Starting phenix.real_space_refine on Tue May 5 13:44:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vek_65010/05_2026/9vek_65010.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vek_65010/05_2026/9vek_65010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vek_65010/05_2026/9vek_65010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vek_65010/05_2026/9vek_65010.map" model { file = "/net/cci-nas-00/data/ceres_data/9vek_65010/05_2026/9vek_65010.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vek_65010/05_2026/9vek_65010.cif" } resolution = 3.31 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= 0.033 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 21 9.91 5 S 70 5.16 5 C 18263 2.51 5 N 4886 2.21 5 O 6062 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29302 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4183 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 519} Chain: "B" Number of atoms: 4183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4183 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 519} Chain: "C" Number of atoms: 4183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4183 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 519} Chain: "D" Number of atoms: 4183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4183 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 519} Chain: "E" Number of atoms: 4183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4183 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 519} Chain: "F" Number of atoms: 4183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4183 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 519} Chain: "G" Number of atoms: 4183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4183 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 519} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.91, per 1000 atoms: 0.24 Number of scatterers: 29302 At special positions: 0 Unit cell: (186.12, 184.24, 181.42, 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 21 19.99 S 70 16.00 O 6062 8.00 N 4886 7.00 C 18263 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: 2.19 Conformation dependent library (CDL) restraints added in 1.2 seconds 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7056 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 78 sheets defined 13.7% alpha, 41.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 234 through 241 removed outlier: 3.715A pdb=" N ASN A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 260 removed outlier: 3.719A pdb=" N SER A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY A 260 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 285 Processing helix chain 'A' and resid 293 through 297 removed outlier: 3.881A pdb=" N PHE A 297 " --> pdb=" O LYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.158A pdb=" N THR A 429 " --> pdb=" O SER A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 472 Processing helix chain 'A' and resid 505 through 512 Processing helix chain 'A' and resid 545 through 554 removed outlier: 3.593A pdb=" N LYS A 551 " --> pdb=" O LYS A 547 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 552 " --> pdb=" O ASP A 548 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 595 removed outlier: 3.550A pdb=" N LYS A 587 " --> pdb=" O GLU A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 609 Processing helix chain 'B' and resid 234 through 241 removed outlier: 3.820A pdb=" N ASN B 240 " --> pdb=" O LEU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 260 removed outlier: 3.691A pdb=" N SER B 258 " --> pdb=" O SER B 255 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY B 260 " --> pdb=" O ALA B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 285 Processing helix chain 'B' and resid 293 through 297 removed outlier: 3.807A pdb=" N PHE B 297 " --> pdb=" O LYS B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 472 Processing helix chain 'B' and resid 505 through 512 Processing helix chain 'B' and resid 545 through 550 Processing helix chain 'B' and resid 582 through 595 removed outlier: 3.768A pdb=" N LYS B 587 " --> pdb=" O GLU B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 602 removed outlier: 3.697A pdb=" N LYS B 601 " --> pdb=" O GLY B 598 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASP B 602 " --> pdb=" O LYS B 599 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 598 through 602' Processing helix chain 'B' and resid 669 through 672 removed outlier: 3.644A pdb=" N LYS B 672 " --> pdb=" O SER B 669 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 669 through 672' Processing helix chain 'C' and resid 234 through 241 removed outlier: 3.563A pdb=" N GLU C 239 " --> pdb=" O ASP C 235 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 258 removed outlier: 3.669A pdb=" N SER C 258 " --> pdb=" O SER C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 285 Processing helix chain 'C' and resid 463 through 472 Processing helix chain 'C' and resid 505 through 512 removed outlier: 3.512A pdb=" N LYS C 510 " --> pdb=" O THR C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 553 removed outlier: 3.595A pdb=" N LYS C 551 " --> pdb=" O LYS C 547 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 552 " --> pdb=" O ASP C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 595 removed outlier: 3.779A pdb=" N LYS C 587 " --> pdb=" O GLU C 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 241 removed outlier: 3.607A pdb=" N GLU D 239 " --> pdb=" O ASP D 235 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN D 240 " --> pdb=" O LEU D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 260 removed outlier: 3.726A pdb=" N SER D 258 " --> pdb=" O SER D 255 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY D 260 " --> pdb=" O ALA D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 285 Processing helix chain 'D' and resid 293 through 297 removed outlier: 3.810A pdb=" N PHE D 297 " --> pdb=" O LYS D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 472 Processing helix chain 'D' and resid 505 through 512 removed outlier: 3.534A pdb=" N LYS D 510 " --> pdb=" O THR D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 554 removed outlier: 3.604A pdb=" N LEU D 552 " --> pdb=" O ASP D 548 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR D 554 " --> pdb=" O LEU D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 595 removed outlier: 3.617A pdb=" N LYS D 587 " --> pdb=" O GLU D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 609 removed outlier: 3.580A pdb=" N ASP D 608 " --> pdb=" O HIS D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 672 removed outlier: 3.684A pdb=" N LYS D 672 " --> pdb=" O SER D 669 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 669 through 672' Processing helix chain 'E' and resid 234 through 241 removed outlier: 3.828A pdb=" N ASN E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 260 removed outlier: 3.733A pdb=" N SER E 258 " --> pdb=" O SER E 255 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY E 260 " --> pdb=" O ALA E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 285 Processing helix chain 'E' and resid 293 through 297 removed outlier: 3.824A pdb=" N PHE E 297 " --> pdb=" O LYS E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 472 Processing helix chain 'E' and resid 505 through 512 removed outlier: 3.618A pdb=" N LYS E 510 " --> pdb=" O THR E 506 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 554 removed outlier: 3.551A pdb=" N LYS E 551 " --> pdb=" O LYS E 547 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU E 552 " --> pdb=" O ASP E 548 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR E 554 " --> pdb=" O LEU E 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 582 through 595 removed outlier: 3.572A pdb=" N LYS E 587 " --> pdb=" O GLU E 583 " (cutoff:3.500A) Processing helix chain 'E' and resid 669 through 672 removed outlier: 3.888A pdb=" N LYS E 672 " --> pdb=" O SER E 669 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 669 through 672' Processing helix chain 'F' and resid 234 through 241 removed outlier: 3.551A pdb=" N GLU F 239 " --> pdb=" O ASP F 235 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN F 240 " --> pdb=" O LEU F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 258 removed outlier: 3.692A pdb=" N SER F 258 " --> pdb=" O SER F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 285 Processing helix chain 'F' and resid 293 through 297 removed outlier: 3.833A pdb=" N PHE F 297 " --> pdb=" O LYS F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 429 removed outlier: 4.120A pdb=" N THR F 429 " --> pdb=" O SER F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 472 Processing helix chain 'F' and resid 505 through 512 removed outlier: 3.567A pdb=" N LYS F 510 " --> pdb=" O THR F 506 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 551 removed outlier: 3.589A pdb=" N LYS F 551 " --> pdb=" O LYS F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 582 through 595 removed outlier: 3.707A pdb=" N LYS F 587 " --> pdb=" O GLU F 583 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 634 removed outlier: 3.512A pdb=" N SER F 633 " --> pdb=" O GLY F 630 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER F 634 " --> pdb=" O GLY F 631 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 630 through 634' Processing helix chain 'F' and resid 669 through 672 removed outlier: 3.802A pdb=" N LYS F 672 " --> pdb=" O SER F 669 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 669 through 672' Processing helix chain 'G' and resid 234 through 241 removed outlier: 3.508A pdb=" N GLU G 239 " --> pdb=" O ASP G 235 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN G 240 " --> pdb=" O LEU G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 258 removed outlier: 3.645A pdb=" N SER G 258 " --> pdb=" O SER G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 285 Processing helix chain 'G' and resid 293 through 297 removed outlier: 3.847A pdb=" N PHE G 297 " --> pdb=" O LYS G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 463 through 472 Processing helix chain 'G' and resid 505 through 512 removed outlier: 3.604A pdb=" N LYS G 510 " --> pdb=" O THR G 506 " (cutoff:3.500A) Processing helix chain 'G' and resid 545 through 551 removed outlier: 3.630A pdb=" N LYS G 551 " --> pdb=" O LYS G 547 " (cutoff:3.500A) Processing helix chain 'G' and resid 582 through 595 Processing helix chain 'G' and resid 669 through 672 removed outlier: 3.831A pdb=" N LYS G 672 " --> pdb=" O SER G 669 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 669 through 672' Processing sheet with id=AA1, first strand: chain 'A' and resid 242 through 245 Processing sheet with id=AA2, first strand: chain 'A' and resid 307 through 317 removed outlier: 5.501A pdb=" N VAL A 309 " --> pdb=" O ASN A 396 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASN A 396 " --> pdb=" O VAL A 309 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N MET A 311 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ARG A 394 " --> pdb=" O MET A 311 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 313 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 438 through 439 removed outlier: 4.659A pdb=" N ILE A 460 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 347 removed outlier: 3.544A pdb=" N GLY A 341 " --> pdb=" O SER A 360 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER A 360 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY G 341 " --> pdb=" O SER G 360 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER G 360 " --> pdb=" O GLY G 341 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL F 344 " --> pdb=" O ALA G 359 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER F 360 " --> pdb=" O GLY F 341 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL E 344 " --> pdb=" O ALA F 359 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER F 379 " --> pdb=" O ASN E 324 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY E 341 " --> pdb=" O SER E 360 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER E 360 " --> pdb=" O GLY E 341 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL D 344 " --> pdb=" O ALA E 359 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY D 341 " --> pdb=" O SER D 360 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER D 360 " --> pdb=" O GLY D 341 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY C 341 " --> pdb=" O SER C 360 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER C 360 " --> pdb=" O GLY C 341 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 379 " --> pdb=" O ASN B 324 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER B 360 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 344 " --> pdb=" O ALA B 359 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER B 379 " --> pdb=" O ASN A 324 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 417 through 423 removed outlier: 5.164A pdb=" N THR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU A 414 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA A 420 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N TYR A 404 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASN A 432 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 417 through 423 removed outlier: 5.164A pdb=" N THR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU A 414 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA A 420 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ILE A 403 " --> pdb=" O TYR A 487 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N TYR A 487 " --> pdb=" O ILE A 403 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLU A 405 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY A 485 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LYS A 407 " --> pdb=" O THR A 483 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N THR A 483 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR A 409 " --> pdb=" O ASN A 481 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N GLY A 485 " --> pdb=" O GLU A 501 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU A 501 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR A 487 " --> pdb=" O GLY A 499 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 524 through 530 removed outlier: 9.012A pdb=" N PHE A 617 " --> pdb=" O THR A 513 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N SER A 515 " --> pdb=" O PHE A 617 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE A 619 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE A 517 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N MET A 621 " --> pdb=" O ILE A 517 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ASP A 519 " --> pdb=" O MET A 621 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 558 through 561 Processing sheet with id=AA9, first strand: chain 'A' and resid 624 through 626 removed outlier: 6.543A pdb=" N ASP A 750 " --> pdb=" O LYS A 654 " (cutoff:3.500A) removed outlier: 12.457A pdb=" N LYS A 654 " --> pdb=" O ASP A 750 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 624 through 626 removed outlier: 4.324A pdb=" N VAL A 751 " --> pdb=" O SER A 684 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N SER A 684 " --> pdb=" O VAL A 751 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE A 753 " --> pdb=" O TYR A 682 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TYR A 682 " --> pdb=" O ILE A 753 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 638 through 641 removed outlier: 6.537A pdb=" N ASP A 734 " --> pdb=" O LEU A 667 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLY A 701 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N THR A 705 " --> pdb=" O GLY A 701 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 242 through 245 Processing sheet with id=AB4, first strand: chain 'B' and resid 307 through 309 Processing sheet with id=AB5, first strand: chain 'B' and resid 313 through 317 removed outlier: 3.621A pdb=" N LYS B 313 " --> pdb=" O ASN B 392 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 313 through 317 removed outlier: 3.621A pdb=" N LYS B 313 " --> pdb=" O ASN B 392 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ILE B 460 " --> pdb=" O LEU B 389 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 403 through 406 removed outlier: 6.958A pdb=" N TYR B 404 " --> pdb=" O ASN B 432 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ASN B 432 " --> pdb=" O TYR B 404 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 418 through 423 removed outlier: 3.968A pdb=" N ALA B 420 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR B 409 " --> pdb=" O ASN B 481 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 486 through 490 removed outlier: 6.283A pdb=" N TYR B 487 " --> pdb=" O GLY B 499 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 524 through 530 removed outlier: 9.017A pdb=" N PHE B 617 " --> pdb=" O THR B 513 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N SER B 515 " --> pdb=" O PHE B 617 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ILE B 619 " --> pdb=" O SER B 515 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE B 517 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N MET B 621 " --> pdb=" O ILE B 517 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASP B 519 " --> pdb=" O MET B 621 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 558 through 560 Processing sheet with id=AC3, first strand: chain 'B' and resid 624 through 626 removed outlier: 6.583A pdb=" N ASP B 750 " --> pdb=" O LYS B 654 " (cutoff:3.500A) removed outlier: 12.508A pdb=" N LYS B 654 " --> pdb=" O ASP B 750 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 624 through 626 removed outlier: 4.282A pdb=" N VAL B 751 " --> pdb=" O SER B 684 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N SER B 684 " --> pdb=" O VAL B 751 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE B 753 " --> pdb=" O TYR B 682 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR B 682 " --> pdb=" O ILE B 753 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N GLU B 755 " --> pdb=" O ASN B 680 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ASN B 680 " --> pdb=" O GLU B 755 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL B 679 " --> pdb=" O ASN B 727 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN B 727 " --> pdb=" O VAL B 679 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 638 through 641 removed outlier: 6.627A pdb=" N ASP B 734 " --> pdb=" O LEU B 667 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N GLY B 701 " --> pdb=" O THR B 705 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N THR B 705 " --> pdb=" O GLY B 701 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 242 through 245 Processing sheet with id=AC7, first strand: chain 'C' and resid 307 through 317 removed outlier: 5.488A pdb=" N VAL C 309 " --> pdb=" O ASN C 396 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN C 396 " --> pdb=" O VAL C 309 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N MET C 311 " --> pdb=" O ARG C 394 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG C 394 " --> pdb=" O MET C 311 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS C 313 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 438 through 439 removed outlier: 4.657A pdb=" N ILE C 460 " --> pdb=" O LEU C 389 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 403 through 406 removed outlier: 6.948A pdb=" N TYR C 404 " --> pdb=" O ASN C 432 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ASN C 432 " --> pdb=" O TYR C 404 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 417 through 423 removed outlier: 5.078A pdb=" N THR C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU C 414 " --> pdb=" O THR C 418 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA C 420 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR C 409 " --> pdb=" O ASN C 481 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 486 through 490 removed outlier: 6.426A pdb=" N TYR C 487 " --> pdb=" O GLY C 499 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 524 through 530 removed outlier: 9.022A pdb=" N PHE C 617 " --> pdb=" O THR C 513 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N SER C 515 " --> pdb=" O PHE C 617 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ILE C 619 " --> pdb=" O SER C 515 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE C 517 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N MET C 621 " --> pdb=" O ILE C 517 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ASP C 519 " --> pdb=" O MET C 621 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 558 through 561 Processing sheet with id=AD5, first strand: chain 'C' and resid 624 through 626 removed outlier: 6.654A pdb=" N ASP C 750 " --> pdb=" O LYS C 654 " (cutoff:3.500A) removed outlier: 12.584A pdb=" N LYS C 654 " --> pdb=" O ASP C 750 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 624 through 626 removed outlier: 5.103A pdb=" N TRP C 748 " --> pdb=" O LYS C 688 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LYS C 688 " --> pdb=" O TRP C 748 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASP C 750 " --> pdb=" O TYR C 686 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR C 686 " --> pdb=" O ASP C 750 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C 679 " --> pdb=" O ASN C 727 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN C 727 " --> pdb=" O VAL C 679 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 638 through 641 removed outlier: 3.983A pdb=" N LYS C 735 " --> pdb=" O VAL C 700 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL C 700 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 242 through 245 Processing sheet with id=AD9, first strand: chain 'D' and resid 307 through 317 removed outlier: 5.492A pdb=" N VAL D 309 " --> pdb=" O ASN D 396 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASN D 396 " --> pdb=" O VAL D 309 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N MET D 311 " --> pdb=" O ARG D 394 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ARG D 394 " --> pdb=" O MET D 311 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS D 313 " --> pdb=" O ASN D 392 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 438 through 439 removed outlier: 4.705A pdb=" N ILE D 460 " --> pdb=" O LEU D 389 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 418 through 423 removed outlier: 6.732A pdb=" N PHE D 412 " --> pdb=" O ILE D 419 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR D 421 " --> pdb=" O THR D 410 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N THR D 410 " --> pdb=" O THR D 421 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N THR D 423 " --> pdb=" O PRO D 408 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N TYR D 404 " --> pdb=" O ASN D 432 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN D 432 " --> pdb=" O TYR D 404 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 418 through 423 removed outlier: 6.732A pdb=" N PHE D 412 " --> pdb=" O ILE D 419 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR D 421 " --> pdb=" O THR D 410 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N THR D 410 " --> pdb=" O THR D 421 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N THR D 423 " --> pdb=" O PRO D 408 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N ILE D 403 " --> pdb=" O TYR D 487 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TYR D 487 " --> pdb=" O ILE D 403 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLU D 405 " --> pdb=" O GLY D 485 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY D 485 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS D 407 " --> pdb=" O THR D 483 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N THR D 483 " --> pdb=" O LYS D 407 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR D 409 " --> pdb=" O ASN D 481 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLY D 485 " --> pdb=" O GLU D 501 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLU D 501 " --> pdb=" O GLY D 485 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR D 487 " --> pdb=" O GLY D 499 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 524 through 530 Processing sheet with id=AE5, first strand: chain 'D' and resid 558 through 561 Processing sheet with id=AE6, first strand: chain 'D' and resid 624 through 626 removed outlier: 6.506A pdb=" N ASP D 750 " --> pdb=" O LYS D 654 " (cutoff:3.500A) removed outlier: 12.424A pdb=" N LYS D 654 " --> pdb=" O ASP D 750 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 624 through 626 removed outlier: 4.994A pdb=" N TRP D 748 " --> pdb=" O LYS D 688 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LYS D 688 " --> pdb=" O TRP D 748 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ASP D 750 " --> pdb=" O TYR D 686 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR D 686 " --> pdb=" O ASP D 750 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 638 through 641 removed outlier: 6.793A pdb=" N ASP D 734 " --> pdb=" O LEU D 667 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLY D 701 " --> pdb=" O THR D 705 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N THR D 705 " --> pdb=" O GLY D 701 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 242 through 245 Processing sheet with id=AF1, first strand: chain 'E' and resid 307 through 317 removed outlier: 5.474A pdb=" N VAL E 309 " --> pdb=" O ASN E 396 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASN E 396 " --> pdb=" O VAL E 309 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N MET E 311 " --> pdb=" O ARG E 394 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ARG E 394 " --> pdb=" O MET E 311 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS E 313 " --> pdb=" O ASN E 392 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 438 through 439 removed outlier: 4.659A pdb=" N ILE E 460 " --> pdb=" O LEU E 389 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 403 through 406 removed outlier: 6.978A pdb=" N TYR E 404 " --> pdb=" O ASN E 432 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ASN E 432 " --> pdb=" O TYR E 404 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 418 through 423 removed outlier: 5.299A pdb=" N THR E 418 " --> pdb=" O LEU E 414 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU E 414 " --> pdb=" O THR E 418 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA E 420 " --> pdb=" O PHE E 412 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR E 409 " --> pdb=" O ASN E 481 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 486 through 490 removed outlier: 6.555A pdb=" N TYR E 487 " --> pdb=" O GLY E 499 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 524 through 530 removed outlier: 9.085A pdb=" N PHE E 617 " --> pdb=" O THR E 513 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N SER E 515 " --> pdb=" O PHE E 617 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ILE E 619 " --> pdb=" O SER E 515 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE E 517 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N MET E 621 " --> pdb=" O ILE E 517 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ASP E 519 " --> pdb=" O MET E 621 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 558 through 560 Processing sheet with id=AF8, first strand: chain 'E' and resid 624 through 626 removed outlier: 6.642A pdb=" N ASP E 750 " --> pdb=" O LYS E 654 " (cutoff:3.500A) removed outlier: 12.573A pdb=" N LYS E 654 " --> pdb=" O ASP E 750 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 624 through 626 removed outlier: 5.051A pdb=" N TRP E 748 " --> pdb=" O LYS E 688 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LYS E 688 " --> pdb=" O TRP E 748 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASP E 750 " --> pdb=" O TYR E 686 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR E 686 " --> pdb=" O ASP E 750 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL E 679 " --> pdb=" O ASN E 727 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN E 727 " --> pdb=" O VAL E 679 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 638 through 641 removed outlier: 6.710A pdb=" N ASP E 734 " --> pdb=" O LEU E 667 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N GLY E 701 " --> pdb=" O THR E 705 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N THR E 705 " --> pdb=" O GLY E 701 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 242 through 245 Processing sheet with id=AG3, first strand: chain 'F' and resid 307 through 317 removed outlier: 5.502A pdb=" N VAL F 309 " --> pdb=" O ASN F 396 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN F 396 " --> pdb=" O VAL F 309 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N MET F 311 " --> pdb=" O ARG F 394 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ARG F 394 " --> pdb=" O MET F 311 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS F 313 " --> pdb=" O ASN F 392 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 438 through 439 removed outlier: 4.652A pdb=" N ILE F 460 " --> pdb=" O LEU F 389 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 403 through 406 removed outlier: 6.942A pdb=" N TYR F 404 " --> pdb=" O ASN F 432 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ASN F 432 " --> pdb=" O TYR F 404 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 417 through 423 removed outlier: 5.144A pdb=" N THR F 418 " --> pdb=" O LEU F 414 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU F 414 " --> pdb=" O THR F 418 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA F 420 " --> pdb=" O PHE F 412 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR F 409 " --> pdb=" O ASN F 481 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 486 through 490 removed outlier: 6.452A pdb=" N TYR F 487 " --> pdb=" O GLY F 499 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 524 through 530 Processing sheet with id=AG9, first strand: chain 'F' and resid 558 through 560 Processing sheet with id=AH1, first strand: chain 'F' and resid 624 through 626 removed outlier: 6.532A pdb=" N ASP F 750 " --> pdb=" O LYS F 654 " (cutoff:3.500A) removed outlier: 12.455A pdb=" N LYS F 654 " --> pdb=" O ASP F 750 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 624 through 626 removed outlier: 4.336A pdb=" N VAL F 751 " --> pdb=" O SER F 684 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER F 684 " --> pdb=" O VAL F 751 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE F 753 " --> pdb=" O TYR F 682 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TYR F 682 " --> pdb=" O ILE F 753 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 638 through 641 removed outlier: 6.603A pdb=" N ASP F 734 " --> pdb=" O LEU F 667 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLY F 701 " --> pdb=" O THR F 705 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N THR F 705 " --> pdb=" O GLY F 701 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 242 through 245 Processing sheet with id=AH5, first strand: chain 'G' and resid 307 through 309 Processing sheet with id=AH6, first strand: chain 'G' and resid 313 through 317 removed outlier: 3.571A pdb=" N LYS G 313 " --> pdb=" O ASN G 392 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 313 through 317 removed outlier: 3.571A pdb=" N LYS G 313 " --> pdb=" O ASN G 392 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ILE G 460 " --> pdb=" O LEU G 389 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 403 through 406 removed outlier: 6.985A pdb=" N TYR G 404 " --> pdb=" O ASN G 432 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ASN G 432 " --> pdb=" O TYR G 404 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 417 through 423 removed outlier: 5.150A pdb=" N THR G 418 " --> pdb=" O LEU G 414 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU G 414 " --> pdb=" O THR G 418 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA G 420 " --> pdb=" O PHE G 412 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR G 409 " --> pdb=" O ASN G 481 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 486 through 490 removed outlier: 6.494A pdb=" N TYR G 487 " --> pdb=" O GLY G 499 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'G' and resid 524 through 530 removed outlier: 9.004A pdb=" N PHE G 617 " --> pdb=" O THR G 513 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N SER G 515 " --> pdb=" O PHE G 617 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE G 619 " --> pdb=" O SER G 515 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE G 517 " --> pdb=" O ILE G 619 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N MET G 621 " --> pdb=" O ILE G 517 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ASP G 519 " --> pdb=" O MET G 621 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'G' and resid 558 through 560 Processing sheet with id=AI4, first strand: chain 'G' and resid 624 through 626 removed outlier: 6.818A pdb=" N ASP G 750 " --> pdb=" O LYS G 654 " (cutoff:3.500A) removed outlier: 12.776A pdb=" N LYS G 654 " --> pdb=" O ASP G 750 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'G' and resid 624 through 626 removed outlier: 4.335A pdb=" N VAL G 751 " --> pdb=" O SER G 684 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N SER G 684 " --> pdb=" O VAL G 751 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE G 753 " --> pdb=" O TYR G 682 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TYR G 682 " --> pdb=" O ILE G 753 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N GLU G 755 " --> pdb=" O ASN G 680 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ASN G 680 " --> pdb=" O GLU G 755 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL G 679 " --> pdb=" O ASN G 727 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN G 727 " --> pdb=" O VAL G 679 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'G' and resid 638 through 641 removed outlier: 3.536A pdb=" N ALA G 663 " --> pdb=" O ILE G 738 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASP G 734 " --> pdb=" O LEU G 667 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL G 697 " --> pdb=" O SER G 708 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N SER G 708 " --> pdb=" O VAL G 697 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL G 699 " --> pdb=" O ILE G 706 " (cutoff:3.500A) 1195 hydrogen bonds defined for protein. 3168 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: 7.85 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5167 1.32 - 1.44: 7682 1.44 - 1.56: 16845 1.56 - 1.68: 0 1.68 - 1.81: 140 Bond restraints: 29834 Sorted by residual: bond pdb=" CA ASP F 289 " pdb=" C ASP F 289 " ideal model delta sigma weight residual 1.524 1.473 0.051 1.35e-02 5.49e+03 1.44e+01 bond pdb=" C ASP F 289 " pdb=" O ASP F 289 " ideal model delta sigma weight residual 1.236 1.202 0.034 1.17e-02 7.31e+03 8.44e+00 bond pdb=" C THR A 296 " pdb=" O THR A 296 " ideal model delta sigma weight residual 1.236 1.198 0.038 1.32e-02 5.74e+03 8.13e+00 bond pdb=" CA ASN A 650 " pdb=" C ASN A 650 " ideal model delta sigma weight residual 1.524 1.491 0.033 1.29e-02 6.01e+03 6.50e+00 bond pdb=" C MET D 476 " pdb=" O MET D 476 " ideal model delta sigma weight residual 1.236 1.211 0.025 1.22e-02 6.72e+03 4.26e+00 ... (remaining 29829 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 39501 1.43 - 2.85: 818 2.85 - 4.28: 153 4.28 - 5.70: 20 5.70 - 7.13: 3 Bond angle restraints: 40495 Sorted by residual: angle pdb=" N THR E 752 " pdb=" CA THR E 752 " pdb=" C THR E 752 " ideal model delta sigma weight residual 108.41 114.51 -6.10 1.63e+00 3.76e-01 1.40e+01 angle pdb=" N THR C 752 " pdb=" CA THR C 752 " pdb=" C THR C 752 " ideal model delta sigma weight residual 108.90 114.49 -5.59 1.63e+00 3.76e-01 1.18e+01 angle pdb=" N ASP F 287 " pdb=" CA ASP F 287 " pdb=" C ASP F 287 " ideal model delta sigma weight residual 112.25 107.65 4.60 1.36e+00 5.41e-01 1.14e+01 angle pdb=" N THR A 752 " pdb=" CA THR A 752 " pdb=" C THR A 752 " ideal model delta sigma weight residual 109.06 114.41 -5.35 1.70e+00 3.46e-01 9.92e+00 angle pdb=" N GLU A 629 " pdb=" CA GLU A 629 " pdb=" C GLU A 629 " ideal model delta sigma weight residual 113.17 109.25 3.92 1.26e+00 6.30e-01 9.70e+00 ... (remaining 40490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 15970 17.95 - 35.90: 1680 35.90 - 53.85: 313 53.85 - 71.80: 45 71.80 - 89.75: 10 Dihedral angle restraints: 18018 sinusoidal: 6986 harmonic: 11032 Sorted by residual: dihedral pdb=" CA LYS C 570 " pdb=" C LYS C 570 " pdb=" N PRO C 571 " pdb=" CA PRO C 571 " ideal model delta harmonic sigma weight residual -180.00 -158.81 -21.19 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA LYS F 570 " pdb=" C LYS F 570 " pdb=" N PRO F 571 " pdb=" CA PRO F 571 " ideal model delta harmonic sigma weight residual -180.00 -163.43 -16.57 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CB GLU G 560 " pdb=" CG GLU G 560 " pdb=" CD GLU G 560 " pdb=" OE1 GLU G 560 " ideal model delta sinusoidal sigma weight residual 0.00 89.75 -89.75 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 18015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3804 0.057 - 0.113: 668 0.113 - 0.170: 77 0.170 - 0.226: 0 0.226 - 0.283: 1 Chirality restraints: 4550 Sorted by residual: chirality pdb=" CG LEU F 288 " pdb=" CB LEU F 288 " pdb=" CD1 LEU F 288 " pdb=" CD2 LEU F 288 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA ILE C 753 " pdb=" N ILE C 753 " pdb=" C ILE C 753 " pdb=" CB ILE C 753 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.83e-01 chirality pdb=" CA VAL E 751 " pdb=" N VAL E 751 " pdb=" C VAL E 751 " pdb=" CB VAL E 751 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.37e-01 ... (remaining 4547 not shown) Planarity restraints: 5257 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP E 415 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.89e+00 pdb=" CG ASP E 415 " -0.045 2.00e-02 2.50e+03 pdb=" OD1 ASP E 415 " 0.017 2.00e-02 2.50e+03 pdb=" OD2 ASP E 415 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 415 " -0.010 2.00e-02 2.50e+03 1.95e-02 3.82e+00 pdb=" C ASP D 415 " 0.034 2.00e-02 2.50e+03 pdb=" O ASP D 415 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS D 416 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 751 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.66e+00 pdb=" C VAL F 751 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL F 751 " -0.011 2.00e-02 2.50e+03 pdb=" N THR F 752 " -0.009 2.00e-02 2.50e+03 ... (remaining 5254 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 87 2.50 - 3.10: 20455 3.10 - 3.70: 41300 3.70 - 4.30: 62927 4.30 - 4.90: 109885 Nonbonded interactions: 234654 Sorted by model distance: nonbonded pdb=" OE2 GLU A 629 " pdb="CA CA A 903 " model vdw 1.901 2.510 nonbonded pdb=" OD1 ASP D 229 " pdb="CA CA D 902 " model vdw 1.919 2.510 nonbonded pdb=" OE2 GLU C 629 " pdb="CA CA C 903 " model vdw 2.064 2.510 nonbonded pdb=" OD1 ASP D 227 " pdb="CA CA D 902 " model vdw 2.072 2.510 nonbonded pdb=" O ILE D 233 " pdb="CA CA D 902 " model vdw 2.117 2.510 ... (remaining 234649 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: 0.02 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: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 28.240 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 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 : 0.003 0.051 29834 Z= 0.148 Angle : 0.544 7.129 40495 Z= 0.321 Chirality : 0.044 0.283 4550 Planarity : 0.003 0.037 5257 Dihedral : 14.630 89.752 10962 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.03 % Allowed : 15.38 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.13), residues: 3766 helix: -1.64 (0.25), residues: 448 sheet: -0.50 (0.13), residues: 1386 loop : -1.52 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 614 TYR 0.009 0.001 TYR F 681 PHE 0.009 0.001 PHE E 656 TRP 0.011 0.001 TRP G 748 HIS 0.003 0.000 HIS G 272 Details of bonding type rmsd covalent geometry : bond 0.00282 (29834) covalent geometry : angle 0.54375 (40495) hydrogen bonds : bond 0.15903 ( 1153) hydrogen bonds : angle 7.85957 ( 3168) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 266 time to evaluate : 0.779 Fit side-chains REVERT: A 336 TYR cc_start: 0.8041 (p90) cc_final: 0.7818 (p90) REVERT: A 415 ASP cc_start: 0.8418 (t70) cc_final: 0.7823 (t0) REVERT: A 590 LYS cc_start: 0.7209 (mtmt) cc_final: 0.6633 (ttpt) REVERT: B 415 ASP cc_start: 0.8283 (t70) cc_final: 0.7917 (t0) REVERT: C 373 THR cc_start: 0.8364 (t) cc_final: 0.8038 (p) REVERT: C 415 ASP cc_start: 0.8492 (t70) cc_final: 0.8001 (t0) REVERT: C 590 LYS cc_start: 0.7655 (mtmt) cc_final: 0.6958 (ttpt) REVERT: D 336 TYR cc_start: 0.8347 (p90) cc_final: 0.7957 (p90) REVERT: D 590 LYS cc_start: 0.7762 (mttt) cc_final: 0.7077 (tttp) REVERT: E 590 LYS cc_start: 0.8063 (mtmt) cc_final: 0.7461 (tttt) REVERT: E 750 ASP cc_start: 0.8710 (m-30) cc_final: 0.8448 (m-30) REVERT: F 287 ASP cc_start: 0.8498 (t0) cc_final: 0.8104 (t70) REVERT: F 415 ASP cc_start: 0.8413 (t70) cc_final: 0.7893 (t0) REVERT: F 686 TYR cc_start: 0.8237 (m-80) cc_final: 0.7876 (m-80) REVERT: G 336 TYR cc_start: 0.8265 (p90) cc_final: 0.8006 (p90) REVERT: G 415 ASP cc_start: 0.8557 (t70) cc_final: 0.8263 (t0) outliers start: 1 outliers final: 1 residues processed: 266 average time/residue: 0.1887 time to fit residues: 79.6361 Evaluate side-chains 248 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 288 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 197 optimal weight: 0.3980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.0170 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 0.5980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 ASN A 655 GLN B 432 ASN C 392 ASN C 432 ASN D 432 ASN ** E 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 432 ASN ** G 432 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 = 0.4038 r_free = 0.4038 target = 0.174357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.121739 restraints weight = 31786.562| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 2.08 r_work: 0.2647 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2511 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.0564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 29834 Z= 0.099 Angle : 0.452 11.220 40495 Z= 0.246 Chirality : 0.044 0.183 4550 Planarity : 0.003 0.040 5257 Dihedral : 3.973 16.635 4034 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.28 % Allowed : 15.90 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.13), residues: 3766 helix: -1.32 (0.24), residues: 448 sheet: -0.09 (0.13), residues: 1386 loop : -1.36 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 614 TYR 0.012 0.001 TYR D 336 PHE 0.011 0.001 PHE F 656 TRP 0.009 0.001 TRP G 748 HIS 0.003 0.000 HIS G 272 Details of bonding type rmsd covalent geometry : bond 0.00232 (29834) covalent geometry : angle 0.45239 (40495) hydrogen bonds : bond 0.02624 ( 1153) hydrogen bonds : angle 5.36752 ( 3168) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 251 time to evaluate : 1.042 Fit side-chains REVERT: A 415 ASP cc_start: 0.8425 (t70) cc_final: 0.7865 (t0) REVERT: A 590 LYS cc_start: 0.7455 (mtmt) cc_final: 0.6855 (ttpt) REVERT: B 415 ASP cc_start: 0.8384 (t70) cc_final: 0.8024 (t0) REVERT: C 415 ASP cc_start: 0.8404 (t70) cc_final: 0.7959 (t0) REVERT: C 590 LYS cc_start: 0.7511 (mtmt) cc_final: 0.6814 (ttpt) REVERT: C 685 MET cc_start: 0.8427 (ptp) cc_final: 0.8084 (ptp) REVERT: C 686 TYR cc_start: 0.8487 (m-80) cc_final: 0.8179 (m-80) REVERT: D 415 ASP cc_start: 0.8344 (t0) cc_final: 0.8097 (t0) REVERT: D 590 LYS cc_start: 0.7442 (mttt) cc_final: 0.6706 (tttt) REVERT: E 415 ASP cc_start: 0.8193 (t70) cc_final: 0.7974 (t0) REVERT: E 588 GLU cc_start: 0.8318 (tp30) cc_final: 0.7783 (tp30) REVERT: E 590 LYS cc_start: 0.7630 (mtmt) cc_final: 0.6901 (ttpt) REVERT: F 369 GLN cc_start: 0.7550 (mt0) cc_final: 0.7327 (mt0) REVERT: F 415 ASP cc_start: 0.8248 (t70) cc_final: 0.7731 (t0) REVERT: F 686 TYR cc_start: 0.8220 (m-80) cc_final: 0.7769 (m-80) REVERT: G 415 ASP cc_start: 0.8477 (t70) cc_final: 0.8161 (t0) outliers start: 42 outliers final: 23 residues processed: 284 average time/residue: 0.1798 time to fit residues: 82.2192 Evaluate side-chains 255 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 232 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 687 MET Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 687 MET Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 721 VAL Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain G residue 296 THR Chi-restraints excluded: chain G residue 564 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 94 optimal weight: 9.9990 chunk 67 optimal weight: 20.0000 chunk 30 optimal weight: 0.6980 chunk 52 optimal weight: 9.9990 chunk 256 optimal weight: 8.9990 chunk 35 optimal weight: 0.6980 chunk 266 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 353 optimal weight: 1.9990 chunk 359 optimal weight: 0.8980 chunk 106 optimal weight: 10.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 660 ASN D 272 HIS E 432 ASN ** F 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 432 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.175237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.124403 restraints weight = 31705.454| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 1.91 r_work: 0.2592 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2459 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 29834 Z= 0.207 Angle : 0.507 11.519 40495 Z= 0.274 Chirality : 0.046 0.202 4550 Planarity : 0.004 0.046 5257 Dihedral : 4.312 16.635 4034 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.98 % Allowed : 16.17 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.13), residues: 3766 helix: -1.64 (0.23), residues: 490 sheet: 0.17 (0.14), residues: 1302 loop : -1.55 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 614 TYR 0.012 0.001 TYR E 567 PHE 0.010 0.001 PHE B 264 TRP 0.009 0.001 TRP D 748 HIS 0.004 0.001 HIS F 272 Details of bonding type rmsd covalent geometry : bond 0.00514 (29834) covalent geometry : angle 0.50672 (40495) hydrogen bonds : bond 0.02738 ( 1153) hydrogen bonds : angle 5.00257 ( 3168) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 242 time to evaluate : 1.049 Fit side-chains REVERT: A 415 ASP cc_start: 0.8424 (t70) cc_final: 0.7848 (t0) REVERT: A 465 GLN cc_start: 0.7542 (mp-120) cc_final: 0.7310 (tt0) REVERT: A 472 ASN cc_start: 0.8441 (t0) cc_final: 0.7807 (t0) REVERT: A 590 LYS cc_start: 0.7544 (mtmt) cc_final: 0.6959 (ttpt) REVERT: B 295 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8417 (pm20) REVERT: B 415 ASP cc_start: 0.8387 (t70) cc_final: 0.8034 (t0) REVERT: C 415 ASP cc_start: 0.8424 (t70) cc_final: 0.7938 (t0) REVERT: C 472 ASN cc_start: 0.8349 (t0) cc_final: 0.8016 (t0) REVERT: C 523 ARG cc_start: 0.8180 (ptt90) cc_final: 0.7931 (ptm-80) REVERT: C 590 LYS cc_start: 0.7602 (mtmt) cc_final: 0.6921 (ttpt) REVERT: C 685 MET cc_start: 0.8470 (ptp) cc_final: 0.8138 (ptp) REVERT: D 415 ASP cc_start: 0.8457 (t0) cc_final: 0.8211 (t0) REVERT: D 590 LYS cc_start: 0.7523 (mttt) cc_final: 0.6690 (tttt) REVERT: D 629 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7726 (mp0) REVERT: E 247 ARG cc_start: 0.8743 (mtm180) cc_final: 0.8455 (mtm180) REVERT: E 415 ASP cc_start: 0.8284 (t70) cc_final: 0.7990 (t0) REVERT: E 588 GLU cc_start: 0.8301 (tp30) cc_final: 0.8079 (tp30) REVERT: F 415 ASP cc_start: 0.8297 (t70) cc_final: 0.7743 (t0) REVERT: F 472 ASN cc_start: 0.8320 (t0) cc_final: 0.7793 (t0) REVERT: F 686 TYR cc_start: 0.8300 (m-80) cc_final: 0.7908 (m-80) REVERT: G 287 ASP cc_start: 0.8811 (t70) cc_final: 0.8052 (t0) REVERT: G 415 ASP cc_start: 0.8519 (t70) cc_final: 0.8168 (t0) outliers start: 65 outliers final: 42 residues processed: 292 average time/residue: 0.1833 time to fit residues: 86.1470 Evaluate side-chains 278 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 234 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 687 MET Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 629 GLU Chi-restraints excluded: chain D residue 687 MET Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain D residue 722 ASP Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 721 VAL Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 317 SER Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 687 MET Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain G residue 295 GLU Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 564 LEU Chi-restraints excluded: chain G residue 609 VAL Chi-restraints excluded: chain G residue 752 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 170 optimal weight: 0.8980 chunk 136 optimal weight: 0.6980 chunk 188 optimal weight: 2.9990 chunk 293 optimal weight: 0.0770 chunk 259 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 312 optimal weight: 0.9980 chunk 350 optimal weight: 0.5980 chunk 338 optimal weight: 4.9990 chunk 255 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.185846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.136570 restraints weight = 32433.249| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.07 r_work: 0.2625 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2489 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 29834 Z= 0.105 Angle : 0.438 10.948 40495 Z= 0.238 Chirality : 0.044 0.199 4550 Planarity : 0.003 0.042 5257 Dihedral : 4.036 15.044 4034 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.73 % Allowed : 17.08 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.13), residues: 3766 helix: -1.49 (0.23), residues: 497 sheet: 0.38 (0.14), residues: 1302 loop : -1.43 (0.13), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 614 TYR 0.009 0.001 TYR D 336 PHE 0.009 0.001 PHE F 656 TRP 0.007 0.001 TRP G 748 HIS 0.003 0.001 HIS G 272 Details of bonding type rmsd covalent geometry : bond 0.00255 (29834) covalent geometry : angle 0.43800 (40495) hydrogen bonds : bond 0.02263 ( 1153) hydrogen bonds : angle 4.67988 ( 3168) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 256 time to evaluate : 1.177 Fit side-chains REVERT: A 415 ASP cc_start: 0.8445 (t70) cc_final: 0.7899 (t0) REVERT: A 465 GLN cc_start: 0.7613 (mp-120) cc_final: 0.7384 (tt0) REVERT: A 472 ASN cc_start: 0.8453 (t0) cc_final: 0.7768 (t0) REVERT: A 590 LYS cc_start: 0.7587 (mtmt) cc_final: 0.7017 (ttpt) REVERT: B 236 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8876 (mm) REVERT: B 295 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8432 (pm20) REVERT: B 415 ASP cc_start: 0.8397 (t70) cc_final: 0.8056 (t0) REVERT: B 590 LYS cc_start: 0.7651 (mttt) cc_final: 0.7016 (ttpt) REVERT: C 415 ASP cc_start: 0.8440 (t70) cc_final: 0.7997 (t0) REVERT: C 472 ASN cc_start: 0.8333 (t0) cc_final: 0.7987 (t0) REVERT: C 523 ARG cc_start: 0.8171 (ptt90) cc_final: 0.7965 (ptm-80) REVERT: C 590 LYS cc_start: 0.7676 (mtmt) cc_final: 0.6967 (ttpt) REVERT: C 685 MET cc_start: 0.8478 (ptp) cc_final: 0.8077 (ptp) REVERT: D 590 LYS cc_start: 0.7549 (mttt) cc_final: 0.6758 (tttt) REVERT: D 629 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7698 (mp0) REVERT: E 415 ASP cc_start: 0.8315 (t70) cc_final: 0.8003 (t0) REVERT: E 588 GLU cc_start: 0.8301 (tp30) cc_final: 0.8088 (tp30) REVERT: F 415 ASP cc_start: 0.8273 (t70) cc_final: 0.7769 (t0) REVERT: F 472 ASN cc_start: 0.8398 (t0) cc_final: 0.7875 (t0) REVERT: F 590 LYS cc_start: 0.7655 (mttt) cc_final: 0.6990 (ttpt) REVERT: F 711 VAL cc_start: 0.7414 (OUTLIER) cc_final: 0.7188 (p) REVERT: G 415 ASP cc_start: 0.8482 (t70) cc_final: 0.8145 (t0) outliers start: 57 outliers final: 45 residues processed: 299 average time/residue: 0.1924 time to fit residues: 92.3936 Evaluate side-chains 288 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 239 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 687 MET Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 629 GLU Chi-restraints excluded: chain D residue 687 MET Chi-restraints excluded: chain D residue 711 VAL Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain D residue 722 ASP Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain E residue 721 VAL Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 428 SER Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 564 LEU Chi-restraints excluded: chain F residue 687 MET Chi-restraints excluded: chain F residue 711 VAL Chi-restraints excluded: chain G residue 564 LEU Chi-restraints excluded: chain G residue 752 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 6 optimal weight: 0.5980 chunk 361 optimal weight: 1.9990 chunk 344 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 292 optimal weight: 0.9980 chunk 254 optimal weight: 0.3980 chunk 305 optimal weight: 0.7980 chunk 46 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.185240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.136073 restraints weight = 32684.787| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.09 r_work: 0.2617 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2480 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 29834 Z= 0.120 Angle : 0.442 11.117 40495 Z= 0.239 Chirality : 0.044 0.198 4550 Planarity : 0.003 0.042 5257 Dihedral : 3.989 15.003 4034 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.37 % Allowed : 16.87 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.13), residues: 3766 helix: -1.38 (0.23), residues: 497 sheet: 0.52 (0.14), residues: 1302 loop : -1.37 (0.13), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 614 TYR 0.009 0.001 TYR A 336 PHE 0.008 0.001 PHE F 656 TRP 0.008 0.001 TRP E 748 HIS 0.003 0.000 HIS A 272 Details of bonding type rmsd covalent geometry : bond 0.00294 (29834) covalent geometry : angle 0.44242 (40495) hydrogen bonds : bond 0.02261 ( 1153) hydrogen bonds : angle 4.51731 ( 3168) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 257 time to evaluate : 1.140 Fit side-chains REVERT: A 415 ASP cc_start: 0.8503 (t70) cc_final: 0.7968 (t0) REVERT: A 465 GLN cc_start: 0.7615 (mp-120) cc_final: 0.7382 (tt0) REVERT: A 472 ASN cc_start: 0.8521 (t0) cc_final: 0.7820 (t0) REVERT: A 590 LYS cc_start: 0.7586 (mtmt) cc_final: 0.7019 (ttpt) REVERT: B 236 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8874 (mm) REVERT: B 295 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8430 (pm20) REVERT: B 415 ASP cc_start: 0.8412 (t70) cc_final: 0.8065 (t0) REVERT: B 590 LYS cc_start: 0.7633 (mttt) cc_final: 0.7019 (ttpt) REVERT: C 415 ASP cc_start: 0.8459 (t70) cc_final: 0.8015 (t0) REVERT: C 472 ASN cc_start: 0.8345 (t0) cc_final: 0.8014 (t0) REVERT: C 523 ARG cc_start: 0.8211 (ptt90) cc_final: 0.7836 (ptt-90) REVERT: C 590 LYS cc_start: 0.7710 (mtmt) cc_final: 0.7032 (ttpt) REVERT: C 685 MET cc_start: 0.8414 (ptp) cc_final: 0.8013 (ptp) REVERT: D 590 LYS cc_start: 0.7565 (mttt) cc_final: 0.6762 (tttt) REVERT: D 629 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7682 (mp0) REVERT: E 415 ASP cc_start: 0.8312 (t70) cc_final: 0.8008 (t0) REVERT: E 588 GLU cc_start: 0.8305 (tp30) cc_final: 0.8080 (tp30) REVERT: F 415 ASP cc_start: 0.8306 (t70) cc_final: 0.7796 (t0) REVERT: F 472 ASN cc_start: 0.8405 (t0) cc_final: 0.7896 (t0) REVERT: F 590 LYS cc_start: 0.7697 (mttt) cc_final: 0.7013 (ttpt) REVERT: F 621 MET cc_start: 0.8813 (mtp) cc_final: 0.8574 (mtp) REVERT: F 711 VAL cc_start: 0.7454 (OUTLIER) cc_final: 0.7226 (p) REVERT: G 415 ASP cc_start: 0.8501 (t70) cc_final: 0.8149 (t0) outliers start: 78 outliers final: 61 residues processed: 321 average time/residue: 0.1822 time to fit residues: 94.7681 Evaluate side-chains 309 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 244 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 687 MET Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 629 GLU Chi-restraints excluded: chain D residue 687 MET Chi-restraints excluded: chain D residue 711 VAL Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain D residue 722 ASP Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain E residue 343 SER Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain E residue 721 VAL Chi-restraints excluded: chain F residue 266 SER Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 317 SER Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 428 SER Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 564 LEU Chi-restraints excluded: chain F residue 609 VAL Chi-restraints excluded: chain F residue 687 MET Chi-restraints excluded: chain F residue 711 VAL Chi-restraints excluded: chain G residue 317 SER Chi-restraints excluded: chain G residue 428 SER Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 564 LEU Chi-restraints excluded: chain G residue 752 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 233 optimal weight: 1.9990 chunk 374 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 145 optimal weight: 0.0370 chunk 125 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 238 optimal weight: 0.6980 chunk 277 optimal weight: 0.6980 chunk 183 optimal weight: 0.4980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 HIS ** F 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 333 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.186317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.137923 restraints weight = 32402.788| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.01 r_work: 0.3268 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 29834 Z= 0.098 Angle : 0.429 10.959 40495 Z= 0.232 Chirality : 0.044 0.268 4550 Planarity : 0.003 0.039 5257 Dihedral : 3.878 14.918 4034 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.37 % Allowed : 17.20 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.13), residues: 3766 helix: -1.26 (0.23), residues: 497 sheet: 0.50 (0.14), residues: 1337 loop : -1.22 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 614 TYR 0.010 0.001 TYR A 573 PHE 0.009 0.001 PHE F 656 TRP 0.007 0.001 TRP E 748 HIS 0.003 0.000 HIS A 272 Details of bonding type rmsd covalent geometry : bond 0.00236 (29834) covalent geometry : angle 0.42859 (40495) hydrogen bonds : bond 0.02156 ( 1153) hydrogen bonds : angle 4.39073 ( 3168) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 261 time to evaluate : 0.789 Fit side-chains REVERT: A 415 ASP cc_start: 0.8679 (t70) cc_final: 0.8166 (t0) REVERT: A 472 ASN cc_start: 0.8636 (t0) cc_final: 0.7941 (t0) REVERT: A 590 LYS cc_start: 0.7751 (mtmt) cc_final: 0.7180 (ttpt) REVERT: B 236 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8917 (mm) REVERT: B 295 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8386 (pm20) REVERT: B 415 ASP cc_start: 0.8542 (t70) cc_final: 0.8232 (t0) REVERT: B 590 LYS cc_start: 0.7848 (mttt) cc_final: 0.7251 (ttpt) REVERT: C 415 ASP cc_start: 0.8607 (t70) cc_final: 0.8206 (t0) REVERT: C 472 ASN cc_start: 0.8479 (t0) cc_final: 0.8149 (t0) REVERT: C 523 ARG cc_start: 0.8180 (ptt90) cc_final: 0.7830 (ptt-90) REVERT: C 588 GLU cc_start: 0.8592 (tp30) cc_final: 0.7745 (mt-10) REVERT: C 590 LYS cc_start: 0.7858 (mtmt) cc_final: 0.7183 (ttpt) REVERT: C 612 THR cc_start: 0.8927 (p) cc_final: 0.8633 (p) REVERT: C 685 MET cc_start: 0.8567 (ptp) cc_final: 0.8194 (ptp) REVERT: D 415 ASP cc_start: 0.8362 (t70) cc_final: 0.8155 (t0) REVERT: D 590 LYS cc_start: 0.7778 (mttt) cc_final: 0.6996 (tttt) REVERT: E 415 ASP cc_start: 0.8449 (t70) cc_final: 0.8156 (t0) REVERT: E 588 GLU cc_start: 0.8378 (tp30) cc_final: 0.8168 (tp30) REVERT: F 415 ASP cc_start: 0.8453 (t70) cc_final: 0.7956 (t0) REVERT: F 472 ASN cc_start: 0.8533 (t0) cc_final: 0.8022 (t0) REVERT: F 590 LYS cc_start: 0.7877 (mttt) cc_final: 0.7212 (ttpt) REVERT: F 621 MET cc_start: 0.8747 (mtp) cc_final: 0.8510 (mtp) REVERT: F 711 VAL cc_start: 0.7501 (OUTLIER) cc_final: 0.7266 (p) REVERT: G 415 ASP cc_start: 0.8621 (t70) cc_final: 0.8289 (t0) outliers start: 78 outliers final: 64 residues processed: 320 average time/residue: 0.1747 time to fit residues: 90.4018 Evaluate side-chains 314 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 247 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 687 MET Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 687 MET Chi-restraints excluded: chain D residue 711 VAL Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain D residue 722 ASP Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 721 VAL Chi-restraints excluded: chain E residue 722 ASP Chi-restraints excluded: chain F residue 266 SER Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 317 SER Chi-restraints excluded: chain F residue 343 SER Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 428 SER Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 564 LEU Chi-restraints excluded: chain F residue 609 VAL Chi-restraints excluded: chain F residue 687 MET Chi-restraints excluded: chain F residue 711 VAL Chi-restraints excluded: chain G residue 295 GLU Chi-restraints excluded: chain G residue 317 SER Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 564 LEU Chi-restraints excluded: chain G residue 752 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 155 optimal weight: 5.9990 chunk 250 optimal weight: 1.9990 chunk 373 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 308 optimal weight: 2.9990 chunk 372 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 295 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 660 ASN F 660 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.172834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.122140 restraints weight = 31723.668| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 1.92 r_work: 0.2565 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2431 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 29834 Z= 0.300 Angle : 0.563 12.014 40495 Z= 0.304 Chirality : 0.050 0.338 4550 Planarity : 0.004 0.045 5257 Dihedral : 4.477 16.581 4034 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.22 % Allowed : 16.63 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.13), residues: 3766 helix: -1.78 (0.21), residues: 539 sheet: 0.42 (0.14), residues: 1302 loop : -1.57 (0.13), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 720 TYR 0.017 0.002 TYR D 686 PHE 0.011 0.002 PHE B 264 TRP 0.010 0.002 TRP C 252 HIS 0.006 0.001 HIS E 272 Details of bonding type rmsd covalent geometry : bond 0.00742 (29834) covalent geometry : angle 0.56307 (40495) hydrogen bonds : bond 0.02743 ( 1153) hydrogen bonds : angle 4.65883 ( 3168) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 235 time to evaluate : 0.972 Fit side-chains REVERT: A 415 ASP cc_start: 0.8457 (t70) cc_final: 0.7895 (t0) REVERT: A 472 ASN cc_start: 0.8613 (t0) cc_final: 0.8164 (t0) REVERT: A 590 LYS cc_start: 0.7581 (mtmt) cc_final: 0.6989 (ttpt) REVERT: A 655 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7780 (pt0) REVERT: B 295 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8433 (pm20) REVERT: B 415 ASP cc_start: 0.8408 (t70) cc_final: 0.8042 (t0) REVERT: C 415 ASP cc_start: 0.8459 (t70) cc_final: 0.7996 (t0) REVERT: C 472 ASN cc_start: 0.8404 (t0) cc_final: 0.7737 (t0) REVERT: C 590 LYS cc_start: 0.7601 (mtmt) cc_final: 0.6941 (ttpt) REVERT: C 685 MET cc_start: 0.8393 (ptp) cc_final: 0.8058 (ptp) REVERT: D 415 ASP cc_start: 0.8330 (t70) cc_final: 0.8117 (t0) REVERT: D 472 ASN cc_start: 0.8395 (t0) cc_final: 0.7823 (t0) REVERT: D 590 LYS cc_start: 0.7552 (mttt) cc_final: 0.6716 (tttt) REVERT: E 247 ARG cc_start: 0.8772 (mtm180) cc_final: 0.8522 (mtm180) REVERT: E 415 ASP cc_start: 0.8347 (t70) cc_final: 0.7995 (t0) REVERT: E 588 GLU cc_start: 0.8213 (tp30) cc_final: 0.7957 (tp30) REVERT: F 415 ASP cc_start: 0.8348 (t70) cc_final: 0.7767 (t0) REVERT: F 472 ASN cc_start: 0.8388 (t0) cc_final: 0.7971 (t0) REVERT: F 590 LYS cc_start: 0.7663 (mttt) cc_final: 0.6997 (ttpt) REVERT: F 711 VAL cc_start: 0.7515 (OUTLIER) cc_final: 0.7306 (p) REVERT: G 287 ASP cc_start: 0.8848 (t70) cc_final: 0.8071 (t0) REVERT: G 415 ASP cc_start: 0.8497 (t70) cc_final: 0.8103 (t0) REVERT: G 581 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8392 (mt) outliers start: 106 outliers final: 76 residues processed: 322 average time/residue: 0.1778 time to fit residues: 92.9851 Evaluate side-chains 312 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 232 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 655 GLN Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 687 MET Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 687 MET Chi-restraints excluded: chain D residue 711 VAL Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain D residue 722 ASP Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain E residue 343 SER Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain E residue 602 ASP Chi-restraints excluded: chain E residue 721 VAL Chi-restraints excluded: chain E residue 722 ASP Chi-restraints excluded: chain F residue 266 SER Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 317 SER Chi-restraints excluded: chain F residue 343 SER Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 426 SER Chi-restraints excluded: chain F residue 428 SER Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 687 MET Chi-restraints excluded: chain F residue 711 VAL Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 295 GLU Chi-restraints excluded: chain G residue 323 SER Chi-restraints excluded: chain G residue 426 SER Chi-restraints excluded: chain G residue 428 SER Chi-restraints excluded: chain G residue 515 SER Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 609 VAL Chi-restraints excluded: chain G residue 752 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 295 optimal weight: 0.8980 chunk 270 optimal weight: 1.9990 chunk 364 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 351 optimal weight: 0.7980 chunk 243 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 chunk 75 optimal weight: 0.6980 chunk 144 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 197 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 660 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.184139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.135717 restraints weight = 32560.689| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.95 r_work: 0.3238 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 29834 Z= 0.115 Angle : 0.449 11.111 40495 Z= 0.244 Chirality : 0.044 0.256 4550 Planarity : 0.003 0.042 5257 Dihedral : 4.124 15.851 4034 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.55 % Allowed : 17.66 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.13), residues: 3766 helix: -1.40 (0.23), residues: 497 sheet: 0.58 (0.14), residues: 1302 loop : -1.36 (0.13), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 614 TYR 0.016 0.001 TYR C 686 PHE 0.009 0.001 PHE F 656 TRP 0.007 0.001 TRP A 371 HIS 0.003 0.001 HIS G 272 Details of bonding type rmsd covalent geometry : bond 0.00278 (29834) covalent geometry : angle 0.44943 (40495) hydrogen bonds : bond 0.02216 ( 1153) hydrogen bonds : angle 4.45219 ( 3168) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 245 time to evaluate : 0.989 Fit side-chains REVERT: A 415 ASP cc_start: 0.8611 (t70) cc_final: 0.8117 (t0) REVERT: A 472 ASN cc_start: 0.8720 (t0) cc_final: 0.8270 (t0) REVERT: A 590 LYS cc_start: 0.7709 (mtmt) cc_final: 0.7136 (ttpt) REVERT: A 655 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7989 (pt0) REVERT: B 295 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8379 (pm20) REVERT: B 415 ASP cc_start: 0.8514 (t70) cc_final: 0.8200 (t0) REVERT: B 590 LYS cc_start: 0.7822 (mttt) cc_final: 0.7200 (ttpt) REVERT: C 415 ASP cc_start: 0.8594 (t70) cc_final: 0.8187 (t0) REVERT: C 472 ASN cc_start: 0.8519 (t0) cc_final: 0.7870 (t0) REVERT: C 588 GLU cc_start: 0.8476 (tp30) cc_final: 0.8117 (tp30) REVERT: C 590 LYS cc_start: 0.7778 (mtmt) cc_final: 0.7133 (ttpt) REVERT: C 685 MET cc_start: 0.8574 (ptp) cc_final: 0.8227 (ptp) REVERT: D 415 ASP cc_start: 0.8475 (t70) cc_final: 0.8246 (t0) REVERT: D 590 LYS cc_start: 0.7695 (mttt) cc_final: 0.6982 (tttt) REVERT: E 236 LEU cc_start: 0.9039 (mt) cc_final: 0.8688 (mt) REVERT: E 247 ARG cc_start: 0.8814 (mtm180) cc_final: 0.8523 (mtm180) REVERT: E 415 ASP cc_start: 0.8485 (t70) cc_final: 0.8175 (t0) REVERT: E 588 GLU cc_start: 0.8325 (tp30) cc_final: 0.8113 (tp30) REVERT: E 686 TYR cc_start: 0.8346 (m-80) cc_final: 0.8096 (m-10) REVERT: F 415 ASP cc_start: 0.8449 (t70) cc_final: 0.7930 (t0) REVERT: F 472 ASN cc_start: 0.8494 (t0) cc_final: 0.8052 (t0) REVERT: F 590 LYS cc_start: 0.7847 (mttt) cc_final: 0.7217 (ttpt) REVERT: F 711 VAL cc_start: 0.7464 (OUTLIER) cc_final: 0.7238 (p) REVERT: G 415 ASP cc_start: 0.8590 (t70) cc_final: 0.8247 (t0) outliers start: 84 outliers final: 73 residues processed: 312 average time/residue: 0.1756 time to fit residues: 89.1094 Evaluate side-chains 317 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 241 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 655 GLN Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 687 MET Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 687 MET Chi-restraints excluded: chain D residue 711 VAL Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain D residue 722 ASP Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain E residue 343 SER Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain E residue 602 ASP Chi-restraints excluded: chain E residue 721 VAL Chi-restraints excluded: chain E residue 722 ASP Chi-restraints excluded: chain F residue 266 SER Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 317 SER Chi-restraints excluded: chain F residue 343 SER Chi-restraints excluded: chain F residue 374 SER Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 687 MET Chi-restraints excluded: chain F residue 711 VAL Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 295 GLU Chi-restraints excluded: chain G residue 426 SER Chi-restraints excluded: chain G residue 428 SER Chi-restraints excluded: chain G residue 515 SER Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 752 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 209 optimal weight: 2.9990 chunk 336 optimal weight: 10.0000 chunk 327 optimal weight: 0.0870 chunk 337 optimal weight: 7.9990 chunk 236 optimal weight: 0.7980 chunk 219 optimal weight: 0.8980 chunk 179 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 255 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 660 ASN ** F 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.185113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.137064 restraints weight = 32476.935| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 1.95 r_work: 0.2630 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2497 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 29834 Z= 0.108 Angle : 0.438 11.042 40495 Z= 0.238 Chirality : 0.044 0.196 4550 Planarity : 0.003 0.041 5257 Dihedral : 3.965 15.180 4034 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.37 % Allowed : 17.84 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.13), residues: 3766 helix: -1.27 (0.23), residues: 497 sheet: 0.68 (0.14), residues: 1302 loop : -1.27 (0.13), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 614 TYR 0.013 0.001 TYR C 686 PHE 0.009 0.001 PHE F 656 TRP 0.007 0.001 TRP E 748 HIS 0.003 0.000 HIS G 272 Details of bonding type rmsd covalent geometry : bond 0.00261 (29834) covalent geometry : angle 0.43849 (40495) hydrogen bonds : bond 0.02150 ( 1153) hydrogen bonds : angle 4.33531 ( 3168) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 260 time to evaluate : 0.991 Fit side-chains REVERT: A 415 ASP cc_start: 0.8486 (t70) cc_final: 0.7954 (t0) REVERT: A 472 ASN cc_start: 0.8610 (t0) cc_final: 0.8156 (t0) REVERT: A 590 LYS cc_start: 0.7524 (mtmt) cc_final: 0.6969 (ttpt) REVERT: A 655 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7812 (pt0) REVERT: B 295 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8383 (pm20) REVERT: B 415 ASP cc_start: 0.8346 (t70) cc_final: 0.8013 (t0) REVERT: B 590 LYS cc_start: 0.7595 (mttt) cc_final: 0.6986 (ttpt) REVERT: B 621 MET cc_start: 0.8962 (mtp) cc_final: 0.8753 (mtp) REVERT: C 415 ASP cc_start: 0.8454 (t70) cc_final: 0.8009 (t0) REVERT: C 472 ASN cc_start: 0.8405 (t0) cc_final: 0.7767 (t0) REVERT: C 588 GLU cc_start: 0.8323 (tp30) cc_final: 0.7926 (tp30) REVERT: C 590 LYS cc_start: 0.7629 (mtmt) cc_final: 0.6955 (ttpt) REVERT: C 685 MET cc_start: 0.8329 (ptp) cc_final: 0.7967 (ptp) REVERT: D 415 ASP cc_start: 0.8342 (t70) cc_final: 0.8097 (t0) REVERT: D 590 LYS cc_start: 0.7524 (mttt) cc_final: 0.6742 (tttt) REVERT: E 415 ASP cc_start: 0.8283 (t70) cc_final: 0.7969 (t0) REVERT: E 588 GLU cc_start: 0.8166 (tp30) cc_final: 0.7856 (tp30) REVERT: E 686 TYR cc_start: 0.8268 (m-80) cc_final: 0.8011 (m-10) REVERT: F 415 ASP cc_start: 0.8292 (t70) cc_final: 0.7775 (t0) REVERT: F 472 ASN cc_start: 0.8412 (t0) cc_final: 0.7993 (t0) REVERT: F 590 LYS cc_start: 0.7704 (mttt) cc_final: 0.7065 (ttpt) REVERT: F 711 VAL cc_start: 0.7494 (OUTLIER) cc_final: 0.7279 (p) REVERT: G 415 ASP cc_start: 0.8453 (t70) cc_final: 0.8087 (t0) outliers start: 78 outliers final: 74 residues processed: 321 average time/residue: 0.1777 time to fit residues: 92.8676 Evaluate side-chains 331 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 254 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 655 GLN Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 687 MET Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 687 MET Chi-restraints excluded: chain D residue 711 VAL Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain D residue 722 ASP Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain E residue 343 SER Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain E residue 602 ASP Chi-restraints excluded: chain E residue 721 VAL Chi-restraints excluded: chain E residue 722 ASP Chi-restraints excluded: chain F residue 266 SER Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 317 SER Chi-restraints excluded: chain F residue 343 SER Chi-restraints excluded: chain F residue 374 SER Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 687 MET Chi-restraints excluded: chain F residue 711 VAL Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 295 GLU Chi-restraints excluded: chain G residue 426 SER Chi-restraints excluded: chain G residue 428 SER Chi-restraints excluded: chain G residue 515 SER Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 609 VAL Chi-restraints excluded: chain G residue 752 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 356 optimal weight: 0.9990 chunk 276 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 304 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 202 optimal weight: 10.0000 chunk 251 optimal weight: 2.9990 chunk 298 optimal weight: 0.3980 chunk 229 optimal weight: 6.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.182304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.133589 restraints weight = 32441.476| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 1.96 r_work: 0.2581 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2449 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 29834 Z= 0.181 Angle : 0.481 11.307 40495 Z= 0.260 Chirality : 0.046 0.199 4550 Planarity : 0.003 0.043 5257 Dihedral : 4.181 15.771 4034 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.52 % Allowed : 17.78 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.13), residues: 3766 helix: -1.37 (0.23), residues: 497 sheet: 0.61 (0.14), residues: 1302 loop : -1.33 (0.13), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 614 TYR 0.015 0.001 TYR A 686 PHE 0.008 0.001 PHE F 656 TRP 0.008 0.001 TRP E 748 HIS 0.003 0.001 HIS E 272 Details of bonding type rmsd covalent geometry : bond 0.00448 (29834) covalent geometry : angle 0.48112 (40495) hydrogen bonds : bond 0.02338 ( 1153) hydrogen bonds : angle 4.41488 ( 3168) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 243 time to evaluate : 1.040 Fit side-chains REVERT: A 415 ASP cc_start: 0.8460 (t70) cc_final: 0.7932 (t0) REVERT: A 472 ASN cc_start: 0.8658 (t0) cc_final: 0.8232 (t0) REVERT: A 590 LYS cc_start: 0.7573 (mtmt) cc_final: 0.6999 (ttpt) REVERT: A 655 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7833 (pt0) REVERT: B 295 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8461 (pm20) REVERT: B 415 ASP cc_start: 0.8359 (t70) cc_final: 0.8011 (t0) REVERT: B 590 LYS cc_start: 0.7660 (mttt) cc_final: 0.7032 (ttpt) REVERT: C 415 ASP cc_start: 0.8488 (t70) cc_final: 0.8037 (t0) REVERT: C 472 ASN cc_start: 0.8448 (t0) cc_final: 0.7822 (t0) REVERT: C 588 GLU cc_start: 0.8370 (tp30) cc_final: 0.7977 (tp30) REVERT: C 590 LYS cc_start: 0.7626 (mtmt) cc_final: 0.6988 (ttpt) REVERT: C 685 MET cc_start: 0.8370 (ptp) cc_final: 0.8019 (ptp) REVERT: D 415 ASP cc_start: 0.8402 (t70) cc_final: 0.8178 (t0) REVERT: D 472 ASN cc_start: 0.8472 (t0) cc_final: 0.8037 (t0) REVERT: D 590 LYS cc_start: 0.7575 (mttt) cc_final: 0.6814 (tttt) REVERT: E 247 ARG cc_start: 0.8778 (mtm180) cc_final: 0.8508 (mtm180) REVERT: E 415 ASP cc_start: 0.8281 (t70) cc_final: 0.7956 (t0) REVERT: E 588 GLU cc_start: 0.8193 (tp30) cc_final: 0.7892 (tp30) REVERT: E 686 TYR cc_start: 0.8261 (m-80) cc_final: 0.8024 (m-10) REVERT: F 415 ASP cc_start: 0.8312 (t70) cc_final: 0.7769 (t0) REVERT: F 472 ASN cc_start: 0.8401 (t0) cc_final: 0.7985 (t0) REVERT: F 590 LYS cc_start: 0.7693 (mttt) cc_final: 0.7041 (ttpt) REVERT: F 711 VAL cc_start: 0.7542 (OUTLIER) cc_final: 0.7314 (p) REVERT: G 287 ASP cc_start: 0.8794 (t70) cc_final: 0.7981 (t0) REVERT: G 415 ASP cc_start: 0.8474 (t70) cc_final: 0.8089 (t0) REVERT: G 472 ASN cc_start: 0.8445 (t0) cc_final: 0.8108 (t0) outliers start: 83 outliers final: 78 residues processed: 307 average time/residue: 0.1822 time to fit residues: 90.9744 Evaluate side-chains 322 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 241 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 655 GLN Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 687 MET Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 477 MET Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 687 MET Chi-restraints excluded: chain D residue 711 VAL Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain D residue 722 ASP Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain E residue 343 SER Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain E residue 602 ASP Chi-restraints excluded: chain E residue 721 VAL Chi-restraints excluded: chain E residue 722 ASP Chi-restraints excluded: chain F residue 266 SER Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 317 SER Chi-restraints excluded: chain F residue 343 SER Chi-restraints excluded: chain F residue 374 SER Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 687 MET Chi-restraints excluded: chain F residue 711 VAL Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 295 GLU Chi-restraints excluded: chain G residue 426 SER Chi-restraints excluded: chain G residue 428 SER Chi-restraints excluded: chain G residue 515 SER Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 609 VAL Chi-restraints excluded: chain G residue 752 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 247 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 363 optimal weight: 0.3980 chunk 366 optimal weight: 8.9990 chunk 333 optimal weight: 0.8980 chunk 323 optimal weight: 7.9990 chunk 268 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 102 optimal weight: 10.0000 chunk 242 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.184076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.135609 restraints weight = 32627.981| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 1.97 r_work: 0.2617 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2484 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 29834 Z= 0.122 Angle : 0.449 11.132 40495 Z= 0.243 Chirality : 0.044 0.198 4550 Planarity : 0.003 0.042 5257 Dihedral : 4.053 15.815 4034 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.52 % Allowed : 17.81 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.13), residues: 3766 helix: -1.27 (0.23), residues: 497 sheet: 0.66 (0.14), residues: 1302 loop : -1.28 (0.13), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 614 TYR 0.014 0.001 TYR D 686 PHE 0.009 0.001 PHE F 656 TRP 0.007 0.001 TRP E 748 HIS 0.003 0.000 HIS A 272 Details of bonding type rmsd covalent geometry : bond 0.00300 (29834) covalent geometry : angle 0.44880 (40495) hydrogen bonds : bond 0.02185 ( 1153) hydrogen bonds : angle 4.33866 ( 3168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8171.57 seconds wall clock time: 140 minutes 15.65 seconds (8415.65 seconds total)