Starting phenix.real_space_refine on Sat Aug 23 14:57:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bu7_44902/08_2025/9bu7_44902.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bu7_44902/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9bu7_44902/08_2025/9bu7_44902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bu7_44902/08_2025/9bu7_44902.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bu7_44902/08_2025/9bu7_44902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bu7_44902/08_2025/9bu7_44902.map" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ARG:plan': 9, 'GLU:plan': 14, 'ASN:plan1': 12, 'ASP:plan': 14, 'GLN:plan1': 9, 'TYR:plan': 5, 'PHE:plan': 13, 'TRP:plan': 6, 'HIS:plan': 5} 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: {'ARG:plan': 10, 'GLU:plan': 16, 'ASP:plan': 15, 'ASN:plan1': 12, 'GLN:plan1': 9, 'TYR:plan': 5, 'PHE:plan': 13, 'TRP:plan': 6, 'HIS:plan': 5} 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: {'ARG:plan': 10, 'GLU:plan': 15, 'ASP:plan': 14, 'GLN:plan1': 11, 'TYR:plan': 6, 'ASN:plan1': 11, 'PHE:plan': 13, 'TRP:plan': 6, 'HIS:plan': 5} 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: {'ARG:plan': 9, 'GLU:plan': 16, 'ASP:plan': 14, 'GLN:plan1': 9, 'ASN:plan1': 11, 'TYR:plan': 5, 'PHE:plan': 13, 'TRP:plan': 6, 'HIS:plan': 5} 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: {'ARG:plan': 3, 'ASP:plan': 6, 'GLN:plan1': 2, 'GLU:plan': 9, 'ASN:plan1': 2, 'TYR:plan': 1} 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: {'ARG:plan': 3, 'GLN:plan1': 3, 'ASP:plan': 8, 'GLU:plan': 9, 'ASN:plan1': 2, 'PHE:plan': 1, 'TYR:plan': 1} 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: 4.00, per 1000 atoms: 0.31 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: 1.38 Conformation dependent library (CDL) restraints added in 773.2 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 218 through 235 Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 246 through 254 removed outlier: 3.655A pdb=" N TYR A 250 " --> pdb=" O ASP A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 278 Processing helix chain 'A' and resid 279 through 285 removed outlier: 3.998A pdb=" N TYR A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 304 Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.545A pdb=" N SER A 314 " --> pdb=" O GLN A 310 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 350 removed outlier: 3.599A pdb=" N ALA A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 removed outlier: 3.982A pdb=" N VAL A 370 " --> pdb=" O ASN A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 395 removed outlier: 4.704A pdb=" N GLU A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N SER A 389 " --> pdb=" O LYS A 385 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 443 Processing helix chain 'A' and resid 462 through 475 removed outlier: 3.947A pdb=" N PHE A 469 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP A 475 " --> pdb=" O ARG A 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 235 Processing helix chain 'B' and resid 238 through 246 Processing helix chain 'B' and resid 246 through 254 removed outlier: 3.688A pdb=" N TYR B 250 " --> pdb=" O ASP B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 276 Processing helix chain 'B' and resid 279 through 284 Processing helix chain 'B' and resid 296 through 305 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 339 through 349 Processing helix chain 'B' and resid 366 through 370 removed outlier: 4.200A pdb=" N VAL B 370 " --> pdb=" O ASN B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 395 Processing helix chain 'B' and resid 437 through 443 Processing helix chain 'B' and resid 462 through 476 Processing helix chain 'C' and resid 218 through 235 Processing helix chain 'C' and resid 238 through 246 Processing helix chain 'C' and resid 246 through 254 removed outlier: 3.895A pdb=" N TYR C 250 " --> pdb=" O ASP C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 278 removed outlier: 3.850A pdb=" N GLN C 262 " --> pdb=" O ASN C 258 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS C 278 " --> pdb=" O MET C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 281 No H-bonds generated for 'chain 'C' and resid 280 through 281' Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 296 through 305 Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.572A pdb=" N SER C 314 " --> pdb=" O GLN C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 349 Processing helix chain 'C' and resid 383 through 394 removed outlier: 4.399A pdb=" N GLU C 388 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N SER C 389 " --> pdb=" O LYS C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 443 Processing helix chain 'C' and resid 455 through 459 removed outlier: 4.430A pdb=" N GLY C 459 " --> pdb=" O HIS C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 476 Processing helix chain 'D' and resid 218 through 235 Processing helix chain 'D' and resid 238 through 246 Processing helix chain 'D' and resid 246 through 253 removed outlier: 4.163A pdb=" N TYR D 250 " --> pdb=" O ASP D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 278 removed outlier: 4.625A pdb=" N LYS D 264 " --> pdb=" O ARG D 260 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA D 265 " --> pdb=" O SER D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 285 Processing helix chain 'D' and resid 296 through 304 Processing helix chain 'D' and resid 308 through 322 Processing helix chain 'D' and resid 339 through 348 removed outlier: 3.760A pdb=" N ALA D 346 " --> pdb=" O ASN D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 395 Processing helix chain 'D' and resid 437 through 443 Processing helix chain 'D' and resid 462 through 476 removed outlier: 4.173A pdb=" N LYS D 474 " --> pdb=" O PHE D 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 235 Processing helix chain 'E' and resid 238 through 246 Processing helix chain 'E' and resid 246 through 256 removed outlier: 3.623A pdb=" N TYR E 250 " --> pdb=" O ASP E 246 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA E 256 " --> pdb=" O SER E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 278 Processing helix chain 'E' and resid 279 through 285 removed outlier: 3.581A pdb=" N TYR E 283 " --> pdb=" O THR E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 295 removed outlier: 4.031A pdb=" N SER E 295 " --> pdb=" O ASP E 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 292 through 295' Processing helix chain 'E' and resid 296 through 306 removed outlier: 3.543A pdb=" N LYS E 300 " --> pdb=" O ASN E 296 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN E 305 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY E 306 " --> pdb=" O LEU E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 339 through 351 removed outlier: 3.647A pdb=" N VAL E 351 " --> pdb=" O ILE E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 385 No H-bonds generated for 'chain 'E' and resid 383 through 385' Processing helix chain 'E' and resid 386 through 394 Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 462 through 475 Processing helix chain 'F' and resid 218 through 234 removed outlier: 3.502A pdb=" N ALA F 222 " --> pdb=" O SER F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 246 Processing helix chain 'F' and resid 246 through 254 removed outlier: 3.931A pdb=" N TYR F 250 " --> pdb=" O ASP F 246 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN F 254 " --> pdb=" O TYR F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 276 removed outlier: 4.148A pdb=" N LYS F 264 " --> pdb=" O ARG F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 285 removed outlier: 3.890A pdb=" N VAL F 285 " --> pdb=" O PRO F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 305 removed outlier: 3.632A pdb=" N LYS F 300 " --> pdb=" O ASN F 296 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN F 305 " --> pdb=" O ILE F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 322 Processing helix chain 'F' and resid 339 through 351 removed outlier: 3.882A pdb=" N ILE F 343 " --> pdb=" O GLY F 339 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL F 351 " --> pdb=" O ILE F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 394 removed outlier: 4.427A pdb=" N ALA F 392 " --> pdb=" O GLU F 388 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE F 393 " --> pdb=" O SER F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 464 through 475 removed outlier: 3.921A pdb=" N ASP F 475 " --> pdb=" O ARG F 471 " (cutoff:3.500A) Processing helix chain 'G' and resid 218 through 234 Processing helix chain 'G' and resid 238 through 246 Processing helix chain 'G' and resid 246 through 254 removed outlier: 3.753A pdb=" N TYR G 250 " --> pdb=" O ASP G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 276 removed outlier: 4.303A pdb=" N SER G 261 " --> pdb=" O SER G 257 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS G 264 " --> pdb=" O ARG G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 285 removed outlier: 4.314A pdb=" N TYR G 283 " --> pdb=" O THR G 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 305 Processing helix chain 'G' and resid 308 through 321 Processing helix chain 'G' and resid 339 through 350 Processing helix chain 'G' and resid 386 through 394 removed outlier: 3.782A pdb=" N ALA G 392 " --> pdb=" O GLU G 388 " (cutoff:3.500A) Processing helix chain 'G' and resid 437 through 443 removed outlier: 3.828A pdb=" N LEU G 441 " --> pdb=" O HIS G 437 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 476 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 356 removed outlier: 6.619A pdb=" N GLY A 355 " --> pdb=" O TRP A 376 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N GLU A 378 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE A 375 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N THR A 419 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TRP A 377 " --> pdb=" O THR A 419 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 382 through 383 removed outlier: 6.554A pdb=" N MET A 382 " --> pdb=" O ILE A 428 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 399 through 403 removed outlier: 4.389A pdb=" N GLN A 403 " --> pdb=" O SER A 407 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N SER A 407 " --> pdb=" O GLN A 403 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 356 removed outlier: 6.322A pdb=" N GLY B 355 " --> pdb=" O TRP B 376 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLU B 378 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE B 330 " --> pdb=" O VAL B 418 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N SER B 420 " --> pdb=" O ILE B 330 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU B 332 " --> pdb=" O SER B 420 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TRP B 331 " --> pdb=" O PHE B 448 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 399 through 403 removed outlier: 3.574A pdb=" N VAL B 399 " --> pdb=" O ILE B 411 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLN B 403 " --> pdb=" O SER B 407 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N SER B 407 " --> pdb=" O GLN B 403 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 427 through 429 Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 356 removed outlier: 6.241A pdb=" N GLY C 355 " --> pdb=" O TRP C 376 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLU C 378 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR C 419 " --> pdb=" O TRP C 377 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 399 through 403 removed outlier: 3.506A pdb=" N VAL C 399 " --> pdb=" O ILE C 411 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLN C 403 " --> pdb=" O SER C 407 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N SER C 407 " --> pdb=" O GLN C 403 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 427 through 429 Processing sheet with id=AB1, first strand: chain 'D' and resid 355 through 356 removed outlier: 6.382A pdb=" N GLY D 355 " --> pdb=" O TRP D 376 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 382 through 383 removed outlier: 6.571A pdb=" N MET D 382 " --> pdb=" O ILE D 428 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 399 through 403 removed outlier: 4.383A pdb=" N GLN D 403 " --> pdb=" O SER D 407 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N SER D 407 " --> pdb=" O GLN D 403 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 354 through 356 removed outlier: 6.928A pdb=" N ILE E 375 " --> pdb=" O ILE E 417 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR E 329 " --> pdb=" O PHE E 446 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N PHE E 448 " --> pdb=" O THR E 329 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TRP E 331 " --> pdb=" O PHE E 448 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 399 through 400 removed outlier: 3.846A pdb=" N VAL E 399 " --> pdb=" O ILE E 411 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 427 through 429 removed outlier: 3.589A pdb=" N VAL E 427 " --> pdb=" O THR E 434 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 354 through 355 removed outlier: 3.510A pdb=" N GLY F 355 " --> pdb=" O VAL F 374 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N THR F 329 " --> pdb=" O PHE F 446 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N PHE F 448 " --> pdb=" O THR F 329 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TRP F 331 " --> pdb=" O PHE F 448 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 399 through 401 removed outlier: 3.986A pdb=" N VAL F 399 " --> pdb=" O ILE F 411 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 355 through 356 removed outlier: 6.325A pdb=" N GLY G 355 " --> pdb=" O TRP G 376 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE G 375 " --> pdb=" O ILE G 417 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N THR G 419 " --> pdb=" O ILE G 375 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TRP G 377 " --> pdb=" O THR G 419 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 399 through 401 removed outlier: 3.810A pdb=" N VAL G 399 " --> pdb=" O ILE G 411 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA G 409 " --> pdb=" O VAL G 401 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 428 through 429 636 hydrogen bonds defined for protein. 1839 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 68 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 1.95 Time building geometry restraints manager: 1.68 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: 20.180 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: 0.500 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.760 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.620 ------------------------------------------------------------------------------- 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 : 7.35 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG E 453 TYR 0.019 0.002 TYR G 311 PHE 0.014 0.001 PHE G 446 TRP 0.014 0.001 TRP A 230 HIS 0.003 0.001 HIS G 482 Details of bonding type rmsd covalent geometry : bond 0.00472 (13089) covalent geometry : angle 0.62767 (18104) hydrogen bonds : bond 0.19325 ( 670) hydrogen bonds : angle 7.32441 ( 1907) *********************** 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 : 0.547 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: 0.1118 time to fit residues: 39.1466 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 : 0.474 ------------------------------------------------------------------------------- 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 98 optimal weight: 8.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 50.0000 chunk 130 optimal weight: 0.0020 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 50.0000 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 269 ASN E 244 GLN E 247 GLN E 254 ASN ** F 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN F 410 GLN G 269 ASN G 296 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 = 0.4187 r_free = 0.4187 target = 0.176806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.130767 restraints weight = 18381.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.128278 restraints weight = 17161.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.127011 restraints weight = 16447.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.127285 restraints weight = 11345.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.127779 restraints weight = 10531.879| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 13089 Z= 0.351 Angle : 0.704 8.088 18104 Z= 0.387 Chirality : 0.050 0.166 2198 Planarity : 0.004 0.042 2294 Dihedral : 14.641 174.091 2337 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 6.53 % Allowed : 13.07 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.19), residues: 1915 helix: 0.11 (0.18), residues: 857 sheet: -2.26 (0.27), residues: 265 loop : -1.40 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 444 TYR 0.018 0.003 TYR E 311 PHE 0.022 0.002 PHE F 446 TRP 0.033 0.002 TRP B 230 HIS 0.004 0.001 HIS E 349 Details of bonding type rmsd covalent geometry : bond 0.00829 (13089) covalent geometry : angle 0.70405 (18104) hydrogen bonds : bond 0.05425 ( 670) hydrogen bonds : angle 4.88926 ( 1907) *********************** 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 218 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 169 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 378 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7255 (tm-30) REVERT: F 282 ASP cc_start: 0.7765 (t70) cc_final: 0.7396 (t0) REVERT: F 471 ARG cc_start: 0.8225 (tpt90) cc_final: 0.7957 (tpt90) REVERT: G 238 SER cc_start: 0.7371 (p) cc_final: 0.7053 (t) REVERT: G 378 GLU cc_start: 0.7343 (pm20) cc_final: 0.7139 (pm20) REVERT: G 424 MET cc_start: 0.8202 (mmm) cc_final: 0.7989 (mtt) outliers start: 49 outliers final: 29 residues processed: 198 average time/residue: 0.0959 time to fit residues: 29.3348 Evaluate side-chains 185 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 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 B residue 243 ILE Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 435 PHE Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 263 ILE 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 261 SER Chi-restraints excluded: chain G residue 296 ASN 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 73 optimal weight: 50.0000 chunk 95 optimal weight: 40.0000 chunk 157 optimal weight: 0.0870 chunk 107 optimal weight: 30.0000 chunk 134 optimal weight: 4.9990 chunk 109 optimal weight: 0.5980 chunk 66 optimal weight: 0.0670 chunk 86 optimal weight: 0.8980 chunk 167 optimal weight: 0.9990 chunk 144 optimal weight: 0.5980 chunk 4 optimal weight: 0.0770 overall best weight: 0.2854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 269 ASN F 247 GLN F 269 ASN F 305 ASN G 241 GLN G 296 ASN G 310 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.182726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.135146 restraints weight = 18487.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.128073 restraints weight = 15709.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.129864 restraints weight = 13170.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.130905 restraints weight = 9767.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.130939 restraints weight = 8206.294| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13089 Z= 0.115 Angle : 0.486 6.490 18104 Z= 0.273 Chirality : 0.043 0.132 2198 Planarity : 0.003 0.035 2294 Dihedral : 14.452 174.527 2334 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.73 % Allowed : 16.80 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.19), residues: 1915 helix: 0.90 (0.18), residues: 858 sheet: -1.81 (0.29), residues: 264 loop : -1.06 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 260 TYR 0.014 0.001 TYR G 311 PHE 0.017 0.001 PHE C 253 TRP 0.023 0.001 TRP B 230 HIS 0.004 0.001 HIS G 482 Details of bonding type rmsd covalent geometry : bond 0.00247 (13089) covalent geometry : angle 0.48623 (18104) hydrogen bonds : bond 0.03780 ( 670) hydrogen bonds : angle 4.03609 ( 1907) *********************** 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 193 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 253 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.7570 (t80) REVERT: E 378 GLU cc_start: 0.7401 (tm-30) cc_final: 0.7159 (tm-30) REVERT: F 282 ASP cc_start: 0.7712 (t70) cc_final: 0.7445 (t0) REVERT: F 471 ARG cc_start: 0.8036 (tpt90) cc_final: 0.7834 (tpt90) REVERT: G 378 GLU cc_start: 0.7381 (pm20) cc_final: 0.7099 (pm20) outliers start: 28 outliers final: 19 residues processed: 179 average time/residue: 0.0999 time to fit residues: 27.3522 Evaluate side-chains 171 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 252 SER Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 435 PHE Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 369 CYS 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 451 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 69 optimal weight: 40.0000 chunk 99 optimal weight: 50.0000 chunk 178 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 42 optimal weight: 30.0000 chunk 148 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 153 optimal weight: 0.5980 chunk 130 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 269 ASN G 241 GLN G 296 ASN G 310 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.180275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.133073 restraints weight = 18374.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.128809 restraints weight = 16361.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.129442 restraints weight = 15932.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.130489 restraints weight = 11254.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.130596 restraints weight = 8673.859| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13089 Z= 0.158 Angle : 0.501 6.820 18104 Z= 0.274 Chirality : 0.045 0.388 2198 Planarity : 0.003 0.037 2294 Dihedral : 14.499 175.392 2329 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.80 % Allowed : 17.33 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.19), residues: 1915 helix: 1.06 (0.18), residues: 861 sheet: -1.64 (0.29), residues: 262 loop : -1.05 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 260 TYR 0.016 0.001 TYR G 311 PHE 0.020 0.001 PHE G 364 TRP 0.016 0.001 TRP B 230 HIS 0.002 0.001 HIS G 482 Details of bonding type rmsd covalent geometry : bond 0.00379 (13089) covalent geometry : angle 0.50098 (18104) hydrogen bonds : bond 0.03616 ( 670) hydrogen bonds : angle 3.86323 ( 1907) *********************** 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 196 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: C 253 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.7551 (t80) REVERT: E 274 MET cc_start: 0.7556 (mtm) cc_final: 0.7343 (mtm) REVERT: E 378 GLU cc_start: 0.7514 (tm-30) cc_final: 0.7289 (tm-30) REVERT: F 282 ASP cc_start: 0.7785 (t70) cc_final: 0.7513 (t0) REVERT: F 411 ILE cc_start: 0.8671 (tt) cc_final: 0.8433 (pt) REVERT: F 471 ARG cc_start: 0.8065 (tpt90) cc_final: 0.7856 (tpt90) REVERT: G 239 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7450 (mt-10) REVERT: G 378 GLU cc_start: 0.7399 (pm20) cc_final: 0.7177 (pm20) outliers start: 36 outliers final: 24 residues processed: 178 average time/residue: 0.0996 time to fit residues: 27.1883 Evaluate side-chains 176 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain C residue 254 ASN 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 237 THR 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 274 MET Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 369 CYS Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 296 ASN Chi-restraints excluded: chain G residue 369 CYS Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 466 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 81 optimal weight: 1.9990 chunk 117 optimal weight: 0.0270 chunk 63 optimal weight: 20.0000 chunk 97 optimal weight: 50.0000 chunk 76 optimal weight: 20.0000 chunk 142 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 11 optimal weight: 50.0000 chunk 176 optimal weight: 4.9990 chunk 110 optimal weight: 0.6980 chunk 153 optimal weight: 1.9990 overall best weight: 0.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 421 ASN G 269 ASN G 296 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 = 0.4231 r_free = 0.4231 target = 0.180641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.130348 restraints weight = 18569.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.122207 restraints weight = 13912.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.123586 restraints weight = 13594.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.124337 restraints weight = 11021.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.124800 restraints weight = 9321.604| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3090 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= 0.142 Angle : 0.482 6.977 18104 Z= 0.265 Chirality : 0.044 0.257 2198 Planarity : 0.003 0.037 2294 Dihedral : 14.502 175.750 2329 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.53 % Allowed : 18.00 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.19), residues: 1915 helix: 1.23 (0.18), residues: 862 sheet: -1.49 (0.29), residues: 262 loop : -0.95 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 297 TYR 0.014 0.001 TYR G 311 PHE 0.014 0.001 PHE G 364 TRP 0.017 0.001 TRP B 230 HIS 0.002 0.001 HIS G 482 Details of bonding type rmsd covalent geometry : bond 0.00334 (13089) covalent geometry : angle 0.48217 (18104) hydrogen bonds : bond 0.03358 ( 670) hydrogen bonds : angle 3.69995 ( 1907) *********************** 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 191 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: C 253 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.7570 (t80) REVERT: E 239 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7614 (mt-10) REVERT: E 378 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7228 (tm-30) REVERT: F 282 ASP cc_start: 0.7904 (t70) cc_final: 0.7572 (t0) REVERT: F 411 ILE cc_start: 0.8670 (tt) cc_final: 0.8461 (pt) REVERT: F 471 ARG cc_start: 0.8050 (tpt90) cc_final: 0.7810 (tpt90) REVERT: G 239 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7545 (mt-10) REVERT: G 378 GLU cc_start: 0.7490 (pm20) cc_final: 0.7244 (pm20) outliers start: 34 outliers final: 22 residues processed: 177 average time/residue: 0.0923 time to fit residues: 25.8817 Evaluate side-chains 174 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 252 SER Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 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 421 ASN Chi-restraints excluded: chain E residue 435 PHE 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 G residue 232 VAL Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 296 ASN Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 466 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 88 optimal weight: 1.9990 chunk 121 optimal weight: 0.4980 chunk 100 optimal weight: 30.0000 chunk 186 optimal weight: 0.5980 chunk 56 optimal weight: 0.1980 chunk 62 optimal weight: 20.0000 chunk 13 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4233 r_free = 0.4233 target = 0.180765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.131948 restraints weight = 18486.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.126585 restraints weight = 17000.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.127756 restraints weight = 14648.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.128946 restraints weight = 11030.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.129133 restraints weight = 9215.332| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3241 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= 0.137 Angle : 0.476 7.065 18104 Z= 0.261 Chirality : 0.044 0.328 2198 Planarity : 0.002 0.037 2294 Dihedral : 14.492 176.051 2327 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.80 % Allowed : 18.93 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.19), residues: 1915 helix: 1.29 (0.18), residues: 863 sheet: -1.39 (0.30), residues: 262 loop : -0.90 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 297 TYR 0.012 0.001 TYR G 311 PHE 0.021 0.001 PHE G 364 TRP 0.016 0.001 TRP B 230 HIS 0.002 0.001 HIS G 482 Details of bonding type rmsd covalent geometry : bond 0.00324 (13089) covalent geometry : angle 0.47589 (18104) hydrogen bonds : bond 0.03248 ( 670) hydrogen bonds : angle 3.61884 ( 1907) *********************** 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 187 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: C 253 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.7603 (t80) REVERT: E 274 MET cc_start: 0.7450 (mtm) cc_final: 0.7223 (mtm) REVERT: E 480 VAL cc_start: 0.8407 (OUTLIER) cc_final: 0.8207 (p) REVERT: F 282 ASP cc_start: 0.7754 (t70) cc_final: 0.7486 (t0) REVERT: F 471 ARG cc_start: 0.8043 (tpt90) cc_final: 0.7816 (tpt90) REVERT: G 239 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7413 (mt-10) REVERT: G 378 GLU cc_start: 0.7471 (pm20) cc_final: 0.7249 (pm20) outliers start: 36 outliers final: 27 residues processed: 173 average time/residue: 0.0987 time to fit residues: 26.5507 Evaluate side-chains 177 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 252 SER 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 E residue 480 VAL Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 369 CYS Chi-restraints excluded: chain F residue 462 THR Chi-restraints excluded: chain G residue 218 SER Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 249 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 34 optimal weight: 10.0000 chunk 117 optimal weight: 0.0870 chunk 51 optimal weight: 50.0000 chunk 175 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 152 optimal weight: 0.3980 chunk 7 optimal weight: 3.9990 chunk 74 optimal weight: 50.0000 chunk 113 optimal weight: 0.7980 chunk 70 optimal weight: 8.9990 chunk 182 optimal weight: 0.2980 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN E 421 ASN F 269 ASN G 241 GLN G 296 ASN G 310 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.181289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.133426 restraints weight = 18591.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.128480 restraints weight = 18289.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.128855 restraints weight = 17872.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.130120 restraints weight = 12948.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.130458 restraints weight = 10134.919| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3438 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= 0.125 Angle : 0.469 7.089 18104 Z= 0.257 Chirality : 0.044 0.340 2198 Planarity : 0.002 0.036 2294 Dihedral : 14.453 176.605 2327 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.20 % Allowed : 18.53 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.19), residues: 1915 helix: 1.42 (0.18), residues: 868 sheet: -1.30 (0.30), residues: 257 loop : -0.86 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 327 TYR 0.011 0.001 TYR G 311 PHE 0.011 0.001 PHE C 253 TRP 0.016 0.001 TRP B 230 HIS 0.002 0.000 HIS G 482 Details of bonding type rmsd covalent geometry : bond 0.00293 (13089) covalent geometry : angle 0.46942 (18104) hydrogen bonds : bond 0.03002 ( 670) hydrogen bonds : angle 3.49026 ( 1907) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: C 253 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.7626 (t80) REVERT: E 274 MET cc_start: 0.7431 (mtm) cc_final: 0.7210 (mtm) REVERT: E 480 VAL cc_start: 0.8402 (OUTLIER) cc_final: 0.8183 (p) REVERT: F 282 ASP cc_start: 0.7745 (t70) cc_final: 0.7481 (t0) REVERT: F 471 ARG cc_start: 0.8002 (tpt90) cc_final: 0.7780 (tpt90) REVERT: G 378 GLU cc_start: 0.7485 (pm20) cc_final: 0.7266 (pm20) outliers start: 39 outliers final: 28 residues processed: 175 average time/residue: 0.0902 time to fit residues: 25.2881 Evaluate side-chains 177 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 252 SER Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 421 ASN Chi-restraints excluded: chain E residue 480 VAL Chi-restraints excluded: chain F residue 231 LEU 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 411 ILE Chi-restraints excluded: chain F residue 462 THR Chi-restraints excluded: chain G residue 218 SER Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain G residue 261 SER Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 296 ASN Chi-restraints excluded: chain G residue 369 CYS Chi-restraints excluded: chain G residue 451 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 57 optimal weight: 0.8980 chunk 39 optimal weight: 50.0000 chunk 6 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 138 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 11 optimal weight: 40.0000 chunk 58 optimal weight: 0.0770 chunk 134 optimal weight: 8.9990 chunk 38 optimal weight: 20.0000 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 269 ASN G 241 GLN G 296 ASN G 310 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.174450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.117685 restraints weight = 19033.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.115825 restraints weight = 11182.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.117860 restraints weight = 8844.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.118947 restraints weight = 6766.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.118860 restraints weight = 5847.398| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3551 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= 0.143 Angle : 0.483 7.128 18104 Z= 0.263 Chirality : 0.044 0.357 2198 Planarity : 0.002 0.035 2294 Dihedral : 14.441 176.931 2327 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.80 % Allowed : 20.13 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.19), residues: 1915 helix: 1.49 (0.18), residues: 868 sheet: -1.25 (0.30), residues: 257 loop : -0.86 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 297 TYR 0.012 0.001 TYR D 250 PHE 0.012 0.001 PHE E 364 TRP 0.013 0.001 TRP B 230 HIS 0.002 0.000 HIS G 482 Details of bonding type rmsd covalent geometry : bond 0.00340 (13089) covalent geometry : angle 0.48328 (18104) hydrogen bonds : bond 0.03045 ( 670) hydrogen bonds : angle 3.50424 ( 1907) *********************** 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 186 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: C 253 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.7591 (t80) REVERT: E 274 MET cc_start: 0.7534 (mtm) cc_final: 0.7248 (mtm) REVERT: E 480 VAL cc_start: 0.8635 (OUTLIER) cc_final: 0.8390 (p) REVERT: F 282 ASP cc_start: 0.8290 (t70) cc_final: 0.7733 (t0) REVERT: F 471 ARG cc_start: 0.7972 (tpt90) cc_final: 0.7596 (tpt90) REVERT: G 378 GLU cc_start: 0.7642 (pm20) cc_final: 0.7285 (pm20) outliers start: 36 outliers final: 28 residues processed: 172 average time/residue: 0.0944 time to fit residues: 25.5680 Evaluate side-chains 178 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 252 SER Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 254 ASN Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 480 VAL Chi-restraints excluded: chain F residue 231 LEU 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 411 ILE Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain G residue 218 SER Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain G residue 261 SER Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 296 ASN Chi-restraints excluded: chain G residue 369 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 49 optimal weight: 50.0000 chunk 147 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 58 optimal weight: 0.4980 chunk 111 optimal weight: 0.6980 chunk 7 optimal weight: 7.9990 chunk 36 optimal weight: 50.0000 chunk 130 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 chunk 77 optimal weight: 50.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 421 ASN F 269 ASN G 296 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 = 0.4213 r_free = 0.4213 target = 0.174663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.117343 restraints weight = 19231.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.116196 restraints weight = 11464.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.118143 restraints weight = 8103.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.118690 restraints weight = 6450.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.119050 restraints weight = 5763.581| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.3668 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= 0.126 Angle : 0.478 7.125 18104 Z= 0.260 Chirality : 0.044 0.367 2198 Planarity : 0.002 0.034 2294 Dihedral : 14.397 177.239 2327 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.80 % Allowed : 20.00 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.19), residues: 1915 helix: 1.57 (0.18), residues: 870 sheet: -1.15 (0.30), residues: 258 loop : -0.83 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 327 TYR 0.010 0.001 TYR G 311 PHE 0.011 0.001 PHE C 253 TRP 0.014 0.001 TRP B 230 HIS 0.002 0.000 HIS G 482 Details of bonding type rmsd covalent geometry : bond 0.00297 (13089) covalent geometry : angle 0.47788 (18104) hydrogen bonds : bond 0.02906 ( 670) hydrogen bonds : angle 3.44142 ( 1907) *********************** 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 180 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: C 253 PHE cc_start: 0.8604 (OUTLIER) cc_final: 0.7591 (t80) REVERT: E 274 MET cc_start: 0.7517 (mtm) cc_final: 0.7244 (mtm) REVERT: E 480 VAL cc_start: 0.8655 (OUTLIER) cc_final: 0.8424 (p) REVERT: F 282 ASP cc_start: 0.8309 (t70) cc_final: 0.7732 (t0) REVERT: F 471 ARG cc_start: 0.7913 (tpt90) cc_final: 0.7518 (tpt90) REVERT: G 378 GLU cc_start: 0.7683 (pm20) cc_final: 0.7321 (pm20) outliers start: 36 outliers final: 30 residues processed: 167 average time/residue: 0.0914 time to fit residues: 24.2947 Evaluate side-chains 174 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 C residue 252 SER Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 421 ASN Chi-restraints excluded: chain E residue 480 VAL Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 246 ASP 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 411 ILE Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain G residue 218 SER Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain G residue 261 SER Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 296 ASN Chi-restraints excluded: chain G residue 369 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 15 optimal weight: 0.9990 chunk 190 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 138 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 137 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 chunk 82 optimal weight: 0.4980 chunk 22 optimal weight: 30.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 421 ASN F 269 ASN G 241 GLN ** 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 = 0.4212 r_free = 0.4212 target = 0.174485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.117086 restraints weight = 19335.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.116100 restraints weight = 11491.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.117845 restraints weight = 8152.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.118926 restraints weight = 6525.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.119024 restraints weight = 5647.319| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.165 13089 Z= 0.186 Angle : 0.794 59.186 18104 Z= 0.484 Chirality : 0.046 0.521 2198 Planarity : 0.004 0.146 2294 Dihedral : 14.408 177.248 2327 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.00 % Allowed : 20.80 % Favored : 75.20 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.19), residues: 1915 helix: 1.56 (0.18), residues: 870 sheet: -1.13 (0.30), residues: 258 loop : -0.84 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 297 TYR 0.010 0.001 TYR G 311 PHE 0.011 0.001 PHE C 253 TRP 0.013 0.001 TRP B 230 HIS 0.002 0.000 HIS G 482 Details of bonding type rmsd covalent geometry : bond 0.00395 (13089) covalent geometry : angle 0.79395 (18104) hydrogen bonds : bond 0.02918 ( 670) hydrogen bonds : angle 3.44348 ( 1907) ********************** 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 173 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: C 253 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.7590 (t80) REVERT: E 274 MET cc_start: 0.7541 (mtm) cc_final: 0.7265 (mtm) REVERT: E 480 VAL cc_start: 0.8655 (OUTLIER) cc_final: 0.8424 (p) REVERT: F 282 ASP cc_start: 0.8321 (t70) cc_final: 0.7746 (t0) REVERT: F 471 ARG cc_start: 0.7914 (tpt90) cc_final: 0.7521 (tpt90) REVERT: G 378 GLU cc_start: 0.7690 (pm20) cc_final: 0.7336 (pm20) outliers start: 30 outliers final: 27 residues processed: 162 average time/residue: 0.0917 time to fit residues: 23.6758 Evaluate side-chains 171 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 C residue 252 SER Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 254 ASN Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 480 VAL Chi-restraints excluded: chain F residue 231 LEU 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 411 ILE Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain G residue 218 SER Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain G residue 261 SER Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 369 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 102 optimal weight: 50.0000 chunk 46 optimal weight: 50.0000 chunk 161 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 70 optimal weight: 30.0000 chunk 41 optimal weight: 5.9990 chunk 71 optimal weight: 50.0000 chunk 77 optimal weight: 50.0000 chunk 123 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 421 ASN F 269 ASN ** G 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.174559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.118423 restraints weight = 19230.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.116489 restraints weight = 11749.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.118958 restraints weight = 8660.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.119350 restraints weight = 6572.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.119547 restraints weight = 5866.208| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.165 13089 Z= 0.186 Angle : 0.794 59.186 18104 Z= 0.484 Chirality : 0.046 0.521 2198 Planarity : 0.004 0.146 2294 Dihedral : 14.408 177.248 2327 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.00 % Allowed : 20.80 % Favored : 75.20 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.19), residues: 1915 helix: 1.56 (0.18), residues: 870 sheet: -1.13 (0.30), residues: 258 loop : -0.84 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 297 TYR 0.010 0.001 TYR G 311 PHE 0.011 0.001 PHE C 253 TRP 0.013 0.001 TRP B 230 HIS 0.002 0.000 HIS G 482 Details of bonding type rmsd covalent geometry : bond 0.00395 (13089) covalent geometry : angle 0.79395 (18104) hydrogen bonds : bond 0.02918 ( 670) hydrogen bonds : angle 3.44348 ( 1907) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2589.05 seconds wall clock time: 45 minutes 28.53 seconds (2728.53 seconds total)