Starting phenix.real_space_refine on Wed Apr 8 04:49:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bp9_30148/04_2026/7bp9_30148.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bp9_30148/04_2026/7bp9_30148.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 { model { file = "/net/cci-nas-00/data/ceres_data/7bp9_30148/04_2026/7bp9_30148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bp9_30148/04_2026/7bp9_30148.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bp9_30148/04_2026/7bp9_30148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bp9_30148/04_2026/7bp9_30148.map" } 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= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 180 5.16 5 C 22008 2.51 5 N 6246 2.21 5 O 6756 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35214 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5815 Classifications: {'peptide': 740} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 699} Chain breaks: 1 Chain: "B" Number of atoms: 5815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5815 Classifications: {'peptide': 740} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 699} Chain breaks: 1 Chain: "C" Number of atoms: 5815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5815 Classifications: {'peptide': 740} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 699} Chain breaks: 1 Chain: "D" Number of atoms: 5815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5815 Classifications: {'peptide': 740} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 699} Chain breaks: 1 Chain: "E" Number of atoms: 5815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5815 Classifications: {'peptide': 740} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 699} Chain breaks: 1 Chain: "F" Number of atoms: 5815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5815 Classifications: {'peptide': 740} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 699} Chain breaks: 1 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.64, per 1000 atoms: 0.22 Number of scatterers: 35214 At special positions: 0 Unit cell: (167.99, 176.55, 100.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 180 16.00 P 24 15.00 O 6756 8.00 N 6246 7.00 C 22008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 1.6 seconds 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8304 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 30 sheets defined 47.6% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 42 through 49 Processing helix chain 'A' and resid 85 through 92 Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 134 through 139 removed outlier: 3.687A pdb=" N TYR A 138 " --> pdb=" O TYR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 226 removed outlier: 3.655A pdb=" N GLN A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 226 through 232 removed outlier: 4.175A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 231 " --> pdb=" O PRO A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'A' and resid 271 through 277 removed outlier: 3.894A pdb=" N LYS A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 296 Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.827A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 318 through 335 removed outlier: 3.833A pdb=" N ARG A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 324 " --> pdb=" O VAL A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.766A pdb=" N ILE A 353 " --> pdb=" O PRO A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 395 through 402 removed outlier: 3.688A pdb=" N VAL A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 426 removed outlier: 3.944A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 445 removed outlier: 4.060A pdb=" N MET A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.632A pdb=" N GLN A 458 " --> pdb=" O TRP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 removed outlier: 3.584A pdb=" N ILE A 479 " --> pdb=" O TRP A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 499 Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 499 through 506 removed outlier: 3.850A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 removed outlier: 3.536A pdb=" N CYS A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.611A pdb=" N LEU A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 557 No H-bonds generated for 'chain 'A' and resid 555 through 557' Processing helix chain 'A' and resid 558 through 569 Processing helix chain 'A' and resid 580 through 586 Processing helix chain 'A' and resid 598 through 610 removed outlier: 3.693A pdb=" N ASN A 602 " --> pdb=" O ASP A 598 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 649 through 662 removed outlier: 4.354A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.680A pdb=" N LEU A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 711 removed outlier: 3.979A pdb=" N CYS A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 740 Processing helix chain 'A' and resid 748 through 765 removed outlier: 3.503A pdb=" N ILE A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 49 Processing helix chain 'B' and resid 85 through 92 Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'B' and resid 134 through 139 removed outlier: 3.687A pdb=" N TYR B 138 " --> pdb=" O TYR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 226 removed outlier: 3.654A pdb=" N GLN B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 232 removed outlier: 4.175A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS B 231 " --> pdb=" O PRO B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 263 Processing helix chain 'B' and resid 271 through 277 removed outlier: 3.894A pdb=" N LYS B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 296 Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.827A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 318 through 335 removed outlier: 3.833A pdb=" N ARG B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE B 324 " --> pdb=" O VAL B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.765A pdb=" N ILE B 353 " --> pdb=" O PRO B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 395 through 402 removed outlier: 3.687A pdb=" N VAL B 399 " --> pdb=" O ASP B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 426 removed outlier: 3.944A pdb=" N LYS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 445 removed outlier: 4.060A pdb=" N MET B 442 " --> pdb=" O ASP B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 458 removed outlier: 3.633A pdb=" N GLN B 458 " --> pdb=" O TRP B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 removed outlier: 3.583A pdb=" N ILE B 479 " --> pdb=" O TRP B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 499 Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 499 through 506 removed outlier: 3.850A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.536A pdb=" N CYS B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 553 removed outlier: 3.611A pdb=" N LEU B 547 " --> pdb=" O LYS B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 557 No H-bonds generated for 'chain 'B' and resid 555 through 557' Processing helix chain 'B' and resid 558 through 569 Processing helix chain 'B' and resid 580 through 586 Processing helix chain 'B' and resid 598 through 610 removed outlier: 3.694A pdb=" N ASN B 602 " --> pdb=" O ASP B 598 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN B 603 " --> pdb=" O ARG B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 634 Processing helix chain 'B' and resid 649 through 662 removed outlier: 4.354A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 679 removed outlier: 3.680A pdb=" N LEU B 675 " --> pdb=" O ASP B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 711 removed outlier: 3.979A pdb=" N CYS B 691 " --> pdb=" O LEU B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 740 Processing helix chain 'B' and resid 748 through 765 removed outlier: 3.503A pdb=" N ILE B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 49 Processing helix chain 'C' and resid 85 through 92 Processing helix chain 'C' and resid 129 through 134 Processing helix chain 'C' and resid 134 through 139 removed outlier: 3.687A pdb=" N TYR C 138 " --> pdb=" O TYR C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 226 removed outlier: 3.654A pdb=" N GLN C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 232 removed outlier: 4.175A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS C 231 " --> pdb=" O PRO C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 263 Processing helix chain 'C' and resid 271 through 277 removed outlier: 3.894A pdb=" N LYS C 277 " --> pdb=" O GLU C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 296 Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.827A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 318 through 335 removed outlier: 3.832A pdb=" N ARG C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE C 324 " --> pdb=" O VAL C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.765A pdb=" N ILE C 353 " --> pdb=" O PRO C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 395 through 402 removed outlier: 3.688A pdb=" N VAL C 399 " --> pdb=" O ASP C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 426 removed outlier: 3.944A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 445 removed outlier: 4.060A pdb=" N MET C 442 " --> pdb=" O ASP C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 458 removed outlier: 3.633A pdb=" N GLN C 458 " --> pdb=" O TRP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 removed outlier: 3.584A pdb=" N ILE C 479 " --> pdb=" O TRP C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 499 Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 499 through 506 removed outlier: 3.851A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 removed outlier: 3.536A pdb=" N CYS C 535 " --> pdb=" O ILE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 553 removed outlier: 3.611A pdb=" N LEU C 547 " --> pdb=" O LYS C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 557 No H-bonds generated for 'chain 'C' and resid 555 through 557' Processing helix chain 'C' and resid 558 through 569 Processing helix chain 'C' and resid 580 through 586 Processing helix chain 'C' and resid 598 through 610 removed outlier: 3.694A pdb=" N ASN C 602 " --> pdb=" O ASP C 598 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 634 Processing helix chain 'C' and resid 649 through 662 removed outlier: 4.355A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 679 removed outlier: 3.680A pdb=" N LEU C 675 " --> pdb=" O ASP C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 711 removed outlier: 3.980A pdb=" N CYS C 691 " --> pdb=" O LEU C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 740 Processing helix chain 'C' and resid 748 through 765 removed outlier: 3.503A pdb=" N ILE C 752 " --> pdb=" O SER C 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 49 Processing helix chain 'D' and resid 85 through 92 Processing helix chain 'D' and resid 129 through 134 Processing helix chain 'D' and resid 134 through 139 removed outlier: 3.686A pdb=" N TYR D 138 " --> pdb=" O TYR D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 226 removed outlier: 3.655A pdb=" N GLN D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 232 removed outlier: 4.175A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 263 Processing helix chain 'D' and resid 271 through 277 removed outlier: 3.894A pdb=" N LYS D 277 " --> pdb=" O GLU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 296 Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.827A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 318 through 335 removed outlier: 3.832A pdb=" N ARG D 322 " --> pdb=" O GLY D 318 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE D 324 " --> pdb=" O VAL D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.765A pdb=" N ILE D 353 " --> pdb=" O PRO D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 395 through 402 removed outlier: 3.688A pdb=" N VAL D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 426 removed outlier: 3.944A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 445 removed outlier: 4.059A pdb=" N MET D 442 " --> pdb=" O ASP D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 458 removed outlier: 3.633A pdb=" N GLN D 458 " --> pdb=" O TRP D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 479 removed outlier: 3.583A pdb=" N ILE D 479 " --> pdb=" O TRP D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 499 Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 499 through 506 removed outlier: 3.850A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.536A pdb=" N CYS D 535 " --> pdb=" O ILE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 553 removed outlier: 3.611A pdb=" N LEU D 547 " --> pdb=" O LYS D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 557 No H-bonds generated for 'chain 'D' and resid 555 through 557' Processing helix chain 'D' and resid 558 through 569 Processing helix chain 'D' and resid 580 through 586 Processing helix chain 'D' and resid 598 through 610 removed outlier: 3.694A pdb=" N ASN D 602 " --> pdb=" O ASP D 598 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN D 603 " --> pdb=" O ARG D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 634 Processing helix chain 'D' and resid 649 through 662 removed outlier: 4.354A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 679 removed outlier: 3.680A pdb=" N LEU D 675 " --> pdb=" O ASP D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 711 removed outlier: 3.979A pdb=" N CYS D 691 " --> pdb=" O LEU D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 735 through 740 Processing helix chain 'D' and resid 748 through 765 removed outlier: 3.503A pdb=" N ILE D 752 " --> pdb=" O SER D 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 49 Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 129 through 134 Processing helix chain 'E' and resid 134 through 139 removed outlier: 3.686A pdb=" N TYR E 138 " --> pdb=" O TYR E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 226 removed outlier: 3.654A pdb=" N GLN E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 226 through 232 removed outlier: 4.174A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'E' and resid 271 through 277 removed outlier: 3.894A pdb=" N LYS E 277 " --> pdb=" O GLU E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 296 Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.827A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 318 through 335 removed outlier: 3.832A pdb=" N ARG E 322 " --> pdb=" O GLY E 318 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE E 324 " --> pdb=" O VAL E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.766A pdb=" N ILE E 353 " --> pdb=" O PRO E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 395 through 402 removed outlier: 3.688A pdb=" N VAL E 399 " --> pdb=" O ASP E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 426 removed outlier: 3.944A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 445 removed outlier: 4.060A pdb=" N MET E 442 " --> pdb=" O ASP E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 458 removed outlier: 3.633A pdb=" N GLN E 458 " --> pdb=" O TRP E 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 479 removed outlier: 3.583A pdb=" N ILE E 479 " --> pdb=" O TRP E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 482 through 499 Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 506 removed outlier: 3.851A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 removed outlier: 3.536A pdb=" N CYS E 535 " --> pdb=" O ILE E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 553 removed outlier: 3.610A pdb=" N LEU E 547 " --> pdb=" O LYS E 543 " (cutoff:3.500A) Processing helix chain 'E' and resid 555 through 557 No H-bonds generated for 'chain 'E' and resid 555 through 557' Processing helix chain 'E' and resid 558 through 569 Processing helix chain 'E' and resid 580 through 586 Processing helix chain 'E' and resid 598 through 610 removed outlier: 3.693A pdb=" N ASN E 602 " --> pdb=" O ASP E 598 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN E 603 " --> pdb=" O ARG E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 634 Processing helix chain 'E' and resid 649 through 662 removed outlier: 4.354A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 679 removed outlier: 3.679A pdb=" N LEU E 675 " --> pdb=" O ASP E 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 685 through 711 removed outlier: 3.979A pdb=" N CYS E 691 " --> pdb=" O LEU E 687 " (cutoff:3.500A) Processing helix chain 'E' and resid 735 through 740 Processing helix chain 'E' and resid 748 through 765 removed outlier: 3.502A pdb=" N ILE E 752 " --> pdb=" O SER E 748 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 49 Processing helix chain 'F' and resid 85 through 92 Processing helix chain 'F' and resid 129 through 134 Processing helix chain 'F' and resid 134 through 139 removed outlier: 3.687A pdb=" N TYR F 138 " --> pdb=" O TYR F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 226 removed outlier: 3.654A pdb=" N GLN F 215 " --> pdb=" O LYS F 211 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 226 through 232 removed outlier: 4.175A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS F 231 " --> pdb=" O PRO F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 263 Processing helix chain 'F' and resid 271 through 277 removed outlier: 3.894A pdb=" N LYS F 277 " --> pdb=" O GLU F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 296 Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.826A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 316 Processing helix chain 'F' and resid 318 through 335 removed outlier: 3.832A pdb=" N ARG F 322 " --> pdb=" O GLY F 318 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE F 324 " --> pdb=" O VAL F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 353 removed outlier: 3.765A pdb=" N ILE F 353 " --> pdb=" O PRO F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 395 through 402 removed outlier: 3.687A pdb=" N VAL F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 426 removed outlier: 3.945A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 445 removed outlier: 4.060A pdb=" N MET F 442 " --> pdb=" O ASP F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 458 removed outlier: 3.633A pdb=" N GLN F 458 " --> pdb=" O TRP F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 479 removed outlier: 3.584A pdb=" N ILE F 479 " --> pdb=" O TRP F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 499 Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 506 removed outlier: 3.850A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 535 removed outlier: 3.537A pdb=" N CYS F 535 " --> pdb=" O ILE F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 553 removed outlier: 3.611A pdb=" N LEU F 547 " --> pdb=" O LYS F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 555 through 557 No H-bonds generated for 'chain 'F' and resid 555 through 557' Processing helix chain 'F' and resid 558 through 569 Processing helix chain 'F' and resid 580 through 586 Processing helix chain 'F' and resid 598 through 610 removed outlier: 3.694A pdb=" N ASN F 602 " --> pdb=" O ASP F 598 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN F 603 " --> pdb=" O ARG F 599 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 634 Processing helix chain 'F' and resid 649 through 662 removed outlier: 4.354A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 679 removed outlier: 3.680A pdb=" N LEU F 675 " --> pdb=" O ASP F 671 " (cutoff:3.500A) Processing helix chain 'F' and resid 685 through 711 removed outlier: 3.979A pdb=" N CYS F 691 " --> pdb=" O LEU F 687 " (cutoff:3.500A) Processing helix chain 'F' and resid 735 through 740 Processing helix chain 'F' and resid 748 through 765 removed outlier: 3.504A pdb=" N ILE F 752 " --> pdb=" O SER F 748 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 29 removed outlier: 3.524A pdb=" N SER A 40 " --> pdb=" O ARG A 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 114 through 118 removed outlier: 7.027A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.410A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLY A 240 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL A 367 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.831A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL A 514 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N THR A 623 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE A 516 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 25 through 29 removed outlier: 3.524A pdb=" N SER B 40 " --> pdb=" O ARG B 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 114 through 118 removed outlier: 7.027A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 145 through 147 Processing sheet with id=AA9, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.411A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLY B 240 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.831A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL B 514 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N THR B 623 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE B 516 " --> pdb=" O THR B 623 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 25 through 29 removed outlier: 3.525A pdb=" N SER C 40 " --> pdb=" O ARG C 83 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 114 through 118 removed outlier: 7.027A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AB5, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.411A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLY C 240 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL C 367 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.832A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL C 514 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N THR C 623 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE C 516 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 25 through 29 removed outlier: 3.524A pdb=" N SER D 40 " --> pdb=" O ARG D 83 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 114 through 118 removed outlier: 7.027A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 145 through 147 Processing sheet with id=AC1, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.410A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLY D 240 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL D 367 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.831A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL D 514 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N THR D 623 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE D 516 " --> pdb=" O THR D 623 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 25 through 29 removed outlier: 3.525A pdb=" N SER E 40 " --> pdb=" O ARG E 83 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 114 through 118 removed outlier: 7.028A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 145 through 147 Processing sheet with id=AC6, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.410A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLY E 240 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL E 367 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.831A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL E 514 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N THR E 623 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE E 516 " --> pdb=" O THR E 623 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 25 through 29 removed outlier: 3.524A pdb=" N SER F 40 " --> pdb=" O ARG F 83 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 114 through 118 removed outlier: 7.027A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 145 through 147 Processing sheet with id=AD2, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.410A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLY F 240 " --> pdb=" O ARG F 365 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL F 367 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.831A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL F 514 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N THR F 623 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE F 516 " --> pdb=" O THR F 623 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) 1404 hydrogen bonds defined for protein. 4086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.58 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7594 1.33 - 1.45: 7136 1.45 - 1.57: 20736 1.57 - 1.69: 42 1.69 - 1.82: 288 Bond restraints: 35796 Sorted by residual: bond pdb=" CB VAL C 123 " pdb=" CG2 VAL C 123 " ideal model delta sigma weight residual 1.521 1.429 0.092 3.30e-02 9.18e+02 7.69e+00 bond pdb=" CB VAL B 123 " pdb=" CG2 VAL B 123 " ideal model delta sigma weight residual 1.521 1.430 0.091 3.30e-02 9.18e+02 7.62e+00 bond pdb=" CB VAL A 123 " pdb=" CG2 VAL A 123 " ideal model delta sigma weight residual 1.521 1.430 0.091 3.30e-02 9.18e+02 7.59e+00 bond pdb=" CB VAL D 123 " pdb=" CG2 VAL D 123 " ideal model delta sigma weight residual 1.521 1.430 0.091 3.30e-02 9.18e+02 7.56e+00 bond pdb=" CB VAL E 123 " pdb=" CG2 VAL E 123 " ideal model delta sigma weight residual 1.521 1.430 0.091 3.30e-02 9.18e+02 7.55e+00 ... (remaining 35791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 44271 2.04 - 4.08: 3262 4.08 - 6.12: 650 6.12 - 8.15: 147 8.15 - 10.19: 54 Bond angle restraints: 48384 Sorted by residual: angle pdb=" CA VAL C 38 " pdb=" CB VAL C 38 " pdb=" CG2 VAL C 38 " ideal model delta sigma weight residual 110.40 117.14 -6.74 1.70e+00 3.46e-01 1.57e+01 angle pdb=" CA VAL F 38 " pdb=" CB VAL F 38 " pdb=" CG2 VAL F 38 " ideal model delta sigma weight residual 110.40 117.13 -6.73 1.70e+00 3.46e-01 1.57e+01 angle pdb=" CA VAL B 38 " pdb=" CB VAL B 38 " pdb=" CG2 VAL B 38 " ideal model delta sigma weight residual 110.40 117.12 -6.72 1.70e+00 3.46e-01 1.56e+01 angle pdb=" CA VAL A 38 " pdb=" CB VAL A 38 " pdb=" CG2 VAL A 38 " ideal model delta sigma weight residual 110.40 117.12 -6.72 1.70e+00 3.46e-01 1.56e+01 angle pdb=" CA VAL E 38 " pdb=" CB VAL E 38 " pdb=" CG2 VAL E 38 " ideal model delta sigma weight residual 110.40 117.10 -6.70 1.70e+00 3.46e-01 1.55e+01 ... (remaining 48379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.49: 21624 31.49 - 62.98: 516 62.98 - 94.47: 66 94.47 - 125.96: 18 125.96 - 157.45: 12 Dihedral angle restraints: 22236 sinusoidal: 9438 harmonic: 12798 Sorted by residual: dihedral pdb=" C5' ADP A 902 " pdb=" O5' ADP A 902 " pdb=" PA ADP A 902 " pdb=" O2A ADP A 902 " ideal model delta sinusoidal sigma weight residual 300.00 142.55 157.45 1 2.00e+01 2.50e-03 4.62e+01 dihedral pdb=" C5' ADP F 902 " pdb=" O5' ADP F 902 " pdb=" PA ADP F 902 " pdb=" O2A ADP F 902 " ideal model delta sinusoidal sigma weight residual 300.00 142.59 157.41 1 2.00e+01 2.50e-03 4.62e+01 dihedral pdb=" C5' ADP C 902 " pdb=" O5' ADP C 902 " pdb=" PA ADP C 902 " pdb=" O2A ADP C 902 " ideal model delta sinusoidal sigma weight residual 300.00 142.60 157.40 1 2.00e+01 2.50e-03 4.62e+01 ... (remaining 22233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 4956 0.128 - 0.257: 432 0.257 - 0.385: 24 0.385 - 0.513: 0 0.513 - 0.642: 6 Chirality restraints: 5418 Sorted by residual: chirality pdb=" CB VAL F 38 " pdb=" CA VAL F 38 " pdb=" CG1 VAL F 38 " pdb=" CG2 VAL F 38 " both_signs ideal model delta sigma weight residual False -2.63 -1.99 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CB VAL C 38 " pdb=" CA VAL C 38 " pdb=" CG1 VAL C 38 " pdb=" CG2 VAL C 38 " both_signs ideal model delta sigma weight residual False -2.63 -1.99 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CB VAL B 38 " pdb=" CA VAL B 38 " pdb=" CG1 VAL B 38 " pdb=" CG2 VAL B 38 " both_signs ideal model delta sigma weight residual False -2.63 -1.99 -0.64 2.00e-01 2.50e+01 1.03e+01 ... (remaining 5415 not shown) Planarity restraints: 6378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 624 " -0.033 2.00e-02 2.50e+03 6.82e-02 4.65e+01 pdb=" CG ASN C 624 " 0.118 2.00e-02 2.50e+03 pdb=" OD1 ASN C 624 " -0.046 2.00e-02 2.50e+03 pdb=" ND2 ASN C 624 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 624 " -0.033 2.00e-02 2.50e+03 6.81e-02 4.64e+01 pdb=" CG ASN A 624 " 0.118 2.00e-02 2.50e+03 pdb=" OD1 ASN A 624 " -0.046 2.00e-02 2.50e+03 pdb=" ND2 ASN A 624 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 624 " -0.033 2.00e-02 2.50e+03 6.78e-02 4.60e+01 pdb=" CG ASN B 624 " 0.117 2.00e-02 2.50e+03 pdb=" OD1 ASN B 624 " -0.045 2.00e-02 2.50e+03 pdb=" ND2 ASN B 624 " -0.039 2.00e-02 2.50e+03 ... (remaining 6375 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3851 2.75 - 3.29: 35472 3.29 - 3.83: 54990 3.83 - 4.36: 66394 4.36 - 4.90: 113703 Nonbonded interactions: 274410 Sorted by model distance: nonbonded pdb=" O ASP C 74 " pdb=" OD1 ASP C 74 " model vdw 2.215 3.040 nonbonded pdb=" O ASP E 74 " pdb=" OD1 ASP E 74 " model vdw 2.215 3.040 nonbonded pdb=" O ASP A 74 " pdb=" OD1 ASP A 74 " model vdw 2.215 3.040 nonbonded pdb=" O ASP D 74 " pdb=" OD1 ASP D 74 " model vdw 2.216 3.040 nonbonded pdb=" O ASP F 74 " pdb=" OD1 ASP F 74 " model vdw 2.216 3.040 ... (remaining 274405 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 31.510 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 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 0.094 35796 Z= 0.376 Angle : 1.259 10.192 48384 Z= 0.687 Chirality : 0.076 0.642 5418 Planarity : 0.008 0.068 6378 Dihedral : 14.690 157.449 13932 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.03 % Favored : 94.84 % Rotamer: Outliers : 0.47 % Allowed : 5.25 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -3.34 (0.10), residues: 4416 helix: -1.39 (0.10), residues: 1812 sheet: -2.31 (0.19), residues: 546 loop : -2.97 (0.11), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 65 TYR 0.038 0.004 TYR E 138 PHE 0.025 0.003 PHE D 575 TRP 0.008 0.003 TRP F 551 HIS 0.011 0.002 HIS F 317 Details of bonding type rmsd covalent geometry : bond 0.00860 (35796) covalent geometry : angle 1.25873 (48384) hydrogen bonds : bond 0.13894 ( 1404) hydrogen bonds : angle 6.57959 ( 4086) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 525 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 465 ARG cc_start: 0.7417 (mmp80) cc_final: 0.6883 (ttp-170) REVERT: A 740 MET cc_start: 0.5517 (ttp) cc_final: 0.4973 (ttp) REVERT: B 159 ARG cc_start: 0.6722 (mmt180) cc_final: 0.6334 (mmt90) REVERT: B 434 ASP cc_start: 0.5918 (OUTLIER) cc_final: 0.4330 (p0) REVERT: B 464 LEU cc_start: 0.6738 (mt) cc_final: 0.6120 (mt) REVERT: C 312 LYS cc_start: 0.6135 (mtpt) cc_final: 0.5872 (mtmt) REVERT: C 465 ARG cc_start: 0.7333 (mmp80) cc_final: 0.6734 (ttp-170) REVERT: D 159 ARG cc_start: 0.6604 (mmt180) cc_final: 0.6370 (mtt90) REVERT: D 434 ASP cc_start: 0.6368 (OUTLIER) cc_final: 0.4878 (p0) REVERT: D 464 LEU cc_start: 0.6521 (mt) cc_final: 0.6025 (mt) REVERT: D 556 GLU cc_start: 0.7978 (pm20) cc_final: 0.7733 (pm20) REVERT: E 312 LYS cc_start: 0.6458 (mtpt) cc_final: 0.6134 (mtmt) REVERT: F 159 ARG cc_start: 0.7158 (mmt180) cc_final: 0.6424 (ttm-80) REVERT: F 434 ASP cc_start: 0.6328 (OUTLIER) cc_final: 0.4805 (p0) REVERT: F 464 LEU cc_start: 0.6477 (mt) cc_final: 0.5660 (mt) REVERT: F 608 MET cc_start: 0.8589 (ttp) cc_final: 0.8323 (ttp) outliers start: 18 outliers final: 5 residues processed: 537 average time/residue: 0.2820 time to fit residues: 226.9588 Evaluate side-chains 309 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 301 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain F residue 434 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 432 optimal weight: 0.9990 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.7980 chunk 401 optimal weight: 6.9990 chunk 424 optimal weight: 0.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 296 ASN A 382 GLN B 90 ASN B 226 HIS ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 GLN B 764 GLN C 90 ASN C 183 HIS C 296 ASN C 404 HIS ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 764 GLN E 90 ASN E 183 HIS E 296 ASN F 90 ASN F 226 HIS F 764 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.154487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.118678 restraints weight = 60438.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.119915 restraints weight = 114994.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.121435 restraints weight = 64327.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.122111 restraints weight = 42913.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.122721 restraints weight = 38575.152| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35796 Z= 0.133 Angle : 0.682 10.495 48384 Z= 0.326 Chirality : 0.047 0.250 5418 Planarity : 0.005 0.058 6378 Dihedral : 10.484 132.382 4981 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.92 % Allowed : 9.02 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -1.78 (0.12), residues: 4416 helix: -0.14 (0.12), residues: 1860 sheet: -1.84 (0.19), residues: 588 loop : -1.95 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 144 TYR 0.027 0.002 TYR E 203 PHE 0.009 0.001 PHE D 575 TRP 0.008 0.001 TRP F 454 HIS 0.007 0.001 HIS D 317 Details of bonding type rmsd covalent geometry : bond 0.00301 (35796) covalent geometry : angle 0.68219 (48384) hydrogen bonds : bond 0.03779 ( 1404) hydrogen bonds : angle 4.95511 ( 4086) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 320 time to evaluate : 1.336 Fit side-chains REVERT: A 203 TYR cc_start: 0.8928 (m-80) cc_final: 0.8694 (m-80) REVERT: A 315 LYS cc_start: 0.6265 (tptt) cc_final: 0.6028 (tptp) REVERT: A 465 ARG cc_start: 0.7082 (mmp80) cc_final: 0.6678 (ttp-170) REVERT: B 159 ARG cc_start: 0.7045 (mmt180) cc_final: 0.6746 (mmm-85) REVERT: B 219 MET cc_start: 0.7525 (mtp) cc_final: 0.7211 (mtp) REVERT: B 427 MET cc_start: 0.6068 (mmm) cc_final: 0.5815 (mmm) REVERT: B 442 MET cc_start: 0.7241 (mmm) cc_final: 0.6902 (mmm) REVERT: C 183 HIS cc_start: 0.6888 (m90) cc_final: 0.6597 (m-70) REVERT: C 312 LYS cc_start: 0.6650 (mtpt) cc_final: 0.6343 (mtmt) REVERT: C 315 LYS cc_start: 0.6303 (tptt) cc_final: 0.6026 (tptp) REVERT: C 465 ARG cc_start: 0.7098 (mmp80) cc_final: 0.6542 (ttp-170) REVERT: D 84 MET cc_start: 0.6794 (mtp) cc_final: 0.6519 (mmm) REVERT: D 159 ARG cc_start: 0.6960 (mmt180) cc_final: 0.6486 (mtt90) REVERT: D 442 MET cc_start: 0.6922 (mmm) cc_final: 0.6673 (mmp) REVERT: E 183 HIS cc_start: 0.6728 (m90) cc_final: 0.6366 (m-70) REVERT: E 312 LYS cc_start: 0.6604 (mtpt) cc_final: 0.6123 (mtmt) REVERT: E 564 ASP cc_start: 0.7279 (t0) cc_final: 0.7028 (t0) REVERT: F 159 ARG cc_start: 0.7488 (mmt180) cc_final: 0.6792 (tpp-160) outliers start: 35 outliers final: 24 residues processed: 333 average time/residue: 0.2460 time to fit residues: 127.7894 Evaluate side-chains 295 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 271 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 492 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 238 optimal weight: 0.0000 chunk 61 optimal weight: 0.6980 chunk 370 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 204 optimal weight: 3.9990 chunk 289 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 chunk 229 optimal weight: 9.9990 chunk 265 optimal weight: 6.9990 chunk 232 optimal weight: 40.0000 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS B 296 ASN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 GLN ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 ASN E 764 GLN F 382 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.154104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.118543 restraints weight = 59938.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.109906 restraints weight = 85047.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.107055 restraints weight = 69775.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.107728 restraints weight = 64988.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.108085 restraints weight = 54807.675| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35796 Z= 0.124 Angle : 0.625 9.258 48384 Z= 0.292 Chirality : 0.045 0.158 5418 Planarity : 0.005 0.061 6378 Dihedral : 9.474 135.322 4968 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.24 % Allowed : 10.89 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -1.12 (0.12), residues: 4416 helix: 0.49 (0.12), residues: 1836 sheet: -1.49 (0.21), residues: 588 loop : -1.67 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 753 TYR 0.025 0.002 TYR C 203 PHE 0.010 0.001 PHE D 575 TRP 0.007 0.001 TRP C 454 HIS 0.003 0.001 HIS D 317 Details of bonding type rmsd covalent geometry : bond 0.00285 (35796) covalent geometry : angle 0.62492 (48384) hydrogen bonds : bond 0.03392 ( 1404) hydrogen bonds : angle 4.42738 ( 4086) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 298 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.9044 (m-80) cc_final: 0.8711 (m-80) REVERT: A 315 LYS cc_start: 0.6394 (tptt) cc_final: 0.6143 (tptp) REVERT: A 465 ARG cc_start: 0.7142 (mmp80) cc_final: 0.6622 (ttp-170) REVERT: B 159 ARG cc_start: 0.7075 (mmt180) cc_final: 0.6786 (mmm-85) REVERT: B 203 TYR cc_start: 0.9000 (m-10) cc_final: 0.8786 (m-10) REVERT: B 442 MET cc_start: 0.7524 (mmm) cc_final: 0.7256 (mmm) REVERT: C 312 LYS cc_start: 0.6585 (mtpt) cc_final: 0.6278 (mtmt) REVERT: C 315 LYS cc_start: 0.6577 (tptt) cc_final: 0.6340 (tptp) REVERT: C 464 LEU cc_start: 0.7347 (mt) cc_final: 0.6953 (mt) REVERT: C 465 ARG cc_start: 0.7172 (mmp80) cc_final: 0.6667 (ttp-170) REVERT: D 158 MET cc_start: 0.7197 (mpp) cc_final: 0.6956 (mtm) REVERT: D 159 ARG cc_start: 0.7174 (mmt180) cc_final: 0.6273 (mtt90) REVERT: D 427 MET cc_start: 0.6928 (mmm) cc_final: 0.6687 (mmm) REVERT: E 312 LYS cc_start: 0.6373 (mtpt) cc_final: 0.6041 (mtmt) REVERT: E 465 ARG cc_start: 0.7194 (mmp80) cc_final: 0.6918 (mmp80) REVERT: E 564 ASP cc_start: 0.7302 (t0) cc_final: 0.7097 (t0) REVERT: F 159 ARG cc_start: 0.7581 (mmt180) cc_final: 0.6699 (mmm-85) outliers start: 47 outliers final: 28 residues processed: 326 average time/residue: 0.2270 time to fit residues: 119.1635 Evaluate side-chains 302 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 274 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 457 SER Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 457 SER Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 623 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 282 optimal weight: 5.9990 chunk 66 optimal weight: 0.2980 chunk 413 optimal weight: 5.9990 chunk 296 optimal weight: 0.5980 chunk 243 optimal weight: 2.9990 chunk 275 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 392 optimal weight: 8.9990 chunk 316 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 268 optimal weight: 0.1980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 HIS D 317 HIS D 382 GLN E 317 HIS E 624 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.154490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.117010 restraints weight = 59490.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.111229 restraints weight = 72781.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.109037 restraints weight = 49058.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.108471 restraints weight = 57437.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.108729 restraints weight = 57059.435| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 35796 Z= 0.103 Angle : 0.584 9.453 48384 Z= 0.271 Chirality : 0.044 0.149 5418 Planarity : 0.004 0.060 6378 Dihedral : 9.201 145.426 4968 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.82 % Allowed : 11.76 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.71 (0.13), residues: 4416 helix: 0.82 (0.12), residues: 1842 sheet: -1.28 (0.21), residues: 588 loop : -1.44 (0.13), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 453 TYR 0.016 0.001 TYR A 244 PHE 0.008 0.001 PHE F 575 TRP 0.008 0.001 TRP F 454 HIS 0.005 0.000 HIS E 317 Details of bonding type rmsd covalent geometry : bond 0.00236 (35796) covalent geometry : angle 0.58390 (48384) hydrogen bonds : bond 0.02985 ( 1404) hydrogen bonds : angle 4.19042 ( 4086) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 305 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.9048 (m-80) cc_final: 0.8814 (m-80) REVERT: A 315 LYS cc_start: 0.6389 (tptt) cc_final: 0.6131 (tptp) REVERT: A 465 ARG cc_start: 0.7208 (mmp80) cc_final: 0.6773 (ttp-170) REVERT: A 740 MET cc_start: 0.5837 (ttp) cc_final: 0.5585 (mtm) REVERT: B 65 ARG cc_start: 0.6719 (OUTLIER) cc_final: 0.6511 (mmm160) REVERT: B 159 ARG cc_start: 0.7126 (mmt180) cc_final: 0.6820 (mmm-85) REVERT: B 442 MET cc_start: 0.7462 (mmm) cc_final: 0.7078 (mmm) REVERT: B 464 LEU cc_start: 0.7007 (mt) cc_final: 0.6623 (mt) REVERT: C 83 ARG cc_start: 0.7675 (mmp80) cc_final: 0.7461 (mmp80) REVERT: C 315 LYS cc_start: 0.6522 (tptt) cc_final: 0.6226 (tptp) REVERT: C 464 LEU cc_start: 0.7311 (mt) cc_final: 0.6910 (mt) REVERT: C 465 ARG cc_start: 0.7169 (mmp80) cc_final: 0.6824 (ttp-170) REVERT: C 711 ARG cc_start: 0.7641 (mmp80) cc_final: 0.7421 (ptp-170) REVERT: D 93 ARG cc_start: 0.8135 (mmp80) cc_final: 0.7595 (mmm160) REVERT: D 159 ARG cc_start: 0.7271 (mmt180) cc_final: 0.6824 (mtp85) REVERT: E 275 MET cc_start: 0.8979 (tpt) cc_final: 0.8750 (mmt) REVERT: E 312 LYS cc_start: 0.6489 (mtpt) cc_final: 0.6170 (mtmt) REVERT: E 465 ARG cc_start: 0.7084 (mmp80) cc_final: 0.6846 (mmp80) REVERT: F 159 ARG cc_start: 0.7596 (mmt180) cc_final: 0.6670 (mmm-85) outliers start: 69 outliers final: 38 residues processed: 354 average time/residue: 0.2301 time to fit residues: 131.9951 Evaluate side-chains 318 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 279 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 608 MET Chi-restraints excluded: chain F residue 623 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 308 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 263 optimal weight: 50.0000 chunk 148 optimal weight: 20.0000 chunk 347 optimal weight: 9.9990 chunk 169 optimal weight: 8.9990 chunk 406 optimal weight: 0.2980 chunk 16 optimal weight: 9.9990 chunk 276 optimal weight: 8.9990 chunk 210 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 overall best weight: 5.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 317 HIS A 499 HIS B 735 HIS C 24 ASN C 499 HIS ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 HIS D 533 ASN D 735 HIS E 24 ASN E 317 HIS E 499 HIS F 735 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.150536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.114269 restraints weight = 59876.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.106780 restraints weight = 89217.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.105090 restraints weight = 65795.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.104625 restraints weight = 68139.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.105033 restraints weight = 64823.466| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 35796 Z= 0.221 Angle : 0.660 8.287 48384 Z= 0.311 Chirality : 0.047 0.194 5418 Planarity : 0.005 0.065 6378 Dihedral : 9.181 146.153 4968 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.98 % Allowed : 13.05 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.13), residues: 4416 helix: 0.50 (0.12), residues: 1872 sheet: -1.28 (0.21), residues: 582 loop : -1.43 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 362 TYR 0.019 0.002 TYR E 203 PHE 0.015 0.001 PHE F 302 TRP 0.008 0.001 TRP F 551 HIS 0.004 0.001 HIS F 183 Details of bonding type rmsd covalent geometry : bond 0.00530 (35796) covalent geometry : angle 0.65969 (48384) hydrogen bonds : bond 0.03754 ( 1404) hydrogen bonds : angle 4.40602 ( 4086) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 290 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.9187 (m-80) cc_final: 0.8934 (m-80) REVERT: A 315 LYS cc_start: 0.6561 (tptt) cc_final: 0.6271 (tptp) REVERT: A 427 MET cc_start: 0.7573 (mmm) cc_final: 0.7349 (mmm) REVERT: A 464 LEU cc_start: 0.7700 (mt) cc_final: 0.7205 (mt) REVERT: A 465 ARG cc_start: 0.7230 (mmp80) cc_final: 0.6646 (ttp-170) REVERT: A 740 MET cc_start: 0.5804 (ttp) cc_final: 0.5533 (mtm) REVERT: B 159 ARG cc_start: 0.7086 (mmt180) cc_final: 0.6710 (mmm-85) REVERT: C 219 MET cc_start: 0.8067 (mtp) cc_final: 0.7829 (mtp) REVERT: C 315 LYS cc_start: 0.6748 (tptt) cc_final: 0.6465 (tptp) REVERT: C 464 LEU cc_start: 0.7652 (mt) cc_final: 0.7222 (mt) REVERT: C 465 ARG cc_start: 0.7273 (mmp80) cc_final: 0.6913 (ttp-170) REVERT: D 427 MET cc_start: 0.6782 (mmm) cc_final: 0.6543 (mmm) REVERT: E 312 LYS cc_start: 0.6436 (mtpt) cc_final: 0.6122 (mtmt) REVERT: F 46 MET cc_start: 0.4767 (tmm) cc_final: 0.4480 (tpp) REVERT: F 159 ARG cc_start: 0.7678 (mmt180) cc_final: 0.6953 (mmm-85) outliers start: 75 outliers final: 51 residues processed: 340 average time/residue: 0.2272 time to fit residues: 125.9945 Evaluate side-chains 319 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 268 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 608 MET Chi-restraints excluded: chain F residue 623 THR Chi-restraints excluded: chain F residue 762 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 439 optimal weight: 20.0000 chunk 329 optimal weight: 5.9990 chunk 96 optimal weight: 0.4980 chunk 348 optimal weight: 0.9990 chunk 258 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 245 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 83 optimal weight: 0.2980 chunk 55 optimal weight: 0.6980 chunk 435 optimal weight: 7.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 443 ASN C 24 ASN ** D 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN D 735 HIS E 24 ASN E 317 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.153689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.108345 restraints weight = 59460.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.106761 restraints weight = 53271.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.106724 restraints weight = 52512.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.107142 restraints weight = 51340.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.107263 restraints weight = 47631.619| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 35796 Z= 0.098 Angle : 0.582 8.469 48384 Z= 0.270 Chirality : 0.044 0.160 5418 Planarity : 0.004 0.061 6378 Dihedral : 8.957 146.851 4968 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.61 % Allowed : 13.69 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.51 (0.13), residues: 4416 helix: 0.90 (0.13), residues: 1842 sheet: -1.14 (0.22), residues: 588 loop : -1.24 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 453 TYR 0.016 0.001 TYR E 203 PHE 0.011 0.001 PHE D 230 TRP 0.010 0.001 TRP D 454 HIS 0.002 0.000 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00221 (35796) covalent geometry : angle 0.58247 (48384) hydrogen bonds : bond 0.02892 ( 1404) hydrogen bonds : angle 4.10058 ( 4086) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 286 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LYS cc_start: 0.6402 (tptt) cc_final: 0.6129 (tptp) REVERT: A 388 MET cc_start: 0.7772 (mmt) cc_final: 0.7555 (tpp) REVERT: A 427 MET cc_start: 0.7377 (mmm) cc_final: 0.7121 (mmm) REVERT: A 464 LEU cc_start: 0.7497 (mt) cc_final: 0.7005 (mt) REVERT: A 465 ARG cc_start: 0.7104 (mmp80) cc_final: 0.6624 (ttp-170) REVERT: A 740 MET cc_start: 0.5657 (ttp) cc_final: 0.5435 (mtm) REVERT: B 159 ARG cc_start: 0.7088 (mmt180) cc_final: 0.6742 (mmm-85) REVERT: B 464 LEU cc_start: 0.6708 (mt) cc_final: 0.6453 (mt) REVERT: C 315 LYS cc_start: 0.6672 (tptt) cc_final: 0.6356 (tptp) REVERT: C 442 MET cc_start: 0.8233 (mmt) cc_final: 0.8033 (mmt) REVERT: C 711 ARG cc_start: 0.7669 (mmp80) cc_final: 0.7375 (ptp-170) REVERT: E 183 HIS cc_start: 0.7168 (m90) cc_final: 0.6875 (m90) REVERT: E 312 LYS cc_start: 0.6496 (mtpt) cc_final: 0.6244 (mtmt) REVERT: F 159 ARG cc_start: 0.7648 (mmt180) cc_final: 0.6952 (mmm-85) outliers start: 61 outliers final: 39 residues processed: 331 average time/residue: 0.2261 time to fit residues: 123.1696 Evaluate side-chains 310 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 271 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 623 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 397 optimal weight: 9.9990 chunk 129 optimal weight: 3.9990 chunk 381 optimal weight: 2.9990 chunk 350 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 172 optimal weight: 20.0000 chunk 124 optimal weight: 0.3980 chunk 270 optimal weight: 4.9990 chunk 310 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 396 optimal weight: 7.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN B 24 ASN C 24 ASN C 183 HIS D 24 ASN ** D 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 HIS E 24 ASN E 317 HIS F 24 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.151612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.113897 restraints weight = 59959.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.109084 restraints weight = 75414.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.106743 restraints weight = 52652.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.106130 restraints weight = 54536.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.106314 restraints weight = 54044.432| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 35796 Z= 0.165 Angle : 0.614 9.606 48384 Z= 0.286 Chirality : 0.045 0.227 5418 Planarity : 0.004 0.064 6378 Dihedral : 8.904 146.596 4968 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.58 % Allowed : 14.77 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.58 (0.13), residues: 4416 helix: 0.80 (0.12), residues: 1854 sheet: -1.09 (0.22), residues: 582 loop : -1.27 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 753 TYR 0.033 0.001 TYR A 203 PHE 0.010 0.001 PHE A 576 TRP 0.006 0.001 TRP D 454 HIS 0.003 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00400 (35796) covalent geometry : angle 0.61371 (48384) hydrogen bonds : bond 0.03237 ( 1404) hydrogen bonds : angle 4.15066 ( 4086) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 271 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LYS cc_start: 0.6386 (tptt) cc_final: 0.6073 (tptp) REVERT: A 388 MET cc_start: 0.7752 (mmt) cc_final: 0.7543 (tpp) REVERT: A 427 MET cc_start: 0.7388 (mmm) cc_final: 0.7182 (mmm) REVERT: A 464 LEU cc_start: 0.7594 (mt) cc_final: 0.7082 (mt) REVERT: A 465 ARG cc_start: 0.7162 (mmp80) cc_final: 0.6723 (ttp-170) REVERT: A 740 MET cc_start: 0.5704 (ttp) cc_final: 0.5463 (mtm) REVERT: B 159 ARG cc_start: 0.7157 (mmt180) cc_final: 0.6778 (mmm-85) REVERT: B 340 HIS cc_start: 0.5630 (OUTLIER) cc_final: 0.5196 (p-80) REVERT: B 464 LEU cc_start: 0.6841 (mt) cc_final: 0.6594 (mt) REVERT: C 315 LYS cc_start: 0.6635 (tptt) cc_final: 0.6400 (tptp) REVERT: E 312 LYS cc_start: 0.6666 (mtpt) cc_final: 0.6401 (mtmt) REVERT: E 465 ARG cc_start: 0.7224 (mmp80) cc_final: 0.6732 (ptp-170) REVERT: F 159 ARG cc_start: 0.7670 (mmt180) cc_final: 0.6935 (mmm-85) REVERT: F 427 MET cc_start: 0.7074 (mmm) cc_final: 0.6613 (mmm) outliers start: 60 outliers final: 50 residues processed: 311 average time/residue: 0.2180 time to fit residues: 112.6653 Evaluate side-chains 313 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 262 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 608 MET Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 608 MET Chi-restraints excluded: chain F residue 623 THR Chi-restraints excluded: chain F residue 762 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 30 optimal weight: 9.9990 chunk 372 optimal weight: 8.9990 chunk 394 optimal weight: 20.0000 chunk 179 optimal weight: 2.9990 chunk 247 optimal weight: 10.0000 chunk 122 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 384 optimal weight: 50.0000 chunk 134 optimal weight: 10.0000 chunk 333 optimal weight: 0.8980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 ASN B 533 ASN C 183 HIS D 24 ASN ** D 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 HIS E 90 ASN E 317 HIS F 24 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.153987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.122271 restraints weight = 59368.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.124904 restraints weight = 130438.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.125564 restraints weight = 59491.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.126015 restraints weight = 44098.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.126568 restraints weight = 37635.586| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 35796 Z= 0.114 Angle : 0.589 8.869 48384 Z= 0.271 Chirality : 0.044 0.200 5418 Planarity : 0.004 0.062 6378 Dihedral : 8.724 145.335 4968 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.37 % Allowed : 15.08 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.37 (0.13), residues: 4416 helix: 0.90 (0.13), residues: 1854 sheet: -1.02 (0.22), residues: 588 loop : -1.06 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 753 TYR 0.024 0.001 TYR A 203 PHE 0.008 0.001 PHE A 576 TRP 0.007 0.001 TRP F 454 HIS 0.003 0.000 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00268 (35796) covalent geometry : angle 0.58886 (48384) hydrogen bonds : bond 0.02889 ( 1404) hydrogen bonds : angle 4.02988 ( 4086) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 269 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 LYS cc_start: 0.6211 (tptt) cc_final: 0.5960 (tptp) REVERT: A 464 LEU cc_start: 0.7447 (mt) cc_final: 0.6969 (mt) REVERT: A 465 ARG cc_start: 0.7107 (mmp80) cc_final: 0.6707 (ttp-170) REVERT: A 740 MET cc_start: 0.5508 (ttp) cc_final: 0.5300 (mtm) REVERT: B 340 HIS cc_start: 0.5518 (OUTLIER) cc_final: 0.5016 (p-80) REVERT: B 464 LEU cc_start: 0.6648 (mt) cc_final: 0.6397 (mt) REVERT: C 315 LYS cc_start: 0.6500 (tptt) cc_final: 0.6277 (tptp) REVERT: E 312 LYS cc_start: 0.6714 (mtpt) cc_final: 0.6455 (mtmt) REVERT: E 465 ARG cc_start: 0.7002 (mmp80) cc_final: 0.6679 (ptp-170) REVERT: F 159 ARG cc_start: 0.7560 (mmt180) cc_final: 0.7117 (mmm-85) REVERT: F 427 MET cc_start: 0.6725 (mmm) cc_final: 0.6330 (mmm) outliers start: 52 outliers final: 45 residues processed: 309 average time/residue: 0.2136 time to fit residues: 109.3879 Evaluate side-chains 307 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 261 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 608 MET Chi-restraints excluded: chain F residue 623 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 139 optimal weight: 2.9990 chunk 231 optimal weight: 7.9990 chunk 159 optimal weight: 8.9990 chunk 334 optimal weight: 10.0000 chunk 185 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 373 optimal weight: 0.7980 chunk 205 optimal weight: 30.0000 chunk 351 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 212 optimal weight: 8.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 ASN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 ASN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 HIS E 317 HIS F 24 ASN ** F 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 533 ASN F 538 ASN F 735 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.150381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.105516 restraints weight = 59665.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.102737 restraints weight = 56485.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.102938 restraints weight = 55886.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.103171 restraints weight = 55956.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.103347 restraints weight = 50788.011| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 35796 Z= 0.199 Angle : 0.644 8.791 48384 Z= 0.301 Chirality : 0.046 0.223 5418 Planarity : 0.005 0.064 6378 Dihedral : 8.799 145.866 4968 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.61 % Allowed : 15.11 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.56 (0.13), residues: 4416 helix: 0.59 (0.12), residues: 1890 sheet: -0.91 (0.23), residues: 528 loop : -1.10 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 753 TYR 0.028 0.002 TYR A 203 PHE 0.012 0.001 PHE F 302 TRP 0.006 0.001 TRP F 551 HIS 0.003 0.001 HIS F 384 Details of bonding type rmsd covalent geometry : bond 0.00483 (35796) covalent geometry : angle 0.64449 (48384) hydrogen bonds : bond 0.03472 ( 1404) hydrogen bonds : angle 4.22276 ( 4086) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 270 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LYS cc_start: 0.6430 (tptt) cc_final: 0.6170 (tptp) REVERT: A 340 HIS cc_start: 0.6428 (p90) cc_final: 0.6097 (p90) REVERT: A 427 MET cc_start: 0.7534 (mmm) cc_final: 0.7256 (mmm) REVERT: A 464 LEU cc_start: 0.7765 (mt) cc_final: 0.7249 (mt) REVERT: A 465 ARG cc_start: 0.7080 (mmp80) cc_final: 0.6725 (ttp-170) REVERT: A 740 MET cc_start: 0.5724 (ttp) cc_final: 0.5447 (mtm) REVERT: B 147 ARG cc_start: 0.7538 (tmt170) cc_final: 0.7244 (tmt170) REVERT: C 315 LYS cc_start: 0.6658 (tptt) cc_final: 0.6433 (tptp) REVERT: C 340 HIS cc_start: 0.6572 (p90) cc_final: 0.6365 (p90) REVERT: C 427 MET cc_start: 0.8001 (mmm) cc_final: 0.7688 (tpt) REVERT: E 183 HIS cc_start: 0.7112 (m90) cc_final: 0.6880 (m90) REVERT: E 465 ARG cc_start: 0.7033 (mmp80) cc_final: 0.6667 (ptp-170) REVERT: F 159 ARG cc_start: 0.7620 (mmt180) cc_final: 0.6851 (mmm-85) REVERT: F 427 MET cc_start: 0.7185 (mmm) cc_final: 0.6823 (mmm) outliers start: 61 outliers final: 54 residues processed: 313 average time/residue: 0.2341 time to fit residues: 118.5827 Evaluate side-chains 318 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 264 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 608 MET Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 608 MET Chi-restraints excluded: chain F residue 623 THR Chi-restraints excluded: chain F residue 762 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 443 optimal weight: 9.9990 chunk 434 optimal weight: 0.3980 chunk 281 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 277 optimal weight: 0.5980 chunk 47 optimal weight: 0.2980 chunk 363 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 341 optimal weight: 0.9990 chunk 408 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 HIS E 317 HIS F 735 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.153686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.121664 restraints weight = 59175.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.123818 restraints weight = 132801.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.124902 restraints weight = 64140.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.125448 restraints weight = 45098.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.126317 restraints weight = 38197.038| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35796 Z= 0.110 Angle : 0.600 9.835 48384 Z= 0.276 Chirality : 0.044 0.241 5418 Planarity : 0.004 0.063 6378 Dihedral : 8.588 141.560 4968 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.27 % Allowed : 15.64 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.34 (0.13), residues: 4416 helix: 0.75 (0.12), residues: 1908 sheet: -0.83 (0.24), residues: 534 loop : -0.95 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 753 TYR 0.022 0.001 TYR A 203 PHE 0.008 0.001 PHE A 576 TRP 0.008 0.001 TRP D 454 HIS 0.003 0.000 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00260 (35796) covalent geometry : angle 0.60027 (48384) hydrogen bonds : bond 0.02872 ( 1404) hydrogen bonds : angle 4.01557 ( 4086) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 270 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LYS cc_start: 0.6312 (tptt) cc_final: 0.6077 (tptp) REVERT: A 427 MET cc_start: 0.6687 (mmm) cc_final: 0.6465 (mmm) REVERT: A 464 LEU cc_start: 0.7494 (mt) cc_final: 0.7049 (mt) REVERT: A 465 ARG cc_start: 0.7108 (mmp80) cc_final: 0.6780 (ttp-170) REVERT: A 740 MET cc_start: 0.5505 (ttp) cc_final: 0.5285 (mtm) REVERT: B 464 LEU cc_start: 0.6724 (mt) cc_final: 0.6519 (mt) REVERT: C 315 LYS cc_start: 0.6443 (tptt) cc_final: 0.6232 (tptp) REVERT: E 465 ARG cc_start: 0.7168 (mmp80) cc_final: 0.6768 (ptp-170) REVERT: F 427 MET cc_start: 0.6657 (mmm) cc_final: 0.6245 (mmm) REVERT: F 447 VAL cc_start: 0.8914 (t) cc_final: 0.8595 (t) outliers start: 48 outliers final: 42 residues processed: 307 average time/residue: 0.2172 time to fit residues: 110.6809 Evaluate side-chains 301 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 259 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 608 MET Chi-restraints excluded: chain F residue 623 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 208 optimal weight: 10.0000 chunk 435 optimal weight: 8.9990 chunk 411 optimal weight: 0.2980 chunk 199 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 381 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 chunk 346 optimal weight: 0.9980 chunk 409 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 HIS C 460 ASN ** D 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 HIS E 317 HIS F 735 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.152508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.120274 restraints weight = 59353.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.122680 restraints weight = 133498.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.123645 restraints weight = 62983.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.124152 restraints weight = 45450.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.125027 restraints weight = 38200.969| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 35796 Z= 0.151 Angle : 0.611 8.946 48384 Z= 0.283 Chirality : 0.045 0.260 5418 Planarity : 0.004 0.064 6378 Dihedral : 8.552 139.008 4968 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.40 % Allowed : 15.72 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.38 (0.13), residues: 4416 helix: 0.68 (0.12), residues: 1908 sheet: -0.72 (0.23), residues: 540 loop : -0.98 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 753 TYR 0.023 0.001 TYR A 203 PHE 0.010 0.001 PHE A 576 TRP 0.006 0.001 TRP D 454 HIS 0.004 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00366 (35796) covalent geometry : angle 0.61113 (48384) hydrogen bonds : bond 0.03083 ( 1404) hydrogen bonds : angle 4.07240 ( 4086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5119.87 seconds wall clock time: 89 minutes 29.89 seconds (5369.89 seconds total)