Starting phenix.real_space_refine on Sat Jul 4 16:09:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8t1e_40961/07_2026/8t1e_40961.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t1e_40961/07_2026/8t1e_40961.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t1e_40961/07_2026/8t1e_40961.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t1e_40961/07_2026/8t1e_40961.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8t1e_40961/07_2026/8t1e_40961.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8t1e_40961/07_2026/8t1e_40961.cif" model { file = "/net/cci-nas-00/data/ceres_data/8t1e_40961/07_2026/8t1e_40961.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t1e_40961/07_2026/8t1e_40961.cif" } resolution = 2.77 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= 0.001 sd= 0.015 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: 6 Type Number sf(0) Gaussians P 28 5.49 5 S 108 5.16 5 Na 3 4.78 5 C 14712 2.51 5 N 3380 2.21 5 O 3884 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22115 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 5061 Classifications: {'peptide': 629} Link IDs: {'PTRANS': 25, 'TRANS': 603} Chain breaks: 1 Chain: "B" Number of atoms: 5061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 5061 Classifications: {'peptide': 629} Link IDs: {'PTRANS': 25, 'TRANS': 603} Chain breaks: 1 Chain: "D" Number of atoms: 5061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 5061 Classifications: {'peptide': 629} Link IDs: {'PTRANS': 25, 'TRANS': 603} Chain breaks: 1 Chain: "A" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 461 Unusual residues: {' NA': 3, '9ZR': 8, 'YJ0': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 279 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'9ZR:plan-4': 2, '9ZR:plan-1': 1, '9ZR:plan-2': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 458 Unusual residues: {'9ZR': 8, 'YJ0': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 279 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'9ZR:plan-4': 2, '9ZR:plan-1': 1, '9ZR:plan-2': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 458 Unusual residues: {'9ZR': 8, 'YJ0': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 279 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'9ZR:plan-4': 2, '9ZR:plan-1': 1, '9ZR:plan-2': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Restraints were copied for chains: C Time building chain proxies: 7.53, per 1000 atoms: 0.34 Number of scatterers: 22115 At special positions: 0 Unit cell: (159.338, 160.126, 122.264, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 108 16.00 P 28 15.00 Na 3 11.00 O 3884 8.00 N 3380 7.00 C 14712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 639 " - pdb=" SG CYS A 660 " distance=2.00 Simple disulfide: pdb=" SG CYS B 639 " - pdb=" SG CYS B 660 " distance=2.00 Simple disulfide: pdb=" SG CYS C 194 " - pdb=" SG CYS C 194 " distance=0.00 Simple disulfide: pdb=" SG CYS C 250 " - pdb=" SG CYS C 250 " distance=0.00 Simple disulfide: pdb=" SG CYS C 294 " - pdb=" SG CYS C 294 " distance=0.00 Simple disulfide: pdb=" SG CYS C 353 " - pdb=" SG CYS C 353 " distance=0.00 Simple disulfide: pdb=" SG CYS C 427 " - pdb=" SG CYS C 427 " distance=0.00 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 480 " distance=0.00 Simple disulfide: pdb=" SG CYS C 537 " - pdb=" SG CYS C 537 " distance=0.00 Simple disulfide: pdb=" SG CYS C 639 " - pdb=" SG CYS C 660 " distance=2.00 Simple disulfide: pdb=" SG CYS C 639 " - pdb=" SG CYS C 639 " distance=0.00 Simple disulfide: pdb=" SG CYS C 639 " - pdb=" SG CYS C 660 " distance=2.00 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 639 " distance=2.00 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 660 " distance=0.00 Simple disulfide: pdb=" SG CYS C 777 " - pdb=" SG CYS C 777 " distance=0.00 Simple disulfide: pdb=" SG CYS C 639 " - pdb=" SG CYS C 660 " distance=2.00 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: 1.77 Conformation dependent library (CDL) restraints added in 795.6 milliseconds 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4752 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 4 sheets defined 65.0% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 150 through 161 removed outlier: 3.573A pdb=" N LEU A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 176 removed outlier: 3.548A pdb=" N HIS A 176 " --> pdb=" O PHE A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 193 through 201 removed outlier: 3.679A pdb=" N LYS A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 221 removed outlier: 4.162A pdb=" N VAL A 212 " --> pdb=" O ASP A 208 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG A 219 " --> pdb=" O ASP A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 227 Processing helix chain 'A' and resid 240 through 248 Processing helix chain 'A' and resid 250 through 260 removed outlier: 3.564A pdb=" N VAL A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 removed outlier: 3.546A pdb=" N GLN A 274 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 297 through 306 removed outlier: 3.528A pdb=" N THR A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 332 Processing helix chain 'A' and resid 335 through 356 removed outlier: 3.607A pdb=" N PHE A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 365 Processing helix chain 'A' and resid 372 through 381 Processing helix chain 'A' and resid 382 through 391 Processing helix chain 'A' and resid 397 through 401 removed outlier: 3.886A pdb=" N ARG A 400 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N HIS A 401 " --> pdb=" O ASP A 398 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 397 through 401' Processing helix chain 'A' and resid 432 through 440 Processing helix chain 'A' and resid 445 through 450 Processing helix chain 'A' and resid 454 through 466 Processing helix chain 'A' and resid 466 through 491 removed outlier: 3.993A pdb=" N VAL A 476 " --> pdb=" O TYR A 472 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 531 Processing helix chain 'A' and resid 546 through 567 removed outlier: 4.036A pdb=" N LEU A 551 " --> pdb=" O GLY A 547 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 587 removed outlier: 3.555A pdb=" N PHE A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 581 " --> pdb=" O VAL A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 595 removed outlier: 4.048A pdb=" N GLY A 595 " --> pdb=" O PHE A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 613 removed outlier: 3.781A pdb=" N TYR A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN A 607 " --> pdb=" O SER A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 634 removed outlier: 3.574A pdb=" N VAL A 620 " --> pdb=" O ARG A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 678 removed outlier: 3.697A pdb=" N THR A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 707 removed outlier: 3.711A pdb=" N PHE A 695 " --> pdb=" O TYR A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 747 removed outlier: 5.412A pdb=" N LYS A 727 " --> pdb=" O GLY A 723 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLU A 728 " --> pdb=" O GLN A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 756 Processing helix chain 'A' and resid 768 through 770 No H-bonds generated for 'chain 'A' and resid 768 through 770' Processing helix chain 'B' and resid 150 through 161 removed outlier: 3.574A pdb=" N LEU B 154 " --> pdb=" O ASN B 150 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 176 removed outlier: 3.548A pdb=" N HIS B 176 " --> pdb=" O PHE B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 186 Processing helix chain 'B' and resid 193 through 201 removed outlier: 3.679A pdb=" N LYS B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 221 removed outlier: 4.162A pdb=" N VAL B 212 " --> pdb=" O ASP B 208 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG B 219 " --> pdb=" O ASP B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'B' and resid 240 through 248 Processing helix chain 'B' and resid 250 through 260 removed outlier: 3.563A pdb=" N VAL B 258 " --> pdb=" O VAL B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 274 removed outlier: 3.545A pdb=" N GLN B 274 " --> pdb=" O ARG B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 297 through 306 removed outlier: 3.528A pdb=" N THR B 305 " --> pdb=" O VAL B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 332 Processing helix chain 'B' and resid 335 through 356 removed outlier: 3.607A pdb=" N PHE B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET B 345 " --> pdb=" O PHE B 341 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'B' and resid 382 through 391 Processing helix chain 'B' and resid 397 through 401 removed outlier: 3.886A pdb=" N ARG B 400 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N HIS B 401 " --> pdb=" O ASP B 398 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 397 through 401' Processing helix chain 'B' and resid 432 through 440 Processing helix chain 'B' and resid 445 through 450 Processing helix chain 'B' and resid 454 through 466 Processing helix chain 'B' and resid 466 through 491 removed outlier: 3.994A pdb=" N VAL B 476 " --> pdb=" O TYR B 472 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA B 489 " --> pdb=" O PHE B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 531 Processing helix chain 'B' and resid 546 through 567 removed outlier: 4.036A pdb=" N LEU B 551 " --> pdb=" O GLY B 547 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 552 " --> pdb=" O SER B 548 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER B 563 " --> pdb=" O LEU B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 587 removed outlier: 3.555A pdb=" N PHE B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B 581 " --> pdb=" O VAL B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 595 removed outlier: 4.047A pdb=" N GLY B 595 " --> pdb=" O PHE B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 613 removed outlier: 3.781A pdb=" N TYR B 602 " --> pdb=" O LEU B 598 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN B 607 " --> pdb=" O SER B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 634 removed outlier: 3.574A pdb=" N VAL B 620 " --> pdb=" O ARG B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 678 removed outlier: 3.697A pdb=" N THR B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 707 removed outlier: 3.710A pdb=" N PHE B 695 " --> pdb=" O TYR B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 747 removed outlier: 5.413A pdb=" N LYS B 727 " --> pdb=" O GLY B 723 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLU B 728 " --> pdb=" O GLN B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 756 Processing helix chain 'B' and resid 768 through 770 No H-bonds generated for 'chain 'B' and resid 768 through 770' Processing helix chain 'C' and resid 150 through 161 removed outlier: 3.573A pdb=" N LEU C 154 " --> pdb=" O ASN C 150 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 176 removed outlier: 3.549A pdb=" N HIS C 176 " --> pdb=" O PHE C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 193 through 201 removed outlier: 3.679A pdb=" N LYS C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 221 removed outlier: 4.162A pdb=" N VAL C 212 " --> pdb=" O ASP C 208 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG C 219 " --> pdb=" O ASP C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 227 Processing helix chain 'C' and resid 240 through 248 Processing helix chain 'C' and resid 250 through 260 removed outlier: 3.564A pdb=" N VAL C 258 " --> pdb=" O VAL C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 274 removed outlier: 3.545A pdb=" N GLN C 274 " --> pdb=" O ARG C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 295 Processing helix chain 'C' and resid 297 through 306 removed outlier: 3.528A pdb=" N THR C 305 " --> pdb=" O VAL C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 332 Processing helix chain 'C' and resid 335 through 356 removed outlier: 3.607A pdb=" N PHE C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET C 345 " --> pdb=" O PHE C 341 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 365 Processing helix chain 'C' and resid 372 through 381 Processing helix chain 'C' and resid 382 through 391 Processing helix chain 'C' and resid 397 through 401 removed outlier: 3.886A pdb=" N ARG C 400 " --> pdb=" O GLU C 397 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N HIS C 401 " --> pdb=" O ASP C 398 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 397 through 401' Processing helix chain 'C' and resid 432 through 440 Processing helix chain 'C' and resid 445 through 450 Processing helix chain 'C' and resid 454 through 466 Processing helix chain 'C' and resid 466 through 491 removed outlier: 3.994A pdb=" N VAL C 476 " --> pdb=" O TYR C 472 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA C 489 " --> pdb=" O PHE C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 531 Processing helix chain 'C' and resid 546 through 567 removed outlier: 4.036A pdb=" N LEU C 551 " --> pdb=" O GLY C 547 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 552 " --> pdb=" O SER C 548 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER C 563 " --> pdb=" O LEU C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 587 removed outlier: 3.556A pdb=" N PHE C 580 " --> pdb=" O ALA C 576 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 581 " --> pdb=" O VAL C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 595 removed outlier: 4.047A pdb=" N GLY C 595 " --> pdb=" O PHE C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 613 removed outlier: 3.781A pdb=" N TYR C 602 " --> pdb=" O LEU C 598 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN C 607 " --> pdb=" O SER C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 634 removed outlier: 3.573A pdb=" N VAL C 620 " --> pdb=" O ARG C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 678 removed outlier: 3.697A pdb=" N THR C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 707 removed outlier: 3.711A pdb=" N PHE C 695 " --> pdb=" O TYR C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 747 removed outlier: 5.412A pdb=" N LYS C 727 " --> pdb=" O GLY C 723 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLU C 728 " --> pdb=" O GLN C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 756 Processing helix chain 'C' and resid 768 through 770 No H-bonds generated for 'chain 'C' and resid 768 through 770' Processing helix chain 'D' and resid 150 through 161 removed outlier: 3.573A pdb=" N LEU D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE D 155 " --> pdb=" O ARG D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 176 removed outlier: 3.548A pdb=" N HIS D 176 " --> pdb=" O PHE D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'D' and resid 193 through 201 removed outlier: 3.679A pdb=" N LYS D 197 " --> pdb=" O THR D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 221 removed outlier: 4.162A pdb=" N VAL D 212 " --> pdb=" O ASP D 208 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 227 Processing helix chain 'D' and resid 240 through 248 Processing helix chain 'D' and resid 250 through 260 removed outlier: 3.563A pdb=" N VAL D 258 " --> pdb=" O VAL D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 274 removed outlier: 3.546A pdb=" N GLN D 274 " --> pdb=" O ARG D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 295 Processing helix chain 'D' and resid 297 through 306 removed outlier: 3.528A pdb=" N THR D 305 " --> pdb=" O VAL D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 332 Processing helix chain 'D' and resid 335 through 356 removed outlier: 3.606A pdb=" N PHE D 341 " --> pdb=" O GLU D 337 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET D 345 " --> pdb=" O PHE D 341 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 372 through 381 Processing helix chain 'D' and resid 382 through 391 Processing helix chain 'D' and resid 397 through 401 removed outlier: 3.887A pdb=" N ARG D 400 " --> pdb=" O GLU D 397 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N HIS D 401 " --> pdb=" O ASP D 398 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 397 through 401' Processing helix chain 'D' and resid 432 through 440 Processing helix chain 'D' and resid 445 through 450 Processing helix chain 'D' and resid 454 through 466 Processing helix chain 'D' and resid 466 through 491 removed outlier: 3.994A pdb=" N VAL D 476 " --> pdb=" O TYR D 472 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA D 489 " --> pdb=" O PHE D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 531 Processing helix chain 'D' and resid 546 through 567 removed outlier: 4.037A pdb=" N LEU D 551 " --> pdb=" O GLY D 547 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU D 552 " --> pdb=" O SER D 548 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER D 563 " --> pdb=" O LEU D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 587 removed outlier: 3.555A pdb=" N PHE D 580 " --> pdb=" O ALA D 576 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA D 581 " --> pdb=" O VAL D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 595 removed outlier: 4.047A pdb=" N GLY D 595 " --> pdb=" O PHE D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 613 removed outlier: 3.781A pdb=" N TYR D 602 " --> pdb=" O LEU D 598 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN D 607 " --> pdb=" O SER D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 634 removed outlier: 3.574A pdb=" N VAL D 620 " --> pdb=" O ARG D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 678 removed outlier: 3.697A pdb=" N THR D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 691 through 707 removed outlier: 3.711A pdb=" N PHE D 695 " --> pdb=" O TYR D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 747 removed outlier: 5.412A pdb=" N LYS D 727 " --> pdb=" O GLY D 723 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLU D 728 " --> pdb=" O GLN D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 756 Processing helix chain 'D' and resid 768 through 770 No H-bonds generated for 'chain 'D' and resid 768 through 770' Processing sheet with id=AA1, first strand: chain 'A' and resid 405 through 406 removed outlier: 6.786A pdb=" N ASP A 773 " --> pdb=" O VAL A 764 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 405 through 406 removed outlier: 6.786A pdb=" N ASP B 773 " --> pdb=" O VAL B 764 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 405 through 406 removed outlier: 6.786A pdb=" N ASP C 773 " --> pdb=" O VAL C 764 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 405 through 406 removed outlier: 6.786A pdb=" N ASP D 773 " --> pdb=" O VAL D 764 " (cutoff:3.500A) 1068 hydrogen bonds defined for protein. 3072 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: 3.42 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3532 1.32 - 1.45: 5720 1.45 - 1.57: 13080 1.57 - 1.69: 56 1.69 - 1.81: 176 Bond restraints: 22564 Sorted by residual: bond pdb=" O32 9ZR C1204 " pdb=" P29 9ZR C1204 " ideal model delta sigma weight residual 1.661 1.593 0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" O32 9ZR A1202 " pdb=" P29 9ZR A1202 " ideal model delta sigma weight residual 1.661 1.593 0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" O32 9ZR D1205 " pdb=" P29 9ZR D1205 " ideal model delta sigma weight residual 1.661 1.593 0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" O32 9ZR B1204 " pdb=" P29 9ZR B1204 " ideal model delta sigma weight residual 1.661 1.594 0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" O32 9ZR C1207 " pdb=" P29 9ZR C1207 " ideal model delta sigma weight residual 1.661 1.595 0.066 2.00e-02 2.50e+03 1.08e+01 ... (remaining 22559 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.36: 29978 4.36 - 8.71: 362 8.71 - 13.07: 8 13.07 - 17.43: 0 17.43 - 21.78: 8 Bond angle restraints: 30356 Sorted by residual: angle pdb=" C10 9ZR C1201 " pdb=" C9 9ZR C1201 " pdb=" C8 9ZR C1201 " ideal model delta sigma weight residual 125.84 147.62 -21.78 3.00e+00 1.11e-01 5.27e+01 angle pdb=" C10 9ZR B1201 " pdb=" C9 9ZR B1201 " pdb=" C8 9ZR B1201 " ideal model delta sigma weight residual 125.84 147.62 -21.78 3.00e+00 1.11e-01 5.27e+01 angle pdb=" C10 9ZR A1209 " pdb=" C9 9ZR A1209 " pdb=" C8 9ZR A1209 " ideal model delta sigma weight residual 125.84 147.61 -21.77 3.00e+00 1.11e-01 5.26e+01 angle pdb=" C10 9ZR D1202 " pdb=" C9 9ZR D1202 " pdb=" C8 9ZR D1202 " ideal model delta sigma weight residual 125.84 147.59 -21.75 3.00e+00 1.11e-01 5.26e+01 angle pdb=" C49 9ZR D1202 " pdb=" C50 9ZR D1202 " pdb=" C51 9ZR D1202 " ideal model delta sigma weight residual 127.36 146.84 -19.48 3.00e+00 1.11e-01 4.21e+01 ... (remaining 30351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 13783 35.63 - 71.26: 503 71.26 - 106.89: 187 106.89 - 142.52: 108 142.52 - 178.15: 56 Dihedral angle restraints: 14637 sinusoidal: 7261 harmonic: 7376 Sorted by residual: dihedral pdb=" CA THR B 497 " pdb=" C THR B 497 " pdb=" N PRO B 498 " pdb=" CA PRO B 498 " ideal model delta harmonic sigma weight residual -180.00 -128.38 -51.62 0 5.00e+00 4.00e-02 1.07e+02 dihedral pdb=" CA THR C 497 " pdb=" C THR C 497 " pdb=" N PRO C 498 " pdb=" CA PRO C 498 " ideal model delta harmonic sigma weight residual -180.00 -128.41 -51.59 0 5.00e+00 4.00e-02 1.06e+02 dihedral pdb=" CA THR A 497 " pdb=" C THR A 497 " pdb=" N PRO A 498 " pdb=" CA PRO A 498 " ideal model delta harmonic sigma weight residual 180.00 -128.43 -51.57 0 5.00e+00 4.00e-02 1.06e+02 ... (remaining 14634 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.248: 3292 0.248 - 0.496: 20 0.496 - 0.744: 12 0.744 - 0.993: 0 0.993 - 1.241: 4 Chirality restraints: 3328 Sorted by residual: chirality pdb=" C26 9ZR A1209 " pdb=" C25 9ZR A1209 " pdb=" C27 9ZR A1209 " pdb=" O39 9ZR A1209 " both_signs ideal model delta sigma weight residual False 2.08 0.84 1.24 2.00e-01 2.50e+01 3.85e+01 chirality pdb=" C26 9ZR C1201 " pdb=" C25 9ZR C1201 " pdb=" C27 9ZR C1201 " pdb=" O39 9ZR C1201 " both_signs ideal model delta sigma weight residual False 2.08 0.85 1.23 2.00e-01 2.50e+01 3.79e+01 chirality pdb=" C26 9ZR D1202 " pdb=" C25 9ZR D1202 " pdb=" C27 9ZR D1202 " pdb=" O39 9ZR D1202 " both_signs ideal model delta sigma weight residual False 2.08 0.85 1.23 2.00e-01 2.50e+01 3.78e+01 ... (remaining 3325 not shown) Planarity restraints: 3632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 YJ0 D1203 " -0.125 2.00e-02 2.50e+03 1.04e-01 1.36e+02 pdb=" C18 YJ0 D1203 " 0.153 2.00e-02 2.50e+03 pdb=" C19 YJ0 D1203 " 0.066 2.00e-02 2.50e+03 pdb=" C20 YJ0 D1203 " 0.012 2.00e-02 2.50e+03 pdb=" C24 YJ0 D1203 " -0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 YJ0 A1210 " 0.125 2.00e-02 2.50e+03 1.04e-01 1.36e+02 pdb=" C18 YJ0 A1210 " -0.153 2.00e-02 2.50e+03 pdb=" C19 YJ0 A1210 " -0.065 2.00e-02 2.50e+03 pdb=" C20 YJ0 A1210 " -0.012 2.00e-02 2.50e+03 pdb=" C24 YJ0 A1210 " 0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 YJ0 B1202 " 0.125 2.00e-02 2.50e+03 1.04e-01 1.36e+02 pdb=" C18 YJ0 B1202 " -0.153 2.00e-02 2.50e+03 pdb=" C19 YJ0 B1202 " -0.065 2.00e-02 2.50e+03 pdb=" C20 YJ0 B1202 " -0.012 2.00e-02 2.50e+03 pdb=" C24 YJ0 B1202 " 0.105 2.00e-02 2.50e+03 ... (remaining 3629 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 250 2.58 - 3.16: 18825 3.16 - 3.74: 32511 3.74 - 4.32: 48179 4.32 - 4.90: 79710 Nonbonded interactions: 179475 Sorted by model distance: nonbonded pdb=" SG CYS D 639 " pdb=" SG CYS D 660 " model vdw 1.997 3.760 nonbonded pdb=" O ASP B 613 " pdb=" O HOH B1301 " model vdw 2.065 3.040 nonbonded pdb=" O ASP C 613 " pdb=" O HOH C1301 " model vdw 2.065 3.040 nonbonded pdb=" O ASP D 613 " pdb=" O HOH D1301 " model vdw 2.065 3.040 nonbonded pdb=" O ASP A 613 " pdb=" O HOH A1301 " model vdw 2.067 3.040 ... (remaining 179470 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 148 through 1201 or resid 1204 or (resid 1205 and (name C1 \ 3 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or nam \ e C20 or name C21 or name C22 or name C25 or name C26 or name C27 or name C33 or \ name C34 or name C36 or name C37 or name C38 or name C40 or name C42 or name C4 \ 3 or name C44 or name C45 or name C46 or name C47 or name C48 or name C49 or nam \ e C50 or name C51 or name C52 or name C53 or name C54 or name C55 or name C56 or \ name N35 or name O23 or name O24 or name O28 or name O30 or name O31 or name O3 \ 2 or name O39 or name O41 or name P29)) or (resid 1206 and (name C44 or name C45 \ or name C46 or name C47 or name C48 or name C49 or name C50 or name C51 or name \ C52 or name C53 or name C54 or name C55 or name C56)) or resid 1208)) selection = (chain 'B' and (resid 148 through 1201 or (resid 1204 and (name C44 or name C45 \ or name C46 or name C47 or name C48 or name C49 or name C50 or name C51 or name \ C52 or name C53 or name C54 or name C55 or name C56)) or resid 1205 through 1206 \ or resid 1208)) selection = (chain 'C' and (resid 148 through 1201 or (resid 1204 and (name C44 or name C45 \ or name C46 or name C47 or name C48 or name C49 or name C50 or name C51 or name \ C52 or name C53 or name C54 or name C55 or name C56)) or resid 1205 through 1206 \ or resid 1208)) selection = (chain 'D' and (resid 148 through 1201 or (resid 1204 and (name C44 or name C45 \ or name C46 or name C47 or name C48 or name C49 or name C50 or name C51 or name \ C52 or name C53 or name C54 or name C55 or name C56)) or (resid 1205 and (name C \ 13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or na \ me C20 or name C21 or name C22 or name C25 or name C26 or name C27 or name C33 o \ r name C34 or name C36 or name C37 or name C38 or name C40 or name C42 or name C \ 43 or name C44 or name C45 or name C46 or name C47 or name C48 or name C49 or na \ me C50 or name C51 or name C52 or name C53 or name C54 or name C55 or name C56 o \ r name N35 or name O23 or name O24 or name O28 or name O30 or name O31 or name O \ 32 or name O39 or name O41 or name P29)) or (resid 1206 and (name C44 or name C4 \ 5 or name C46 or name C47 or name C48 or name C49 or name C50 or name C51 or nam \ e C52 or name C53 or name C54 or name C55 or name C56)) or resid 1208)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.310 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: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 21.770 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 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 : 0.011 0.124 22567 Z= 0.462 Angle : 1.275 21.782 30372 Z= 0.639 Chirality : 0.083 1.241 3328 Planarity : 0.008 0.104 3632 Dihedral : 26.382 178.148 9856 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.48 % Favored : 87.20 % Rotamer: Outliers : 0.18 % Allowed : 4.14 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 12.00 % Twisted General : 0.17 % 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: -4.98 (0.13), residues: 2500 helix: -2.90 (0.10), residues: 1452 sheet: -3.20 (0.44), residues: 92 loop : -3.81 (0.18), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG C 594 TYR 0.022 0.003 TYR D 602 PHE 0.033 0.003 PHE A 485 TRP 0.026 0.003 TRP C 733 HIS 0.008 0.002 HIS B 787 Details of bonding type rmsd/Z covalent geometry : bond 0.01066 / 0.46 (22564) covalent geometry : angle 1.27446 / 0.64 (30356) SS BOND : bond 0.03430 / 1.59 ( 3) SS BOND : angle 1.50499 / 1.11 ( 16) hydrogen bonds : bond 0.28951 / 19.21 ( 1068) hydrogen bonds : angle 9.77455 / 6.76 ( 3072) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 547 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 HIS cc_start: 0.7292 (m-70) cc_final: 0.7084 (m90) REVERT: A 615 PHE cc_start: 0.7593 (m-80) cc_final: 0.7144 (t80) REVERT: A 713 MET cc_start: 0.8338 (ttt) cc_final: 0.8067 (ttp) REVERT: A 760 GLU cc_start: 0.7727 (pt0) cc_final: 0.7522 (pt0) REVERT: B 615 PHE cc_start: 0.7552 (m-80) cc_final: 0.7157 (t80) REVERT: C 615 PHE cc_start: 0.7578 (m-80) cc_final: 0.7070 (t80) REVERT: C 774 ARG cc_start: 0.7448 (mmm160) cc_final: 0.7144 (mmm160) REVERT: D 615 PHE cc_start: 0.7552 (m-80) cc_final: 0.7152 (t80) outliers start: 4 outliers final: 4 residues processed: 551 average time/residue: 0.5973 time to fit residues: 372.3832 Evaluate side-chains 317 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 313 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain D residue 435 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 247 optimal weight: 0.0670 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 8.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 ASN A 207 ASN A 243 HIS A 326 HIS A 550 GLN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN B 204 ASN B 207 ASN B 252 HIS B 274 GLN B 317 GLN B 326 HIS B 387 GLN ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 ASN ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 ASN C 207 ASN C 252 HIS C 274 GLN C 317 GLN C 326 HIS C 387 GLN ** C 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** C 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN D 207 ASN D 243 HIS D 252 HIS D 274 GLN D 317 GLN D 326 HIS D 387 GLN ** D 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 ASN ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.216479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.167119 restraints weight = 26518.341| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 2.17 r_work: 0.3784 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 22567 Z= 0.261 Angle : 0.910 9.961 30372 Z= 0.445 Chirality : 0.050 0.267 3328 Planarity : 0.007 0.071 3632 Dihedral : 31.785 179.790 5080 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.52 % Favored : 89.48 % Rotamer: Outliers : 4.59 % Allowed : 12.52 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 12.00 % Twisted General : 0.17 % 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: -2.74 (0.15), residues: 2500 helix: -0.78 (0.12), residues: 1468 sheet: -2.40 (0.52), residues: 64 loop : -3.45 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 391 TYR 0.015 0.002 TYR A 657 PHE 0.029 0.003 PHE D 485 TRP 0.025 0.003 TRP C 733 HIS 0.008 0.002 HIS C 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.26 (22564) covalent geometry : angle 0.90866 / 0.44 (30356) SS BOND : bond 0.00612 / 0.28 ( 3) SS BOND : angle 2.38046 / 1.69 ( 16) hydrogen bonds : bond 0.05667 / 3.79 ( 1068) hydrogen bonds : angle 5.10717 / 3.55 ( 3072) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 381 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 LYS cc_start: 0.7613 (ttmt) cc_final: 0.7202 (tttt) REVERT: A 206 ARG cc_start: 0.5954 (mmm160) cc_final: 0.5408 (mmm160) REVERT: A 233 ASP cc_start: 0.6286 (t0) cc_final: 0.5945 (p0) REVERT: A 253 TYR cc_start: 0.7400 (m-10) cc_final: 0.7131 (m-80) REVERT: A 267 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.6744 (mm110) REVERT: A 299 HIS cc_start: 0.7489 (m-70) cc_final: 0.7068 (m90) REVERT: A 472 TYR cc_start: 0.8032 (m-80) cc_final: 0.7808 (m-80) REVERT: A 484 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7939 (mp) REVERT: A 615 PHE cc_start: 0.8293 (m-80) cc_final: 0.7104 (t80) REVERT: A 774 ARG cc_start: 0.7593 (mmm160) cc_final: 0.7225 (mmm160) REVERT: A 785 TRP cc_start: 0.6782 (m-90) cc_final: 0.6432 (m-90) REVERT: B 192 LYS cc_start: 0.7524 (ttmt) cc_final: 0.7121 (tttt) REVERT: B 206 ARG cc_start: 0.5838 (mmm160) cc_final: 0.5416 (mmm160) REVERT: B 233 ASP cc_start: 0.6301 (t0) cc_final: 0.6031 (p0) REVERT: B 435 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8099 (mp0) REVERT: B 484 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.8041 (mp) REVERT: B 615 PHE cc_start: 0.8294 (m-80) cc_final: 0.7071 (t80) REVERT: C 192 LYS cc_start: 0.7533 (ttmt) cc_final: 0.7121 (tttt) REVERT: C 206 ARG cc_start: 0.5862 (mmm160) cc_final: 0.5435 (mmm160) REVERT: C 233 ASP cc_start: 0.6335 (t0) cc_final: 0.6126 (p0) REVERT: C 435 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8107 (mp0) REVERT: C 484 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.8026 (mp) REVERT: C 613 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.8208 (m-30) REVERT: C 615 PHE cc_start: 0.8292 (m-80) cc_final: 0.7081 (t80) REVERT: D 192 LYS cc_start: 0.7525 (ttmt) cc_final: 0.7119 (tttt) REVERT: D 206 ARG cc_start: 0.5854 (mmm160) cc_final: 0.5417 (mmm160) REVERT: D 233 ASP cc_start: 0.6310 (t0) cc_final: 0.6042 (p0) REVERT: D 236 TYR cc_start: 0.5545 (m-80) cc_final: 0.5038 (m-80) REVERT: D 253 TYR cc_start: 0.7556 (m-80) cc_final: 0.7204 (m-80) REVERT: D 435 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8091 (mp0) REVERT: D 484 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.8034 (mp) REVERT: D 615 PHE cc_start: 0.8296 (m-80) cc_final: 0.7067 (t80) outliers start: 102 outliers final: 32 residues processed: 438 average time/residue: 0.5977 time to fit residues: 296.8467 Evaluate side-chains 343 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 302 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 727 LYS Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 613 ASP Chi-restraints excluded: chain C residue 672 ASP Chi-restraints excluded: chain C residue 727 LYS Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 440 ASN Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 660 CYS Chi-restraints excluded: chain D residue 672 ASP Chi-restraints excluded: chain D residue 727 LYS Chi-restraints excluded: chain D residue 764 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 223 optimal weight: 2.9990 chunk 189 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 160 optimal weight: 10.0000 chunk 63 optimal weight: 0.0970 chunk 22 optimal weight: 1.9990 chunk 193 optimal weight: 8.9990 chunk 222 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 44 optimal weight: 0.2980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 HIS A 302 ASN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 HIS B 302 ASN B 550 GLN ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 HIS C 302 ASN C 338 ASN C 550 GLN ** C 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 HIS D 243 HIS D 302 ASN D 550 GLN ** D 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.220341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.171862 restraints weight = 26766.395| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 2.22 r_work: 0.3837 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22567 Z= 0.146 Angle : 0.731 12.754 30372 Z= 0.361 Chirality : 0.042 0.176 3328 Planarity : 0.006 0.062 3632 Dihedral : 29.209 171.517 5077 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 3.60 % Allowed : 15.72 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 12.00 % 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: -1.49 (0.17), residues: 2500 helix: 0.27 (0.13), residues: 1480 sheet: -1.22 (0.61), residues: 64 loop : -3.09 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 400 TYR 0.016 0.001 TYR A 303 PHE 0.016 0.001 PHE A 341 TRP 0.017 0.002 TRP B 733 HIS 0.008 0.001 HIS D 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (22564) covalent geometry : angle 0.73002 / 0.36 (30356) SS BOND : bond 0.02676 / 1.40 ( 3) SS BOND : angle 1.44617 / 1.05 ( 16) hydrogen bonds : bond 0.04642 / 3.11 ( 1068) hydrogen bonds : angle 4.61160 / 3.23 ( 3072) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 372 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: A 192 LYS cc_start: 0.7586 (ttmt) cc_final: 0.7194 (tttt) REVERT: A 233 ASP cc_start: 0.6016 (t0) cc_final: 0.5807 (p0) REVERT: A 253 TYR cc_start: 0.7456 (m-10) cc_final: 0.7062 (m-10) REVERT: A 299 HIS cc_start: 0.7283 (m-70) cc_final: 0.6864 (m-70) REVERT: A 340 LYS cc_start: 0.7792 (tppp) cc_final: 0.7588 (tppt) REVERT: A 435 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7936 (mm-30) REVERT: A 457 GLU cc_start: 0.7717 (mp0) cc_final: 0.7445 (mt-10) REVERT: A 484 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7856 (mp) REVERT: A 613 ASP cc_start: 0.8604 (m-30) cc_final: 0.8122 (m-30) REVERT: A 615 PHE cc_start: 0.8286 (m-80) cc_final: 0.7109 (t80) REVERT: A 774 ARG cc_start: 0.7487 (mmm160) cc_final: 0.7278 (mmm160) REVERT: A 783 VAL cc_start: 0.8520 (t) cc_final: 0.8185 (p) REVERT: B 192 LYS cc_start: 0.7497 (ttmt) cc_final: 0.7106 (tttt) REVERT: B 206 ARG cc_start: 0.5872 (mmm160) cc_final: 0.5341 (mmm160) REVERT: B 233 ASP cc_start: 0.6201 (t0) cc_final: 0.5861 (p0) REVERT: B 253 TYR cc_start: 0.7448 (m-80) cc_final: 0.7091 (m-80) REVERT: B 457 GLU cc_start: 0.7725 (mp0) cc_final: 0.7507 (mt-10) REVERT: B 484 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7961 (mt) REVERT: B 613 ASP cc_start: 0.8612 (m-30) cc_final: 0.8019 (m-30) REVERT: B 615 PHE cc_start: 0.8283 (m-80) cc_final: 0.7076 (t80) REVERT: B 774 ARG cc_start: 0.7461 (mmm160) cc_final: 0.7252 (mmm160) REVERT: C 192 LYS cc_start: 0.7527 (ttmt) cc_final: 0.7142 (tttt) REVERT: C 206 ARG cc_start: 0.5876 (mmm160) cc_final: 0.5342 (mmm160) REVERT: C 233 ASP cc_start: 0.6225 (t0) cc_final: 0.5873 (p0) REVERT: C 253 TYR cc_start: 0.7455 (m-80) cc_final: 0.7103 (m-80) REVERT: C 457 GLU cc_start: 0.7732 (mp0) cc_final: 0.7517 (mt-10) REVERT: C 484 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7967 (mt) REVERT: C 615 PHE cc_start: 0.8298 (m-80) cc_final: 0.7100 (t80) REVERT: C 783 VAL cc_start: 0.8364 (t) cc_final: 0.8145 (p) REVERT: D 192 LYS cc_start: 0.7522 (ttmt) cc_final: 0.7143 (tttt) REVERT: D 206 ARG cc_start: 0.5877 (mmm160) cc_final: 0.5450 (mmm160) REVERT: D 233 ASP cc_start: 0.6224 (t0) cc_final: 0.5873 (p0) REVERT: D 253 TYR cc_start: 0.7520 (m-10) cc_final: 0.7213 (m-80) REVERT: D 340 LYS cc_start: 0.7873 (tppp) cc_final: 0.7658 (tppt) REVERT: D 457 GLU cc_start: 0.7732 (mp0) cc_final: 0.7522 (mt-10) REVERT: D 484 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7979 (mt) REVERT: D 613 ASP cc_start: 0.8621 (m-30) cc_final: 0.8102 (m-30) REVERT: D 615 PHE cc_start: 0.8288 (m-80) cc_final: 0.7080 (t80) REVERT: D 774 ARG cc_start: 0.7437 (mmm160) cc_final: 0.7227 (mmm160) outliers start: 80 outliers final: 24 residues processed: 426 average time/residue: 0.5475 time to fit residues: 266.8137 Evaluate side-chains 334 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 305 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 579 VAL Chi-restraints excluded: chain C residue 696 ILE Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 440 ASN Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 764 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 131 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 122 optimal weight: 0.3980 chunk 52 optimal weight: 8.9990 chunk 80 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 209 optimal weight: 0.7980 chunk 39 optimal weight: 0.4980 chunk 130 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 307 ASN A 338 ASN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 ASN B 474 ASN ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 307 ASN ** C 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 ASN ** D 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.219799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.171107 restraints weight = 26860.471| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.20 r_work: 0.3841 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22567 Z= 0.136 Angle : 0.686 8.033 30372 Z= 0.340 Chirality : 0.041 0.171 3328 Planarity : 0.005 0.063 3632 Dihedral : 27.257 172.853 5068 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 3.78 % Allowed : 16.71 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.00 % 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: -0.94 (0.17), residues: 2500 helix: 0.73 (0.13), residues: 1468 sheet: -1.06 (0.64), residues: 72 loop : -2.84 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 400 TYR 0.020 0.001 TYR A 303 PHE 0.023 0.001 PHE C 341 TRP 0.019 0.002 TRP C 785 HIS 0.009 0.001 HIS A 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (22564) covalent geometry : angle 0.68624 / 0.34 (30356) SS BOND : bond 0.01126 / 0.48 ( 3) SS BOND : angle 0.69047 / 0.39 ( 16) hydrogen bonds : bond 0.04252 / 2.86 ( 1068) hydrogen bonds : angle 4.39101 / 3.06 ( 3072) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 350 time to evaluate : 0.756 Fit side-chains revert: symmetry clash REVERT: A 192 LYS cc_start: 0.7573 (ttmt) cc_final: 0.7133 (tttt) REVERT: A 225 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6279 (pt0) REVERT: A 233 ASP cc_start: 0.6131 (t0) cc_final: 0.5783 (p0) REVERT: A 253 TYR cc_start: 0.7453 (m-10) cc_final: 0.7128 (m-10) REVERT: A 299 HIS cc_start: 0.7395 (m-70) cc_final: 0.6984 (m-70) REVERT: A 572 GLU cc_start: 0.6022 (tt0) cc_final: 0.5728 (mt-10) REVERT: A 613 ASP cc_start: 0.8591 (m-30) cc_final: 0.8090 (m-30) REVERT: A 615 PHE cc_start: 0.8289 (m-80) cc_final: 0.7111 (t80) REVERT: A 774 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.7156 (mmm160) REVERT: A 781 ASP cc_start: 0.7921 (t0) cc_final: 0.7515 (m-30) REVERT: A 783 VAL cc_start: 0.8496 (t) cc_final: 0.8182 (p) REVERT: B 187 GLU cc_start: 0.6305 (OUTLIER) cc_final: 0.5912 (tm-30) REVERT: B 192 LYS cc_start: 0.7460 (ttmt) cc_final: 0.7018 (tttt) REVERT: B 225 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.6226 (pt0) REVERT: B 232 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.6551 (ttt90) REVERT: B 400 ARG cc_start: 0.7418 (mmm-85) cc_final: 0.7200 (mmm-85) REVERT: B 613 ASP cc_start: 0.8594 (m-30) cc_final: 0.8025 (m-30) REVERT: B 615 PHE cc_start: 0.8305 (m-80) cc_final: 0.7131 (t80) REVERT: B 774 ARG cc_start: 0.7325 (mmm160) cc_final: 0.6951 (mmm160) REVERT: B 783 VAL cc_start: 0.8144 (t) cc_final: 0.7921 (p) REVERT: C 187 GLU cc_start: 0.6360 (OUTLIER) cc_final: 0.5957 (tm-30) REVERT: C 192 LYS cc_start: 0.7532 (ttmt) cc_final: 0.7093 (tttt) REVERT: C 218 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7363 (pm20) REVERT: C 225 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.6182 (pt0) REVERT: C 232 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.6576 (ttt90) REVERT: C 400 ARG cc_start: 0.7427 (mmm-85) cc_final: 0.7211 (mmm-85) REVERT: C 613 ASP cc_start: 0.8633 (m-30) cc_final: 0.8155 (m-30) REVERT: C 615 PHE cc_start: 0.8311 (m-80) cc_final: 0.7129 (t80) REVERT: C 781 ASP cc_start: 0.7849 (t0) cc_final: 0.7645 (m-30) REVERT: D 187 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.5977 (tm-30) REVERT: D 192 LYS cc_start: 0.7501 (ttmt) cc_final: 0.7062 (tttt) REVERT: D 206 ARG cc_start: 0.6064 (mmm160) cc_final: 0.5582 (mmm160) REVERT: D 218 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7368 (pm20) REVERT: D 225 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6201 (pt0) REVERT: D 232 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.6572 (ttt90) REVERT: D 233 ASP cc_start: 0.6200 (t0) cc_final: 0.5999 (p0) REVERT: D 253 TYR cc_start: 0.7507 (m-10) cc_final: 0.7210 (m-80) REVERT: D 613 ASP cc_start: 0.8580 (m-30) cc_final: 0.8054 (m-30) REVERT: D 615 PHE cc_start: 0.8299 (m-80) cc_final: 0.7112 (t80) REVERT: D 774 ARG cc_start: 0.7334 (mmm160) cc_final: 0.6971 (mmm160) outliers start: 84 outliers final: 26 residues processed: 407 average time/residue: 0.5739 time to fit residues: 268.1501 Evaluate side-chains 347 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 308 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 774 ARG Chi-restraints excluded: chain A residue 784 ASN Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 579 VAL Chi-restraints excluded: chain C residue 672 ASP Chi-restraints excluded: chain C residue 696 ILE Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 252 HIS Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 440 ASN Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain D residue 672 ASP Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 784 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 169 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 168 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 207 optimal weight: 0.6980 chunk 158 optimal weight: 2.9990 chunk 223 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 302 ASN A 474 ASN A 588 ASN B 302 ASN B 588 ASN B 637 ASN C 302 ASN C 474 ASN C 588 ASN C 637 ASN D 302 ASN D 474 ASN D 588 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.216988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.167362 restraints weight = 26680.056| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.22 r_work: 0.3801 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22567 Z= 0.157 Angle : 0.702 9.940 30372 Z= 0.344 Chirality : 0.042 0.228 3328 Planarity : 0.005 0.060 3632 Dihedral : 26.452 173.785 5068 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 4.05 % Allowed : 17.93 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.17), residues: 2500 helix: 0.70 (0.13), residues: 1480 sheet: -0.72 (0.64), residues: 72 loop : -2.72 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 391 TYR 0.021 0.002 TYR D 303 PHE 0.029 0.001 PHE B 341 TRP 0.016 0.002 TRP B 785 HIS 0.010 0.001 HIS B 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (22564) covalent geometry : angle 0.70150 / 0.34 (30356) SS BOND : bond 0.00183 / 0.08 ( 3) SS BOND : angle 0.75213 / 0.43 ( 16) hydrogen bonds : bond 0.04334 / 2.91 ( 1068) hydrogen bonds : angle 4.40873 / 3.07 ( 3072) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 329 time to evaluate : 0.611 Fit side-chains REVERT: A 192 LYS cc_start: 0.7567 (ttmt) cc_final: 0.7071 (tttt) REVERT: A 225 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6263 (pt0) REVERT: A 232 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.6543 (ttt90) REVERT: A 233 ASP cc_start: 0.6086 (t0) cc_final: 0.5794 (p0) REVERT: A 253 TYR cc_start: 0.7493 (m-10) cc_final: 0.7124 (m-10) REVERT: A 299 HIS cc_start: 0.7397 (m-70) cc_final: 0.6995 (m-70) REVERT: A 572 GLU cc_start: 0.5984 (tt0) cc_final: 0.5697 (mt-10) REVERT: A 615 PHE cc_start: 0.8292 (m-80) cc_final: 0.7111 (t80) REVERT: A 774 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.7097 (mmm160) REVERT: A 781 ASP cc_start: 0.8040 (t0) cc_final: 0.7658 (m-30) REVERT: A 783 VAL cc_start: 0.8640 (t) cc_final: 0.8391 (p) REVERT: B 187 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.6073 (tm-30) REVERT: B 192 LYS cc_start: 0.7503 (ttmt) cc_final: 0.7040 (tttt) REVERT: B 400 ARG cc_start: 0.7475 (mmm-85) cc_final: 0.7247 (mmm-85) REVERT: B 507 ASP cc_start: 0.6214 (m-30) cc_final: 0.5425 (t0) REVERT: B 613 ASP cc_start: 0.8648 (m-30) cc_final: 0.8018 (m-30) REVERT: B 615 PHE cc_start: 0.8310 (m-80) cc_final: 0.7123 (t80) REVERT: B 774 ARG cc_start: 0.7247 (mmm160) cc_final: 0.6898 (mmm160) REVERT: B 781 ASP cc_start: 0.7649 (OUTLIER) cc_final: 0.7357 (m-30) REVERT: C 187 GLU cc_start: 0.6413 (OUTLIER) cc_final: 0.6097 (tm-30) REVERT: C 192 LYS cc_start: 0.7548 (ttmt) cc_final: 0.7084 (tttt) REVERT: C 218 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7280 (pm20) REVERT: C 400 ARG cc_start: 0.7493 (mmm-85) cc_final: 0.7262 (mmm-85) REVERT: C 507 ASP cc_start: 0.6206 (m-30) cc_final: 0.5485 (t0) REVERT: C 615 PHE cc_start: 0.8314 (m-80) cc_final: 0.7114 (t80) REVERT: D 187 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.6077 (tm-30) REVERT: D 192 LYS cc_start: 0.7536 (ttmt) cc_final: 0.7069 (tttt) REVERT: D 218 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7253 (pm20) REVERT: D 225 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6370 (pt0) REVERT: D 253 TYR cc_start: 0.7541 (m-10) cc_final: 0.7157 (m-10) REVERT: D 267 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.6429 (mm110) REVERT: D 344 LYS cc_start: 0.8272 (tppt) cc_final: 0.7827 (tppt) REVERT: D 507 ASP cc_start: 0.6242 (m-30) cc_final: 0.5471 (t0) REVERT: D 613 ASP cc_start: 0.8639 (m-30) cc_final: 0.8055 (m-30) REVERT: D 615 PHE cc_start: 0.8279 (m-80) cc_final: 0.7090 (t80) REVERT: D 774 ARG cc_start: 0.7251 (mmm160) cc_final: 0.6909 (mmm160) REVERT: D 781 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.7371 (m-30) outliers start: 90 outliers final: 39 residues processed: 394 average time/residue: 0.5796 time to fit residues: 261.5834 Evaluate side-chains 337 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 286 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 774 ARG Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 781 ASP Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 579 VAL Chi-restraints excluded: chain C residue 672 ASP Chi-restraints excluded: chain C residue 696 ILE Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 252 HIS Chi-restraints excluded: chain D residue 267 GLN Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 440 ASN Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain D residue 660 CYS Chi-restraints excluded: chain D residue 672 ASP Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 781 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 116 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 159 optimal weight: 0.4980 chunk 212 optimal weight: 0.0670 chunk 30 optimal weight: 0.7980 chunk 205 optimal weight: 0.4980 chunk 54 optimal weight: 0.6980 chunk 222 optimal weight: 10.0000 chunk 167 optimal weight: 0.8980 chunk 123 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.219842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.171032 restraints weight = 26960.444| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 2.23 r_work: 0.3844 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22567 Z= 0.124 Angle : 0.665 9.982 30372 Z= 0.327 Chirality : 0.040 0.191 3328 Planarity : 0.005 0.054 3632 Dihedral : 25.484 176.878 5068 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 3.65 % Allowed : 19.95 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.17), residues: 2500 helix: 0.81 (0.13), residues: 1476 sheet: -0.41 (0.65), residues: 72 loop : -2.61 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 400 TYR 0.024 0.001 TYR B 303 PHE 0.016 0.001 PHE B 341 TRP 0.023 0.002 TRP B 785 HIS 0.011 0.001 HIS A 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (22564) covalent geometry : angle 0.66527 / 0.33 (30356) SS BOND : bond 0.00103 / 0.04 ( 3) SS BOND : angle 0.77648 / 0.46 ( 16) hydrogen bonds : bond 0.03991 / 2.70 ( 1068) hydrogen bonds : angle 4.30222 / 2.98 ( 3072) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 329 time to evaluate : 0.580 Fit side-chains REVERT: A 192 LYS cc_start: 0.7541 (ttmt) cc_final: 0.7025 (tttt) REVERT: A 223 MET cc_start: 0.6844 (tpp) cc_final: 0.6458 (tpt) REVERT: A 225 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6550 (mp0) REVERT: A 232 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.6506 (ttt90) REVERT: A 233 ASP cc_start: 0.6065 (t0) cc_final: 0.5805 (p0) REVERT: A 253 TYR cc_start: 0.7513 (m-10) cc_final: 0.7214 (m-10) REVERT: A 299 HIS cc_start: 0.7374 (m-70) cc_final: 0.6986 (m-70) REVERT: A 314 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7585 (mtm) REVERT: A 572 GLU cc_start: 0.5813 (tt0) cc_final: 0.5595 (mt-10) REVERT: A 613 ASP cc_start: 0.8558 (m-30) cc_final: 0.8013 (m-30) REVERT: A 615 PHE cc_start: 0.8302 (m-80) cc_final: 0.7099 (t80) REVERT: A 774 ARG cc_start: 0.7335 (mmm160) cc_final: 0.7081 (mmm160) REVERT: A 781 ASP cc_start: 0.8004 (t0) cc_final: 0.7578 (m-30) REVERT: A 783 VAL cc_start: 0.8701 (t) cc_final: 0.8365 (p) REVERT: B 187 GLU cc_start: 0.6208 (OUTLIER) cc_final: 0.5949 (tm-30) REVERT: B 192 LYS cc_start: 0.7421 (ttmt) cc_final: 0.6945 (tttt) REVERT: B 225 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6544 (mp0) REVERT: B 232 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.6425 (ttt90) REVERT: B 253 TYR cc_start: 0.7516 (m-80) cc_final: 0.7305 (m-80) REVERT: B 391 ARG cc_start: 0.6360 (ptp-170) cc_final: 0.5766 (ptp-110) REVERT: B 507 ASP cc_start: 0.6112 (m-30) cc_final: 0.5456 (t0) REVERT: B 615 PHE cc_start: 0.8288 (m-80) cc_final: 0.7089 (t80) REVERT: B 680 MET cc_start: 0.7335 (ptp) cc_final: 0.7133 (ptp) REVERT: C 187 GLU cc_start: 0.6281 (OUTLIER) cc_final: 0.6020 (tm-30) REVERT: C 192 LYS cc_start: 0.7468 (ttmt) cc_final: 0.6994 (tttt) REVERT: C 218 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7257 (pm20) REVERT: C 225 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6521 (mp0) REVERT: C 232 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.6436 (ttt90) REVERT: C 253 TYR cc_start: 0.7513 (m-80) cc_final: 0.7299 (m-80) REVERT: C 391 ARG cc_start: 0.6326 (ptp-170) cc_final: 0.5814 (ptp-110) REVERT: C 507 ASP cc_start: 0.6118 (m-30) cc_final: 0.5474 (t0) REVERT: C 615 PHE cc_start: 0.8310 (m-80) cc_final: 0.7079 (t80) REVERT: D 187 GLU cc_start: 0.6239 (OUTLIER) cc_final: 0.5981 (tm-30) REVERT: D 192 LYS cc_start: 0.7488 (ttmt) cc_final: 0.7014 (tttt) REVERT: D 218 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7196 (pm20) REVERT: D 225 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6553 (mp0) REVERT: D 232 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.6411 (ttm110) REVERT: D 253 TYR cc_start: 0.7503 (m-10) cc_final: 0.7112 (m-10) REVERT: D 391 ARG cc_start: 0.6339 (ptp-170) cc_final: 0.5740 (ptp-110) REVERT: D 507 ASP cc_start: 0.6098 (m-30) cc_final: 0.5447 (t0) REVERT: D 615 PHE cc_start: 0.8278 (m-80) cc_final: 0.7077 (t80) REVERT: D 774 ARG cc_start: 0.7258 (mmm160) cc_final: 0.6961 (mmm160) outliers start: 81 outliers final: 28 residues processed: 393 average time/residue: 0.5572 time to fit residues: 251.6682 Evaluate side-chains 336 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 294 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 579 VAL Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 440 ASN Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain D residue 764 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 188 optimal weight: 0.0070 chunk 131 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 112 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 100 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 214 optimal weight: 0.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 637 ASN B 201 ASN C 201 ASN D 201 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.214480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.163335 restraints weight = 26775.751| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.25 r_work: 0.3759 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22567 Z= 0.178 Angle : 0.730 11.920 30372 Z= 0.356 Chirality : 0.043 0.240 3328 Planarity : 0.005 0.051 3632 Dihedral : 24.974 179.652 5068 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 3.96 % Allowed : 20.05 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.17), residues: 2500 helix: 0.61 (0.13), residues: 1472 sheet: -0.48 (0.63), residues: 72 loop : -2.58 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 400 TYR 0.024 0.002 TYR C 303 PHE 0.022 0.002 PHE B 341 TRP 0.015 0.002 TRP B 785 HIS 0.007 0.001 HIS A 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (22564) covalent geometry : angle 0.72994 / 0.36 (30356) SS BOND : bond 0.00102 / 0.05 ( 3) SS BOND : angle 0.91285 / 0.56 ( 16) hydrogen bonds : bond 0.04524 / 3.04 ( 1068) hydrogen bonds : angle 4.48571 / 3.10 ( 3072) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 305 time to evaluate : 0.717 Fit side-chains REVERT: A 187 GLU cc_start: 0.6342 (OUTLIER) cc_final: 0.5345 (tm-30) REVERT: A 232 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.6459 (ttm110) REVERT: A 253 TYR cc_start: 0.7479 (m-10) cc_final: 0.7134 (m-10) REVERT: A 299 HIS cc_start: 0.7394 (m-70) cc_final: 0.7007 (m-70) REVERT: A 572 GLU cc_start: 0.5992 (tt0) cc_final: 0.5786 (mt-10) REVERT: A 613 ASP cc_start: 0.8709 (m-30) cc_final: 0.8019 (m-30) REVERT: A 615 PHE cc_start: 0.8268 (m-80) cc_final: 0.7057 (t80) REVERT: A 781 ASP cc_start: 0.8135 (t0) cc_final: 0.7817 (m-30) REVERT: B 192 LYS cc_start: 0.7434 (ttmt) cc_final: 0.6911 (tttt) REVERT: B 267 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.6410 (mm110) REVERT: B 507 ASP cc_start: 0.6245 (m-30) cc_final: 0.5513 (t0) REVERT: B 572 GLU cc_start: 0.5998 (tt0) cc_final: 0.5724 (mt-10) REVERT: B 615 PHE cc_start: 0.8264 (m-80) cc_final: 0.7070 (t80) REVERT: C 192 LYS cc_start: 0.7443 (ttmt) cc_final: 0.6927 (tttt) REVERT: C 218 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7108 (pm20) REVERT: C 253 TYR cc_start: 0.7564 (m-80) cc_final: 0.7338 (m-80) REVERT: C 267 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.6424 (mm110) REVERT: C 507 ASP cc_start: 0.6238 (m-30) cc_final: 0.5505 (t0) REVERT: C 572 GLU cc_start: 0.6013 (tt0) cc_final: 0.5738 (mt-10) REVERT: C 615 PHE cc_start: 0.8275 (m-80) cc_final: 0.7050 (t80) REVERT: D 192 LYS cc_start: 0.7459 (ttmt) cc_final: 0.6934 (tttt) REVERT: D 218 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7091 (pm20) REVERT: D 232 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.6476 (ttm110) REVERT: D 267 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.6431 (mm110) REVERT: D 507 ASP cc_start: 0.6210 (m-30) cc_final: 0.5473 (t0) REVERT: D 572 GLU cc_start: 0.6017 (tt0) cc_final: 0.5733 (mt-10) REVERT: D 615 PHE cc_start: 0.8255 (m-80) cc_final: 0.7062 (t80) REVERT: D 774 ARG cc_start: 0.7326 (mmm160) cc_final: 0.6995 (mmm160) REVERT: D 781 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7420 (m-30) outliers start: 88 outliers final: 41 residues processed: 369 average time/residue: 0.5455 time to fit residues: 231.1954 Evaluate side-chains 340 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 290 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 267 GLN Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 579 VAL Chi-restraints excluded: chain C residue 672 ASP Chi-restraints excluded: chain C residue 696 ILE Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 267 GLN Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 440 ASN Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 660 CYS Chi-restraints excluded: chain D residue 672 ASP Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 781 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 35 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 207 optimal weight: 0.1980 chunk 18 optimal weight: 0.8980 chunk 171 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 235 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 139 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 252 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.218819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.169521 restraints weight = 26862.263| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.26 r_work: 0.3826 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22567 Z= 0.126 Angle : 0.669 10.406 30372 Z= 0.328 Chirality : 0.041 0.206 3328 Planarity : 0.005 0.055 3632 Dihedral : 24.084 179.398 5068 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 3.02 % Allowed : 21.71 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.17), residues: 2500 helix: 0.83 (0.13), residues: 1472 sheet: -0.19 (0.62), residues: 72 loop : -2.49 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 400 TYR 0.024 0.002 TYR C 303 PHE 0.029 0.001 PHE D 707 TRP 0.022 0.002 TRP B 785 HIS 0.007 0.001 HIS A 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (22564) covalent geometry : angle 0.66919 / 0.33 (30356) SS BOND : bond 0.00040 / 0.02 ( 3) SS BOND : angle 0.91785 / 0.56 ( 16) hydrogen bonds : bond 0.03990 / 2.71 ( 1068) hydrogen bonds : angle 4.31095 / 2.98 ( 3072) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 302 time to evaluate : 0.818 Fit side-chains REVERT: A 187 GLU cc_start: 0.6245 (OUTLIER) cc_final: 0.5199 (tm-30) REVERT: A 223 MET cc_start: 0.6710 (tpp) cc_final: 0.6326 (tpt) REVERT: A 232 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.6367 (ttt90) REVERT: A 253 TYR cc_start: 0.7492 (m-10) cc_final: 0.6911 (m-10) REVERT: A 299 HIS cc_start: 0.7358 (m-70) cc_final: 0.6952 (m-70) REVERT: A 337 GLU cc_start: 0.7998 (pm20) cc_final: 0.7789 (tp30) REVERT: A 615 PHE cc_start: 0.8292 (m-80) cc_final: 0.7093 (t80) REVERT: A 781 ASP cc_start: 0.8065 (t0) cc_final: 0.7773 (m-30) REVERT: A 782 GLU cc_start: 0.8366 (tt0) cc_final: 0.8038 (tt0) REVERT: B 192 LYS cc_start: 0.7399 (ttmt) cc_final: 0.6890 (tttt) REVERT: B 232 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.6315 (ttt90) REVERT: B 253 TYR cc_start: 0.7532 (m-80) cc_final: 0.7298 (m-80) REVERT: B 507 ASP cc_start: 0.6192 (m-30) cc_final: 0.5587 (t0) REVERT: B 572 GLU cc_start: 0.5876 (tt0) cc_final: 0.5631 (mt-10) REVERT: B 615 PHE cc_start: 0.8280 (m-80) cc_final: 0.7089 (t80) REVERT: C 192 LYS cc_start: 0.7430 (ttmt) cc_final: 0.6922 (tttt) REVERT: C 218 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7225 (pm20) REVERT: C 232 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.6343 (ttt90) REVERT: C 253 TYR cc_start: 0.7598 (m-80) cc_final: 0.7338 (m-80) REVERT: C 507 ASP cc_start: 0.6201 (m-30) cc_final: 0.5605 (t0) REVERT: C 572 GLU cc_start: 0.5873 (tt0) cc_final: 0.5631 (mt-10) REVERT: C 615 PHE cc_start: 0.8303 (m-80) cc_final: 0.7092 (t80) REVERT: C 680 MET cc_start: 0.7696 (ptp) cc_final: 0.7472 (ptp) REVERT: D 192 LYS cc_start: 0.7442 (ttmt) cc_final: 0.6940 (tttt) REVERT: D 218 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7215 (pm20) REVERT: D 232 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.6315 (ttt90) REVERT: D 507 ASP cc_start: 0.6185 (m-30) cc_final: 0.5584 (t0) REVERT: D 572 GLU cc_start: 0.5905 (tt0) cc_final: 0.5651 (mt-10) REVERT: D 615 PHE cc_start: 0.8271 (m-80) cc_final: 0.7067 (t80) REVERT: D 774 ARG cc_start: 0.7329 (mmm160) cc_final: 0.7104 (mmm160) outliers start: 67 outliers final: 33 residues processed: 354 average time/residue: 0.5622 time to fit residues: 229.4243 Evaluate side-chains 327 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 287 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 579 VAL Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 440 ASN Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 660 CYS Chi-restraints excluded: chain D residue 764 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 84 optimal weight: 0.4980 chunk 186 optimal weight: 20.0000 chunk 118 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 chunk 148 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 170 optimal weight: 0.9980 chunk 212 optimal weight: 3.9990 chunk 193 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.216151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.166384 restraints weight = 26865.549| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.22 r_work: 0.3792 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22567 Z= 0.162 Angle : 0.704 11.018 30372 Z= 0.343 Chirality : 0.043 0.218 3328 Planarity : 0.005 0.054 3632 Dihedral : 23.762 179.774 5068 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 3.15 % Allowed : 21.49 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.17), residues: 2500 helix: 0.75 (0.13), residues: 1472 sheet: -0.24 (0.62), residues: 72 loop : -2.43 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 400 TYR 0.023 0.002 TYR D 303 PHE 0.031 0.002 PHE D 707 TRP 0.013 0.002 TRP A 733 HIS 0.005 0.001 HIS C 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (22564) covalent geometry : angle 0.70360 / 0.34 (30356) SS BOND : bond 0.00055 / 0.03 ( 3) SS BOND : angle 0.93408 / 0.57 ( 16) hydrogen bonds : bond 0.04294 / 2.89 ( 1068) hydrogen bonds : angle 4.37900 / 3.04 ( 3072) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 293 time to evaluate : 0.777 Fit side-chains REVERT: A 187 GLU cc_start: 0.6304 (OUTLIER) cc_final: 0.5259 (tm-30) REVERT: A 192 LYS cc_start: 0.7633 (ttmt) cc_final: 0.7390 (ttmm) REVERT: A 223 MET cc_start: 0.6588 (tpp) cc_final: 0.6140 (tpt) REVERT: A 232 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.6380 (ttt90) REVERT: A 253 TYR cc_start: 0.7506 (m-10) cc_final: 0.6921 (m-10) REVERT: A 299 HIS cc_start: 0.7357 (m-70) cc_final: 0.6958 (m-70) REVERT: A 337 GLU cc_start: 0.8093 (pm20) cc_final: 0.7808 (tp30) REVERT: A 518 LEU cc_start: 0.8243 (tm) cc_final: 0.7535 (tp) REVERT: A 615 PHE cc_start: 0.8277 (m-80) cc_final: 0.7057 (t80) REVERT: A 781 ASP cc_start: 0.8176 (t0) cc_final: 0.7890 (m-30) REVERT: B 187 GLU cc_start: 0.6130 (OUTLIER) cc_final: 0.5870 (tm-30) REVERT: B 192 LYS cc_start: 0.7519 (ttmt) cc_final: 0.7002 (tttt) REVERT: B 232 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.6313 (ttt90) REVERT: B 267 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.6361 (mm110) REVERT: B 507 ASP cc_start: 0.6302 (m-30) cc_final: 0.5647 (t0) REVERT: B 615 PHE cc_start: 0.8274 (m-80) cc_final: 0.7066 (t80) REVERT: C 187 GLU cc_start: 0.6124 (OUTLIER) cc_final: 0.5886 (tm-30) REVERT: C 218 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7195 (pm20) REVERT: C 232 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.6345 (ttt90) REVERT: C 253 TYR cc_start: 0.7585 (m-80) cc_final: 0.7318 (m-80) REVERT: C 267 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.6356 (mm110) REVERT: C 507 ASP cc_start: 0.6283 (m-30) cc_final: 0.5648 (t0) REVERT: C 615 PHE cc_start: 0.8287 (m-80) cc_final: 0.7068 (t80) REVERT: C 680 MET cc_start: 0.7737 (ptp) cc_final: 0.7502 (ptp) REVERT: C 781 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7623 (m-30) REVERT: D 187 GLU cc_start: 0.6156 (OUTLIER) cc_final: 0.5898 (tm-30) REVERT: D 218 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7208 (pm20) REVERT: D 223 MET cc_start: 0.6574 (ttm) cc_final: 0.6318 (tpt) REVERT: D 232 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.6335 (ttt90) REVERT: D 267 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.6401 (mm110) REVERT: D 507 ASP cc_start: 0.6260 (m-30) cc_final: 0.5618 (t0) REVERT: D 615 PHE cc_start: 0.8262 (m-80) cc_final: 0.7054 (t80) outliers start: 70 outliers final: 32 residues processed: 348 average time/residue: 0.6197 time to fit residues: 247.6126 Evaluate side-chains 328 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 282 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 727 LYS Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 267 GLN Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 579 VAL Chi-restraints excluded: chain C residue 613 ASP Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 267 GLN Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 440 ASN Chi-restraints excluded: chain D residue 660 CYS Chi-restraints excluded: chain D residue 764 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 210 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 212 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 151 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 HIS ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.216472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.167025 restraints weight = 27088.032| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.21 r_work: 0.3789 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.5297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 22567 Z= 0.152 Angle : 0.712 12.666 30372 Z= 0.348 Chirality : 0.043 0.239 3328 Planarity : 0.005 0.056 3632 Dihedral : 23.479 178.819 5068 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 2.52 % Allowed : 22.57 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.17), residues: 2500 helix: 0.77 (0.13), residues: 1472 sheet: -0.39 (0.59), residues: 72 loop : -2.40 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 400 TYR 0.023 0.002 TYR D 303 PHE 0.034 0.001 PHE D 707 TRP 0.015 0.002 TRP B 785 HIS 0.006 0.001 HIS A 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (22564) covalent geometry : angle 0.71210 / 0.35 (30356) SS BOND : bond 0.00048 / 0.02 ( 3) SS BOND : angle 0.99488 / 0.61 ( 16) hydrogen bonds : bond 0.04250 / 2.87 ( 1068) hydrogen bonds : angle 4.34968 / 3.03 ( 3072) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 297 time to evaluate : 0.734 Fit side-chains REVERT: A 187 GLU cc_start: 0.6287 (OUTLIER) cc_final: 0.5240 (tm-30) REVERT: A 223 MET cc_start: 0.6583 (tpp) cc_final: 0.6367 (tpt) REVERT: A 232 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.6252 (ttt180) REVERT: A 253 TYR cc_start: 0.7516 (m-10) cc_final: 0.6906 (m-10) REVERT: A 299 HIS cc_start: 0.7356 (m-70) cc_final: 0.6943 (m-70) REVERT: A 336 ARG cc_start: 0.7505 (ptm160) cc_final: 0.7167 (ptp90) REVERT: A 615 PHE cc_start: 0.8277 (m-80) cc_final: 0.7073 (t80) REVERT: A 781 ASP cc_start: 0.8173 (t0) cc_final: 0.7932 (m-30) REVERT: B 232 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.6336 (ttt90) REVERT: B 267 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.6289 (mm110) REVERT: B 507 ASP cc_start: 0.6302 (m-30) cc_final: 0.5673 (t0) REVERT: B 615 PHE cc_start: 0.8290 (m-80) cc_final: 0.7083 (t80) REVERT: C 218 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7222 (pm20) REVERT: C 232 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.6347 (ttt90) REVERT: C 253 TYR cc_start: 0.7591 (m-80) cc_final: 0.7321 (m-80) REVERT: C 267 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.6293 (mm110) REVERT: C 507 ASP cc_start: 0.6317 (m-30) cc_final: 0.5686 (t0) REVERT: C 615 PHE cc_start: 0.8295 (m-80) cc_final: 0.7088 (t80) REVERT: C 680 MET cc_start: 0.7824 (ptp) cc_final: 0.7566 (ptp) REVERT: C 781 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7615 (m-30) REVERT: D 218 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7073 (pm20) REVERT: D 223 MET cc_start: 0.6445 (ttm) cc_final: 0.6047 (tpt) REVERT: D 232 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.6339 (ttt90) REVERT: D 267 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.6338 (mm110) REVERT: D 507 ASP cc_start: 0.6293 (m-30) cc_final: 0.5662 (t0) REVERT: D 615 PHE cc_start: 0.8258 (m-80) cc_final: 0.7064 (t80) outliers start: 56 outliers final: 29 residues processed: 337 average time/residue: 0.5689 time to fit residues: 220.0618 Evaluate side-chains 327 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 287 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 267 GLN Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 579 VAL Chi-restraints excluded: chain C residue 613 ASP Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 267 GLN Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 440 ASN Chi-restraints excluded: chain D residue 660 CYS Chi-restraints excluded: chain D residue 727 LYS Chi-restraints excluded: chain D residue 764 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 205 optimal weight: 0.7980 chunk 212 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 210 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 29 optimal weight: 0.0770 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.218629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.169848 restraints weight = 26951.101| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.21 r_work: 0.3825 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22567 Z= 0.128 Angle : 0.700 15.683 30372 Z= 0.339 Chirality : 0.042 0.229 3328 Planarity : 0.005 0.056 3632 Dihedral : 23.071 179.911 5068 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 2.21 % Allowed : 23.47 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.17), residues: 2500 helix: 0.91 (0.13), residues: 1484 sheet: -0.11 (0.57), residues: 76 loop : -2.38 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 400 TYR 0.021 0.001 TYR D 303 PHE 0.035 0.001 PHE D 707 TRP 0.017 0.002 TRP B 785 HIS 0.005 0.001 HIS A 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (22564) covalent geometry : angle 0.69939 / 0.34 (30356) SS BOND : bond 0.00023 / 0.01 ( 3) SS BOND : angle 1.03138 / 0.63 ( 16) hydrogen bonds : bond 0.04011 / 2.72 ( 1068) hydrogen bonds : angle 4.25026 / 2.95 ( 3072) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7841.44 seconds wall clock time: 134 minutes 13.31 seconds (8053.31 seconds total)