Starting phenix.real_space_refine on Mon Jul 6 09:30:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u2z_41847/07_2026/8u2z_41847_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u2z_41847/07_2026/8u2z_41847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u2z_41847/07_2026/8u2z_41847.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u2z_41847/07_2026/8u2z_41847.map" model { file = "/net/cci-nas-00/data/ceres_data/8u2z_41847/07_2026/8u2z_41847_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u2z_41847/07_2026/8u2z_41847_trim.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 16 5.49 5 S 92 5.16 5 Na 1 4.78 5 C 11200 2.51 5 N 2652 2.21 5 O 3084 1.98 5 H 16620 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33665 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 8269 Classifications: {'peptide': 510} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 495} Chain breaks: 3 Chain: "D" Number of atoms: 8269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 8269 Classifications: {'peptide': 510} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 495} Chain breaks: 3 Chain: "B" Number of atoms: 8269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 8269 Classifications: {'peptide': 510} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 495} Chain breaks: 3 Chain: "C" Number of atoms: 8269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 8269 Classifications: {'peptide': 510} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 495} Chain breaks: 3 Chain: "A" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'CLR': 1, 'PCW': 1, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 1 Chain: "D" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'CLR': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 183 Unusual residues: {'CLR': 1, 'PCW': 2, 'PIO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'CLR': 1, 'PCW': 1, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 18 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 18 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 21 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 15 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 5.10, per 1000 atoms: 0.15 Number of scatterers: 33665 At special positions: 0 Unit cell: (122.745, 122.745, 111.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 92 16.00 P 16 15.00 Na 1 11.00 O 3084 8.00 N 2652 7.00 C 11200 6.00 H 16620 1.00 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: 2.79 Conformation dependent library (CDL) restraints added in 764.9 milliseconds 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3856 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 8 sheets defined 65.7% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 203 through 212 Processing helix chain 'A' and resid 213 through 224 removed outlier: 3.513A pdb=" N GLY A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 261 through 269 removed outlier: 3.851A pdb=" N GLN A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'A' and resid 335 through 343 Processing helix chain 'A' and resid 345 through 354 removed outlier: 3.668A pdb=" N GLN A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 Processing helix chain 'A' and resid 394 through 402 Processing helix chain 'A' and resid 410 through 414 removed outlier: 3.806A pdb=" N LEU A 414 " --> pdb=" O ASP A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 429 removed outlier: 3.653A pdb=" N ASN A 419 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 454 removed outlier: 3.540A pdb=" N TYR A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 500 Processing helix chain 'A' and resid 502 through 509 removed outlier: 4.544A pdb=" N PHE A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 531 Processing helix chain 'A' and resid 536 through 552 Processing helix chain 'A' and resid 553 through 557 removed outlier: 3.803A pdb=" N ARG A 557 " --> pdb=" O TYR A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 563 Processing helix chain 'A' and resid 567 through 573 removed outlier: 3.501A pdb=" N LYS A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 599 Processing helix chain 'A' and resid 629 through 643 removed outlier: 3.534A pdb=" N LYS A 639 " --> pdb=" O LEU A 635 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 642 " --> pdb=" O PHE A 638 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY A 643 " --> pdb=" O LYS A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 692 removed outlier: 4.252A pdb=" N ASN A 687 " --> pdb=" O GLY A 683 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU A 692 " --> pdb=" O LYS A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 710 removed outlier: 3.800A pdb=" N LEU A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 212 Processing helix chain 'D' and resid 213 through 224 removed outlier: 3.513A pdb=" N GLY D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 258 Processing helix chain 'D' and resid 261 through 269 removed outlier: 3.851A pdb=" N GLN D 269 " --> pdb=" O LYS D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 295 Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'D' and resid 335 through 343 Processing helix chain 'D' and resid 345 through 354 removed outlier: 3.667A pdb=" N GLN D 354 " --> pdb=" O ALA D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 366 Processing helix chain 'D' and resid 394 through 402 Processing helix chain 'D' and resid 410 through 414 removed outlier: 3.805A pdb=" N LEU D 414 " --> pdb=" O ASP D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 429 removed outlier: 3.653A pdb=" N ASN D 419 " --> pdb=" O VAL D 415 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 454 removed outlier: 3.540A pdb=" N TYR D 454 " --> pdb=" O ALA D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 500 Processing helix chain 'D' and resid 502 through 509 removed outlier: 4.544A pdb=" N PHE D 507 " --> pdb=" O LEU D 503 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL D 508 " --> pdb=" O LYS D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 531 Processing helix chain 'D' and resid 536 through 552 Processing helix chain 'D' and resid 553 through 557 removed outlier: 3.803A pdb=" N ARG D 557 " --> pdb=" O TYR D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 563 Processing helix chain 'D' and resid 567 through 573 removed outlier: 3.501A pdb=" N LYS D 571 " --> pdb=" O VAL D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 599 Processing helix chain 'D' and resid 629 through 643 removed outlier: 3.534A pdb=" N LYS D 639 " --> pdb=" O LEU D 635 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE D 642 " --> pdb=" O PHE D 638 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY D 643 " --> pdb=" O LYS D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 692 removed outlier: 4.252A pdb=" N ASN D 687 " --> pdb=" O GLY D 683 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU D 692 " --> pdb=" O LYS D 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 700 through 710 removed outlier: 3.800A pdb=" N LEU D 706 " --> pdb=" O ALA D 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 212 Processing helix chain 'B' and resid 213 through 224 removed outlier: 3.513A pdb=" N GLY B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 261 through 269 removed outlier: 3.851A pdb=" N GLN B 269 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 298 through 320 Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 345 through 354 removed outlier: 3.668A pdb=" N GLN B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 410 through 414 removed outlier: 3.806A pdb=" N LEU B 414 " --> pdb=" O ASP B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 429 removed outlier: 3.653A pdb=" N ASN B 419 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 454 removed outlier: 3.539A pdb=" N TYR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 500 Processing helix chain 'B' and resid 502 through 509 removed outlier: 4.543A pdb=" N PHE B 507 " --> pdb=" O LEU B 503 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL B 508 " --> pdb=" O LYS B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 531 Processing helix chain 'B' and resid 536 through 552 Processing helix chain 'B' and resid 553 through 557 removed outlier: 3.803A pdb=" N ARG B 557 " --> pdb=" O TYR B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 563 Processing helix chain 'B' and resid 567 through 573 removed outlier: 3.500A pdb=" N LYS B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 599 Processing helix chain 'B' and resid 629 through 643 removed outlier: 3.535A pdb=" N LYS B 639 " --> pdb=" O LEU B 635 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 642 " --> pdb=" O PHE B 638 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY B 643 " --> pdb=" O LYS B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 692 removed outlier: 4.252A pdb=" N ASN B 687 " --> pdb=" O GLY B 683 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU B 692 " --> pdb=" O LYS B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 710 removed outlier: 3.800A pdb=" N LEU B 706 " --> pdb=" O ALA B 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 212 Processing helix chain 'C' and resid 213 through 224 removed outlier: 3.514A pdb=" N GLY C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 261 through 269 removed outlier: 3.850A pdb=" N GLN C 269 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 298 through 320 Processing helix chain 'C' and resid 335 through 343 Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.667A pdb=" N GLN C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 366 Processing helix chain 'C' and resid 394 through 402 Processing helix chain 'C' and resid 410 through 414 removed outlier: 3.805A pdb=" N LEU C 414 " --> pdb=" O ASP C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 429 removed outlier: 3.653A pdb=" N ASN C 419 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 454 removed outlier: 3.540A pdb=" N TYR C 454 " --> pdb=" O ALA C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 500 Processing helix chain 'C' and resid 502 through 509 removed outlier: 4.544A pdb=" N PHE C 507 " --> pdb=" O LEU C 503 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL C 508 " --> pdb=" O LYS C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 531 Processing helix chain 'C' and resid 536 through 552 Processing helix chain 'C' and resid 553 through 557 removed outlier: 3.803A pdb=" N ARG C 557 " --> pdb=" O TYR C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 563 Processing helix chain 'C' and resid 567 through 573 removed outlier: 3.501A pdb=" N LYS C 571 " --> pdb=" O VAL C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 599 Processing helix chain 'C' and resid 629 through 643 removed outlier: 3.534A pdb=" N LYS C 639 " --> pdb=" O LEU C 635 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE C 642 " --> pdb=" O PHE C 638 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY C 643 " --> pdb=" O LYS C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 692 removed outlier: 4.253A pdb=" N ASN C 687 " --> pdb=" O GLY C 683 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU C 692 " --> pdb=" O LYS C 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 700 through 710 removed outlier: 3.800A pdb=" N LEU C 706 " --> pdb=" O ALA C 702 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 368 through 374 removed outlier: 7.278A pdb=" N LYS A 368 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASP A 383 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TRP A 372 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS A 378 " --> pdb=" O GLU A 746 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 727 through 730 removed outlier: 4.885A pdb=" N GLY A 729 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 368 through 374 removed outlier: 7.278A pdb=" N LYS D 368 " --> pdb=" O ASP D 383 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASP D 383 " --> pdb=" O LYS D 368 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TRP D 372 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS D 378 " --> pdb=" O GLU D 746 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 727 through 730 removed outlier: 4.886A pdb=" N GLY D 729 " --> pdb=" O ASP D 737 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 368 through 374 removed outlier: 7.278A pdb=" N LYS B 368 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASP B 383 " --> pdb=" O LYS B 368 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TRP B 372 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS B 378 " --> pdb=" O GLU B 746 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 727 through 730 removed outlier: 4.885A pdb=" N GLY B 729 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 368 through 374 removed outlier: 7.278A pdb=" N LYS C 368 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASP C 383 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TRP C 372 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS C 378 " --> pdb=" O GLU C 746 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 727 through 730 removed outlier: 4.884A pdb=" N GLY C 729 " --> pdb=" O ASP C 737 " (cutoff:3.500A) 936 hydrogen bonds defined for protein. 2724 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: 5.96 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16588 1.03 - 1.23: 89 1.23 - 1.42: 7303 1.42 - 1.62: 9860 1.62 - 1.82: 196 Bond restraints: 34036 Sorted by residual: bond pdb=" C11 CLR D 801 " pdb=" C9 CLR D 801 " ideal model delta sigma weight residual 1.533 1.711 -0.178 2.00e-02 2.50e+03 7.93e+01 bond pdb=" C11 CLR A 803 " pdb=" C9 CLR A 803 " ideal model delta sigma weight residual 1.533 1.711 -0.178 2.00e-02 2.50e+03 7.90e+01 bond pdb=" C11 CLR C 802 " pdb=" C9 CLR C 802 " ideal model delta sigma weight residual 1.533 1.710 -0.177 2.00e-02 2.50e+03 7.87e+01 bond pdb=" C11 CLR B 804 " pdb=" C9 CLR B 804 " ideal model delta sigma weight residual 1.533 1.710 -0.177 2.00e-02 2.50e+03 7.87e+01 bond pdb=" C11 CLR C 802 " pdb=" C12 CLR C 802 " ideal model delta sigma weight residual 1.531 1.694 -0.163 2.00e-02 2.50e+03 6.60e+01 ... (remaining 34031 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.55: 60710 7.55 - 15.09: 190 15.09 - 22.64: 36 22.64 - 30.19: 68 30.19 - 37.73: 32 Bond angle restraints: 61036 Sorted by residual: angle pdb=" CG LYS D 710 " pdb=" CD LYS D 710 " pdb=" HD2 LYS D 710 " ideal model delta sigma weight residual 109.00 71.27 37.73 3.00e+00 1.11e-01 1.58e+02 angle pdb=" CG LYS C 710 " pdb=" CD LYS C 710 " pdb=" HD2 LYS C 710 " ideal model delta sigma weight residual 109.00 71.27 37.73 3.00e+00 1.11e-01 1.58e+02 angle pdb=" CG LYS A 710 " pdb=" CD LYS A 710 " pdb=" HD2 LYS A 710 " ideal model delta sigma weight residual 109.00 71.30 37.70 3.00e+00 1.11e-01 1.58e+02 angle pdb=" CG LYS B 710 " pdb=" CD LYS B 710 " pdb=" HD2 LYS B 710 " ideal model delta sigma weight residual 109.00 71.33 37.67 3.00e+00 1.11e-01 1.58e+02 angle pdb=" NZ LYS D 710 " pdb=" CE LYS D 710 " pdb=" HE2 LYS D 710 " ideal model delta sigma weight residual 108.00 70.75 37.25 3.00e+00 1.11e-01 1.54e+02 ... (remaining 61031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.84: 15372 27.84 - 55.68: 812 55.68 - 83.52: 72 83.52 - 111.36: 12 111.36 - 139.20: 4 Dihedral angle restraints: 16272 sinusoidal: 8816 harmonic: 7456 Sorted by residual: dihedral pdb=" N PCW B 802 " pdb=" C4 PCW B 802 " pdb=" C5 PCW B 802 " pdb=" O4P PCW B 802 " ideal model delta sinusoidal sigma weight residual 293.34 154.14 139.20 1 3.00e+01 1.11e-03 1.87e+01 dihedral pdb=" N PCW A 802 " pdb=" C4 PCW A 802 " pdb=" C5 PCW A 802 " pdb=" O4P PCW A 802 " ideal model delta sinusoidal sigma weight residual 293.34 154.15 139.19 1 3.00e+01 1.11e-03 1.87e+01 dihedral pdb=" N PCW B 803 " pdb=" C4 PCW B 803 " pdb=" C5 PCW B 803 " pdb=" O4P PCW B 803 " ideal model delta sinusoidal sigma weight residual 293.34 154.16 139.18 1 3.00e+01 1.11e-03 1.87e+01 ... (remaining 16269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.347: 2652 0.347 - 0.693: 4 0.693 - 1.040: 0 1.040 - 1.386: 0 1.386 - 1.733: 8 Chirality restraints: 2664 Sorted by residual: chirality pdb=" CG LEU B 726 " pdb=" CB LEU B 726 " pdb=" CD1 LEU B 726 " pdb=" CD2 LEU B 726 " both_signs ideal model delta sigma weight residual False -2.59 -0.86 -1.73 2.00e-01 2.50e+01 7.51e+01 chirality pdb=" CG LEU D 726 " pdb=" CB LEU D 726 " pdb=" CD1 LEU D 726 " pdb=" CD2 LEU D 726 " both_signs ideal model delta sigma weight residual False -2.59 -0.86 -1.73 2.00e-01 2.50e+01 7.50e+01 chirality pdb=" CG LEU A 726 " pdb=" CB LEU A 726 " pdb=" CD1 LEU A 726 " pdb=" CD2 LEU A 726 " both_signs ideal model delta sigma weight residual False -2.59 -0.86 -1.73 2.00e-01 2.50e+01 7.48e+01 ... (remaining 2661 not shown) Planarity restraints: 4836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN D 700 " -0.136 2.00e-02 2.50e+03 1.45e-01 3.16e+02 pdb=" CD GLN D 700 " 0.011 2.00e-02 2.50e+03 pdb=" OE1 GLN D 700 " 0.128 2.00e-02 2.50e+03 pdb=" NE2 GLN D 700 " 0.003 2.00e-02 2.50e+03 pdb="HE21 GLN D 700 " -0.217 2.00e-02 2.50e+03 pdb="HE22 GLN D 700 " 0.211 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 700 " 0.136 2.00e-02 2.50e+03 1.45e-01 3.16e+02 pdb=" CD GLN B 700 " -0.010 2.00e-02 2.50e+03 pdb=" OE1 GLN B 700 " -0.128 2.00e-02 2.50e+03 pdb=" NE2 GLN B 700 " -0.003 2.00e-02 2.50e+03 pdb="HE21 GLN B 700 " 0.217 2.00e-02 2.50e+03 pdb="HE22 GLN B 700 " -0.211 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 700 " -0.136 2.00e-02 2.50e+03 1.45e-01 3.16e+02 pdb=" CD GLN A 700 " 0.010 2.00e-02 2.50e+03 pdb=" OE1 GLN A 700 " 0.128 2.00e-02 2.50e+03 pdb=" NE2 GLN A 700 " 0.003 2.00e-02 2.50e+03 pdb="HE21 GLN A 700 " -0.217 2.00e-02 2.50e+03 pdb="HE22 GLN A 700 " 0.211 2.00e-02 2.50e+03 ... (remaining 4833 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.10: 679 2.10 - 2.73: 56309 2.73 - 3.35: 96158 3.35 - 3.98: 115438 3.98 - 4.60: 183931 Nonbonded interactions: 452515 Sorted by model distance: nonbonded pdb=" HE3 LYS B 710 " pdb=" HZ3 LYS B 710 " model vdw 1.477 1.816 nonbonded pdb=" HE3 LYS C 710 " pdb=" HZ3 LYS C 710 " model vdw 1.477 1.816 nonbonded pdb=" HE3 LYS A 710 " pdb=" HZ3 LYS A 710 " model vdw 1.477 1.816 nonbonded pdb=" HE3 LYS D 710 " pdb=" HZ3 LYS D 710 " model vdw 1.478 1.816 nonbonded pdb=" HG3 LYS A 710 " pdb=" HD3 LYS A 710 " model vdw 1.478 1.952 ... (remaining 452510 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 201 through 752) selection = (chain 'B' and resid 201 through 752) selection = (chain 'C' and resid 201 through 752) selection = (chain 'D' and resid 201 through 752) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.220 Extract box with map and model: 0.490 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.590 Find NCS groups from input model: 0.580 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 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 : 0.009 0.178 17416 Z= 0.469 Angle : 1.157 19.950 23584 Z= 0.512 Chirality : 0.103 1.733 2664 Planarity : 0.006 0.065 2864 Dihedral : 16.423 139.202 6552 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 1.34 % Allowed : 0.89 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.19), residues: 2008 helix: 1.50 (0.15), residues: 1180 sheet: -1.30 (0.60), residues: 64 loop : -2.16 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 212 TYR 0.021 0.002 TYR C 374 PHE 0.019 0.001 PHE B 304 TRP 0.012 0.001 TRP C 740 HIS 0.024 0.003 HIS B 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00933 / 0.47 (17416) covalent geometry : angle 1.15729 / 0.51 (23584) hydrogen bonds : bond 0.14036 / 9.67 ( 936) hydrogen bonds : angle 5.72842 / 4.03 ( 2724) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 350 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 ARG cc_start: 0.7071 (ttm110) cc_final: 0.6788 (ttp80) REVERT: A 710 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7473 (mtmt) REVERT: D 374 TYR cc_start: 0.5539 (OUTLIER) cc_final: 0.5194 (t80) REVERT: D 710 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7410 (tppt) REVERT: B 374 TYR cc_start: 0.5474 (OUTLIER) cc_final: 0.5247 (t80) REVERT: B 710 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7394 (tppt) REVERT: C 710 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7411 (tppt) outliers start: 24 outliers final: 0 residues processed: 358 average time/residue: 0.2275 time to fit residues: 131.2208 Evaluate side-chains 300 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 294 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 LYS Chi-restraints excluded: chain D residue 374 TYR Chi-restraints excluded: chain D residue 710 LYS Chi-restraints excluded: chain B residue 374 TYR Chi-restraints excluded: chain B residue 710 LYS Chi-restraints excluded: chain C residue 710 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.0470 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.197306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.153873 restraints weight = 62568.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.154315 restraints weight = 39338.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.157436 restraints weight = 25922.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.157443 restraints weight = 18349.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.158268 restraints weight = 17657.750| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17416 Z= 0.166 Angle : 0.729 11.967 23584 Z= 0.352 Chirality : 0.118 1.708 2664 Planarity : 0.005 0.069 2864 Dihedral : 12.634 151.329 2760 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 1.22 % Allowed : 7.74 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.46 (0.20), residues: 2008 helix: 1.75 (0.15), residues: 1196 sheet: -0.77 (0.58), residues: 64 loop : -2.12 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 409 TYR 0.016 0.001 TYR D 653 PHE 0.015 0.001 PHE B 659 TRP 0.008 0.001 TRP D 740 HIS 0.006 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 (17416) covalent geometry : angle 0.72938 / 0.35 (23584) hydrogen bonds : bond 0.05765 / 3.93 ( 936) hydrogen bonds : angle 4.81186 / 3.40 ( 2724) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 319 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 710 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7717 (mtpt) REVERT: D 364 HIS cc_start: 0.7085 (p-80) cc_final: 0.6750 (p90) REVERT: D 374 TYR cc_start: 0.5771 (OUTLIER) cc_final: 0.5490 (t80) REVERT: D 710 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7852 (mtpt) REVERT: B 364 HIS cc_start: 0.7093 (p-80) cc_final: 0.6767 (p90) REVERT: B 710 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7816 (mtpt) REVERT: C 364 HIS cc_start: 0.7078 (p-80) cc_final: 0.6752 (p90) REVERT: C 710 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7836 (mtpt) outliers start: 22 outliers final: 10 residues processed: 328 average time/residue: 0.2200 time to fit residues: 117.6582 Evaluate side-chains 298 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 283 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 710 LYS Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain D residue 374 TYR Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 572 MET Chi-restraints excluded: chain D residue 710 LYS Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 710 LYS Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 710 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 198 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 201 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 301 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.194318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.150581 restraints weight = 62492.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.150358 restraints weight = 45916.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.154223 restraints weight = 31276.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.154136 restraints weight = 20479.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.155251 restraints weight = 19051.253| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17416 Z= 0.143 Angle : 0.650 11.480 23584 Z= 0.314 Chirality : 0.118 1.703 2664 Planarity : 0.004 0.059 2864 Dihedral : 11.898 163.340 2758 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.97 % Favored : 92.83 % Rotamer: Outliers : 1.28 % Allowed : 9.86 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.70 (0.20), residues: 2008 helix: 2.01 (0.15), residues: 1204 sheet: -1.66 (0.57), residues: 84 loop : -2.09 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 409 TYR 0.015 0.001 TYR D 671 PHE 0.011 0.001 PHE B 659 TRP 0.006 0.001 TRP C 740 HIS 0.004 0.001 HIS B 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (17416) covalent geometry : angle 0.65026 / 0.31 (23584) hydrogen bonds : bond 0.05392 / 3.68 ( 936) hydrogen bonds : angle 4.40237 / 3.10 ( 2724) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 326 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 710 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7838 (ttmt) REVERT: D 254 LEU cc_start: 0.7946 (tp) cc_final: 0.7661 (tp) REVERT: D 364 HIS cc_start: 0.6930 (p-80) cc_final: 0.6600 (p90) REVERT: B 364 HIS cc_start: 0.6890 (p-80) cc_final: 0.6563 (p90) REVERT: C 254 LEU cc_start: 0.7992 (tp) cc_final: 0.7702 (tp) REVERT: C 364 HIS cc_start: 0.6919 (p-80) cc_final: 0.6557 (p90) outliers start: 23 outliers final: 17 residues processed: 338 average time/residue: 0.2439 time to fit residues: 134.4853 Evaluate side-chains 314 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 296 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 710 LYS Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 710 LYS Chi-restraints excluded: chain D residue 748 ASN Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 710 LYS Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 710 LYS Chi-restraints excluded: chain C residue 748 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 166 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 71 optimal weight: 0.2980 chunk 0 optimal weight: 5.9990 chunk 173 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 223 ASN C 223 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.192509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.148918 restraints weight = 61608.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.148528 restraints weight = 41347.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.152582 restraints weight = 29090.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.152306 restraints weight = 20213.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.155109 restraints weight = 18308.068| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17416 Z= 0.153 Angle : 0.638 11.593 23584 Z= 0.311 Chirality : 0.119 1.754 2664 Planarity : 0.004 0.055 2864 Dihedral : 11.780 172.127 2756 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.27 % Favored : 92.53 % Rotamer: Outliers : 1.22 % Allowed : 11.92 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.89 (0.20), residues: 2008 helix: 2.21 (0.14), residues: 1200 sheet: -1.75 (0.56), residues: 84 loop : -2.05 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 409 TYR 0.016 0.001 TYR A 671 PHE 0.012 0.001 PHE D 659 TRP 0.006 0.001 TRP C 740 HIS 0.003 0.001 HIS B 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (17416) covalent geometry : angle 0.63823 / 0.31 (23584) hydrogen bonds : bond 0.05130 / 3.50 ( 936) hydrogen bonds : angle 4.24196 / 2.98 ( 2724) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 310 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 628 ASN cc_start: 0.7795 (t0) cc_final: 0.7459 (t0) REVERT: A 710 LYS cc_start: 0.8215 (ttmt) cc_final: 0.7888 (mtpt) REVERT: D 364 HIS cc_start: 0.6995 (p-80) cc_final: 0.6628 (p90) REVERT: D 710 LYS cc_start: 0.8153 (ttmt) cc_final: 0.7907 (mtpt) REVERT: B 364 HIS cc_start: 0.6976 (p-80) cc_final: 0.6601 (p90) REVERT: B 374 TYR cc_start: 0.6042 (t80) cc_final: 0.5798 (t80) REVERT: B 710 LYS cc_start: 0.8129 (ttmt) cc_final: 0.7887 (mtpt) REVERT: C 364 HIS cc_start: 0.6973 (p-80) cc_final: 0.6611 (p90) REVERT: C 710 LYS cc_start: 0.8154 (ttmt) cc_final: 0.7902 (mtpt) outliers start: 22 outliers final: 19 residues processed: 321 average time/residue: 0.2435 time to fit residues: 125.6503 Evaluate side-chains 315 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 296 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 572 MET Chi-restraints excluded: chain D residue 748 ASN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 748 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 180 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 135 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 223 ASN D 223 ASN B 223 ASN C 223 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.184339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.140071 restraints weight = 61825.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.142322 restraints weight = 40867.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.144321 restraints weight = 29915.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.144919 restraints weight = 20352.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.145451 restraints weight = 18315.049| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 17416 Z= 0.229 Angle : 0.697 13.742 23584 Z= 0.341 Chirality : 0.120 1.748 2664 Planarity : 0.004 0.061 2864 Dihedral : 12.187 179.837 2740 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.57 % Favored : 91.24 % Rotamer: Outliers : 1.78 % Allowed : 12.03 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.19), residues: 2008 helix: 1.98 (0.14), residues: 1208 sheet: -1.94 (0.56), residues: 84 loop : -2.21 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 409 TYR 0.019 0.002 TYR D 671 PHE 0.014 0.002 PHE B 640 TRP 0.008 0.001 TRP D 426 HIS 0.005 0.001 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.23 (17416) covalent geometry : angle 0.69711 / 0.34 (23584) hydrogen bonds : bond 0.05858 / 4.00 ( 936) hydrogen bonds : angle 4.31619 / 3.04 ( 2724) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 324 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 628 ASN cc_start: 0.8187 (t0) cc_final: 0.7719 (t0) REVERT: A 710 LYS cc_start: 0.8199 (ttmt) cc_final: 0.7968 (ttmt) REVERT: D 364 HIS cc_start: 0.6941 (p-80) cc_final: 0.6667 (p-80) REVERT: D 601 ASP cc_start: 0.7471 (m-30) cc_final: 0.7057 (m-30) REVERT: B 710 LYS cc_start: 0.8149 (ttmt) cc_final: 0.7610 (tptp) REVERT: C 364 HIS cc_start: 0.6958 (p-80) cc_final: 0.6680 (p-80) REVERT: C 601 ASP cc_start: 0.7449 (m-30) cc_final: 0.7027 (m-30) outliers start: 32 outliers final: 21 residues processed: 336 average time/residue: 0.2696 time to fit residues: 142.5435 Evaluate side-chains 323 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 302 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 707 ASP Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain D residue 748 ASN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 498 GLN Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 748 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 33 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 182 optimal weight: 0.0050 chunk 196 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 chunk 197 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 161 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 223 ASN B 223 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.187780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.144707 restraints weight = 61429.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.145482 restraints weight = 42066.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.148367 restraints weight = 28668.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.149667 restraints weight = 19338.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.150068 restraints weight = 17715.804| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17416 Z= 0.124 Angle : 0.610 10.727 23584 Z= 0.297 Chirality : 0.119 1.761 2664 Planarity : 0.004 0.050 2864 Dihedral : 11.526 179.800 2740 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.23 % Favored : 93.58 % Rotamer: Outliers : 1.28 % Allowed : 13.81 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.06 (0.20), residues: 2008 helix: 2.35 (0.15), residues: 1208 sheet: -1.86 (0.56), residues: 84 loop : -2.02 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 409 TYR 0.014 0.001 TYR D 671 PHE 0.011 0.001 PHE B 439 TRP 0.006 0.001 TRP D 740 HIS 0.003 0.001 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (17416) covalent geometry : angle 0.60986 / 0.30 (23584) hydrogen bonds : bond 0.05059 / 3.45 ( 936) hydrogen bonds : angle 4.12640 / 2.91 ( 2724) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 323 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 PHE cc_start: 0.7803 (t80) cc_final: 0.7500 (t80) REVERT: A 628 ASN cc_start: 0.8100 (t0) cc_final: 0.7634 (t0) REVERT: A 710 LYS cc_start: 0.8167 (ttmt) cc_final: 0.7945 (ttmt) REVERT: D 581 MET cc_start: 0.8107 (mmt) cc_final: 0.7838 (mmt) REVERT: D 601 ASP cc_start: 0.7511 (m-30) cc_final: 0.7101 (m-30) REVERT: D 710 LYS cc_start: 0.8207 (ttmt) cc_final: 0.7963 (ttmt) REVERT: B 601 ASP cc_start: 0.7393 (m-30) cc_final: 0.6916 (m-30) REVERT: C 601 ASP cc_start: 0.7493 (m-30) cc_final: 0.7077 (m-30) REVERT: C 710 LYS cc_start: 0.8183 (ttmt) cc_final: 0.7939 (ttmt) outliers start: 23 outliers final: 20 residues processed: 331 average time/residue: 0.2833 time to fit residues: 144.6359 Evaluate side-chains 332 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 312 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 748 ASN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 498 GLN Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 748 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 50 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 179 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 158 optimal weight: 0.2980 chunk 95 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 191 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.189745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.145423 restraints weight = 62013.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.149054 restraints weight = 39266.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.150364 restraints weight = 28482.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.150993 restraints weight = 18139.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.151322 restraints weight = 16339.430| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17416 Z= 0.133 Angle : 0.604 10.742 23584 Z= 0.293 Chirality : 0.118 1.730 2664 Planarity : 0.004 0.051 2864 Dihedral : 11.293 177.664 2740 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.87 % Favored : 92.93 % Rotamer: Outliers : 1.22 % Allowed : 14.14 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.21 (0.20), residues: 2008 helix: 2.43 (0.15), residues: 1208 sheet: -1.85 (0.56), residues: 84 loop : -1.86 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 409 TYR 0.014 0.001 TYR D 671 PHE 0.009 0.001 PHE B 439 TRP 0.004 0.001 TRP A 426 HIS 0.003 0.001 HIS C 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (17416) covalent geometry : angle 0.60374 / 0.29 (23584) hydrogen bonds : bond 0.04944 / 3.36 ( 936) hydrogen bonds : angle 4.08840 / 2.88 ( 2724) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 317 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 PHE cc_start: 0.7792 (t80) cc_final: 0.7492 (t80) REVERT: A 628 ASN cc_start: 0.8195 (t0) cc_final: 0.7727 (t0) REVERT: A 710 LYS cc_start: 0.8160 (ttmt) cc_final: 0.7912 (ttmt) REVERT: D 581 MET cc_start: 0.8119 (mmt) cc_final: 0.7846 (mmt) REVERT: D 601 ASP cc_start: 0.7568 (m-30) cc_final: 0.7121 (m-30) REVERT: D 710 LYS cc_start: 0.8197 (ttmt) cc_final: 0.7961 (ttmt) REVERT: B 374 TYR cc_start: 0.6397 (t80) cc_final: 0.6050 (t80) REVERT: B 601 ASP cc_start: 0.7469 (m-30) cc_final: 0.7021 (m-30) REVERT: C 496 PHE cc_start: 0.7783 (t80) cc_final: 0.7465 (t80) REVERT: C 581 MET cc_start: 0.8093 (mmt) cc_final: 0.7823 (mmt) REVERT: C 601 ASP cc_start: 0.7515 (m-30) cc_final: 0.7031 (m-30) REVERT: C 710 LYS cc_start: 0.8199 (ttmt) cc_final: 0.7981 (ttmt) outliers start: 22 outliers final: 22 residues processed: 325 average time/residue: 0.2711 time to fit residues: 136.8808 Evaluate side-chains 331 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 309 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 572 MET Chi-restraints excluded: chain D residue 748 ASN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 498 GLN Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 748 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 2.9990 chunk 149 optimal weight: 0.0670 chunk 81 optimal weight: 0.9980 chunk 178 optimal weight: 0.1980 chunk 100 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 182 optimal weight: 0.0050 chunk 172 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 overall best weight: 0.4532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.191042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.145929 restraints weight = 61701.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.150341 restraints weight = 37354.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.151911 restraints weight = 22963.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.153397 restraints weight = 17709.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.154161 restraints weight = 16585.810| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17416 Z= 0.110 Angle : 0.584 10.421 23584 Z= 0.281 Chirality : 0.118 1.743 2664 Planarity : 0.004 0.044 2864 Dihedral : 10.786 176.345 2740 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.37 % Favored : 93.43 % Rotamer: Outliers : 1.11 % Allowed : 14.59 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.48 (0.20), residues: 2008 helix: 2.64 (0.15), residues: 1208 sheet: -1.80 (0.57), residues: 84 loop : -1.74 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 491 TYR 0.012 0.001 TYR B 671 PHE 0.010 0.001 PHE B 439 TRP 0.005 0.001 TRP A 740 HIS 0.003 0.001 HIS B 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (17416) covalent geometry : angle 0.58386 / 0.28 (23584) hydrogen bonds : bond 0.04443 / 3.02 ( 936) hydrogen bonds : angle 3.96615 / 2.80 ( 2724) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 325 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 HIS cc_start: 0.7529 (m170) cc_final: 0.7095 (m170) REVERT: A 628 ASN cc_start: 0.8136 (t0) cc_final: 0.7666 (t0) REVERT: D 581 MET cc_start: 0.8019 (mmt) cc_final: 0.7772 (mmt) REVERT: D 601 ASP cc_start: 0.7541 (m-30) cc_final: 0.7042 (m-30) REVERT: B 601 ASP cc_start: 0.7456 (m-30) cc_final: 0.7010 (m-30) REVERT: C 581 MET cc_start: 0.7992 (mmt) cc_final: 0.7750 (mmt) REVERT: C 601 ASP cc_start: 0.7510 (m-30) cc_final: 0.7026 (m-30) outliers start: 20 outliers final: 20 residues processed: 332 average time/residue: 0.2658 time to fit residues: 137.2650 Evaluate side-chains 328 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 308 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 748 ASN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 748 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 108 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 141 optimal weight: 0.0870 chunk 178 optimal weight: 0.9980 chunk 198 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.184428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.139422 restraints weight = 62076.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.140359 restraints weight = 46397.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.143296 restraints weight = 33409.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.143319 restraints weight = 21835.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.144128 restraints weight = 20397.059| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17416 Z= 0.163 Angle : 0.615 10.976 23584 Z= 0.300 Chirality : 0.118 1.725 2664 Planarity : 0.004 0.048 2864 Dihedral : 11.074 177.559 2740 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.07 % Favored : 92.73 % Rotamer: Outliers : 1.45 % Allowed : 14.53 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.20), residues: 2008 helix: 2.51 (0.15), residues: 1212 sheet: -1.83 (0.57), residues: 84 loop : -1.82 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 409 TYR 0.016 0.001 TYR D 671 PHE 0.011 0.001 PHE A 649 TRP 0.007 0.001 TRP A 426 HIS 0.002 0.001 HIS B 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (17416) covalent geometry : angle 0.61452 / 0.30 (23584) hydrogen bonds : bond 0.04900 / 3.34 ( 936) hydrogen bonds : angle 4.03130 / 2.85 ( 2724) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 310 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 628 ASN cc_start: 0.8299 (t0) cc_final: 0.7838 (t0) REVERT: D 601 ASP cc_start: 0.7662 (m-30) cc_final: 0.7142 (m-30) REVERT: B 601 ASP cc_start: 0.7549 (m-30) cc_final: 0.7050 (m-30) REVERT: C 601 ASP cc_start: 0.7652 (m-30) cc_final: 0.7126 (m-30) outliers start: 26 outliers final: 25 residues processed: 318 average time/residue: 0.2688 time to fit residues: 132.9027 Evaluate side-chains 330 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 305 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 748 ASN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 498 GLN Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 748 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 150 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 178 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 160 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 127 optimal weight: 0.3980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.185299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.141358 restraints weight = 61662.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.140933 restraints weight = 44789.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.143745 restraints weight = 31357.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.145913 restraints weight = 20296.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.145936 restraints weight = 17967.187| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17416 Z= 0.137 Angle : 0.602 10.452 23584 Z= 0.293 Chirality : 0.118 1.725 2664 Planarity : 0.004 0.046 2864 Dihedral : 11.007 177.481 2740 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.77 % Favored : 93.18 % Rotamer: Outliers : 1.50 % Allowed : 14.70 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.39 (0.20), residues: 2008 helix: 2.58 (0.15), residues: 1212 sheet: -1.89 (0.56), residues: 84 loop : -1.81 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 409 TYR 0.015 0.001 TYR D 671 PHE 0.012 0.001 PHE B 439 TRP 0.005 0.001 TRP D 426 HIS 0.002 0.001 HIS C 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (17416) covalent geometry : angle 0.60218 / 0.29 (23584) hydrogen bonds : bond 0.04795 / 3.27 ( 936) hydrogen bonds : angle 3.99118 / 2.83 ( 2724) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 303 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 628 ASN cc_start: 0.8429 (t0) cc_final: 0.7943 (t0) REVERT: A 710 LYS cc_start: 0.8037 (mtpt) cc_final: 0.7810 (ttmt) REVERT: D 581 MET cc_start: 0.8139 (mmt) cc_final: 0.7871 (mmt) REVERT: D 601 ASP cc_start: 0.7717 (m-30) cc_final: 0.7131 (m-30) REVERT: B 601 ASP cc_start: 0.7690 (m-30) cc_final: 0.7138 (m-30) REVERT: C 581 MET cc_start: 0.8127 (mmt) cc_final: 0.7863 (mmt) REVERT: C 601 ASP cc_start: 0.7739 (m-30) cc_final: 0.7188 (m-30) outliers start: 27 outliers final: 25 residues processed: 313 average time/residue: 0.2579 time to fit residues: 126.6378 Evaluate side-chains 324 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 299 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 748 ASN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 498 GLN Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 748 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 177 optimal weight: 1.9990 chunk 180 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 184 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 chunk 178 optimal weight: 0.0970 chunk 119 optimal weight: 3.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.185746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.141138 restraints weight = 62434.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.141783 restraints weight = 46696.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.145014 restraints weight = 32755.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.144936 restraints weight = 21518.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.145788 restraints weight = 20152.496| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17416 Z= 0.119 Angle : 0.590 11.244 23584 Z= 0.285 Chirality : 0.119 1.793 2664 Planarity : 0.004 0.045 2864 Dihedral : 10.777 177.789 2740 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 1.45 % Allowed : 14.87 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.55 (0.20), residues: 2008 helix: 2.65 (0.15), residues: 1220 sheet: -1.90 (0.57), residues: 84 loop : -1.69 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 409 TYR 0.014 0.001 TYR C 671 PHE 0.012 0.001 PHE B 439 TRP 0.019 0.001 TRP A 740 HIS 0.002 0.001 HIS B 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (17416) covalent geometry : angle 0.58975 / 0.29 (23584) hydrogen bonds : bond 0.04531 / 3.09 ( 936) hydrogen bonds : angle 3.93216 / 2.79 ( 2724) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4645.32 seconds wall clock time: 80 minutes 5.19 seconds (4805.19 seconds total)