Starting phenix.real_space_refine on Sun Jul 5 20:45:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vek_65010/07_2026/9vek_65010.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vek_65010/07_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_65010/07_2026/9vek_65010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vek_65010/07_2026/9vek_65010.map" model { file = "/net/cci-nas-00/data/ceres_data/9vek_65010/07_2026/9vek_65010.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vek_65010/07_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-dev-6108/lib/python3.11/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, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Time building chain proxies: 5.72, per 1000 atoms: 0.20 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: 2.35 Conformation dependent library (CDL) restraints added in 1.1 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: 1.09 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: 5.72 Time building geometry restraints manager: 2.96 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 3.250 nonbonded pdb=" OD1 ASP D 229 " pdb="CA CA D 902 " model vdw 1.919 3.250 nonbonded pdb=" OE2 GLU C 629 " pdb="CA CA C 903 " model vdw 2.064 3.250 nonbonded pdb=" OD1 ASP D 227 " pdb="CA CA D 902 " model vdw 2.072 3.250 nonbonded pdb=" O ILE D 233 " pdb="CA CA D 902 " model vdw 2.117 3.250 ... (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: 0.01 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: 5.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.510 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 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/Z covalent geometry : bond 0.00282 / 0.15 (29834) covalent geometry : angle 0.54375 / 0.32 (40495) hydrogen bonds : bond 0.15903 / 10.57 ( 1153) hydrogen bonds : angle 7.85957 / 5.33 ( 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 : 1.190 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: 0.1772 time to fit residues: 75.4469 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 : 1.181 ------------------------------------------------------------------------------- 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... 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 = 0.4118 r_free = 0.4118 target = 0.180381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.130060 restraints weight = 31373.096| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 1.83 r_work: 0.2676 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.0597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 29834 Z= 0.104 Angle : 0.462 11.075 40495 Z= 0.252 Chirality : 0.044 0.178 4550 Planarity : 0.004 0.047 5257 Dihedral : 4.037 16.823 4034 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % 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: -1.38 (0.13), residues: 3766 helix: -1.49 (0.24), residues: 441 sheet: -0.09 (0.13), residues: 1386 loop : -1.38 (0.13), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 614 TYR 0.011 0.001 TYR D 336 PHE 0.011 0.001 PHE F 656 TRP 0.010 0.001 TRP G 748 HIS 0.003 0.000 HIS G 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 (29834) covalent geometry : angle 0.46209 / 0.25 (40495) hydrogen bonds : bond 0.02793 / 1.87 ( 1153) hydrogen bonds : angle 5.47991 / 3.75 ( 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 : 1.133 Fit side-chains REVERT: A 415 ASP cc_start: 0.8415 (t70) cc_final: 0.7859 (t0) REVERT: A 590 LYS cc_start: 0.7580 (mtmt) cc_final: 0.6991 (ttpt) REVERT: B 415 ASP cc_start: 0.8384 (t70) cc_final: 0.8036 (t0) REVERT: C 415 ASP cc_start: 0.8417 (t70) cc_final: 0.7973 (t0) REVERT: C 590 LYS cc_start: 0.7625 (mtmt) cc_final: 0.6920 (ttpt) REVERT: C 685 MET cc_start: 0.8540 (ptp) cc_final: 0.8201 (ptp) REVERT: C 686 TYR cc_start: 0.8528 (m-80) cc_final: 0.8226 (m-80) REVERT: D 415 ASP cc_start: 0.8285 (t0) cc_final: 0.8058 (t0) REVERT: D 590 LYS cc_start: 0.7520 (mttt) cc_final: 0.6789 (tttt) REVERT: D 629 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: E 415 ASP cc_start: 0.8160 (t70) cc_final: 0.7933 (t0) REVERT: E 588 GLU cc_start: 0.8326 (tp30) cc_final: 0.7827 (tp30) REVERT: E 590 LYS cc_start: 0.7710 (mtmt) cc_final: 0.6969 (ttpt) REVERT: F 369 GLN cc_start: 0.7560 (mt0) cc_final: 0.7331 (mt0) REVERT: F 415 ASP cc_start: 0.8232 (t70) cc_final: 0.7722 (t0) REVERT: F 686 TYR cc_start: 0.8268 (m-80) cc_final: 0.7805 (m-80) REVERT: G 415 ASP cc_start: 0.8475 (t70) cc_final: 0.8160 (t0) outliers start: 42 outliers final: 21 residues processed: 283 average time/residue: 0.1922 time to fit residues: 88.0313 Evaluate side-chains 256 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 234 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 752 THR 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 629 GLU 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 524 VAL 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: 1.9990 chunk 52 optimal weight: 9.9990 chunk 256 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 266 optimal weight: 6.9990 chunk 179 optimal weight: 0.9980 chunk 353 optimal weight: 1.9990 chunk 359 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 660 ASN C 392 ASN D 272 HIS ** E 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.173749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.122609 restraints weight = 31680.544| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 1.92 r_work: 0.2577 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2446 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 29834 Z= 0.277 Angle : 0.556 11.807 40495 Z= 0.302 Chirality : 0.049 0.198 4550 Planarity : 0.004 0.055 5257 Dihedral : 4.577 17.333 4034 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.16 % Allowed : 16.66 % 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: -1.56 (0.13), residues: 3766 helix: -1.87 (0.22), residues: 490 sheet: 0.09 (0.14), residues: 1302 loop : -1.61 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 614 TYR 0.013 0.002 TYR E 567 PHE 0.011 0.002 PHE B 264 TRP 0.009 0.001 TRP C 502 HIS 0.006 0.001 HIS F 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00683 / 0.28 (29834) covalent geometry : angle 0.55621 / 0.30 (40495) hydrogen bonds : bond 0.02924 / 1.97 ( 1153) hydrogen bonds : angle 5.14837 / 3.53 ( 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 308 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 237 time to evaluate : 0.851 Fit side-chains REVERT: A 415 ASP cc_start: 0.8418 (t70) cc_final: 0.7827 (t0) REVERT: A 465 GLN cc_start: 0.7591 (mp-120) cc_final: 0.7331 (tt0) REVERT: A 472 ASN cc_start: 0.8465 (t0) cc_final: 0.8045 (t0) REVERT: A 590 LYS cc_start: 0.7583 (mttt) cc_final: 0.6966 (ttpt) REVERT: B 295 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8445 (pm20) REVERT: B 415 ASP cc_start: 0.8368 (t70) cc_final: 0.8006 (t0) REVERT: C 415 ASP cc_start: 0.8436 (t70) cc_final: 0.7939 (t0) REVERT: C 472 ASN cc_start: 0.8397 (t0) cc_final: 0.8089 (t0) REVERT: C 523 ARG cc_start: 0.8214 (ptt90) cc_final: 0.7966 (ptm-80) REVERT: C 590 LYS cc_start: 0.7619 (mtmt) cc_final: 0.6928 (ttpt) REVERT: C 685 MET cc_start: 0.8490 (ptp) cc_final: 0.8123 (ptp) REVERT: C 686 TYR cc_start: 0.8576 (m-80) cc_final: 0.8286 (m-80) REVERT: D 415 ASP cc_start: 0.8455 (t0) cc_final: 0.8224 (t0) REVERT: D 590 LYS cc_start: 0.7558 (mttt) cc_final: 0.6706 (tttt) REVERT: E 247 ARG cc_start: 0.8706 (mtm180) cc_final: 0.8441 (mtm180) REVERT: E 415 ASP cc_start: 0.8325 (t70) cc_final: 0.8025 (t0) REVERT: E 588 GLU cc_start: 0.8339 (tp30) cc_final: 0.8134 (tp30) REVERT: F 415 ASP cc_start: 0.8305 (t70) cc_final: 0.7741 (t0) REVERT: F 472 ASN cc_start: 0.8304 (t0) cc_final: 0.7845 (t0) REVERT: F 614 ARG cc_start: 0.8347 (mtt90) cc_final: 0.8146 (mtt-85) REVERT: F 686 TYR cc_start: 0.8304 (m-80) cc_final: 0.7949 (m-80) REVERT: G 287 ASP cc_start: 0.8832 (t70) cc_final: 0.8085 (t0) REVERT: G 415 ASP cc_start: 0.8502 (t70) cc_final: 0.8134 (t0) outliers start: 71 outliers final: 48 residues processed: 291 average time/residue: 0.1767 time to fit residues: 83.6654 Evaluate side-chains 279 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 230 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 428 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 296 THR 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 428 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 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 609 VAL 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 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: 0.9980 chunk 136 optimal weight: 0.5980 chunk 188 optimal weight: 1.9990 chunk 293 optimal weight: 0.9990 chunk 259 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 312 optimal weight: 4.9990 chunk 350 optimal weight: 2.9990 chunk 338 optimal weight: 5.9990 chunk 255 optimal weight: 0.7980 chunk 31 optimal weight: 0.2980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 392 ASN E 432 ASN ** F 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 432 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.178576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.127738 restraints weight = 31197.286| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 1.83 r_work: 0.2646 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 29834 Z= 0.122 Angle : 0.455 11.125 40495 Z= 0.248 Chirality : 0.045 0.200 4550 Planarity : 0.003 0.051 5257 Dihedral : 4.238 15.240 4034 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.98 % Allowed : 17.29 % Favored : 80.73 % 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: -1.32 (0.13), residues: 3766 helix: -1.69 (0.22), residues: 497 sheet: 0.30 (0.14), residues: 1302 loop : -1.49 (0.13), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 614 TYR 0.009 0.001 TYR D 336 PHE 0.010 0.001 PHE F 656 TRP 0.007 0.001 TRP D 748 HIS 0.003 0.001 HIS A 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 (29834) covalent geometry : angle 0.45458 / 0.25 (40495) hydrogen bonds : bond 0.02354 / 1.57 ( 1153) hydrogen bonds : angle 4.77596 / 3.29 ( 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 323 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 258 time to evaluate : 1.020 Fit side-chains REVERT: A 415 ASP cc_start: 0.8382 (t70) cc_final: 0.7826 (t0) REVERT: A 465 GLN cc_start: 0.7541 (mp-120) cc_final: 0.7325 (tt0) REVERT: A 472 ASN cc_start: 0.8450 (t0) cc_final: 0.7812 (t0) REVERT: A 590 LYS cc_start: 0.7556 (mttt) cc_final: 0.6956 (ttpt) REVERT: B 295 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8368 (pm20) REVERT: B 415 ASP cc_start: 0.8361 (t70) cc_final: 0.8011 (t0) REVERT: B 590 LYS cc_start: 0.7584 (mttt) cc_final: 0.6931 (ttpt) REVERT: C 415 ASP cc_start: 0.8394 (t70) cc_final: 0.7958 (t0) REVERT: C 472 ASN cc_start: 0.8325 (t0) cc_final: 0.8005 (t0) REVERT: C 523 ARG cc_start: 0.8178 (ptt90) cc_final: 0.7938 (ptm-80) REVERT: C 590 LYS cc_start: 0.7651 (mtmt) cc_final: 0.6927 (ttpt) REVERT: C 685 MET cc_start: 0.8477 (ptp) cc_final: 0.8074 (ptp) REVERT: C 686 TYR cc_start: 0.8446 (m-80) cc_final: 0.8148 (m-80) REVERT: D 415 ASP cc_start: 0.8442 (t0) cc_final: 0.8219 (t0) REVERT: D 590 LYS cc_start: 0.7492 (mttt) cc_final: 0.6712 (tttt) REVERT: D 614 ARG cc_start: 0.8534 (mtt-85) cc_final: 0.8309 (mtt90) REVERT: D 629 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: D 686 TYR cc_start: 0.8383 (m-80) cc_final: 0.8143 (m-80) REVERT: E 229 ASP cc_start: 0.8906 (p0) cc_final: 0.8614 (p0) REVERT: E 247 ARG cc_start: 0.8700 (mtm180) cc_final: 0.8430 (mtm180) REVERT: E 415 ASP cc_start: 0.8280 (t70) cc_final: 0.7962 (t0) REVERT: E 588 GLU cc_start: 0.8257 (tp30) cc_final: 0.8021 (tp30) REVERT: F 415 ASP cc_start: 0.8261 (t70) cc_final: 0.7737 (t0) REVERT: F 472 ASN cc_start: 0.8377 (t0) cc_final: 0.7903 (t0) REVERT: F 614 ARG cc_start: 0.8364 (mtt90) cc_final: 0.8147 (mtt-85) REVERT: F 711 VAL cc_start: 0.7353 (OUTLIER) cc_final: 0.7126 (p) REVERT: G 415 ASP cc_start: 0.8468 (t70) cc_final: 0.8098 (t0) outliers start: 65 outliers final: 49 residues processed: 306 average time/residue: 0.1870 time to fit residues: 91.4594 Evaluate side-chains 298 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 246 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 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 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 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 752 THR Chi-restraints excluded: chain E residue 266 SER 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 683 LEU 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 609 VAL Chi-restraints excluded: chain F residue 687 MET Chi-restraints excluded: chain F residue 711 VAL Chi-restraints excluded: chain G residue 428 SER 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: 0.7980 chunk 36 optimal weight: 2.9990 chunk 292 optimal weight: 0.9990 chunk 254 optimal weight: 0.3980 chunk 305 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 152 optimal weight: 0.0020 chunk 173 optimal weight: 0.9980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 392 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 = 0.4160 r_free = 0.4160 target = 0.186341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.137985 restraints weight = 32243.444| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.91 r_work: 0.2649 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2519 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1121 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= 0.104 Angle : 0.435 10.998 40495 Z= 0.237 Chirality : 0.044 0.195 4550 Planarity : 0.003 0.048 5257 Dihedral : 4.053 15.052 4034 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.34 % Allowed : 17.08 % Favored : 80.58 % 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: -1.11 (0.13), residues: 3766 helix: -1.50 (0.23), residues: 497 sheet: 0.48 (0.14), residues: 1302 loop : -1.39 (0.13), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 614 TYR 0.008 0.001 TYR A 336 PHE 0.009 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/Z covalent geometry : bond 0.00248 / 0.10 (29834) covalent geometry : angle 0.43508 / 0.24 (40495) hydrogen bonds : bond 0.02222 / 1.48 ( 1153) hydrogen bonds : angle 4.56105 / 3.14 ( 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 340 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 263 time to evaluate : 1.027 Fit side-chains REVERT: A 415 ASP cc_start: 0.8462 (t70) cc_final: 0.7920 (t0) REVERT: A 465 GLN cc_start: 0.7589 (mp-120) cc_final: 0.7375 (tt0) REVERT: A 472 ASN cc_start: 0.8515 (t0) cc_final: 0.7830 (t0) REVERT: A 590 LYS cc_start: 0.7579 (mttt) cc_final: 0.7003 (ttpt) REVERT: B 295 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8420 (pm20) REVERT: B 415 ASP cc_start: 0.8372 (t70) cc_final: 0.8027 (t0) REVERT: B 590 LYS cc_start: 0.7645 (mttt) cc_final: 0.7003 (ttpt) REVERT: C 415 ASP cc_start: 0.8434 (t70) cc_final: 0.7987 (t0) REVERT: C 472 ASN cc_start: 0.8384 (t0) cc_final: 0.8065 (t0) REVERT: C 523 ARG cc_start: 0.8183 (ptt90) cc_final: 0.7959 (ptm-80) REVERT: C 590 LYS cc_start: 0.7710 (mtmt) cc_final: 0.6991 (ttpt) REVERT: C 685 MET cc_start: 0.8445 (ptp) cc_final: 0.8036 (ptp) REVERT: C 686 TYR cc_start: 0.8417 (m-80) cc_final: 0.8134 (m-80) REVERT: D 590 LYS cc_start: 0.7565 (mttt) cc_final: 0.6783 (tttt) REVERT: D 629 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7568 (mp0) REVERT: E 229 ASP cc_start: 0.8833 (OUTLIER) cc_final: 0.8563 (p0) REVERT: E 415 ASP cc_start: 0.8300 (t70) cc_final: 0.7970 (t0) REVERT: E 588 GLU cc_start: 0.8291 (tp30) cc_final: 0.8044 (tp30) REVERT: F 415 ASP cc_start: 0.8269 (t70) cc_final: 0.7759 (t0) REVERT: F 472 ASN cc_start: 0.8393 (t0) cc_final: 0.7912 (t0) REVERT: F 590 LYS cc_start: 0.7659 (mttt) cc_final: 0.6974 (ttpt) REVERT: F 614 ARG cc_start: 0.8342 (mtt90) cc_final: 0.8085 (mtt90) REVERT: F 711 VAL cc_start: 0.7493 (OUTLIER) cc_final: 0.7260 (p) REVERT: G 415 ASP cc_start: 0.8472 (t70) cc_final: 0.8107 (t0) REVERT: G 564 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7700 (mp) outliers start: 77 outliers final: 58 residues processed: 326 average time/residue: 0.1810 time to fit residues: 95.7831 Evaluate side-chains 309 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 246 time to evaluate : 1.291 ------------------------------------------------------------------------------- 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 295 GLU Chi-restraints excluded: chain B residue 377 ASN 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 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 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 229 ASP Chi-restraints excluded: chain E residue 266 SER 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 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 609 VAL Chi-restraints excluded: chain F residue 687 MET Chi-restraints excluded: chain F residue 711 VAL Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 295 GLU Chi-restraints excluded: chain G residue 343 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: 10.0000 chunk 30 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 145 optimal weight: 0.6980 chunk 125 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 238 optimal weight: 1.9990 chunk 277 optimal weight: 0.8980 chunk 183 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 392 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 = 0.4154 r_free = 0.4154 target = 0.186327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.137970 restraints weight = 32254.955| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.06 r_work: 0.2623 rms_B_bonded: 2.36 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: 0.8622 moved from start: 0.1186 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= 0.124 Angle : 0.448 11.097 40495 Z= 0.243 Chirality : 0.045 0.269 4550 Planarity : 0.003 0.048 5257 Dihedral : 4.058 15.133 4034 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.67 % Allowed : 17.05 % Favored : 80.27 % 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: -1.04 (0.13), residues: 3766 helix: -1.47 (0.23), residues: 504 sheet: 0.53 (0.14), residues: 1302 loop : -1.35 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 614 TYR 0.011 0.001 TYR A 573 PHE 0.009 0.001 PHE F 656 TRP 0.008 0.001 TRP E 748 HIS 0.003 0.001 HIS A 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.12 (29834) covalent geometry : angle 0.44821 / 0.24 (40495) hydrogen bonds : bond 0.02234 / 1.50 ( 1153) hydrogen bonds : angle 4.48396 / 3.09 ( 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 348 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 260 time to evaluate : 0.997 Fit side-chains REVERT: A 415 ASP cc_start: 0.8491 (t70) cc_final: 0.7961 (t0) REVERT: A 465 GLN cc_start: 0.7636 (mp-120) cc_final: 0.7394 (tt0) REVERT: A 472 ASN cc_start: 0.8541 (t0) cc_final: 0.7863 (t0) REVERT: A 590 LYS cc_start: 0.7592 (mttt) cc_final: 0.7009 (ttpt) REVERT: A 655 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7789 (pt0) REVERT: B 295 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8435 (pm20) REVERT: B 415 ASP cc_start: 0.8398 (t70) cc_final: 0.8051 (t0) REVERT: B 590 LYS cc_start: 0.7653 (mttt) cc_final: 0.7020 (ttpt) REVERT: C 415 ASP cc_start: 0.8469 (t70) cc_final: 0.8019 (t0) REVERT: C 472 ASN cc_start: 0.8398 (t0) cc_final: 0.8082 (t0) REVERT: C 523 ARG cc_start: 0.8231 (ptt90) cc_final: 0.8021 (ptm-80) REVERT: C 588 GLU cc_start: 0.8536 (tp30) cc_final: 0.7749 (mt-10) REVERT: C 590 LYS cc_start: 0.7732 (mtmt) cc_final: 0.7053 (ttpt) REVERT: C 685 MET cc_start: 0.8417 (ptp) cc_final: 0.7987 (ptp) REVERT: C 686 TYR cc_start: 0.8408 (m-80) cc_final: 0.8186 (m-80) REVERT: D 590 LYS cc_start: 0.7592 (mttt) cc_final: 0.6784 (tttt) REVERT: D 629 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: E 229 ASP cc_start: 0.8840 (OUTLIER) cc_final: 0.8559 (p0) REVERT: E 415 ASP cc_start: 0.8342 (t70) cc_final: 0.8014 (t0) REVERT: E 588 GLU cc_start: 0.8237 (tp30) cc_final: 0.7989 (tp30) REVERT: F 415 ASP cc_start: 0.8280 (t70) cc_final: 0.7767 (t0) REVERT: F 472 ASN cc_start: 0.8405 (t0) cc_final: 0.7928 (t0) REVERT: F 590 LYS cc_start: 0.7716 (mttt) cc_final: 0.6980 (ttpt) REVERT: F 614 ARG cc_start: 0.8359 (mtt90) cc_final: 0.8106 (mtt90) REVERT: F 621 MET cc_start: 0.8820 (mtp) cc_final: 0.8567 (mtp) REVERT: F 711 VAL cc_start: 0.7502 (OUTLIER) cc_final: 0.7282 (p) REVERT: G 415 ASP cc_start: 0.8495 (t70) cc_final: 0.8137 (t0) REVERT: G 564 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7687 (mp) REVERT: G 581 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8359 (mt) outliers start: 88 outliers final: 71 residues processed: 331 average time/residue: 0.1767 time to fit residues: 94.9630 Evaluate side-chains 327 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 249 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 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 266 SER 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 722 ASP 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 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 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 229 ASP Chi-restraints excluded: chain E residue 266 SER 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 609 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 317 SER Chi-restraints excluded: chain G residue 343 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 564 LEU Chi-restraints excluded: chain G residue 581 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: 8.9990 chunk 250 optimal weight: 3.9990 chunk 373 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 308 optimal weight: 2.9990 chunk 372 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 295 optimal weight: 0.9980 chunk 224 optimal weight: 1.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 660 ASN C 392 ASN F 660 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.136731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.082930 restraints weight = 33352.412| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 1.82 r_work: 0.2565 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2438 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 29834 Z= 0.302 Angle : 0.565 11.864 40495 Z= 0.306 Chirality : 0.050 0.323 4550 Planarity : 0.004 0.051 5257 Dihedral : 4.607 16.698 4034 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.19 % Allowed : 16.75 % Favored : 80.06 % 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: -1.44 (0.13), residues: 3766 helix: -1.92 (0.21), residues: 546 sheet: 0.35 (0.14), residues: 1302 loop : -1.62 (0.13), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 614 TYR 0.015 0.002 TYR D 336 PHE 0.012 0.002 PHE D 264 TRP 0.010 0.002 TRP C 252 HIS 0.007 0.001 HIS F 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00745 / 0.30 (29834) covalent geometry : angle 0.56534 / 0.31 (40495) hydrogen bonds : bond 0.02758 / 1.86 ( 1153) hydrogen bonds : angle 4.71952 / 3.25 ( 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 348 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 243 time to evaluate : 1.088 Fit side-chains REVERT: A 415 ASP cc_start: 0.8457 (t70) cc_final: 0.7880 (t0) REVERT: A 465 GLN cc_start: 0.7675 (mp-120) cc_final: 0.7447 (tt0) REVERT: A 472 ASN cc_start: 0.8672 (t0) cc_final: 0.8244 (t0) REVERT: A 590 LYS cc_start: 0.7637 (mttt) cc_final: 0.7049 (ttpt) REVERT: A 655 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7855 (pt0) REVERT: B 295 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8414 (pm20) REVERT: B 415 ASP cc_start: 0.8368 (t70) cc_final: 0.8004 (t0) REVERT: C 415 ASP cc_start: 0.8489 (t70) cc_final: 0.8023 (t0) REVERT: C 472 ASN cc_start: 0.8456 (t0) cc_final: 0.7794 (t0) REVERT: C 523 ARG cc_start: 0.8248 (ptt90) cc_final: 0.8008 (ptm-80) REVERT: C 588 GLU cc_start: 0.8568 (tp30) cc_final: 0.8328 (tp30) REVERT: C 590 LYS cc_start: 0.7772 (mtmt) cc_final: 0.7067 (ttpt) REVERT: C 685 MET cc_start: 0.8574 (ptp) cc_final: 0.8191 (ptp) REVERT: C 686 TYR cc_start: 0.8581 (m-80) cc_final: 0.8323 (m-80) REVERT: D 472 ASN cc_start: 0.8459 (t0) cc_final: 0.7882 (t0) REVERT: D 590 LYS cc_start: 0.7663 (mttt) cc_final: 0.6824 (tttt) REVERT: D 629 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7575 (mp0) REVERT: E 229 ASP cc_start: 0.9021 (OUTLIER) cc_final: 0.8750 (p0) REVERT: E 247 ARG cc_start: 0.8741 (mtm180) cc_final: 0.8499 (mtm180) REVERT: E 415 ASP cc_start: 0.8411 (t70) cc_final: 0.8041 (t0) REVERT: E 588 GLU cc_start: 0.8242 (tp30) cc_final: 0.8037 (tp30) REVERT: F 415 ASP cc_start: 0.8363 (t70) cc_final: 0.7789 (t0) REVERT: F 472 ASN cc_start: 0.8466 (t0) cc_final: 0.8054 (t0) REVERT: F 614 ARG cc_start: 0.8337 (mtt90) cc_final: 0.8092 (mtt90) REVERT: G 287 ASP cc_start: 0.8840 (t70) cc_final: 0.8081 (t0) REVERT: G 415 ASP cc_start: 0.8514 (t70) cc_final: 0.8114 (t0) REVERT: G 581 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8466 (mt) outliers start: 105 outliers final: 79 residues processed: 329 average time/residue: 0.1675 time to fit residues: 89.5964 Evaluate side-chains 323 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 239 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 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 529 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 266 SER 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 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 722 ASP Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain C residue 266 SER 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 529 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 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 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 229 ASP Chi-restraints excluded: chain E residue 266 SER 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 602 ASP 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 343 SER Chi-restraints excluded: chain F residue 374 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 343 SER Chi-restraints excluded: chain G residue 374 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: 0.7980 chunk 270 optimal weight: 0.9990 chunk 364 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 351 optimal weight: 0.9990 chunk 243 optimal weight: 0.7980 chunk 95 optimal weight: 0.0020 chunk 75 optimal weight: 0.6980 chunk 144 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 197 optimal weight: 0.0370 overall best weight: 0.4666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 392 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 = 0.4154 r_free = 0.4154 target = 0.186049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.138229 restraints weight = 32353.602| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 1.93 r_work: 0.2635 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2505 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1356 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= 0.100 Angle : 0.447 10.940 40495 Z= 0.243 Chirality : 0.044 0.233 4550 Planarity : 0.003 0.049 5257 Dihedral : 4.168 15.601 4034 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.46 % Allowed : 17.57 % Favored : 79.97 % 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: -1.48 (0.22), residues: 504 sheet: 0.53 (0.14), residues: 1302 loop : -1.36 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 614 TYR 0.009 0.001 TYR A 573 PHE 0.010 0.001 PHE F 656 TRP 0.008 0.001 TRP A 371 HIS 0.003 0.001 HIS A 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 (29834) covalent geometry : angle 0.44718 / 0.24 (40495) hydrogen bonds : bond 0.02204 / 1.47 ( 1153) hydrogen bonds : angle 4.47408 / 3.08 ( 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 331 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 250 time to evaluate : 1.127 Fit side-chains REVERT: A 415 ASP cc_start: 0.8445 (t70) cc_final: 0.7907 (t0) REVERT: A 465 GLN cc_start: 0.7625 (mp-120) cc_final: 0.7376 (tt0) REVERT: A 472 ASN cc_start: 0.8602 (t0) cc_final: 0.8162 (t0) REVERT: A 590 LYS cc_start: 0.7609 (mttt) cc_final: 0.7038 (ttpt) REVERT: B 295 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8358 (pm20) REVERT: B 415 ASP cc_start: 0.8374 (t70) cc_final: 0.8029 (t0) REVERT: B 590 LYS cc_start: 0.7584 (mttt) cc_final: 0.6960 (ttpt) REVERT: C 415 ASP cc_start: 0.8415 (t70) cc_final: 0.7972 (t0) REVERT: C 472 ASN cc_start: 0.8395 (t0) cc_final: 0.7758 (t0) REVERT: C 588 GLU cc_start: 0.8486 (tp30) cc_final: 0.7699 (mt-10) REVERT: C 590 LYS cc_start: 0.7680 (mtmt) cc_final: 0.6994 (ttpt) REVERT: C 685 MET cc_start: 0.8435 (ptp) cc_final: 0.7986 (ptp) REVERT: C 686 TYR cc_start: 0.8387 (m-80) cc_final: 0.8114 (m-80) REVERT: D 590 LYS cc_start: 0.7491 (mttt) cc_final: 0.6772 (tttt) REVERT: D 629 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7524 (mp0) REVERT: E 229 ASP cc_start: 0.8787 (OUTLIER) cc_final: 0.8483 (p0) REVERT: E 415 ASP cc_start: 0.8320 (t70) cc_final: 0.7987 (t0) REVERT: E 588 GLU cc_start: 0.8136 (tp30) cc_final: 0.7888 (tp30) REVERT: F 415 ASP cc_start: 0.8270 (t70) cc_final: 0.7742 (t0) REVERT: F 472 ASN cc_start: 0.8392 (t0) cc_final: 0.7965 (t0) REVERT: F 590 LYS cc_start: 0.7665 (mttt) cc_final: 0.6993 (ttpt) REVERT: F 711 VAL cc_start: 0.7494 (OUTLIER) cc_final: 0.7261 (p) REVERT: G 415 ASP cc_start: 0.8458 (t70) cc_final: 0.8070 (t0) REVERT: G 581 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8299 (mt) outliers start: 81 outliers final: 68 residues processed: 316 average time/residue: 0.1818 time to fit residues: 93.7761 Evaluate side-chains 320 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 247 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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 515 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 266 SER 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 C residue 266 SER Chi-restraints excluded: chain C residue 317 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 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 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 E residue 229 ASP Chi-restraints excluded: chain E residue 266 SER 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 374 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 564 LEU Chi-restraints excluded: chain E residue 602 ASP 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 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 687 MET Chi-restraints excluded: chain F residue 711 VAL Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 343 SER Chi-restraints excluded: chain G residue 426 SER Chi-restraints excluded: chain G residue 515 SER Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 581 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 209 optimal weight: 0.9980 chunk 336 optimal weight: 10.0000 chunk 327 optimal weight: 0.8980 chunk 337 optimal weight: 10.0000 chunk 236 optimal weight: 0.9990 chunk 219 optimal weight: 0.1980 chunk 179 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 255 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 655 GLN ** 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 = 0.4096 r_free = 0.4096 target = 0.178191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.127755 restraints weight = 31370.641| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 1.82 r_work: 0.2647 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1396 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= 0.130 Angle : 0.455 11.089 40495 Z= 0.248 Chirality : 0.045 0.194 4550 Planarity : 0.003 0.049 5257 Dihedral : 4.134 15.494 4034 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.49 % Allowed : 17.54 % Favored : 79.97 % 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: -0.98 (0.13), residues: 3766 helix: -1.39 (0.23), residues: 504 sheet: 0.60 (0.14), residues: 1302 loop : -1.33 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 614 TYR 0.010 0.001 TYR A 336 PHE 0.010 0.001 PHE A 656 TRP 0.007 0.001 TRP G 748 HIS 0.003 0.001 HIS A 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (29834) covalent geometry : angle 0.45550 / 0.25 (40495) hydrogen bonds : bond 0.02227 / 1.49 ( 1153) hydrogen bonds : angle 4.42067 / 3.05 ( 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 331 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 249 time to evaluate : 1.098 Fit side-chains REVERT: A 415 ASP cc_start: 0.8452 (t70) cc_final: 0.7913 (t0) REVERT: A 465 GLN cc_start: 0.7569 (mp-120) cc_final: 0.7327 (tt0) REVERT: A 472 ASN cc_start: 0.8582 (t0) cc_final: 0.8143 (t0) REVERT: A 590 LYS cc_start: 0.7543 (mttt) cc_final: 0.6972 (ttpt) REVERT: B 295 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8397 (pm20) REVERT: B 415 ASP cc_start: 0.8332 (t70) cc_final: 0.7994 (t0) REVERT: B 590 LYS cc_start: 0.7561 (mttt) cc_final: 0.6925 (ttpt) REVERT: C 415 ASP cc_start: 0.8443 (t70) cc_final: 0.7979 (t0) REVERT: C 472 ASN cc_start: 0.8386 (t0) cc_final: 0.7752 (t0) REVERT: C 588 GLU cc_start: 0.8467 (tp30) cc_final: 0.7661 (mt-10) REVERT: C 590 LYS cc_start: 0.7609 (mtmt) cc_final: 0.6940 (ttpt) REVERT: C 685 MET cc_start: 0.8384 (ptp) cc_final: 0.7939 (ptp) REVERT: C 686 TYR cc_start: 0.8363 (m-80) cc_final: 0.8145 (m-80) REVERT: D 590 LYS cc_start: 0.7472 (mttt) cc_final: 0.6694 (tttt) REVERT: D 629 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7538 (mp0) REVERT: E 229 ASP cc_start: 0.8816 (OUTLIER) cc_final: 0.8538 (p0) REVERT: E 247 ARG cc_start: 0.8691 (mtm180) cc_final: 0.8424 (mtm180) REVERT: E 415 ASP cc_start: 0.8339 (t70) cc_final: 0.8001 (t0) REVERT: E 588 GLU cc_start: 0.8118 (tp30) cc_final: 0.7860 (tp30) REVERT: E 686 TYR cc_start: 0.8238 (m-80) cc_final: 0.7962 (m-10) REVERT: F 415 ASP cc_start: 0.8275 (t70) cc_final: 0.7740 (t0) REVERT: F 472 ASN cc_start: 0.8383 (t0) cc_final: 0.7964 (t0) REVERT: F 590 LYS cc_start: 0.7605 (mttt) cc_final: 0.6950 (ttpt) REVERT: F 711 VAL cc_start: 0.7452 (OUTLIER) cc_final: 0.7223 (p) REVERT: G 415 ASP cc_start: 0.8456 (t70) cc_final: 0.8062 (t0) REVERT: G 581 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8264 (mt) outliers start: 82 outliers final: 72 residues processed: 318 average time/residue: 0.1761 time to fit residues: 91.5505 Evaluate side-chains 323 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 246 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 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 266 SER 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 C residue 266 SER 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 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 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 E residue 229 ASP Chi-restraints excluded: chain E residue 266 SER 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 374 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 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 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 687 MET Chi-restraints excluded: chain F residue 711 VAL Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 323 SER Chi-restraints excluded: chain G residue 343 SER Chi-restraints excluded: chain G residue 426 SER Chi-restraints excluded: chain G residue 428 SER Chi-restraints excluded: chain G residue 438 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 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: 0.6980 chunk 26 optimal weight: 0.9980 chunk 304 optimal weight: 2.9990 chunk 238 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 202 optimal weight: 10.0000 chunk 251 optimal weight: 0.9980 chunk 298 optimal weight: 0.6980 chunk 229 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4096 r_free = 0.4096 target = 0.178203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.127787 restraints weight = 31335.963| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 1.84 r_work: 0.2634 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2503 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1422 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= 0.134 Angle : 0.456 11.111 40495 Z= 0.248 Chirality : 0.045 0.195 4550 Planarity : 0.003 0.049 5257 Dihedral : 4.132 15.423 4034 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % 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: -0.97 (0.13), residues: 3766 helix: -1.36 (0.23), residues: 504 sheet: 0.59 (0.14), residues: 1302 loop : -1.32 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 614 TYR 0.015 0.001 TYR A 686 PHE 0.009 0.001 PHE F 656 TRP 0.007 0.001 TRP E 748 HIS 0.003 0.001 HIS G 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.13 (29834) covalent geometry : angle 0.45621 / 0.25 (40495) hydrogen bonds : bond 0.02218 / 1.48 ( 1153) hydrogen bonds : angle 4.39016 / 3.03 ( 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 337 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 253 time to evaluate : 1.182 Fit side-chains REVERT: A 415 ASP cc_start: 0.8459 (t70) cc_final: 0.7925 (t0) REVERT: A 465 GLN cc_start: 0.7598 (mp-120) cc_final: 0.7352 (tt0) REVERT: A 472 ASN cc_start: 0.8597 (t0) cc_final: 0.8164 (t0) REVERT: A 590 LYS cc_start: 0.7530 (mttt) cc_final: 0.6953 (ttpt) REVERT: B 295 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8408 (pm20) REVERT: B 415 ASP cc_start: 0.8336 (t70) cc_final: 0.7993 (t0) REVERT: B 590 LYS cc_start: 0.7588 (mttt) cc_final: 0.6958 (ttpt) REVERT: C 415 ASP cc_start: 0.8455 (t70) cc_final: 0.8007 (t0) REVERT: C 472 ASN cc_start: 0.8395 (t0) cc_final: 0.7764 (t0) REVERT: C 588 GLU cc_start: 0.8481 (tp30) cc_final: 0.7684 (mt-10) REVERT: C 590 LYS cc_start: 0.7638 (mtmt) cc_final: 0.6970 (ttpt) REVERT: C 685 MET cc_start: 0.8396 (ptp) cc_final: 0.7962 (ptp) REVERT: C 686 TYR cc_start: 0.8370 (m-80) cc_final: 0.8149 (m-80) REVERT: D 590 LYS cc_start: 0.7497 (mttt) cc_final: 0.6734 (tttt) REVERT: D 629 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7542 (mp0) REVERT: E 229 ASP cc_start: 0.8804 (OUTLIER) cc_final: 0.8559 (p0) REVERT: E 247 ARG cc_start: 0.8705 (mtm180) cc_final: 0.8422 (mtm180) REVERT: E 415 ASP cc_start: 0.8296 (t70) cc_final: 0.7964 (t0) REVERT: E 564 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7772 (mp) REVERT: E 588 GLU cc_start: 0.8137 (tp30) cc_final: 0.7888 (tp30) REVERT: E 686 TYR cc_start: 0.8236 (m-80) cc_final: 0.8030 (m-10) REVERT: F 415 ASP cc_start: 0.8282 (t70) cc_final: 0.7747 (t0) REVERT: F 472 ASN cc_start: 0.8399 (t0) cc_final: 0.7981 (t0) REVERT: F 590 LYS cc_start: 0.7639 (mttt) cc_final: 0.6976 (ttpt) REVERT: F 711 VAL cc_start: 0.7499 (OUTLIER) cc_final: 0.7273 (p) REVERT: G 415 ASP cc_start: 0.8461 (t70) cc_final: 0.8068 (t0) REVERT: G 581 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8230 (mt) outliers start: 84 outliers final: 76 residues processed: 321 average time/residue: 0.1751 time to fit residues: 91.9757 Evaluate side-chains 332 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 250 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 515 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 564 LEU 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 266 SER 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 266 SER 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 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 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 E residue 229 ASP Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain E residue 374 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 564 LEU Chi-restraints excluded: chain E residue 602 ASP 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 343 SER Chi-restraints excluded: chain F residue 374 SER Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 426 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 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 343 SER Chi-restraints excluded: chain G residue 426 SER Chi-restraints excluded: chain G residue 428 SER Chi-restraints excluded: chain G residue 438 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 247 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 363 optimal weight: 0.9990 chunk 366 optimal weight: 10.0000 chunk 333 optimal weight: 0.6980 chunk 323 optimal weight: 9.9990 chunk 268 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 102 optimal weight: 10.0000 chunk 242 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 655 GLN ** 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 = 0.4143 r_free = 0.4143 target = 0.184858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.137322 restraints weight = 32470.428| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.88 r_work: 0.3232 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29834 Z= 0.136 Angle : 0.456 11.094 40495 Z= 0.248 Chirality : 0.045 0.195 4550 Planarity : 0.003 0.049 5257 Dihedral : 4.128 16.121 4034 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.64 % Allowed : 17.51 % Favored : 79.85 % 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: -0.95 (0.13), residues: 3766 helix: -1.31 (0.23), residues: 504 sheet: 0.59 (0.14), residues: 1302 loop : -1.30 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 614 TYR 0.012 0.001 TYR D 686 PHE 0.009 0.001 PHE F 656 TRP 0.007 0.001 TRP E 748 HIS 0.003 0.001 HIS G 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (29834) covalent geometry : angle 0.45630 / 0.25 (40495) hydrogen bonds : bond 0.02217 / 1.48 ( 1153) hydrogen bonds : angle 4.36371 / 3.01 ( 3168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8130.53 seconds wall clock time: 139 minutes 58.98 seconds (8398.98 seconds total)