final: 0.7446 (t0) REVERT: F 471 ARG cc_start: 0.8116 (tpt90) cc_final: 0.7824 (tpt90) REVERT: G 353 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.7952 (p90) outliers start: 33 outliers final: 24 residues processed: 174 average time/residue: 0.1975 time to fit residues: 53.7470 Evaluate side-chains 178 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 252 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 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 387 VAL Chi-restraints excluded: chain F residue 412 ASP Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 218 SER 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 353 PHE Chi-restraints excluded: chain G residue 369 CYS 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: 0.8980 chunk 43 optimal weight: 10.0000 chunk 108 optimal weight: 0.0770 chunk 100 optimal weight: 1.9990 chunk 105 optimal weight: 20.0000 chunk 73 optimal weight: 6.9990 chunk 12 optimal weight: 40.0000 chunk 53 optimal weight: 6.9990 chunk 119 optimal weight: 0.6980 overall best weight: 2.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 ASN F 254 ASN F 269 ASN G 310 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.173715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.126938 restraints weight = 18944.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.121720 restraints weight = 21406.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.122625 restraints weight = 20981.927| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 13089 Z= 0.269 Angle : 0.603 11.334 18104 Z= 0.322 Chirality : 0.047 0.360 2198 Planarity : 0.003 0.037 2294 Dihedral : 14.558 177.506 2327 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.13 % Allowed : 23.20 % Favored : 72.67 % 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: 0.07 (0.19), residues: 1915 helix: 1.32 (0.18), residues: 872 sheet: -1.26 (0.31), residues: 243 loop : -0.90 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 230 HIS 0.003 0.001 HIS G 482 PHE 0.020 0.002 PHE F 446 TYR 0.018 0.002 TYR D 250 ARG 0.004 0.000 ARG F 260 Details of bonding type rmsd hydrogen bonds : bond 0.04020 ( 670) hydrogen bonds : angle 3.86306 ( 1907) covalent geometry : bond 0.00650 (13089) covalent geometry : angle 0.60276 (18104) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4182.52 seconds wall clock time: 73 minutes 51.87 seconds (4431.87 seconds total)