Starting phenix.real_space_refine on Fri Jul 3 07:20:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bu7_44902/07_2026/9bu7_44902.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bu7_44902/07_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_44902/07_2026/9bu7_44902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bu7_44902/07_2026/9bu7_44902.map" model { file = "/net/cci-nas-00/data/ceres_data/9bu7_44902/07_2026/9bu7_44902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bu7_44902/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 3.29, per 1000 atoms: 0.26 Number of scatterers: 12831 At special positions: 0 Unit cell: (87.648, 137.28, 137.808, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 35 16.00 P 37 15.00 Mg 2 11.99 O 2509 8.00 N 2348 7.00 C 7900 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 790.6 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: 1.41 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: 1.92 Time building geometry restraints manager: 1.56 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: 17711 2.23 - 4.45: 355 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: 21.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.760 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.240 ------------------------------------------------------------------------------- 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 : 0.728 11.130 18104 Z= 0.473 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 0.72769 / 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 : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 SER cc_start: 0.7964 (p) cc_final: 0.7680 (p) REVERT: E 323 LYS cc_start: 0.7431 (ttmt) cc_final: 0.7007 (ttpp) REVERT: E 480 VAL cc_start: 0.8510 (OUTLIER) cc_final: 0.8278 (p) REVERT: F 216 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.7442 (mt) REVERT: F 282 ASP cc_start: 0.7573 (t70) cc_final: 0.7285 (t0) REVERT: G 238 SER cc_start: 0.7659 (p) cc_final: 0.7451 (t) REVERT: G 241 GLN cc_start: 0.8063 (mt0) cc_final: 0.7641 (tp-100) REVERT: G 439 GLN cc_start: 0.8315 (tp40) cc_final: 0.7863 (mm-40) outliers start: 16 outliers final: 5 residues processed: 237 average time/residue: 0.1074 time to fit residues: 37.8204 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 : 0.481 ------------------------------------------------------------------------------- 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 305 ASN F 410 GLN G 269 ASN G 476 HIS G 482 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.179008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.135438 restraints weight = 18219.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.131478 restraints weight = 20687.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.132532 restraints weight = 18521.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.130280 restraints weight = 13173.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.130638 restraints weight = 11911.946| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.124 13089 Z= 0.357 Angle : 0.720 10.703 18104 Z= 0.390 Chirality : 0.051 0.334 2192 Planarity : 0.004 0.039 2294 Dihedral : 17.690 178.437 2391 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 5.33 % Allowed : 14.40 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.19), residues: 1915 helix: 0.17 (0.18), residues: 847 sheet: -2.24 (0.28), residues: 264 loop : -1.38 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 327 TYR 0.018 0.002 TYR D 250 PHE 0.018 0.002 PHE F 446 TRP 0.030 0.002 TRP B 230 HIS 0.004 0.001 HIS F 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00858 / 0.36 (13089) covalent geometry : angle 0.71965 / 0.39 (18104) hydrogen bonds : bond 0.06128 / 4.57 ( 670) hydrogen bonds : angle 5.16744 / 3.77 ( 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 210 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 240 LYS cc_start: 0.8642 (mttm) cc_final: 0.8359 (mtpp) REVERT: F 282 ASP cc_start: 0.7705 (t70) cc_final: 0.7393 (t0) REVERT: G 238 SER cc_start: 0.7326 (p) cc_final: 0.7108 (t) REVERT: G 424 MET cc_start: 0.8205 (mmm) cc_final: 0.7791 (mtt) outliers start: 40 outliers final: 26 residues processed: 195 average time/residue: 0.0937 time to fit residues: 28.3504 Evaluate side-chains 182 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain C residue 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 401 VAL Chi-restraints excluded: chain E residue 435 PHE 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 274 MET 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: 10.0000 chunk 95 optimal weight: 40.0000 chunk 157 optimal weight: 0.7980 chunk 107 optimal weight: 30.0000 chunk 134 optimal weight: 4.9990 chunk 109 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 167 optimal weight: 0.8980 chunk 144 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 G 241 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.182441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.136600 restraints weight = 18444.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.131193 restraints weight = 17412.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.132608 restraints weight = 16268.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.133211 restraints weight = 10486.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.133546 restraints weight = 8734.563| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13089 Z= 0.141 Angle : 0.530 6.665 18104 Z= 0.295 Chirality : 0.046 0.302 2192 Planarity : 0.003 0.032 2294 Dihedral : 17.243 178.575 2388 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 5.07 % Allowed : 15.47 % 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: -0.61 (0.19), residues: 1915 helix: 0.81 (0.18), residues: 855 sheet: -1.97 (0.28), residues: 265 loop : -1.11 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 327 TYR 0.012 0.001 TYR D 250 PHE 0.016 0.001 PHE D 253 TRP 0.020 0.001 TRP B 230 HIS 0.003 0.001 HIS G 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (13089) covalent geometry : angle 0.52984 / 0.29 (18104) hydrogen bonds : bond 0.04440 / 3.30 ( 670) hydrogen bonds : angle 4.30648 / 3.15 ( 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 197 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 0.471 Fit side-chains REVERT: C 253 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.7586 (t80) REVERT: F 282 ASP cc_start: 0.7738 (t70) cc_final: 0.7439 (t0) outliers start: 38 outliers final: 27 residues processed: 181 average time/residue: 0.0884 time to fit residues: 25.4657 Evaluate side-chains 179 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 284 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 435 PHE Chi-restraints excluded: chain E residue 466 VAL 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 386 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 69 optimal weight: 20.0000 chunk 99 optimal weight: 40.0000 chunk 178 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 148 optimal weight: 0.5980 chunk 149 optimal weight: 0.9980 chunk 43 optimal weight: 0.0980 chunk 160 optimal weight: 0.0670 chunk 153 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 247 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.183066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.136763 restraints weight = 18340.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.132338 restraints weight = 16548.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.132498 restraints weight = 15743.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.133413 restraints weight = 11289.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.133650 restraints weight = 8791.389| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13089 Z= 0.120 Angle : 0.497 6.788 18104 Z= 0.273 Chirality : 0.045 0.287 2192 Planarity : 0.002 0.033 2294 Dihedral : 16.932 179.928 2384 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.93 % Allowed : 16.80 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.19), residues: 1915 helix: 1.10 (0.18), residues: 859 sheet: -1.76 (0.29), residues: 263 loop : -1.02 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 327 TYR 0.017 0.001 TYR G 311 PHE 0.020 0.001 PHE G 364 TRP 0.019 0.001 TRP B 230 HIS 0.002 0.001 HIS G 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (13089) covalent geometry : angle 0.49711 / 0.27 (18104) hydrogen bonds : bond 0.03719 / 2.77 ( 670) hydrogen bonds : angle 3.91470 / 2.86 ( 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 192 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 253 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.7617 (t80) REVERT: F 282 ASP cc_start: 0.7739 (t70) cc_final: 0.7486 (t0) REVERT: F 292 ASP cc_start: 0.7579 (t0) cc_final: 0.7347 (t0) outliers start: 37 outliers final: 26 residues processed: 175 average time/residue: 0.0891 time to fit residues: 24.7353 Evaluate side-chains 174 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 254 ASN Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 435 PHE Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 369 CYS Chi-restraints excluded: chain 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 274 MET Chi-restraints excluded: chain G residue 353 PHE Chi-restraints excluded: chain G residue 369 CYS Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 466 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 81 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 chunk 63 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 76 optimal weight: 30.0000 chunk 142 optimal weight: 3.9990 chunk 56 optimal weight: 0.3980 chunk 11 optimal weight: 50.0000 chunk 176 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 153 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 421 ASN F 254 ASN G 269 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.178865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.131079 restraints weight = 18404.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.126133 restraints weight = 17405.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.126747 restraints weight = 16430.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.127572 restraints weight = 11742.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.127587 restraints weight = 9149.222| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13089 Z= 0.129 Angle : 0.487 7.325 18104 Z= 0.268 Chirality : 0.045 0.278 2192 Planarity : 0.002 0.032 2294 Dihedral : 16.786 179.018 2383 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.93 % Allowed : 16.27 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.10 (0.19), residues: 1915 helix: 1.22 (0.18), residues: 864 sheet: -1.52 (0.30), residues: 263 loop : -0.92 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 471 TYR 0.011 0.001 TYR F 311 PHE 0.011 0.001 PHE C 253 TRP 0.014 0.001 TRP B 230 HIS 0.002 0.001 HIS G 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (13089) covalent geometry : angle 0.48708 / 0.27 (18104) hydrogen bonds : bond 0.03478 / 2.58 ( 670) hydrogen bonds : angle 3.73445 / 2.74 ( 1907) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 253 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.7626 (t80) REVERT: F 282 ASP cc_start: 0.7838 (t70) cc_final: 0.7544 (t0) outliers start: 37 outliers final: 30 residues processed: 175 average time/residue: 0.0871 time to fit residues: 24.5335 Evaluate side-chains 174 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 254 ASN Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 421 ASN Chi-restraints excluded: chain E residue 435 PHE Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 369 CYS Chi-restraints excluded: chain 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 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: 4.9990 chunk 121 optimal weight: 0.5980 chunk 100 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 62 optimal weight: 30.0000 chunk 13 optimal weight: 7.9990 chunk 119 optimal weight: 0.5980 chunk 169 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 = 0.4238 r_free = 0.4238 target = 0.181686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.136143 restraints weight = 18073.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.130832 restraints weight = 22113.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.132784 restraints weight = 18213.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.133400 restraints weight = 12103.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.133167 restraints weight = 10237.519| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 13089 Z= 0.218 Angle : 0.545 7.251 18104 Z= 0.295 Chirality : 0.046 0.278 2192 Planarity : 0.003 0.033 2294 Dihedral : 16.792 178.790 2383 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 5.47 % Allowed : 17.47 % 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: -0.12 (0.19), residues: 1915 helix: 1.20 (0.18), residues: 862 sheet: -1.47 (0.30), residues: 263 loop : -0.96 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 260 TYR 0.018 0.002 TYR C 250 PHE 0.019 0.002 PHE G 364 TRP 0.014 0.001 TRP F 242 HIS 0.004 0.001 HIS G 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.22 (13089) covalent geometry : angle 0.54530 / 0.29 (18104) hydrogen bonds : bond 0.03776 / 2.81 ( 670) hydrogen bonds : angle 3.80077 / 2.79 ( 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 193 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 152 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: C 253 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.7677 (t80) REVERT: F 282 ASP cc_start: 0.7683 (t70) cc_final: 0.7435 (t0) outliers start: 41 outliers final: 33 residues processed: 175 average time/residue: 0.0908 time to fit residues: 25.2462 Evaluate side-chains 180 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 263 ILE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 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 E residue 466 VAL Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 369 CYS Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 34 optimal weight: 9.9990 chunk 117 optimal weight: 0.8980 chunk 51 optimal weight: 50.0000 chunk 175 optimal weight: 2.9990 chunk 160 optimal weight: 0.0670 chunk 152 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 74 optimal weight: 50.0000 chunk 113 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 182 optimal weight: 2.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 421 ASN F 269 ASN G 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.183478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.137429 restraints weight = 18314.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.133058 restraints weight = 18251.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.134488 restraints weight = 16359.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.134709 restraints weight = 11205.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.134840 restraints weight = 9221.620| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 13089 Z= 0.122 Angle : 0.485 7.195 18104 Z= 0.266 Chirality : 0.045 0.277 2192 Planarity : 0.002 0.033 2294 Dihedral : 16.737 178.824 2381 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.53 % Allowed : 18.67 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.06 (0.19), residues: 1915 helix: 1.35 (0.18), residues: 863 sheet: -1.37 (0.30), residues: 264 loop : -0.88 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 471 TYR 0.012 0.001 TYR E 311 PHE 0.016 0.001 PHE G 364 TRP 0.017 0.001 TRP E 242 HIS 0.002 0.000 HIS G 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (13089) covalent geometry : angle 0.48461 / 0.27 (18104) hydrogen bonds : bond 0.03349 / 2.48 ( 670) hydrogen bonds : angle 3.63756 / 2.67 ( 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 183 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.515 Fit side-chains REVERT: C 253 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.7698 (t80) REVERT: E 274 MET cc_start: 0.7388 (mtm) cc_final: 0.7178 (mtm) REVERT: F 282 ASP cc_start: 0.7768 (t70) cc_final: 0.7482 (t0) outliers start: 34 outliers final: 26 residues processed: 168 average time/residue: 0.0904 time to fit residues: 24.0577 Evaluate side-chains 167 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 225 MET 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 421 ASN Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 369 CYS Chi-restraints excluded: chain 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 296 ASN Chi-restraints excluded: chain G residue 451 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 57 optimal weight: 0.9990 chunk 39 optimal weight: 50.0000 chunk 6 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 11 optimal weight: 50.0000 chunk 58 optimal weight: 0.5980 chunk 134 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 241 GLN G 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.181639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.134339 restraints weight = 18393.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.129140 restraints weight = 17288.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.130434 restraints weight = 15033.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.130656 restraints weight = 10288.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.131029 restraints weight = 8783.567| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13089 Z= 0.134 Angle : 0.491 7.205 18104 Z= 0.269 Chirality : 0.045 0.276 2192 Planarity : 0.002 0.032 2294 Dihedral : 16.654 178.611 2381 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.80 % Allowed : 19.60 % Favored : 75.60 % 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: 0.10 (0.19), residues: 1915 helix: 1.40 (0.18), residues: 863 sheet: -1.33 (0.30), residues: 263 loop : -0.88 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 297 TYR 0.013 0.001 TYR E 311 PHE 0.011 0.001 PHE C 253 TRP 0.012 0.001 TRP E 242 HIS 0.002 0.000 HIS G 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (13089) covalent geometry : angle 0.49093 / 0.27 (18104) hydrogen bonds : bond 0.03300 / 2.45 ( 670) hydrogen bonds : angle 3.59834 / 2.64 ( 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 178 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 0.419 Fit side-chains REVERT: C 253 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.7702 (t80) REVERT: E 274 MET cc_start: 0.7452 (mtm) cc_final: 0.7219 (mtm) REVERT: F 282 ASP cc_start: 0.7865 (t70) cc_final: 0.7529 (t0) outliers start: 36 outliers final: 32 residues processed: 163 average time/residue: 0.0851 time to fit residues: 22.3064 Evaluate side-chains 175 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 263 ILE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 225 MET Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 254 ASN Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 369 CYS Chi-restraints excluded: chain 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 373 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: 2.9990 chunk 147 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 36 optimal weight: 50.0000 chunk 130 optimal weight: 0.5980 chunk 75 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 77 optimal weight: 50.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 296 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.181874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.134292 restraints weight = 18433.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.128208 restraints weight = 17298.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.130126 restraints weight = 15511.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.130473 restraints weight = 10995.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.130747 restraints weight = 8658.275| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13089 Z= 0.126 Angle : 0.487 7.187 18104 Z= 0.267 Chirality : 0.044 0.275 2192 Planarity : 0.002 0.032 2294 Dihedral : 16.588 178.367 2381 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.67 % Allowed : 19.33 % Favored : 76.00 % 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: 1.51 (0.18), residues: 860 sheet: -1.27 (0.30), residues: 263 loop : -0.83 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 297 TYR 0.013 0.001 TYR E 311 PHE 0.011 0.001 PHE C 253 TRP 0.011 0.001 TRP E 242 HIS 0.002 0.000 HIS G 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (13089) covalent geometry : angle 0.48733 / 0.27 (18104) hydrogen bonds : bond 0.03179 / 2.35 ( 670) hydrogen bonds : angle 3.54042 / 2.60 ( 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 182 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 0.385 Fit side-chains REVERT: C 253 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.7706 (t80) REVERT: E 274 MET cc_start: 0.7457 (mtm) cc_final: 0.7227 (mtm) REVERT: F 282 ASP cc_start: 0.7862 (t70) cc_final: 0.7531 (t0) outliers start: 35 outliers final: 32 residues processed: 168 average time/residue: 0.0803 time to fit residues: 21.5611 Evaluate side-chains 174 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 263 ILE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 225 MET Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 254 ASN Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 435 PHE Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 369 CYS Chi-restraints excluded: chain 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 373 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: 0.0570 chunk 190 optimal weight: 20.0000 chunk 27 optimal weight: 0.0050 chunk 66 optimal weight: 0.6980 chunk 138 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 137 optimal weight: 0.6980 chunk 79 optimal weight: 6.9990 chunk 82 optimal weight: 0.5980 chunk 22 optimal weight: 9.9990 overall best weight: 0.4112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 296 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.181422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.133143 restraints weight = 18503.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.126039 restraints weight = 15856.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.128518 restraints weight = 13402.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.128876 restraints weight = 8942.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.128868 restraints weight = 8202.059| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3397 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= 0.107 Angle : 0.480 7.328 18104 Z= 0.263 Chirality : 0.044 0.273 2192 Planarity : 0.002 0.033 2294 Dihedral : 16.530 178.167 2381 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.27 % Allowed : 19.87 % Favored : 75.87 % 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: 0.30 (0.19), residues: 1915 helix: 1.57 (0.18), residues: 864 sheet: -1.19 (0.30), residues: 264 loop : -0.79 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 297 TYR 0.011 0.001 TYR E 311 PHE 0.010 0.001 PHE C 253 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 0.00231 / 0.11 (13089) covalent geometry : angle 0.47991 / 0.26 (18104) hydrogen bonds : bond 0.03003 / 2.22 ( 670) hydrogen bonds : angle 3.46310 / 2.54 ( 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 179 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.463 Fit side-chains REVERT: C 253 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.7701 (t80) REVERT: E 274 MET cc_start: 0.7484 (mtm) cc_final: 0.7249 (mtm) REVERT: F 240 LYS cc_start: 0.8574 (mtpp) cc_final: 0.8307 (mmmt) REVERT: F 282 ASP cc_start: 0.7922 (t70) cc_final: 0.7572 (t0) outliers start: 32 outliers final: 29 residues processed: 165 average time/residue: 0.0763 time to fit residues: 20.1263 Evaluate side-chains 176 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 221 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 225 MET Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 254 ASN Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 435 PHE Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 369 CYS Chi-restraints excluded: chain 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 373 MET Chi-restraints excluded: chain G residue 451 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 102 optimal weight: 30.0000 chunk 46 optimal weight: 50.0000 chunk 161 optimal weight: 3.9990 chunk 183 optimal weight: 0.1980 chunk 70 optimal weight: 30.0000 chunk 41 optimal weight: 0.0270 chunk 71 optimal weight: 40.0000 chunk 77 optimal weight: 50.0000 chunk 123 optimal weight: 0.2980 chunk 9 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 421 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.180649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.134790 restraints weight = 18439.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.129313 restraints weight = 19516.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.131081 restraints weight = 16891.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.131730 restraints weight = 11834.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.131814 restraints weight = 9557.077| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13089 Z= 0.133 Angle : 0.488 7.336 18104 Z= 0.265 Chirality : 0.044 0.273 2192 Planarity : 0.002 0.032 2294 Dihedral : 16.481 177.845 2381 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.67 % Allowed : 19.73 % Favored : 75.60 % 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: 1.59 (0.18), residues: 864 sheet: -1.21 (0.30), residues: 258 loop : -0.77 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 297 TYR 0.013 0.001 TYR E 311 PHE 0.010 0.001 PHE C 253 TRP 0.010 0.001 TRP B 230 HIS 0.002 0.000 HIS G 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (13089) covalent geometry : angle 0.48801 / 0.27 (18104) hydrogen bonds : bond 0.03033 / 2.24 ( 670) hydrogen bonds : angle 3.45840 / 2.54 ( 1907) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2437.59 seconds wall clock time: 42 minutes 45.77 seconds (2565.77 seconds total)