Starting phenix.real_space_refine on Mon Aug 25 03:58:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6klw_0720/08_2025/6klw_0720.cif Found real_map, /net/cci-nas-00/data/ceres_data/6klw_0720/08_2025/6klw_0720.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6klw_0720/08_2025/6klw_0720.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6klw_0720/08_2025/6klw_0720.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6klw_0720/08_2025/6klw_0720.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6klw_0720/08_2025/6klw_0720.map" } resolution = 2.9 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= 0.006 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: 5 Type Number sf(0) Gaussians Ca 14 9.91 5 S 38 5.16 5 C 15711 2.51 5 N 4163 2.21 5 O 5253 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 113 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25179 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3135 Classifications: {'peptide': 406} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 391} Chain: "B" Number of atoms: 3135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3135 Classifications: {'peptide': 406} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 391} Chain: "C" Number of atoms: 3135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3135 Classifications: {'peptide': 406} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 391} Chain: "D" Number of atoms: 3135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3135 Classifications: {'peptide': 406} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 391} Chain: "E" Number of atoms: 3135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3135 Classifications: {'peptide': 406} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 391} Chain: "F" Number of atoms: 3135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3135 Classifications: {'peptide': 406} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 391} Chain: "G" Number of atoms: 3135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3135 Classifications: {'peptide': 406} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 391} Chain: "H" Number of atoms: 3220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3220 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 20, 'TRANS': 375} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.10, per 1000 atoms: 0.24 Number of scatterers: 25179 At special positions: 0 Unit cell: (148.03, 148.03, 230.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 14 19.99 S 38 16.00 O 5253 8.00 N 4163 7.00 C 15711 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: 2.31 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 6444 Ramachandran restraints generated. 3222 Oldfield, 0 Emsley, 3222 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6032 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 57 sheets defined 22.3% alpha, 46.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 226 through 232 Processing helix chain 'A' and resid 245 through 250 removed outlier: 3.792A pdb=" N PHE A 248 " --> pdb=" O ASN A 245 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA A 249 " --> pdb=" O ASP A 246 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU A 250 " --> pdb=" O SER A 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 245 through 250' Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 424 through 428 removed outlier: 3.634A pdb=" N ILE A 428 " --> pdb=" O ASP A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 470 Processing helix chain 'A' and resid 502 through 512 removed outlier: 4.446A pdb=" N SER A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLN A 508 " --> pdb=" O ASN A 504 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 555 removed outlier: 3.524A pdb=" N PHE A 554 " --> pdb=" O ILE A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 592 removed outlier: 3.675A pdb=" N LYS A 592 " --> pdb=" O LYS A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 602 Processing helix chain 'B' and resid 226 through 233 Processing helix chain 'B' and resid 245 through 250 removed outlier: 3.516A pdb=" N PHE B 248 " --> pdb=" O ASN B 245 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA B 249 " --> pdb=" O ASP B 246 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU B 250 " --> pdb=" O SER B 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 245 through 250' Processing helix chain 'B' and resid 271 through 277 Processing helix chain 'B' and resid 285 through 290 Processing helix chain 'B' and resid 424 through 428 removed outlier: 3.741A pdb=" N ILE B 428 " --> pdb=" O ASP B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 470 Processing helix chain 'B' and resid 502 through 511 removed outlier: 4.714A pdb=" N SER B 507 " --> pdb=" O SER B 503 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N GLN B 508 " --> pdb=" O ASN B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 555 removed outlier: 3.583A pdb=" N PHE B 554 " --> pdb=" O ILE B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 575 removed outlier: 3.787A pdb=" N VAL B 575 " --> pdb=" O GLU B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 591 Processing helix chain 'B' and resid 598 through 602 Processing helix chain 'C' and resid 226 through 233 Processing helix chain 'C' and resid 245 through 250 removed outlier: 3.555A pdb=" N ALA C 249 " --> pdb=" O ASP C 246 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU C 250 " --> pdb=" O SER C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 277 Processing helix chain 'C' and resid 285 through 290 Processing helix chain 'C' and resid 424 through 428 removed outlier: 3.574A pdb=" N ILE C 428 " --> pdb=" O ASP C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 470 Processing helix chain 'C' and resid 502 through 511 removed outlier: 4.460A pdb=" N SER C 507 " --> pdb=" O SER C 503 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLN C 508 " --> pdb=" O ASN C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 554 removed outlier: 3.507A pdb=" N PHE C 554 " --> pdb=" O ILE C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 575 removed outlier: 3.977A pdb=" N VAL C 575 " --> pdb=" O GLU C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 593 removed outlier: 3.717A pdb=" N LYS C 592 " --> pdb=" O LYS C 588 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR C 593 " --> pdb=" O GLU C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 602 removed outlier: 3.630A pdb=" N VAL C 602 " --> pdb=" O ILE C 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 233 Processing helix chain 'D' and resid 245 through 250 removed outlier: 3.728A pdb=" N ALA D 249 " --> pdb=" O ASP D 246 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU D 250 " --> pdb=" O SER D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 278 Processing helix chain 'D' and resid 285 through 290 Processing helix chain 'D' and resid 424 through 428 Processing helix chain 'D' and resid 462 through 470 Processing helix chain 'D' and resid 501 through 504 removed outlier: 3.546A pdb=" N ASN D 504 " --> pdb=" O SER D 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 501 through 504' Processing helix chain 'D' and resid 505 through 512 removed outlier: 3.523A pdb=" N VAL D 512 " --> pdb=" O GLN D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 554 Processing helix chain 'D' and resid 580 through 591 Processing helix chain 'D' and resid 598 through 602 Processing helix chain 'E' and resid 226 through 233 removed outlier: 3.533A pdb=" N ASN E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 250 removed outlier: 3.526A pdb=" N PHE E 248 " --> pdb=" O ASN E 245 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA E 249 " --> pdb=" O ASP E 246 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU E 250 " --> pdb=" O SER E 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 245 through 250' Processing helix chain 'E' and resid 271 through 278 Processing helix chain 'E' and resid 285 through 290 Processing helix chain 'E' and resid 424 through 428 removed outlier: 3.587A pdb=" N ILE E 428 " --> pdb=" O ASP E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 470 Processing helix chain 'E' and resid 502 through 511 removed outlier: 4.607A pdb=" N SER E 507 " --> pdb=" O SER E 503 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N GLN E 508 " --> pdb=" O ASN E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 554 Processing helix chain 'E' and resid 580 through 591 Processing helix chain 'E' and resid 598 through 602 Processing helix chain 'F' and resid 226 through 233 Processing helix chain 'F' and resid 245 through 250 removed outlier: 3.561A pdb=" N ALA F 249 " --> pdb=" O ASP F 246 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU F 250 " --> pdb=" O SER F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 278 Processing helix chain 'F' and resid 285 through 290 Processing helix chain 'F' and resid 424 through 428 removed outlier: 3.508A pdb=" N ILE F 428 " --> pdb=" O ASP F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 470 Processing helix chain 'F' and resid 502 through 510 removed outlier: 4.558A pdb=" N SER F 507 " --> pdb=" O SER F 503 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N GLN F 508 " --> pdb=" O ASN F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 555 Processing helix chain 'F' and resid 571 through 575 removed outlier: 3.847A pdb=" N VAL F 575 " --> pdb=" O GLU F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 593 removed outlier: 3.844A pdb=" N LYS F 592 " --> pdb=" O LYS F 588 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR F 593 " --> pdb=" O GLU F 589 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 602 Processing helix chain 'G' and resid 226 through 233 Processing helix chain 'G' and resid 245 through 249 removed outlier: 3.589A pdb=" N ALA G 249 " --> pdb=" O ASP G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 278 Processing helix chain 'G' and resid 285 through 290 Processing helix chain 'G' and resid 424 through 428 removed outlier: 3.628A pdb=" N ILE G 428 " --> pdb=" O ASP G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 470 Processing helix chain 'G' and resid 501 through 504 removed outlier: 3.604A pdb=" N ASN G 504 " --> pdb=" O SER G 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 501 through 504' Processing helix chain 'G' and resid 505 through 510 Processing helix chain 'G' and resid 545 through 554 removed outlier: 3.620A pdb=" N PHE G 554 " --> pdb=" O ILE G 550 " (cutoff:3.500A) Processing helix chain 'G' and resid 571 through 575 removed outlier: 3.703A pdb=" N VAL G 575 " --> pdb=" O GLU G 572 " (cutoff:3.500A) Processing helix chain 'G' and resid 580 through 591 Processing helix chain 'G' and resid 598 through 602 Processing helix chain 'H' and resid 19 through 28 Processing helix chain 'H' and resid 32 through 41 Processing helix chain 'H' and resid 45 through 55 Processing helix chain 'H' and resid 60 through 66 Processing helix chain 'H' and resid 69 through 82 Processing helix chain 'H' and resid 96 through 101 Processing helix chain 'H' and resid 115 through 126 Processing helix chain 'H' and resid 216 through 229 removed outlier: 3.903A pdb=" N GLY H 220 " --> pdb=" O ASP H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 234 removed outlier: 4.178A pdb=" N LYS H 234 " --> pdb=" O TRP H 231 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 248 removed outlier: 3.764A pdb=" N LEU H 240 " --> pdb=" O THR H 236 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ARG H 248 " --> pdb=" O ASN H 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 249 through 259 removed outlier: 3.749A pdb=" N ALA H 253 " --> pdb=" O GLY H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 261 through 266 removed outlier: 3.857A pdb=" N ASN H 265 " --> pdb=" O ASN H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 280 Processing helix chain 'H' and resid 315 through 327 removed outlier: 3.680A pdb=" N ILE H 319 " --> pdb=" O LYS H 315 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 234 through 236 Processing sheet with id=AA2, first strand: chain 'A' and resid 299 through 310 removed outlier: 6.717A pdb=" N ASN A 391 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU A 306 " --> pdb=" O ASN A 389 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASN A 389 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE A 308 " --> pdb=" O TYR A 387 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N TYR A 387 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU A 436 " --> pdb=" O ASN A 396 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 299 through 310 removed outlier: 6.717A pdb=" N ASN A 391 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU A 306 " --> pdb=" O ASN A 389 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASN A 389 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE A 308 " --> pdb=" O TYR A 387 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N TYR A 387 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE A 459 " --> pdb=" O ILE A 388 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 313 through 343 removed outlier: 3.537A pdb=" N SER A 373 " --> pdb=" O GLY A 319 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 323 " --> pdb=" O SER A 369 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS G 320 " --> pdb=" O TRP A 374 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN G 375 " --> pdb=" O ASP G 317 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER G 373 " --> pdb=" O GLY G 319 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR G 321 " --> pdb=" O GLY G 371 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER G 369 " --> pdb=" O SER G 323 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR G 353 " --> pdb=" O SER G 339 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY G 350 " --> pdb=" O TYR F 344 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR F 321 " --> pdb=" O GLY F 371 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER F 369 " --> pdb=" O SER F 323 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER F 363 " --> pdb=" O SER F 329 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE F 352 " --> pdb=" O ALA E 342 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER E 373 " --> pdb=" O GLY E 319 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER E 339 " --> pdb=" O THR E 353 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS D 320 " --> pdb=" O TRP E 374 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 313 through 341 current: chain 'C' and resid 313 through 314 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 350 through 381 current: chain 'B' and resid 363 through 381 removed outlier: 3.627A pdb=" N SER B 373 " --> pdb=" O GLY B 319 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR C 364 " --> pdb=" O LYS B 330 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY C 350 " --> pdb=" O TYR B 344 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN C 351 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR C 331 " --> pdb=" O ASP C 361 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER C 363 " --> pdb=" O SER C 329 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS D 358 " --> pdb=" O VAL C 336 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER D 329 " --> pdb=" O SER D 363 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER D 373 " --> pdb=" O GLY D 319 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER C 363 " --> pdb=" O SER C 329 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR C 331 " --> pdb=" O ASP C 361 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN C 351 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY C 350 " --> pdb=" O TYR B 344 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR C 364 " --> pdb=" O LYS B 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 417 through 422 removed outlier: 6.930A pdb=" N LEU A 411 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N THR A 420 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N THR A 409 " --> pdb=" O THR A 420 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LYS A 422 " --> pdb=" O PRO A 407 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LYS A 404 " --> pdb=" O GLY A 484 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLY A 484 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N THR A 406 " --> pdb=" O VAL A 482 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL A 482 " --> pdb=" O THR A 406 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR A 408 " --> pdb=" O THR A 480 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 488 through 489 Processing sheet with id=AA7, first strand: chain 'A' and resid 524 through 530 removed outlier: 9.075A pdb=" N ILE A 610 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N SER A 515 " --> pdb=" O ILE A 610 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE A 612 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE A 517 " --> pdb=" O ILE A 612 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 557 through 559 Processing sheet with id=AA9, first strand: chain 'B' and resid 234 through 236 Processing sheet with id=AB1, first strand: chain 'B' and resid 299 through 309 removed outlier: 6.877A pdb=" N ASN B 391 " --> pdb=" O GLU B 304 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU B 306 " --> pdb=" O ASN B 389 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ASN B 389 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE B 308 " --> pdb=" O TYR B 387 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N TYR B 387 " --> pdb=" O ILE B 308 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 299 through 309 removed outlier: 6.877A pdb=" N ASN B 391 " --> pdb=" O GLU B 304 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU B 306 " --> pdb=" O ASN B 389 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ASN B 389 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE B 308 " --> pdb=" O TYR B 387 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N TYR B 387 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA B 386 " --> pdb=" O ILE B 461 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ILE B 459 " --> pdb=" O ILE B 388 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 416 through 422 removed outlier: 6.837A pdb=" N LEU B 411 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR B 420 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR B 409 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LYS B 422 " --> pdb=" O PRO B 407 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N TYR B 403 " --> pdb=" O ASN B 431 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASN B 431 " --> pdb=" O TYR B 403 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 416 through 422 removed outlier: 6.837A pdb=" N LEU B 411 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR B 420 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR B 409 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LYS B 422 " --> pdb=" O PRO B 407 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LYS B 404 " --> pdb=" O GLY B 484 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY B 484 " --> pdb=" O LYS B 404 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N THR B 406 " --> pdb=" O VAL B 482 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL B 482 " --> pdb=" O THR B 406 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR B 408 " --> pdb=" O THR B 480 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 488 through 489 Processing sheet with id=AB6, first strand: chain 'B' and resid 524 through 530 removed outlier: 7.470A pdb=" N ILE B 612 " --> pdb=" O SER B 515 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE B 517 " --> pdb=" O ILE B 612 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 557 through 558 Processing sheet with id=AB8, first strand: chain 'C' and resid 234 through 237 Processing sheet with id=AB9, first strand: chain 'C' and resid 299 through 310 removed outlier: 5.617A pdb=" N VAL C 301 " --> pdb=" O TYR C 395 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TYR C 395 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N MET C 303 " --> pdb=" O ARG C 393 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ARG C 393 " --> pdb=" O MET C 303 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN C 305 " --> pdb=" O ASN C 391 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 299 through 310 removed outlier: 5.617A pdb=" N VAL C 301 " --> pdb=" O TYR C 395 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TYR C 395 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N MET C 303 " --> pdb=" O ARG C 393 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ARG C 393 " --> pdb=" O MET C 303 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN C 305 " --> pdb=" O ASN C 391 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE C 459 " --> pdb=" O ILE C 388 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 417 through 422 removed outlier: 6.818A pdb=" N LEU C 411 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N THR C 420 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N THR C 409 " --> pdb=" O THR C 420 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LYS C 422 " --> pdb=" O PRO C 407 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N TYR C 403 " --> pdb=" O ASN C 431 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASN C 431 " --> pdb=" O TYR C 403 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 417 through 422 removed outlier: 6.818A pdb=" N LEU C 411 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N THR C 420 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N THR C 409 " --> pdb=" O THR C 420 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LYS C 422 " --> pdb=" O PRO C 407 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LYS C 404 " --> pdb=" O GLY C 484 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLY C 484 " --> pdb=" O LYS C 404 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N THR C 406 " --> pdb=" O VAL C 482 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N VAL C 482 " --> pdb=" O THR C 406 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR C 408 " --> pdb=" O THR C 480 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 488 through 489 Processing sheet with id=AC5, first strand: chain 'C' and resid 525 through 530 removed outlier: 9.376A pdb=" N ILE C 610 " --> pdb=" O SER C 513 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N SER C 515 " --> pdb=" O ILE C 610 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ILE C 612 " --> pdb=" O SER C 515 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE C 517 " --> pdb=" O ILE C 612 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 557 through 559 Processing sheet with id=AC7, first strand: chain 'D' and resid 234 through 236 Processing sheet with id=AC8, first strand: chain 'D' and resid 299 through 310 removed outlier: 6.874A pdb=" N ASN D 391 " --> pdb=" O GLU D 304 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU D 306 " --> pdb=" O ASN D 389 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN D 389 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE D 308 " --> pdb=" O TYR D 387 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR D 387 " --> pdb=" O ILE D 308 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 299 through 310 removed outlier: 6.874A pdb=" N ASN D 391 " --> pdb=" O GLU D 304 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU D 306 " --> pdb=" O ASN D 389 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN D 389 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE D 308 " --> pdb=" O TYR D 387 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR D 387 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE D 459 " --> pdb=" O ILE D 388 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 416 through 422 removed outlier: 6.810A pdb=" N LEU D 411 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N THR D 420 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR D 409 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS D 422 " --> pdb=" O PRO D 407 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TYR D 403 " --> pdb=" O ASN D 431 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN D 431 " --> pdb=" O TYR D 403 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 416 through 422 removed outlier: 6.810A pdb=" N LEU D 411 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N THR D 420 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR D 409 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS D 422 " --> pdb=" O PRO D 407 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LYS D 404 " --> pdb=" O ASN D 485 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ASN D 485 " --> pdb=" O LYS D 404 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN D 481 " --> pdb=" O THR D 408 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN D 410 " --> pdb=" O THR D 479 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N THR D 479 " --> pdb=" O ASN D 410 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL D 412 " --> pdb=" O LEU D 477 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N LEU D 477 " --> pdb=" O VAL D 412 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 488 through 489 Processing sheet with id=AD4, first strand: chain 'D' and resid 524 through 530 removed outlier: 7.640A pdb=" N ILE D 612 " --> pdb=" O SER D 515 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE D 517 " --> pdb=" O ILE D 612 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 557 through 559 removed outlier: 3.546A pdb=" N LEU D 562 " --> pdb=" O ASN D 559 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 234 through 237 Processing sheet with id=AD7, first strand: chain 'E' and resid 299 through 310 removed outlier: 6.855A pdb=" N ASN E 391 " --> pdb=" O GLU E 304 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU E 306 " --> pdb=" O ASN E 389 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASN E 389 " --> pdb=" O LEU E 306 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE E 308 " --> pdb=" O TYR E 387 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TYR E 387 " --> pdb=" O ILE E 308 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 299 through 310 removed outlier: 6.855A pdb=" N ASN E 391 " --> pdb=" O GLU E 304 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU E 306 " --> pdb=" O ASN E 389 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASN E 389 " --> pdb=" O LEU E 306 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE E 308 " --> pdb=" O TYR E 387 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TYR E 387 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE E 459 " --> pdb=" O ILE E 388 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 416 through 422 removed outlier: 3.542A pdb=" N GLU E 416 " --> pdb=" O LEU E 413 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU E 411 " --> pdb=" O LEU E 418 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR E 420 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N THR E 409 " --> pdb=" O THR E 420 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LYS E 422 " --> pdb=" O PRO E 407 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL E 405 " --> pdb=" O SER E 483 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER E 483 " --> pdb=" O VAL E 405 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLN E 481 " --> pdb=" O PRO E 407 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR E 409 " --> pdb=" O THR E 479 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N THR E 479 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU E 411 " --> pdb=" O LEU E 477 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LEU E 477 " --> pdb=" O LEU E 411 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 525 through 530 removed outlier: 9.114A pdb=" N ILE E 610 " --> pdb=" O SER E 513 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N SER E 515 " --> pdb=" O ILE E 610 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ILE E 612 " --> pdb=" O SER E 515 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE E 517 " --> pdb=" O ILE E 612 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 557 through 559 removed outlier: 3.766A pdb=" N LEU E 562 " --> pdb=" O ASN E 559 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 234 through 237 Processing sheet with id=AE4, first strand: chain 'F' and resid 299 through 310 removed outlier: 5.743A pdb=" N VAL F 301 " --> pdb=" O TYR F 395 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N TYR F 395 " --> pdb=" O VAL F 301 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N MET F 303 " --> pdb=" O ARG F 393 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG F 393 " --> pdb=" O MET F 303 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN F 305 " --> pdb=" O ASN F 391 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 299 through 310 removed outlier: 5.743A pdb=" N VAL F 301 " --> pdb=" O TYR F 395 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N TYR F 395 " --> pdb=" O VAL F 301 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N MET F 303 " --> pdb=" O ARG F 393 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG F 393 " --> pdb=" O MET F 303 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN F 305 " --> pdb=" O ASN F 391 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ILE F 459 " --> pdb=" O ILE F 388 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 417 through 422 removed outlier: 6.683A pdb=" N LEU F 411 " --> pdb=" O LEU F 418 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N THR F 420 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N THR F 409 " --> pdb=" O THR F 420 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LYS F 422 " --> pdb=" O PRO F 407 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TYR F 403 " --> pdb=" O ASN F 431 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN F 431 " --> pdb=" O TYR F 403 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 417 through 422 removed outlier: 6.683A pdb=" N LEU F 411 " --> pdb=" O LEU F 418 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N THR F 420 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N THR F 409 " --> pdb=" O THR F 420 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LYS F 422 " --> pdb=" O PRO F 407 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL F 405 " --> pdb=" O SER F 483 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N SER F 483 " --> pdb=" O VAL F 405 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLN F 481 " --> pdb=" O PRO F 407 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR F 409 " --> pdb=" O THR F 479 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR F 479 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU F 411 " --> pdb=" O LEU F 477 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU F 477 " --> pdb=" O LEU F 411 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU F 413 " --> pdb=" O ILE F 475 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ILE F 475 " --> pdb=" O LEU F 413 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 488 through 489 removed outlier: 3.573A pdb=" N ILE F 496 " --> pdb=" O THR F 488 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 524 through 530 Processing sheet with id=AF1, first strand: chain 'G' and resid 234 through 236 Processing sheet with id=AF2, first strand: chain 'G' and resid 299 through 310 removed outlier: 5.636A pdb=" N VAL G 301 " --> pdb=" O TYR G 395 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N TYR G 395 " --> pdb=" O VAL G 301 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N MET G 303 " --> pdb=" O ARG G 393 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG G 393 " --> pdb=" O MET G 303 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN G 305 " --> pdb=" O ASN G 391 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA G 390 " --> pdb=" O LEU G 448 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 437 through 438 removed outlier: 4.569A pdb=" N ILE G 459 " --> pdb=" O ILE G 388 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 416 through 422 removed outlier: 3.585A pdb=" N GLU G 416 " --> pdb=" O LEU G 413 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU G 411 " --> pdb=" O LEU G 418 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR G 420 " --> pdb=" O THR G 409 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N THR G 409 " --> pdb=" O THR G 420 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LYS G 422 " --> pdb=" O PRO G 407 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LYS G 404 " --> pdb=" O GLY G 484 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY G 484 " --> pdb=" O LYS G 404 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N THR G 406 " --> pdb=" O VAL G 482 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL G 482 " --> pdb=" O THR G 406 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR G 408 " --> pdb=" O THR G 480 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 488 through 489 Processing sheet with id=AF6, first strand: chain 'G' and resid 524 through 530 Processing sheet with id=AF7, first strand: chain 'G' and resid 557 through 559 removed outlier: 3.882A pdb=" N LEU G 562 " --> pdb=" O ASN G 559 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 89 through 95 removed outlier: 3.867A pdb=" N LEU H 154 " --> pdb=" O GLU H 95 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS H 189 " --> pdb=" O GLU H 204 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 131 through 132 Processing sheet with id=AG1, first strand: chain 'H' and resid 136 through 139 Processing sheet with id=AG2, first strand: chain 'H' and resid 291 through 297 removed outlier: 3.527A pdb=" N LEU H 411 " --> pdb=" O ASN H 359 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR H 410 " --> pdb=" O ILE H 391 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ILE H 391 " --> pdb=" O THR H 410 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER H 387 " --> pdb=" O TYR H 333 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 337 through 340 removed outlier: 4.090A pdb=" N ILE H 337 " --> pdb=" O LEU H 383 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU H 383 " --> pdb=" O ILE H 337 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU H 382 " --> pdb=" O ALA H 367 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA H 367 " --> pdb=" O LEU H 382 " (cutoff:3.500A) 1101 hydrogen bonds defined for protein. 2946 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.43 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8310 1.34 - 1.45: 3672 1.45 - 1.57: 13544 1.57 - 1.69: 0 1.69 - 1.81: 69 Bond restraints: 25595 Sorted by residual: bond pdb=" C LEU D 432 " pdb=" N SER D 433 " ideal model delta sigma weight residual 1.331 1.278 0.053 2.83e-02 1.25e+03 3.56e+00 bond pdb=" CG PRO B 439 " pdb=" CD PRO B 439 " ideal model delta sigma weight residual 1.512 1.463 0.049 2.70e-02 1.37e+03 3.32e+00 bond pdb=" CA ALA D 288 " pdb=" C ALA D 288 " ideal model delta sigma weight residual 1.523 1.491 0.032 1.80e-02 3.09e+03 3.13e+00 bond pdb=" CG PRO D 439 " pdb=" CD PRO D 439 " ideal model delta sigma weight residual 1.512 1.465 0.047 2.70e-02 1.37e+03 3.09e+00 bond pdb=" CG PRO A 439 " pdb=" CD PRO A 439 " ideal model delta sigma weight residual 1.512 1.465 0.047 2.70e-02 1.37e+03 2.98e+00 ... (remaining 25590 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 33058 1.40 - 2.81: 1464 2.81 - 4.21: 166 4.21 - 5.61: 29 5.61 - 7.01: 6 Bond angle restraints: 34723 Sorted by residual: angle pdb=" C ASN C 381 " pdb=" N LYS C 382 " pdb=" CA LYS C 382 " ideal model delta sigma weight residual 122.65 116.36 6.29 1.60e+00 3.91e-01 1.54e+01 angle pdb=" N VAL C 602 " pdb=" CA VAL C 602 " pdb=" C VAL C 602 " ideal model delta sigma weight residual 110.21 105.93 4.28 1.13e+00 7.83e-01 1.43e+01 angle pdb=" C ARG D 289 " pdb=" N ASP D 290 " pdb=" CA ASP D 290 " ideal model delta sigma weight residual 121.83 127.12 -5.29 1.56e+00 4.11e-01 1.15e+01 angle pdb=" N ILE G 459 " pdb=" CA ILE G 459 " pdb=" C ILE G 459 " ideal model delta sigma weight residual 107.56 110.55 -2.99 9.10e-01 1.21e+00 1.08e+01 angle pdb=" C PHE H 213 " pdb=" N LYS H 214 " pdb=" CA LYS H 214 " ideal model delta sigma weight residual 120.82 125.73 -4.91 1.50e+00 4.44e-01 1.07e+01 ... (remaining 34718 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 14114 17.55 - 35.10: 1167 35.10 - 52.66: 180 52.66 - 70.21: 41 70.21 - 87.76: 24 Dihedral angle restraints: 15526 sinusoidal: 6087 harmonic: 9439 Sorted by residual: dihedral pdb=" CA LYS C 603 " pdb=" C LYS C 603 " pdb=" N LEU C 604 " pdb=" CA LEU C 604 " ideal model delta harmonic sigma weight residual 180.00 147.11 32.89 0 5.00e+00 4.00e-02 4.33e+01 dihedral pdb=" CA LEU F 448 " pdb=" C LEU F 448 " pdb=" N ASN F 449 " pdb=" CA ASN F 449 " ideal model delta harmonic sigma weight residual -180.00 -155.81 -24.19 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA PHE F 248 " pdb=" C PHE F 248 " pdb=" N ALA F 249 " pdb=" CA ALA F 249 " ideal model delta harmonic sigma weight residual 180.00 157.92 22.08 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 15523 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2574 0.041 - 0.083: 936 0.083 - 0.124: 350 0.124 - 0.165: 55 0.165 - 0.206: 2 Chirality restraints: 3917 Sorted by residual: chirality pdb=" CB ILE B 352 " pdb=" CA ILE B 352 " pdb=" CG1 ILE B 352 " pdb=" CG2 ILE B 352 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB ILE H 337 " pdb=" CA ILE H 337 " pdb=" CG1 ILE H 337 " pdb=" CG2 ILE H 337 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.15e-01 chirality pdb=" CA ILE F 352 " pdb=" N ILE F 352 " pdb=" C ILE F 352 " pdb=" CB ILE F 352 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.69e-01 ... (remaining 3914 not shown) Planarity restraints: 4554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 268 " 0.040 5.00e-02 4.00e+02 6.07e-02 5.90e+00 pdb=" N PRO C 269 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 269 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 269 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 268 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO D 269 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO D 269 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 269 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 268 " 0.036 5.00e-02 4.00e+02 5.49e-02 4.83e+00 pdb=" N PRO B 269 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 269 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 269 " 0.031 5.00e-02 4.00e+02 ... (remaining 4551 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 772 2.69 - 3.24: 23877 3.24 - 3.79: 37930 3.79 - 4.35: 54435 4.35 - 4.90: 91038 Nonbonded interactions: 208052 Sorted by model distance: nonbonded pdb=" O LYS H 225 " pdb=" OG SER H 229 " model vdw 2.135 3.040 nonbonded pdb=" O SER B 239 " pdb=" OH TYR B 273 " model vdw 2.136 3.040 nonbonded pdb=" OE2 GLU G 230 " pdb="CA CA G1002 " model vdw 2.138 2.510 nonbonded pdb=" O GLU G 262 " pdb="CA CA G1002 " model vdw 2.166 2.510 nonbonded pdb=" OE2 GLU D 230 " pdb="CA CA D1001 " model vdw 2.194 2.510 ... (remaining 208047 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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 individual isotropic 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: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.120 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 25595 Z= 0.237 Angle : 0.658 7.013 34723 Z= 0.384 Chirality : 0.049 0.206 3917 Planarity : 0.005 0.061 4554 Dihedral : 13.672 87.762 9494 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.60 (0.12), residues: 3222 helix: -2.79 (0.15), residues: 612 sheet: -1.50 (0.16), residues: 917 loop : -2.78 (0.12), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 295 TYR 0.032 0.002 TYR E 394 PHE 0.013 0.002 PHE F 618 TRP 0.010 0.002 TRP H 326 HIS 0.004 0.001 HIS H 157 Details of bonding type rmsd covalent geometry : bond 0.00540 (25595) covalent geometry : angle 0.65842 (34723) hydrogen bonds : bond 0.21814 ( 1010) hydrogen bonds : angle 9.84015 ( 2946) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6444 Ramachandran restraints generated. 3222 Oldfield, 0 Emsley, 3222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6444 Ramachandran restraints generated. 3222 Oldfield, 0 Emsley, 3222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 1.226 Fit side-chains REVERT: A 372 GLU cc_start: 0.7898 (pt0) cc_final: 0.7667 (pt0) REVERT: A 534 GLN cc_start: 0.7476 (tp40) cc_final: 0.6977 (mm110) REVERT: A 564 TYR cc_start: 0.8207 (m-80) cc_final: 0.8003 (m-10) REVERT: A 605 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7257 (mm-30) REVERT: B 523 GLN cc_start: 0.7993 (mt0) cc_final: 0.7753 (tt0) REVERT: C 597 LYS cc_start: 0.7441 (mttm) cc_final: 0.7114 (mmtm) REVERT: D 404 LYS cc_start: 0.8622 (tttm) cc_final: 0.8398 (mtpm) REVERT: D 474 GLN cc_start: 0.8521 (mm-40) cc_final: 0.8297 (mp10) REVERT: E 320 LYS cc_start: 0.8762 (ttmm) cc_final: 0.8300 (tppp) REVERT: E 441 LYS cc_start: 0.8372 (tttp) cc_final: 0.8134 (tptp) REVERT: E 566 ASN cc_start: 0.8049 (m-40) cc_final: 0.7846 (m110) REVERT: E 608 MET cc_start: 0.8660 (mtt) cc_final: 0.8285 (mmm) REVERT: F 222 ASN cc_start: 0.8144 (t0) cc_final: 0.7915 (t0) REVERT: F 320 LYS cc_start: 0.8241 (ttmm) cc_final: 0.7957 (tttp) REVERT: F 330 LYS cc_start: 0.7928 (tttp) cc_final: 0.7292 (tmmt) REVERT: F 362 ASN cc_start: 0.7766 (m-40) cc_final: 0.7553 (m-40) REVERT: G 222 ASN cc_start: 0.8479 (t0) cc_final: 0.8194 (m-40) REVERT: G 321 THR cc_start: 0.8968 (m) cc_final: 0.8735 (p) REVERT: G 381 ASN cc_start: 0.8264 (t0) cc_final: 0.7996 (t0) REVERT: G 564 TYR cc_start: 0.8250 (m-10) cc_final: 0.7909 (m-10) REVERT: H 65 GLU cc_start: 0.4119 (mp0) cc_final: 0.3885 (pp20) REVERT: H 95 GLU cc_start: 0.6503 (mm-30) cc_final: 0.6049 (tp30) REVERT: H 105 GLU cc_start: 0.4822 (tp30) cc_final: 0.4524 (pm20) REVERT: H 398 LYS cc_start: 0.5205 (ttpp) cc_final: 0.4924 (ttpt) outliers start: 0 outliers final: 0 residues processed: 401 average time/residue: 0.7319 time to fit residues: 335.8430 Evaluate side-chains 266 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN B 370 ASN B 582 ASN B 609 ASN C 455 ASN D 609 ASN E 318 GLN E 334 ASN F 590 GLN G 370 ASN ** G 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 300 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.138128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.102292 restraints weight = 33025.436| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.83 r_work: 0.2956 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25595 Z= 0.172 Angle : 0.581 9.738 34723 Z= 0.319 Chirality : 0.048 0.171 3917 Planarity : 0.005 0.051 4554 Dihedral : 5.433 32.340 3467 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.21 % Allowed : 9.68 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.53 (0.13), residues: 3222 helix: -1.60 (0.19), residues: 620 sheet: -0.42 (0.17), residues: 845 loop : -2.43 (0.12), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 528 TYR 0.026 0.002 TYR H 52 PHE 0.028 0.002 PHE C 248 TRP 0.012 0.001 TRP H 223 HIS 0.005 0.001 HIS H 157 Details of bonding type rmsd covalent geometry : bond 0.00404 (25595) covalent geometry : angle 0.58108 (34723) hydrogen bonds : bond 0.03776 ( 1010) hydrogen bonds : angle 5.91102 ( 2946) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6444 Ramachandran restraints generated. 3222 Oldfield, 0 Emsley, 3222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6444 Ramachandran restraints generated. 3222 Oldfield, 0 Emsley, 3222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 306 time to evaluate : 1.072 Fit side-chains revert: symmetry clash REVERT: A 490 ASN cc_start: 0.7509 (p0) cc_final: 0.7240 (p0) REVERT: A 564 TYR cc_start: 0.8326 (m-80) cc_final: 0.8112 (m-10) REVERT: A 589 GLU cc_start: 0.7378 (mm-30) cc_final: 0.7130 (mp0) REVERT: A 592 LYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6868 (mttt) REVERT: A 605 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8107 (mm-30) REVERT: B 240 ILE cc_start: 0.8436 (pt) cc_final: 0.7902 (mp) REVERT: B 318 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8217 (mt0) REVERT: B 523 GLN cc_start: 0.8088 (mt0) cc_final: 0.7877 (tt0) REVERT: B 563 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8670 (mp) REVERT: B 605 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8329 (mt-10) REVERT: C 585 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7728 (tp30) REVERT: C 588 LYS cc_start: 0.8376 (ttpt) cc_final: 0.7933 (ttmt) REVERT: C 597 LYS cc_start: 0.7341 (mttm) cc_final: 0.6939 (mmtm) REVERT: D 324 ARG cc_start: 0.8388 (ttm-80) cc_final: 0.8166 (tpp80) REVERT: D 414 ASP cc_start: 0.8438 (t70) cc_final: 0.8162 (t70) REVERT: D 474 GLN cc_start: 0.8905 (mm-40) cc_final: 0.8619 (mp10) REVERT: D 576 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7692 (tm-30) REVERT: E 566 ASN cc_start: 0.8298 (m-40) cc_final: 0.8032 (m110) REVERT: E 589 GLU cc_start: 0.7050 (mm-30) cc_final: 0.6711 (mm-30) REVERT: E 608 MET cc_start: 0.8820 (mtt) cc_final: 0.8517 (mmm) REVERT: F 222 ASN cc_start: 0.8588 (t0) cc_final: 0.8318 (t0) REVERT: F 254 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8522 (mttm) REVERT: F 330 LYS cc_start: 0.8141 (tttp) cc_final: 0.7162 (tmtt) REVERT: G 222 ASN cc_start: 0.8978 (t0) cc_final: 0.8715 (m-40) REVERT: G 384 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8162 (mt-10) REVERT: G 543 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8008 (tp30) REVERT: G 564 TYR cc_start: 0.8499 (m-10) cc_final: 0.8156 (m-10) REVERT: G 589 GLU cc_start: 0.8504 (tm-30) cc_final: 0.7508 (tp30) REVERT: H 65 GLU cc_start: 0.3907 (mp0) cc_final: 0.3572 (pp20) REVERT: H 93 TYR cc_start: 0.6799 (p90) cc_final: 0.6399 (p90) REVERT: H 95 GLU cc_start: 0.6416 (mm-30) cc_final: 0.6168 (tp30) REVERT: H 105 GLU cc_start: 0.4712 (tp30) cc_final: 0.4448 (pm20) REVERT: H 137 LYS cc_start: 0.4740 (OUTLIER) cc_final: 0.4378 (ttmt) REVERT: H 166 MET cc_start: 0.3405 (OUTLIER) cc_final: 0.3021 (mpt) outliers start: 62 outliers final: 26 residues processed: 335 average time/residue: 0.7046 time to fit residues: 271.8936 Evaluate side-chains 314 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 278 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 592 LYS Chi-restraints excluded: chain B residue 318 GLN Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 515 SER Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 515 SER Chi-restraints excluded: chain C residue 585 GLU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 467 LYS Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 576 GLU Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain F residue 254 LYS Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 374 TRP Chi-restraints excluded: chain F residue 402 MET Chi-restraints excluded: chain G residue 240 ILE Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 373 SER Chi-restraints excluded: chain G residue 441 LYS Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain H residue 137 LYS Chi-restraints excluded: chain H residue 166 MET Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 370 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 148 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 279 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 ASN ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 ASN C 601 ASN E 318 GLN E 590 GLN F 311 ASN F 449 ASN F 590 GLN ** H 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.136191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.100210 restraints weight = 33011.830| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.82 r_work: 0.2923 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 25595 Z= 0.280 Angle : 0.636 9.572 34723 Z= 0.345 Chirality : 0.050 0.185 3917 Planarity : 0.005 0.057 4554 Dihedral : 5.658 32.195 3467 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.77 % Allowed : 12.24 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.06 (0.13), residues: 3222 helix: -1.02 (0.21), residues: 572 sheet: 0.11 (0.17), residues: 805 loop : -2.28 (0.12), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 528 TYR 0.021 0.002 TYR H 251 PHE 0.033 0.002 PHE C 248 TRP 0.014 0.002 TRP H 223 HIS 0.004 0.001 HIS C 313 Details of bonding type rmsd covalent geometry : bond 0.00675 (25595) covalent geometry : angle 0.63571 (34723) hydrogen bonds : bond 0.03760 ( 1010) hydrogen bonds : angle 5.52432 ( 2946) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6444 Ramachandran restraints generated. 3222 Oldfield, 0 Emsley, 3222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6444 Ramachandran restraints generated. 3222 Oldfield, 0 Emsley, 3222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 270 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: A 490 ASN cc_start: 0.7504 (p0) cc_final: 0.7267 (p0) REVERT: A 498 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8176 (tp30) REVERT: A 589 GLU cc_start: 0.7380 (mm-30) cc_final: 0.7178 (mp0) REVERT: A 592 LYS cc_start: 0.7162 (OUTLIER) cc_final: 0.6823 (mttt) REVERT: A 605 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7722 (mm-30) REVERT: B 318 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8205 (mt0) REVERT: B 523 GLN cc_start: 0.8085 (mt0) cc_final: 0.7860 (tt0) REVERT: B 605 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8391 (mt-10) REVERT: C 585 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7739 (tp30) REVERT: C 588 LYS cc_start: 0.8392 (ttpt) cc_final: 0.7990 (ttmt) REVERT: C 597 LYS cc_start: 0.7225 (mttm) cc_final: 0.6919 (mmtm) REVERT: D 324 ARG cc_start: 0.8414 (ttm-80) cc_final: 0.8185 (tpp80) REVERT: D 414 ASP cc_start: 0.8541 (t70) cc_final: 0.8164 (t70) REVERT: D 451 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.8919 (ptp) REVERT: D 576 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7580 (tm-30) REVERT: E 324 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7808 (ttp80) REVERT: E 498 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7207 (mm-30) REVERT: E 566 ASN cc_start: 0.8322 (m-40) cc_final: 0.8053 (m110) REVERT: E 589 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6673 (mm-30) REVERT: E 608 MET cc_start: 0.8844 (mtt) cc_final: 0.8530 (mmm) REVERT: F 217 ASP cc_start: 0.7771 (p0) cc_final: 0.6838 (m-30) REVERT: F 222 ASN cc_start: 0.8519 (t0) cc_final: 0.8285 (t0) REVERT: F 254 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8665 (mttm) REVERT: F 330 LYS cc_start: 0.8105 (tttp) cc_final: 0.7150 (tmtt) REVERT: F 378 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8477 (tt) REVERT: F 402 MET cc_start: 0.9361 (OUTLIER) cc_final: 0.9120 (ttm) REVERT: G 384 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8126 (mt-10) REVERT: G 564 TYR cc_start: 0.8629 (m-10) cc_final: 0.8257 (m-10) REVERT: G 589 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7755 (tp30) REVERT: G 605 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8080 (pt0) REVERT: H 44 LYS cc_start: 0.4362 (mmmm) cc_final: 0.4040 (mmpt) REVERT: H 62 TYR cc_start: 0.3891 (p90) cc_final: 0.3262 (p90) REVERT: H 65 GLU cc_start: 0.3957 (mp0) cc_final: 0.3560 (pp20) REVERT: H 95 GLU cc_start: 0.6489 (mm-30) cc_final: 0.6250 (tp30) REVERT: H 105 GLU cc_start: 0.4762 (tp30) cc_final: 0.4461 (pm20) REVERT: H 137 LYS cc_start: 0.4542 (OUTLIER) cc_final: 0.4271 (ttmt) REVERT: H 399 ASP cc_start: 0.1316 (OUTLIER) cc_final: 0.1095 (m-30) outliers start: 78 outliers final: 43 residues processed: 316 average time/residue: 0.6765 time to fit residues: 247.3468 Evaluate side-chains 309 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 252 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 592 LYS Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 318 GLN Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 515 SER Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 515 SER Chi-restraints excluded: chain C residue 585 GLU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 362 ASN Chi-restraints excluded: chain D residue 451 MET Chi-restraints excluded: chain D residue 467 LYS Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 559 ASN Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 576 GLU Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 324 ARG Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain E residue 451 MET Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 523 GLN Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain F residue 254 LYS Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 374 TRP Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 384 GLU Chi-restraints excluded: chain F residue 399 THR Chi-restraints excluded: chain F residue 402 MET Chi-restraints excluded: chain F residue 441 LYS Chi-restraints excluded: chain F residue 449 ASN Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain G residue 240 ILE Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 373 SER Chi-restraints excluded: chain G residue 384 GLU Chi-restraints excluded: chain G residue 441 LYS Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 605 GLU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 137 LYS Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 370 SER Chi-restraints excluded: chain H residue 399 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 187 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 chunk 246 optimal weight: 0.9980 chunk 265 optimal weight: 0.9990 chunk 285 optimal weight: 5.9990 chunk 280 optimal weight: 3.9990 chunk 226 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 108 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN A 455 ASN B 362 ASN B 391 ASN B 582 ASN E 318 GLN E 485 ASN F 311 ASN F 590 GLN ** G 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.138981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.103164 restraints weight = 32745.352| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.84 r_work: 0.2965 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25595 Z= 0.123 Angle : 0.520 7.916 34723 Z= 0.285 Chirality : 0.046 0.171 3917 Planarity : 0.004 0.047 4554 Dihedral : 5.191 32.495 3467 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.21 % Allowed : 14.02 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.66 (0.13), residues: 3222 helix: -0.67 (0.21), residues: 564 sheet: 0.44 (0.17), residues: 824 loop : -2.09 (0.12), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 289 TYR 0.015 0.001 TYR C 356 PHE 0.022 0.001 PHE C 248 TRP 0.012 0.001 TRP H 223 HIS 0.006 0.001 HIS H 157 Details of bonding type rmsd covalent geometry : bond 0.00285 (25595) covalent geometry : angle 0.52039 (34723) hydrogen bonds : bond 0.02823 ( 1010) hydrogen bonds : angle 5.03100 ( 2946) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6444 Ramachandran restraints generated. 3222 Oldfield, 0 Emsley, 3222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6444 Ramachandran restraints generated. 3222 Oldfield, 0 Emsley, 3222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 288 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: A 498 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8117 (tp30) REVERT: A 589 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7077 (mp0) REVERT: A 592 LYS cc_start: 0.7016 (OUTLIER) cc_final: 0.6711 (mttt) REVERT: A 605 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7676 (mm-30) REVERT: B 240 ILE cc_start: 0.8489 (pt) cc_final: 0.7956 (mm) REVERT: B 523 GLN cc_start: 0.8091 (mt0) cc_final: 0.7876 (mt0) REVERT: B 563 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8672 (mp) REVERT: B 605 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8278 (mt-10) REVERT: C 216 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.5576 (tm-30) REVERT: C 585 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7711 (tp30) REVERT: C 588 LYS cc_start: 0.8375 (ttpt) cc_final: 0.7949 (ttmt) REVERT: C 589 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7523 (tm-30) REVERT: C 597 LYS cc_start: 0.7197 (mttm) cc_final: 0.6876 (mmtm) REVERT: D 324 ARG cc_start: 0.8397 (ttm-80) cc_final: 0.8182 (tpp80) REVERT: D 414 ASP cc_start: 0.8597 (t70) cc_final: 0.8039 (t70) REVERT: D 568 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8292 (pt) REVERT: D 576 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7451 (tm-30) REVERT: E 566 ASN cc_start: 0.8302 (m-40) cc_final: 0.8051 (m110) REVERT: E 589 GLU cc_start: 0.7059 (mm-30) cc_final: 0.6761 (mm-30) REVERT: E 608 MET cc_start: 0.8781 (mtt) cc_final: 0.8560 (mmm) REVERT: F 222 ASN cc_start: 0.8584 (t0) cc_final: 0.8327 (t0) REVERT: F 330 LYS cc_start: 0.8104 (tttp) cc_final: 0.7166 (tmtt) REVERT: F 378 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8504 (tp) REVERT: G 222 ASN cc_start: 0.8953 (t0) cc_final: 0.8720 (m-40) REVERT: G 357 SER cc_start: 0.8238 (t) cc_final: 0.7998 (p) REVERT: G 384 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8137 (mt-10) REVERT: G 589 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7794 (tp30) REVERT: G 593 TYR cc_start: 0.6548 (m-80) cc_final: 0.6057 (m-10) REVERT: G 605 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8019 (pt0) REVERT: H 44 LYS cc_start: 0.4405 (mmmm) cc_final: 0.4142 (mmpt) REVERT: H 62 TYR cc_start: 0.4315 (p90) cc_final: 0.3517 (p90) REVERT: H 65 GLU cc_start: 0.4086 (OUTLIER) cc_final: 0.3612 (pp20) REVERT: H 379 TYR cc_start: 0.5149 (m-80) cc_final: 0.4592 (m-80) REVERT: H 399 ASP cc_start: 0.1796 (OUTLIER) cc_final: 0.1572 (m-30) outliers start: 62 outliers final: 27 residues processed: 323 average time/residue: 0.6737 time to fit residues: 251.6903 Evaluate side-chains 304 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 265 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 592 LYS Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 515 SER Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 515 SER Chi-restraints excluded: chain C residue 585 GLU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 467 LYS Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 559 ASN Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain D residue 576 GLU Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain F residue 374 TRP Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 399 THR Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 384 GLU Chi-restraints excluded: chain G residue 441 LYS Chi-restraints excluded: chain G residue 452 ASP Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 605 GLU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 370 SER Chi-restraints excluded: chain H residue 399 ASP Chi-restraints excluded: chain H residue 402 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 231 optimal weight: 5.9990 chunk 204 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 269 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 189 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 ASN B 582 ASN E 318 GLN E 582 ASN F 311 ASN F 590 GLN ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.136810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.100842 restraints weight = 32848.779| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.80 r_work: 0.2931 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 25595 Z= 0.250 Angle : 0.598 9.285 34723 Z= 0.324 Chirality : 0.049 0.176 3917 Planarity : 0.005 0.054 4554 Dihedral : 5.470 31.302 3467 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.06 % Allowed : 14.16 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.13), residues: 3222 helix: -0.61 (0.21), residues: 571 sheet: 0.61 (0.17), residues: 810 loop : -2.08 (0.12), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 289 TYR 0.021 0.002 TYR D 356 PHE 0.028 0.002 PHE C 248 TRP 0.014 0.002 TRP H 223 HIS 0.005 0.001 HIS H 157 Details of bonding type rmsd covalent geometry : bond 0.00604 (25595) covalent geometry : angle 0.59829 (34723) hydrogen bonds : bond 0.03278 ( 1010) hydrogen bonds : angle 5.09658 ( 2946) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6444 Ramachandran restraints generated. 3222 Oldfield, 0 Emsley, 3222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6444 Ramachandran restraints generated. 3222 Oldfield, 0 Emsley, 3222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 262 time to evaluate : 1.044 Fit side-chains REVERT: A 498 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8241 (tp30) REVERT: A 589 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7154 (mp0) REVERT: A 592 LYS cc_start: 0.7097 (OUTLIER) cc_final: 0.6792 (mttt) REVERT: A 605 GLU cc_start: 0.8353 (mm-30) cc_final: 0.7733 (mm-30) REVERT: B 318 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8278 (mt0) REVERT: B 523 GLN cc_start: 0.8088 (mt0) cc_final: 0.7869 (mt0) REVERT: B 605 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8333 (mt-10) REVERT: C 216 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.5604 (tm-30) REVERT: C 585 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7747 (tp30) REVERT: C 588 LYS cc_start: 0.8380 (ttpt) cc_final: 0.7972 (ttmt) REVERT: C 589 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7497 (tm-30) REVERT: C 597 LYS cc_start: 0.7268 (mttm) cc_final: 0.6903 (mmtm) REVERT: D 324 ARG cc_start: 0.8433 (ttm-80) cc_final: 0.8190 (tpp80) REVERT: D 414 ASP cc_start: 0.8600 (t70) cc_final: 0.8002 (t70) REVERT: D 576 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7450 (tm-30) REVERT: E 330 LYS cc_start: 0.8244 (ttmt) cc_final: 0.7985 (ttpt) REVERT: E 566 ASN cc_start: 0.8346 (m-40) cc_final: 0.8084 (m110) REVERT: E 588 LYS cc_start: 0.7978 (mtpp) cc_final: 0.7778 (mtpp) REVERT: E 589 GLU cc_start: 0.7062 (mm-30) cc_final: 0.6814 (mm-30) REVERT: E 608 MET cc_start: 0.8843 (mtt) cc_final: 0.8528 (mmm) REVERT: F 222 ASN cc_start: 0.8583 (t0) cc_final: 0.8317 (t0) REVERT: F 254 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8672 (mttm) REVERT: F 320 LYS cc_start: 0.8386 (ttmm) cc_final: 0.7804 (tttp) REVERT: F 330 LYS cc_start: 0.8098 (tttp) cc_final: 0.7138 (tmtt) REVERT: F 378 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8487 (tt) REVERT: F 585 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7494 (tm-30) REVERT: G 384 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8165 (mt-10) REVERT: G 576 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7706 (tp30) REVERT: G 589 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7764 (tp30) REVERT: G 605 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8020 (pt0) REVERT: H 62 TYR cc_start: 0.4387 (p90) cc_final: 0.3556 (p90) REVERT: H 65 GLU cc_start: 0.4049 (OUTLIER) cc_final: 0.3493 (pp20) REVERT: H 93 TYR cc_start: 0.6675 (p90) cc_final: 0.6465 (p90) REVERT: H 370 SER cc_start: 0.3255 (OUTLIER) cc_final: 0.3035 (p) REVERT: H 379 TYR cc_start: 0.5004 (m-80) cc_final: 0.4586 (m-80) outliers start: 86 outliers final: 45 residues processed: 318 average time/residue: 0.6583 time to fit residues: 243.0265 Evaluate side-chains 313 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 254 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 592 LYS Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 318 GLN Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 515 SER Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 515 SER Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 585 GLU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 467 LYS Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 576 GLU Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 451 MET Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain F residue 254 LYS Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 374 TRP Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 384 GLU Chi-restraints excluded: chain F residue 399 THR Chi-restraints excluded: chain F residue 441 LYS Chi-restraints excluded: chain F residue 585 GLU Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain G residue 240 ILE Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 352 ILE Chi-restraints excluded: chain G residue 384 GLU Chi-restraints excluded: chain G residue 441 LYS Chi-restraints excluded: chain G residue 452 ASP Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 576 GLU Chi-restraints excluded: chain G residue 605 GLU Chi-restraints excluded: chain G residue 619 THR Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 370 SER Chi-restraints excluded: chain H residue 381 VAL Chi-restraints excluded: chain H residue 402 VAL Chi-restraints excluded: chain H residue 408 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 310 optimal weight: 10.0000 chunk 169 optimal weight: 1.9990 chunk 282 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 chunk 261 optimal weight: 0.3980 chunk 59 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 120 optimal weight: 0.0970 chunk 299 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 262 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN B 362 ASN B 370 ASN B 582 ASN E 311 ASN E 318 GLN F 311 ASN F 590 GLN ** G 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.139719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.103871 restraints weight = 32756.055| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.83 r_work: 0.2969 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25595 Z= 0.108 Angle : 0.503 8.569 34723 Z= 0.274 Chirality : 0.045 0.156 3917 Planarity : 0.004 0.045 4554 Dihedral : 5.014 31.893 3467 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.28 % Allowed : 16.12 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.14), residues: 3222 helix: -0.38 (0.21), residues: 564 sheet: 0.91 (0.17), residues: 817 loop : -1.95 (0.13), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 289 TYR 0.017 0.001 TYR C 356 PHE 0.019 0.001 PHE C 248 TRP 0.012 0.001 TRP H 223 HIS 0.006 0.001 HIS H 157 Details of bonding type rmsd covalent geometry : bond 0.00250 (25595) covalent geometry : angle 0.50271 (34723) hydrogen bonds : bond 0.02577 ( 1010) hydrogen bonds : angle 4.76656 ( 2946) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6444 Ramachandran restraints generated. 3222 Oldfield, 0 Emsley, 3222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6444 Ramachandran restraints generated. 3222 Oldfield, 0 Emsley, 3222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 291 time to evaluate : 1.232 Fit side-chains REVERT: A 498 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8144 (tp30) REVERT: A 589 GLU cc_start: 0.7349 (mm-30) cc_final: 0.7098 (mp0) REVERT: A 592 LYS cc_start: 0.6965 (OUTLIER) cc_final: 0.6677 (mttt) REVERT: A 605 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7730 (mm-30) REVERT: B 240 ILE cc_start: 0.8495 (pt) cc_final: 0.7979 (mm) REVERT: B 559 ASN cc_start: 0.7243 (m110) cc_final: 0.7038 (m110) REVERT: B 576 GLU cc_start: 0.7769 (tt0) cc_final: 0.7253 (mt-10) REVERT: B 605 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8268 (mt-10) REVERT: C 216 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.5274 (tm-30) REVERT: C 585 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7717 (tp30) REVERT: C 588 LYS cc_start: 0.8355 (ttpt) cc_final: 0.7934 (ttmt) REVERT: C 589 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7509 (tm-30) REVERT: C 597 LYS cc_start: 0.7101 (mttm) cc_final: 0.6865 (mmtm) REVERT: D 414 ASP cc_start: 0.8693 (t70) cc_final: 0.8034 (t70) REVERT: D 568 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8437 (pt) REVERT: D 576 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7617 (mt-10) REVERT: E 330 LYS cc_start: 0.8255 (ttmt) cc_final: 0.7986 (ttpt) REVERT: E 566 ASN cc_start: 0.8223 (m-40) cc_final: 0.7988 (m110) REVERT: E 589 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6785 (mm-30) REVERT: F 222 ASN cc_start: 0.8612 (t0) cc_final: 0.8356 (t0) REVERT: F 330 LYS cc_start: 0.8134 (tttp) cc_final: 0.7183 (tmtt) REVERT: F 374 TRP cc_start: 0.7759 (OUTLIER) cc_final: 0.4814 (p90) REVERT: F 378 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8521 (tp) REVERT: G 222 ASN cc_start: 0.8949 (t0) cc_final: 0.8731 (m-40) REVERT: G 357 SER cc_start: 0.8282 (t) cc_final: 0.8065 (p) REVERT: G 589 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7805 (tp30) REVERT: G 593 TYR cc_start: 0.6518 (m-80) cc_final: 0.5915 (m-80) REVERT: G 605 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8003 (pt0) REVERT: H 44 LYS cc_start: 0.3186 (mmpt) cc_final: 0.2980 (mttt) REVERT: H 65 GLU cc_start: 0.4286 (OUTLIER) cc_final: 0.3703 (pp20) REVERT: H 93 TYR cc_start: 0.6799 (p90) cc_final: 0.6440 (p90) REVERT: H 379 TYR cc_start: 0.5086 (m-80) cc_final: 0.4708 (m-80) outliers start: 64 outliers final: 29 residues processed: 332 average time/residue: 0.6529 time to fit residues: 252.1654 Evaluate side-chains 300 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 261 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 592 LYS Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 515 SER Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 585 GLU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 467 LYS Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 559 ASN Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain D residue 576 GLU Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain F residue 374 TRP Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 399 THR Chi-restraints excluded: chain F residue 548 GLU Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 441 LYS Chi-restraints excluded: chain G residue 452 ASP Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 605 GLU Chi-restraints excluded: chain G residue 619 THR Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 370 SER Chi-restraints excluded: chain H residue 381 VAL Chi-restraints excluded: chain H residue 402 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 274 optimal weight: 6.9990 chunk 224 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 251 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 chunk 159 optimal weight: 2.9990 chunk 203 optimal weight: 0.6980 chunk 199 optimal weight: 0.9980 chunk 241 optimal weight: 0.7980 chunk 188 optimal weight: 2.9990 chunk 172 optimal weight: 8.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 ASN B 370 ASN B 582 ASN E 318 GLN E 582 ASN F 311 ASN F 590 GLN ** G 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.139164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.103411 restraints weight = 32700.957| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.84 r_work: 0.2967 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25595 Z= 0.141 Angle : 0.519 9.662 34723 Z= 0.282 Chirality : 0.046 0.157 3917 Planarity : 0.004 0.045 4554 Dihedral : 5.002 31.101 3467 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.42 % Allowed : 16.72 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.14), residues: 3222 helix: -0.24 (0.22), residues: 564 sheet: 1.05 (0.17), residues: 817 loop : -1.89 (0.13), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 324 TYR 0.031 0.001 TYR H 52 PHE 0.020 0.001 PHE G 248 TRP 0.014 0.001 TRP H 223 HIS 0.006 0.001 HIS H 157 Details of bonding type rmsd covalent geometry : bond 0.00335 (25595) covalent geometry : angle 0.51909 (34723) hydrogen bonds : bond 0.02675 ( 1010) hydrogen bonds : angle 4.71571 ( 2946) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6444 Ramachandran restraints generated. 3222 Oldfield, 0 Emsley, 3222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6444 Ramachandran restraints generated. 3222 Oldfield, 0 Emsley, 3222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 277 time to evaluate : 1.007 Fit side-chains REVERT: A 498 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8247 (tp30) REVERT: A 589 GLU cc_start: 0.7356 (mm-30) cc_final: 0.7101 (mp0) REVERT: A 592 LYS cc_start: 0.7026 (OUTLIER) cc_final: 0.6716 (mttt) REVERT: A 605 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7562 (mm-30) REVERT: B 240 ILE cc_start: 0.8468 (pt) cc_final: 0.7953 (mm) REVERT: B 318 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8253 (mt0) REVERT: B 576 GLU cc_start: 0.7797 (tt0) cc_final: 0.7250 (mt-10) REVERT: B 605 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8270 (mt-10) REVERT: C 216 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.5302 (tm-30) REVERT: C 585 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7626 (tp30) REVERT: C 588 LYS cc_start: 0.8349 (ttpt) cc_final: 0.7981 (tmmt) REVERT: C 589 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7585 (tm-30) REVERT: C 597 LYS cc_start: 0.7105 (mttm) cc_final: 0.6861 (mmtm) REVERT: D 414 ASP cc_start: 0.8677 (t70) cc_final: 0.8002 (t70) REVERT: D 576 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7591 (mt-10) REVERT: E 330 LYS cc_start: 0.8242 (ttmt) cc_final: 0.7973 (ttpt) REVERT: E 566 ASN cc_start: 0.8214 (m-40) cc_final: 0.7984 (m110) REVERT: E 589 GLU cc_start: 0.6997 (mm-30) cc_final: 0.6783 (mm-30) REVERT: F 222 ASN cc_start: 0.8557 (t0) cc_final: 0.8288 (t0) REVERT: F 330 LYS cc_start: 0.8104 (tttp) cc_final: 0.7042 (tmmt) REVERT: F 374 TRP cc_start: 0.7815 (OUTLIER) cc_final: 0.4744 (p90) REVERT: F 378 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8536 (tt) REVERT: F 384 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8207 (mt-10) REVERT: G 222 ASN cc_start: 0.8951 (t0) cc_final: 0.8725 (m-40) REVERT: G 357 SER cc_start: 0.8202 (t) cc_final: 0.7944 (p) REVERT: G 589 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7739 (tp30) REVERT: G 593 TYR cc_start: 0.6515 (m-80) cc_final: 0.5851 (m-80) REVERT: G 605 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8095 (pt0) REVERT: H 64 ILE cc_start: 0.5394 (mt) cc_final: 0.4890 (tp) REVERT: H 65 GLU cc_start: 0.4499 (OUTLIER) cc_final: 0.3862 (pp20) REVERT: H 93 TYR cc_start: 0.6764 (p90) cc_final: 0.6373 (p90) REVERT: H 247 MET cc_start: 0.3902 (mtt) cc_final: 0.3511 (ptp) REVERT: H 339 THR cc_start: 0.6031 (t) cc_final: 0.5656 (m) REVERT: H 379 TYR cc_start: 0.5135 (m-80) cc_final: 0.4772 (m-80) outliers start: 68 outliers final: 41 residues processed: 323 average time/residue: 0.6465 time to fit residues: 243.5078 Evaluate side-chains 320 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 268 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 592 LYS Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 318 GLN Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 515 SER Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 585 GLU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 467 LYS Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 576 GLU Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 451 MET Chi-restraints excluded: chain F residue 374 TRP Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 384 GLU Chi-restraints excluded: chain F residue 399 THR Chi-restraints excluded: chain F residue 441 LYS Chi-restraints excluded: chain F residue 548 GLU Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 352 ILE Chi-restraints excluded: chain G residue 441 LYS Chi-restraints excluded: chain G residue 452 ASP Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 605 GLU Chi-restraints excluded: chain G residue 619 THR Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 356 LEU Chi-restraints excluded: chain H residue 370 SER Chi-restraints excluded: chain H residue 381 VAL Chi-restraints excluded: chain H residue 402 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 155 optimal weight: 4.9990 chunk 273 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 275 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 305 ASN B 362 ASN B 370 ASN B 391 ASN B 582 ASN E 318 GLN F 311 ASN F 590 GLN ** G 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.137012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.101080 restraints weight = 32942.350| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.89 r_work: 0.2931 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 25595 Z= 0.247 Angle : 0.594 9.610 34723 Z= 0.321 Chirality : 0.049 0.175 3917 Planarity : 0.005 0.050 4554 Dihedral : 5.384 31.770 3467 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.99 % Allowed : 16.47 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.14), residues: 3222 helix: -0.31 (0.21), residues: 571 sheet: 0.89 (0.17), residues: 825 loop : -1.93 (0.13), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 324 TYR 0.020 0.002 TYR E 296 PHE 0.027 0.002 PHE G 248 TRP 0.014 0.002 TRP H 223 HIS 0.006 0.001 HIS H 157 Details of bonding type rmsd covalent geometry : bond 0.00598 (25595) covalent geometry : angle 0.59354 (34723) hydrogen bonds : bond 0.03172 ( 1010) hydrogen bonds : angle 4.92042 ( 2946) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6444 Ramachandran restraints generated. 3222 Oldfield, 0 Emsley, 3222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6444 Ramachandran restraints generated. 3222 Oldfield, 0 Emsley, 3222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 260 time to evaluate : 1.011 Fit side-chains REVERT: A 498 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8311 (tp30) REVERT: A 589 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7196 (mp0) REVERT: A 592 LYS cc_start: 0.7080 (OUTLIER) cc_final: 0.6785 (mttt) REVERT: A 605 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7768 (mm-30) REVERT: B 318 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8260 (mt0) REVERT: B 605 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8342 (mt-10) REVERT: C 216 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.5322 (tm-30) REVERT: C 585 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7813 (tp30) REVERT: C 588 LYS cc_start: 0.8388 (ttpt) cc_final: 0.7986 (ttmt) REVERT: C 589 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7680 (tm-30) REVERT: C 597 LYS cc_start: 0.7110 (mttm) cc_final: 0.6856 (mmtm) REVERT: D 414 ASP cc_start: 0.8681 (t70) cc_final: 0.8039 (t70) REVERT: D 576 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7430 (tm-30) REVERT: E 330 LYS cc_start: 0.8260 (ttmt) cc_final: 0.7976 (ttpt) REVERT: E 566 ASN cc_start: 0.8301 (m-40) cc_final: 0.8050 (m110) REVERT: F 222 ASN cc_start: 0.8596 (t0) cc_final: 0.8329 (t0) REVERT: F 330 LYS cc_start: 0.8122 (tttp) cc_final: 0.7059 (tmmt) REVERT: F 374 TRP cc_start: 0.7793 (OUTLIER) cc_final: 0.5060 (p90) REVERT: F 378 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8535 (tt) REVERT: G 576 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7694 (tp30) REVERT: G 589 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7811 (tp30) REVERT: G 605 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8079 (pt0) REVERT: H 23 GLU cc_start: 0.6564 (OUTLIER) cc_final: 0.6056 (tt0) REVERT: H 64 ILE cc_start: 0.5258 (mt) cc_final: 0.4771 (tp) REVERT: H 65 GLU cc_start: 0.4522 (OUTLIER) cc_final: 0.3874 (pp20) REVERT: H 192 ARG cc_start: 0.6071 (ptt180) cc_final: 0.5845 (ptt180) REVERT: H 339 THR cc_start: 0.6038 (t) cc_final: 0.5624 (m) REVERT: H 379 TYR cc_start: 0.5142 (m-80) cc_final: 0.4729 (m-80) outliers start: 84 outliers final: 50 residues processed: 316 average time/residue: 0.6266 time to fit residues: 231.0633 Evaluate side-chains 311 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 249 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 592 LYS Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 318 GLN Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 515 SER Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 585 GLU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 467 LYS Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 559 ASN Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 576 GLU Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 451 MET Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 374 TRP Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 384 GLU Chi-restraints excluded: chain F residue 399 THR Chi-restraints excluded: chain F residue 441 LYS Chi-restraints excluded: chain G residue 240 ILE Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 352 ILE Chi-restraints excluded: chain G residue 441 LYS Chi-restraints excluded: chain G residue 452 ASP Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 576 GLU Chi-restraints excluded: chain G residue 605 GLU Chi-restraints excluded: chain G residue 619 THR Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 337 ILE Chi-restraints excluded: chain H residue 370 SER Chi-restraints excluded: chain H residue 381 VAL Chi-restraints excluded: chain H residue 402 VAL Chi-restraints excluded: chain H residue 408 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.2451 > 50: distance: 15 - 95: 32.003 distance: 18 - 92: 26.875 distance: 63 - 68: 20.110 distance: 68 - 69: 10.367 distance: 69 - 70: 5.323 distance: 69 - 72: 35.765 distance: 70 - 71: 19.741 distance: 70 - 76: 24.267 distance: 72 - 73: 5.406 distance: 73 - 74: 43.478 distance: 73 - 75: 9.661 distance: 76 - 77: 25.053 distance: 77 - 78: 19.101 distance: 77 - 80: 19.305 distance: 78 - 79: 29.963 distance: 78 - 85: 7.925 distance: 80 - 81: 4.797 distance: 81 - 82: 4.437 distance: 82 - 83: 15.902 distance: 82 - 84: 22.112 distance: 85 - 86: 24.259 distance: 86 - 87: 43.078 distance: 86 - 89: 17.583 distance: 87 - 88: 33.674 distance: 87 - 92: 3.077 distance: 89 - 90: 23.150 distance: 89 - 91: 24.649 distance: 92 - 93: 19.768 distance: 93 - 94: 25.922 distance: 93 - 96: 20.863 distance: 94 - 95: 46.109 distance: 94 - 104: 9.014 distance: 96 - 97: 19.412 distance: 97 - 98: 20.168 distance: 97 - 99: 12.179 distance: 99 - 101: 16.336 distance: 100 - 102: 17.168 distance: 101 - 102: 7.763 distance: 102 - 103: 10.303 distance: 104 - 105: 11.280 distance: 104 - 110: 5.978 distance: 105 - 106: 7.473 distance: 105 - 108: 9.249 distance: 106 - 107: 25.473 distance: 106 - 111: 5.919 distance: 108 - 109: 37.029 distance: 109 - 110: 29.404 distance: 111 - 112: 10.518 distance: 112 - 113: 31.338 distance: 112 - 115: 15.580 distance: 113 - 114: 18.880 distance: 113 - 120: 20.882 distance: 115 - 116: 18.298 distance: 116 - 117: 42.216 distance: 117 - 118: 44.419 distance: 118 - 119: 30.912 distance: 120 - 121: 23.849 distance: 121 - 122: 24.736 distance: 121 - 124: 39.205 distance: 122 - 123: 41.038 distance: 122 - 129: 23.227 distance: 124 - 125: 23.757 distance: 125 - 126: 25.796 distance: 126 - 127: 17.087 distance: 127 - 128: 30.075 distance: 129 - 130: 14.377 distance: 130 - 131: 20.082 distance: 131 - 132: 16.600 distance: 131 - 133: 19.426 distance: 133 - 134: 12.868 distance: 134 - 135: 30.012 distance: 134 - 137: 43.641 distance: 135 - 141: 6.632 distance: 137 - 138: 36.469 distance: 138 - 139: 15.673 distance: 138 - 140: 56.757 distance: 141 - 142: 15.448 distance: 142 - 143: 17.750 distance: 142 - 145: 32.431 distance: 143 - 144: 31.492 distance: 143 - 147: 23.199 distance: 145 - 146: 6.737