Starting phenix.real_space_refine on Thu Aug 6 01:40:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bu7_44902/08_2026/9bu7_44902.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bu7_44902/08_2026/9bu7_44902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bu7_44902/08_2026/9bu7_44902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bu7_44902/08_2026/9bu7_44902.map" model { file = "/net/cci-nas-00/data/ceres_data/9bu7_44902/08_2026/9bu7_44902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bu7_44902/08_2026/9bu7_44902.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/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: 4.05, per 1000 atoms: 0.32 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: 0.93 Conformation dependent library (CDL) restraints added in 760.9 milliseconds 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: 1.43 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: 1.69 Time building geometry restraints manager: 1.28 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=" O3B AGS F 501 " pdb=" PB AGS F 501 " ideal model delta sigma weight residual 1.673 1.569 0.104 2.00e-02 2.50e+03 2.73e+01 bond pdb=" O3B AGS G 501 " pdb=" PB AGS G 501 " ideal model delta sigma weight residual 1.673 1.571 0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" O3A AGS E 501 " pdb=" PA AGS E 501 " ideal model delta sigma weight residual 1.664 1.566 0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" O3A AGS F 501 " pdb=" PA AGS F 501 " ideal model delta sigma weight residual 1.664 1.567 0.097 2.00e-02 2.50e+03 2.38e+01 bond pdb=" O3B AGS E 501 " pdb=" PB AGS E 501 " ideal model delta sigma weight residual 1.673 1.577 0.096 2.00e-02 2.50e+03 2.29e+01 ... (remaining 13084 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 17710 2.23 - 4.45: 356 4.45 - 6.68: 17 6.68 - 8.90: 14 8.90 - 11.13: 7 Bond angle restraints: 18104 Sorted by residual: angle pdb=" N3 DT H 16 " pdb=" C4 DT H 16 " pdb=" O4 DT H 16 " ideal model delta sigma weight residual 119.90 122.82 -2.92 6.00e-01 2.78e+00 2.37e+01 angle pdb=" N3 DT H 9 " pdb=" C4 DT H 9 " pdb=" O4 DT H 9 " ideal model delta sigma weight residual 119.90 122.72 -2.82 6.00e-01 2.78e+00 2.21e+01 angle pdb=" O4 DT H 9 " pdb=" C4 DT H 9 " pdb=" C5 DT H 9 " ideal model delta sigma weight residual 124.90 121.62 3.28 7.00e-01 2.04e+00 2.20e+01 angle pdb=" O4 DT H 16 " pdb=" C4 DT H 16 " pdb=" C5 DT H 16 " ideal model delta sigma weight residual 124.90 121.98 2.92 7.00e-01 2.04e+00 1.73e+01 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 ... (remaining 18099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.06: 7355 35.06 - 70.12: 217 70.12 - 105.18: 6 105.18 - 140.24: 9 140.24 - 175.30: 6 Dihedral angle restraints: 7593 sinusoidal: 2002 harmonic: 5591 Sorted by residual: dihedral pdb=" O1B AGS F 501 " pdb=" O3B AGS F 501 " pdb=" PB AGS F 501 " pdb=" PG AGS F 501 " ideal model delta sinusoidal sigma weight residual 138.55 -46.15 -175.30 1 3.00e+01 1.11e-03 2.13e+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 138.55 -50.06 -171.39 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O1A AGS G 501 " pdb=" O3A AGS G 501 " pdb=" PA AGS G 501 " pdb=" PB AGS G 501 " ideal model delta sinusoidal sigma weight residual 82.37 -52.43 134.80 1 3.00e+01 1.11e-03 1.82e+01 ... (remaining 7590 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1673 0.051 - 0.101: 373 0.101 - 0.152: 111 0.152 - 0.203: 30 0.203 - 0.253: 5 Chirality restraints: 2192 Sorted by residual: chirality pdb=" C3' AGS F 501 " pdb=" C2' AGS F 501 " pdb=" C4' AGS F 501 " pdb=" O3' AGS F 501 " both_signs ideal model delta sigma weight residual False -2.37 -2.62 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" C3' AGS E 501 " pdb=" C2' AGS E 501 " pdb=" C4' AGS E 501 " pdb=" O3' AGS E 501 " both_signs ideal model delta sigma weight residual False -2.37 -2.62 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C3' AGS G 501 " pdb=" C2' AGS G 501 " pdb=" C4' AGS G 501 " pdb=" O3' AGS G 501 " both_signs ideal model delta sigma weight residual False -2.37 -2.62 0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 2189 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: 20.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.880 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 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 : 0.006 0.104 13089 Z= 0.372 Angle : 0.729 11.130 18104 Z= 0.474 Chirality : 0.051 0.253 2192 Planarity : 0.003 0.035 2294 Dihedral : 17.080 175.299 3959 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 are 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/Z covalent geometry : bond 0.00570 / 0.37 (13089) covalent geometry : angle 0.72860 / 0.47 (18104) hydrogen bonds : bond 0.19325 / 13.89 ( 670) hydrogen bonds : angle 7.32441 / 5.31 ( 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 : 0.466 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: 0.7443 (mt) REVERT: F 282 ASP cc_start: 0.7573 (t70) cc_final: 0.7286 (t0) REVERT: G 238 SER cc_start: 0.7659 (p) cc_final: 0.7449 (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: 0.7864 (mm-40) outliers start: 16 outliers final: 5 residues processed: 237 average time/residue: 0.0987 time to fit residues: 34.9230 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 : 0.323 ------------------------------------------------------------------------------- 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... 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 = 0.4205 r_free = 0.4205 target = 0.178619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.134287 restraints weight = 18208.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.128595 restraints weight = 22134.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.130731 restraints weight = 18824.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.130924 restraints weight = 12323.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.130855 restraints weight = 10377.875| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 13089 Z= 0.341 Angle : 0.713 10.935 18104 Z= 0.386 Chirality : 0.052 0.438 2192 Planarity : 0.004 0.038 2294 Dihedral : 17.634 176.454 2391 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 6.13 % Allowed : 13.33 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.19), residues: 1915 helix: 0.11 (0.18), residues: 849 sheet: -2.25 (0.28), residues: 264 loop : -1.37 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 327 TYR 0.019 0.002 TYR D 250 PHE 0.018 0.002 PHE F 446 TRP 0.029 0.002 TRP B 230 HIS 0.004 0.001 HIS F 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00801 / 0.34 (13089) covalent geometry : angle 0.71336 / 0.39 (18104) hydrogen bonds : bond 0.06121 / 4.55 ( 670) hydrogen bonds : angle 5.12357 / 3.74 ( 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 215 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 169 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 378 GLU cc_start: 0.7466 (tm-30) cc_final: 0.7163 (tm-30) REVERT: F 282 ASP cc_start: 0.7672 (t70) cc_final: 0.7347 (t0) REVERT: F 471 ARG cc_start: 0.8154 (tpt90) cc_final: 0.7926 (tpt90) REVERT: G 238 SER cc_start: 0.7262 (p) cc_final: 0.7028 (t) REVERT: G 424 MET cc_start: 0.8184 (mmm) cc_final: 0.7799 (mtt) outliers start: 46 outliers final: 33 residues processed: 199 average time/residue: 0.0913 time to fit residues: 28.2761 Evaluate side-chains 190 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 241 GLN Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 435 PHE Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 232 VAL 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 218 SER Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 261 SER Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 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: 4.9990 chunk 95 optimal weight: 40.0000 chunk 157 optimal weight: 0.9990 chunk 107 optimal weight: 20.0000 chunk 134 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 167 optimal weight: 0.8980 chunk 144 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 269 ASN ** F 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 269 ASN F 305 ASN G 241 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.181540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.136074 restraints weight = 18377.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.130491 restraints weight = 17973.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.131539 restraints weight = 16915.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.132118 restraints weight = 11127.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.132304 restraints weight = 9113.981| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13089 Z= 0.146 Angle : 0.541 6.646 18104 Z= 0.299 Chirality : 0.046 0.324 2192 Planarity : 0.003 0.033 2294 Dihedral : 17.254 177.328 2388 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.33 % Allowed : 15.20 % 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 are not related in a simple way. whole: -0.69 (0.19), residues: 1915 helix: 0.74 (0.18), residues: 855 sheet: -2.02 (0.28), residues: 264 loop : -1.13 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 297 TYR 0.016 0.002 TYR G 311 PHE 0.023 0.001 PHE G 364 TRP 0.019 0.001 TRP B 230 HIS 0.003 0.001 HIS G 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (13089) covalent geometry : angle 0.54118 / 0.30 (18104) hydrogen bonds : bond 0.04630 / 3.44 ( 670) hydrogen bonds : angle 4.38413 / 3.20 ( 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 199 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 159 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: C 253 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.7574 (t80) REVERT: E 378 GLU cc_start: 0.7424 (tm-30) cc_final: 0.7170 (tm-30) REVERT: F 240 LYS cc_start: 0.8630 (mtpp) cc_final: 0.8407 (mtpp) REVERT: F 282 ASP cc_start: 0.7812 (t70) cc_final: 0.7481 (t0) REVERT: F 471 ARG cc_start: 0.8121 (tpt90) cc_final: 0.7916 (tpt90) REVERT: G 424 MET cc_start: 0.8149 (mmm) cc_final: 0.7935 (mtt) outliers start: 40 outliers final: 28 residues processed: 180 average time/residue: 0.0931 time to fit residues: 26.3326 Evaluate side-chains 180 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 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 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 401 VAL Chi-restraints excluded: chain E residue 435 PHE Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 254 ASN Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 369 CYS Chi-restraints excluded: chain F residue 455 ASP Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 353 PHE Chi-restraints excluded: chain G residue 369 CYS Chi-restraints excluded: chain G residue 412 ASP Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 466 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 69 optimal weight: 40.0000 chunk 99 optimal weight: 50.0000 chunk 178 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 chunk 42 optimal weight: 8.9990 chunk 148 optimal weight: 0.3980 chunk 149 optimal weight: 0.6980 chunk 43 optimal weight: 0.0770 chunk 160 optimal weight: 0.5980 chunk 153 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 247 GLN G 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.182989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.136291 restraints weight = 18476.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.133911 restraints weight = 15240.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.133935 restraints weight = 12619.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.133145 restraints weight = 8977.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.133758 restraints weight = 8821.098| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 13089 Z= 0.117 Angle : 0.492 6.801 18104 Z= 0.272 Chirality : 0.045 0.314 2192 Planarity : 0.002 0.032 2294 Dihedral : 16.917 179.153 2386 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 5.07 % Allowed : 16.40 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.19), residues: 1915 helix: 1.03 (0.18), residues: 865 sheet: -1.68 (0.29), residues: 263 loop : -1.03 (0.22), residues: 787 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 0.015 0.001 PHE G 364 TRP 0.019 0.001 TRP B 230 HIS 0.002 0.001 HIS F 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (13089) covalent geometry : angle 0.49209 / 0.27 (18104) hydrogen bonds : bond 0.03690 / 2.75 ( 670) hydrogen bonds : angle 3.88989 / 2.85 ( 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 194 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: C 253 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.7644 (t80) REVERT: F 282 ASP cc_start: 0.7777 (t70) cc_final: 0.7498 (t0) outliers start: 38 outliers final: 28 residues processed: 178 average time/residue: 0.0917 time to fit residues: 26.0284 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 : 0.576 ------------------------------------------------------------------------------- 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 245 GLU 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 263 ILE Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 369 CYS Chi-restraints excluded: chain F residue 455 ASP Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 261 SER Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain G residue 296 ASN Chi-restraints excluded: chain G residue 353 PHE Chi-restraints excluded: chain G residue 451 THR 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: 0.8980 chunk 63 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 76 optimal weight: 30.0000 chunk 142 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 11 optimal weight: 50.0000 chunk 176 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 153 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 254 ASN F 269 ASN G 269 ASN G 296 ASN 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 = 0.180374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.134004 restraints weight = 18587.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.126259 restraints weight = 18853.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.127896 restraints weight = 16148.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.128620 restraints weight = 11880.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.128908 restraints weight = 9730.918| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13089 Z= 0.184 Angle : 0.530 7.085 18104 Z= 0.287 Chirality : 0.046 0.308 2192 Planarity : 0.003 0.032 2294 Dihedral : 16.849 179.996 2383 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 5.47 % Allowed : 16.00 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.19), residues: 1915 helix: 1.11 (0.18), residues: 860 sheet: -1.60 (0.29), residues: 264 loop : -0.98 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 327 TYR 0.014 0.002 TYR E 311 PHE 0.018 0.001 PHE G 364 TRP 0.014 0.001 TRP B 230 HIS 0.003 0.001 HIS G 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (13089) covalent geometry : angle 0.53039 / 0.29 (18104) hydrogen bonds : bond 0.03827 / 2.85 ( 670) hydrogen bonds : angle 3.88657 / 2.85 ( 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 197 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 156 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: C 253 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.7645 (t80) REVERT: F 282 ASP cc_start: 0.7786 (t70) cc_final: 0.7504 (t0) outliers start: 41 outliers final: 30 residues processed: 181 average time/residue: 0.0791 time to fit residues: 22.8347 Evaluate side-chains 181 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 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 304 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 435 PHE Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 369 CYS Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 218 SER Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain G residue 353 PHE Chi-restraints excluded: chain G residue 369 CYS Chi-restraints excluded: chain G residue 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: 9.9990 chunk 121 optimal weight: 0.5980 chunk 100 optimal weight: 10.0000 chunk 186 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 62 optimal weight: 30.0000 chunk 13 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 chunk 169 optimal weight: 0.6980 chunk 176 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.179797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.133202 restraints weight = 17968.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.128438 restraints weight = 18516.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.129492 restraints weight = 16409.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.128843 restraints weight = 11506.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.128979 restraints weight = 10118.187| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13089 Z= 0.131 Angle : 0.491 7.110 18104 Z= 0.270 Chirality : 0.045 0.305 2192 Planarity : 0.002 0.031 2294 Dihedral : 16.772 179.586 2383 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.53 % Allowed : 17.60 % 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 are not related in a simple way. whole: -0.03 (0.19), residues: 1915 helix: 1.27 (0.18), residues: 862 sheet: -1.43 (0.29), residues: 263 loop : -0.91 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 217 TYR 0.011 0.001 TYR E 311 PHE 0.019 0.001 PHE G 364 TRP 0.016 0.001 TRP B 230 HIS 0.002 0.000 HIS G 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (13089) covalent geometry : angle 0.49117 / 0.27 (18104) hydrogen bonds : bond 0.03433 / 2.55 ( 670) hydrogen bonds : angle 3.67754 / 2.70 ( 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 191 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: C 253 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.7661 (t80) REVERT: E 274 MET cc_start: 0.7372 (mtm) cc_final: 0.7156 (mtm) REVERT: F 282 ASP cc_start: 0.7759 (t70) cc_final: 0.7491 (t0) outliers start: 34 outliers final: 26 residues processed: 175 average time/residue: 0.0819 time to fit residues: 23.2474 Evaluate side-chains 173 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 218 SER Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 254 ASN Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 435 PHE Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 369 CYS Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 218 SER Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain G residue 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: 0.9990 chunk 51 optimal weight: 50.0000 chunk 175 optimal weight: 0.3980 chunk 160 optimal weight: 0.6980 chunk 152 optimal weight: 0.0270 chunk 7 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 182 optimal weight: 0.0470 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 269 ASN G 241 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.183536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.138310 restraints weight = 18294.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.134730 restraints weight = 18086.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.134925 restraints weight = 16668.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.133054 restraints weight = 12332.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.133860 restraints weight = 12046.819| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 13089 Z= 0.106 Angle : 0.470 7.112 18104 Z= 0.259 Chirality : 0.044 0.301 2192 Planarity : 0.002 0.034 2294 Dihedral : 16.590 179.100 2381 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.60 % Allowed : 18.67 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.19), residues: 1915 helix: 1.38 (0.18), residues: 871 sheet: -1.29 (0.29), residues: 264 loop : -0.84 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 217 TYR 0.011 0.001 TYR E 311 PHE 0.018 0.001 PHE G 364 TRP 0.021 0.001 TRP E 242 HIS 0.001 0.000 HIS G 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (13089) covalent geometry : angle 0.47023 / 0.26 (18104) hydrogen bonds : bond 0.03092 / 2.29 ( 670) hydrogen bonds : angle 3.51936 / 2.59 ( 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 182 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.476 Fit side-chains REVERT: C 253 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.7634 (t80) REVERT: E 274 MET cc_start: 0.7308 (mtm) cc_final: 0.7103 (mtm) REVERT: F 240 LYS cc_start: 0.8509 (mtpp) cc_final: 0.8288 (mmmt) outliers start: 27 outliers final: 21 residues processed: 171 average time/residue: 0.0872 time to fit residues: 23.8245 Evaluate side-chains 169 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 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 284 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 369 CYS Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 218 SER Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 466 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 57 optimal weight: 0.8980 chunk 39 optimal weight: 50.0000 chunk 6 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 138 optimal weight: 0.5980 chunk 107 optimal weight: 0.0970 chunk 85 optimal weight: 0.5980 chunk 11 optimal weight: 50.0000 chunk 58 optimal weight: 0.6980 chunk 134 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 241 GLN ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.178758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.132595 restraints weight = 18459.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.126747 restraints weight = 18923.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.127766 restraints weight = 18611.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.128607 restraints weight = 12184.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.128669 restraints weight = 9790.756| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13089 Z= 0.114 Angle : 0.481 7.151 18104 Z= 0.262 Chirality : 0.045 0.404 2192 Planarity : 0.002 0.033 2294 Dihedral : 16.516 178.725 2381 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.33 % Allowed : 19.33 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.19), residues: 1915 helix: 1.44 (0.18), residues: 878 sheet: -1.17 (0.30), residues: 265 loop : -0.82 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 297 TYR 0.013 0.001 TYR G 311 PHE 0.018 0.001 PHE G 364 TRP 0.013 0.001 TRP F 376 HIS 0.002 0.000 HIS G 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (13089) covalent geometry : angle 0.48105 / 0.26 (18104) hydrogen bonds : bond 0.02995 / 2.22 ( 670) hydrogen bonds : angle 3.46350 / 2.55 ( 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 176 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.485 Fit side-chains REVERT: C 253 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.7667 (t80) REVERT: E 274 MET cc_start: 0.7400 (mtm) cc_final: 0.7188 (mtm) outliers start: 25 outliers final: 22 residues processed: 165 average time/residue: 0.0827 time to fit residues: 22.1398 Evaluate side-chains 171 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 218 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 401 VAL Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 369 CYS Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 218 SER Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 466 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 49 optimal weight: 30.0000 chunk 147 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 36 optimal weight: 50.0000 chunk 130 optimal weight: 0.0870 chunk 75 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 chunk 77 optimal weight: 50.0000 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 241 GLN ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.177740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.130972 restraints weight = 18369.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.124874 restraints weight = 17757.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.125966 restraints weight = 17003.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.126397 restraints weight = 11584.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.126631 restraints weight = 9811.570| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13089 Z= 0.132 Angle : 0.495 7.195 18104 Z= 0.268 Chirality : 0.045 0.331 2192 Planarity : 0.002 0.032 2294 Dihedral : 16.458 178.374 2381 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.00 % Allowed : 18.93 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.19), residues: 1915 helix: 1.55 (0.18), residues: 874 sheet: -1.12 (0.30), residues: 258 loop : -0.80 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 297 TYR 0.013 0.001 TYR E 311 PHE 0.017 0.001 PHE G 364 TRP 0.010 0.001 TRP B 230 HIS 0.002 0.001 HIS F 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (13089) covalent geometry : angle 0.49456 / 0.27 (18104) hydrogen bonds : bond 0.03041 / 2.25 ( 670) hydrogen bonds : angle 3.45340 / 2.54 ( 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 187 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.572 Fit side-chains REVERT: C 253 PHE cc_start: 0.8641 (OUTLIER) cc_final: 0.7714 (t80) REVERT: G 406 LYS cc_start: 0.8950 (mtmt) cc_final: 0.8709 (mtpp) outliers start: 30 outliers final: 26 residues processed: 177 average time/residue: 0.0882 time to fit residues: 25.1067 Evaluate side-chains 178 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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 218 SER Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 252 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 401 VAL Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 369 CYS Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 218 SER Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 466 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 15 optimal weight: 0.0870 chunk 190 optimal weight: 10.0000 chunk 27 optimal weight: 0.4980 chunk 66 optimal weight: 4.9990 chunk 138 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 137 optimal weight: 0.3980 chunk 79 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 22 optimal weight: 30.0000 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 328 ASN G 241 GLN ** G 296 ASN ** 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 = 0.4206 r_free = 0.4206 target = 0.178964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.131780 restraints weight = 18436.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.126378 restraints weight = 17125.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.126591 restraints weight = 17121.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.127741 restraints weight = 11808.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.128040 restraints weight = 9144.430| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13089 Z= 0.109 Angle : 0.482 8.574 18104 Z= 0.262 Chirality : 0.045 0.372 2192 Planarity : 0.002 0.032 2294 Dihedral : 16.403 178.095 2381 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.33 % Allowed : 20.00 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.19), residues: 1915 helix: 1.62 (0.18), residues: 878 sheet: -1.03 (0.31), residues: 248 loop : -0.75 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 471 TYR 0.011 0.001 TYR E 311 PHE 0.018 0.001 PHE G 364 TRP 0.011 0.001 TRP B 230 HIS 0.001 0.000 HIS G 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (13089) covalent geometry : angle 0.48197 / 0.26 (18104) hydrogen bonds : bond 0.02818 / 2.07 ( 670) hydrogen bonds : angle 3.39590 / 2.49 ( 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 180 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.488 Fit side-chains REVERT: C 253 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.7715 (t80) REVERT: G 406 LYS cc_start: 0.8933 (mtmt) cc_final: 0.8708 (mtpp) outliers start: 25 outliers final: 22 residues processed: 171 average time/residue: 0.0851 time to fit residues: 23.7430 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 : 0.483 ------------------------------------------------------------------------------- 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 218 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 252 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 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 412 ASP Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 218 SER Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain G residue 274 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 102 optimal weight: 40.0000 chunk 46 optimal weight: 50.0000 chunk 161 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 70 optimal weight: 30.0000 chunk 41 optimal weight: 0.0070 chunk 71 optimal weight: 30.0000 chunk 77 optimal weight: 50.0000 chunk 123 optimal weight: 0.7980 chunk 9 optimal weight: 8.9990 chunk 136 optimal weight: 0.3980 overall best weight: 1.6402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 269 ASN F 349 HIS G 241 GLN ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.174901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.128444 restraints weight = 18383.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.124459 restraints weight = 18897.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.125167 restraints weight = 17449.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.126013 restraints weight = 12454.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.126102 restraints weight = 9697.250| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 13089 Z= 0.221 Angle : 0.574 7.918 18104 Z= 0.304 Chirality : 0.047 0.327 2192 Planarity : 0.003 0.031 2294 Dihedral : 16.448 178.021 2381 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.73 % Allowed : 19.73 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.19), residues: 1915 helix: 1.46 (0.18), residues: 875 sheet: -1.09 (0.31), residues: 238 loop : -0.84 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 471 TYR 0.020 0.002 TYR C 250 PHE 0.016 0.002 PHE G 446 TRP 0.017 0.001 TRP F 377 HIS 0.004 0.001 HIS G 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.22 (13089) covalent geometry : angle 0.57447 / 0.30 (18104) hydrogen bonds : bond 0.03565 / 2.63 ( 670) hydrogen bonds : angle 3.64116 / 2.67 ( 1907) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2360.40 seconds wall clock time: 41 minutes 21.77 seconds (2481.77 seconds total)