Starting phenix.real_space_refine on Thu Aug 6 18:55:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zq1_74540/08_2026/9zq1_74540.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zq1_74540/08_2026/9zq1_74540.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zq1_74540/08_2026/9zq1_74540.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zq1_74540/08_2026/9zq1_74540.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zq1_74540/08_2026/9zq1_74540.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zq1_74540/08_2026/9zq1_74540.map" } resolution = 2.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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 K 5 8.98 5 P 40 5.49 5 S 76 5.16 5 C 10701 2.51 5 N 2400 2.21 5 O 2970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16192 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3680 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 14, 'TRANS': 434} Chain: "B" Number of atoms: 3680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3680 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 14, 'TRANS': 434} Chain: "C" Number of atoms: 3680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3680 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 14, 'TRANS': 434} Chain: "D" Number of atoms: 3680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3680 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 14, 'TRANS': 434} Chain: "A" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 411 Unusual residues: {' K': 4, 'CLR': 1, 'PCG': 1, 'PCW': 8, 'PIO': 1} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 114 Planarities with less than four sites: {'PCW:plan-4': 3, 'PCW:plan-2': 3} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 330 Unusual residues: {' K': 1, 'CLR': 1, 'PCG': 1, 'PCW': 6, 'PIO': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-2': 2, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 366 Unusual residues: {'CLR': 1, 'PCG': 1, 'PCW': 7, 'PIO': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-4': 3, 'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 365 Unusual residues: {'CLR': 1, 'PCG': 1, 'PCW': 7, 'PIO': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 102 Planarities with less than four sites: {'PCW:plan-2': 4, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 3.05, per 1000 atoms: 0.19 Number of scatterers: 16192 At special positions: 0 Unit cell: (96.3, 96.3, 121.5, 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) K 5 19.00 S 76 16.00 P 40 15.00 O 2970 8.00 N 2400 7.00 C 10701 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 579.2 milliseconds 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3408 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 12 sheets defined 67.9% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 162 through 189 Proline residue: A 175 - end of helix removed outlier: 5.153A pdb=" N ILE A 184 " --> pdb=" O TRP A 180 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.862A pdb=" N TYR A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 220 Processing helix chain 'A' and resid 234 through 241 Processing helix chain 'A' and resid 243 through 253 removed outlier: 4.097A pdb=" N LYS A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 258 removed outlier: 3.503A pdb=" N LEU A 258 " --> pdb=" O PRO A 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 255 through 258' Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 267 through 276 removed outlier: 3.686A pdb=" N ILE A 270 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASN A 273 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 291 removed outlier: 3.874A pdb=" N MET A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 326 Processing helix chain 'A' and resid 344 through 361 Processing helix chain 'A' and resid 371 through 404 Processing helix chain 'A' and resid 404 through 424 Processing helix chain 'A' and resid 427 through 444 Processing helix chain 'A' and resid 449 through 455 Processing helix chain 'A' and resid 458 through 477 removed outlier: 5.300A pdb=" N ASP A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N THR A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 481 Processing helix chain 'A' and resid 485 through 493 removed outlier: 3.509A pdb=" N VAL A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 588 removed outlier: 4.015A pdb=" N GLU A 587 " --> pdb=" O GLU A 583 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TYR A 588 " --> pdb=" O ALA A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 603 removed outlier: 3.505A pdb=" N LEU A 595 " --> pdb=" O ALA A 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 189 removed outlier: 3.568A pdb=" N TYR B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) Proline residue: B 175 - end of helix removed outlier: 5.194A pdb=" N ILE B 184 " --> pdb=" O TRP B 180 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 196 removed outlier: 3.787A pdb=" N TYR B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 220 Processing helix chain 'B' and resid 232 through 241 Processing helix chain 'B' and resid 243 through 253 removed outlier: 4.027A pdb=" N LYS B 247 " --> pdb=" O ASN B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 258 removed outlier: 3.501A pdb=" N LEU B 258 " --> pdb=" O PRO B 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 255 through 258' Processing helix chain 'B' and resid 259 through 264 Processing helix chain 'B' and resid 267 through 276 removed outlier: 3.656A pdb=" N ILE B 270 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASN B 273 " --> pdb=" O ILE B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 292 removed outlier: 3.930A pdb=" N MET B 281 " --> pdb=" O ARG B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 326 Processing helix chain 'B' and resid 344 through 361 Processing helix chain 'B' and resid 371 through 404 Processing helix chain 'B' and resid 404 through 424 Processing helix chain 'B' and resid 427 through 444 Processing helix chain 'B' and resid 449 through 455 Processing helix chain 'B' and resid 458 through 477 removed outlier: 5.430A pdb=" N ASP B 472 " --> pdb=" O ASN B 468 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N THR B 473 " --> pdb=" O VAL B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 494 Processing helix chain 'B' and resid 578 through 588 removed outlier: 3.873A pdb=" N GLU B 587 " --> pdb=" O GLU B 583 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR B 588 " --> pdb=" O ALA B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 600 removed outlier: 4.147A pdb=" N MET B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS B 600 " --> pdb=" O GLU B 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 189 removed outlier: 3.572A pdb=" N TYR C 166 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Proline residue: C 175 - end of helix removed outlier: 5.196A pdb=" N ILE C 184 " --> pdb=" O TRP C 180 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 196 removed outlier: 3.846A pdb=" N TYR C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 220 Processing helix chain 'C' and resid 232 through 241 Processing helix chain 'C' and resid 243 through 253 removed outlier: 4.079A pdb=" N LYS C 247 " --> pdb=" O ASN C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 257 No H-bonds generated for 'chain 'C' and resid 255 through 257' Processing helix chain 'C' and resid 258 through 263 removed outlier: 4.357A pdb=" N LYS C 262 " --> pdb=" O LEU C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 276 removed outlier: 3.708A pdb=" N ILE C 270 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASN C 273 " --> pdb=" O ILE C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 292 removed outlier: 3.928A pdb=" N MET C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 326 Processing helix chain 'C' and resid 344 through 361 Processing helix chain 'C' and resid 371 through 404 Processing helix chain 'C' and resid 404 through 424 Processing helix chain 'C' and resid 427 through 444 Processing helix chain 'C' and resid 449 through 456 removed outlier: 4.100A pdb=" N TYR C 456 " --> pdb=" O GLU C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 477 removed outlier: 5.406A pdb=" N ASP C 472 " --> pdb=" O ASN C 468 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N THR C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 482 Processing helix chain 'C' and resid 486 through 493 removed outlier: 3.669A pdb=" N LEU C 493 " --> pdb=" O VAL C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 586 Processing helix chain 'C' and resid 588 through 599 removed outlier: 3.576A pdb=" N LYS C 592 " --> pdb=" O TYR C 588 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR C 593 " --> pdb=" O PRO C 589 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY C 599 " --> pdb=" O LEU C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 604 removed outlier: 3.691A pdb=" N LEU C 603 " --> pdb=" O GLY C 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 189 removed outlier: 3.569A pdb=" N TYR D 166 " --> pdb=" O GLY D 162 " (cutoff:3.500A) Proline residue: D 175 - end of helix removed outlier: 5.155A pdb=" N ILE D 184 " --> pdb=" O TRP D 180 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA D 185 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 196 removed outlier: 3.503A pdb=" N GLN D 193 " --> pdb=" O PHE D 189 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 220 Processing helix chain 'D' and resid 232 through 241 Processing helix chain 'D' and resid 243 through 253 removed outlier: 4.080A pdb=" N LYS D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 258 Processing helix chain 'D' and resid 259 through 264 Processing helix chain 'D' and resid 267 through 276 removed outlier: 3.662A pdb=" N ILE D 270 " --> pdb=" O TYR D 267 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASN D 273 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 292 removed outlier: 3.934A pdb=" N MET D 281 " --> pdb=" O ARG D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 326 Processing helix chain 'D' and resid 344 through 361 Processing helix chain 'D' and resid 371 through 404 Processing helix chain 'D' and resid 404 through 424 Processing helix chain 'D' and resid 427 through 444 Processing helix chain 'D' and resid 449 through 455 Processing helix chain 'D' and resid 458 through 477 removed outlier: 5.072A pdb=" N ASP D 472 " --> pdb=" O ASN D 468 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N THR D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS D 476 " --> pdb=" O ASP D 472 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL D 477 " --> pdb=" O THR D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 481 Processing helix chain 'D' and resid 484 through 490 Processing helix chain 'D' and resid 578 through 588 removed outlier: 4.249A pdb=" N GLU D 587 " --> pdb=" O GLU D 583 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR D 588 " --> pdb=" O ALA D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 602 removed outlier: 3.764A pdb=" N LYS D 592 " --> pdb=" O TYR D 588 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY D 599 " --> pdb=" O LEU D 595 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS D 600 " --> pdb=" O GLU D 596 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLN D 601 " --> pdb=" O GLU D 597 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE D 602 " --> pdb=" O LYS D 598 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA2, first strand: chain 'A' and resid 496 through 500 removed outlier: 6.654A pdb=" N ASP A 572 " --> pdb=" O LYS A 520 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 505 through 507 removed outlier: 6.513A pdb=" N TYR A 505 " --> pdb=" O SER A 567 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER A 567 " --> pdb=" O TYR A 505 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS A 507 " --> pdb=" O ILE A 565 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN A 564 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LEU A 524 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL A 537 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL A 526 " --> pdb=" O PHE A 535 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AA5, first strand: chain 'B' and resid 496 through 500 removed outlier: 6.614A pdb=" N ASP B 572 " --> pdb=" O LYS B 520 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 505 through 507 removed outlier: 6.455A pdb=" N TYR B 505 " --> pdb=" O SER B 567 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N SER B 567 " --> pdb=" O TYR B 505 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASN B 564 " --> pdb=" O VAL B 527 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL B 536 " --> pdb=" O VAL B 526 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AA8, first strand: chain 'C' and resid 496 through 498 Processing sheet with id=AA9, first strand: chain 'C' and resid 505 through 507 removed outlier: 6.433A pdb=" N TYR C 505 " --> pdb=" O SER C 567 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER C 567 " --> pdb=" O TYR C 505 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS C 507 " --> pdb=" O ILE C 565 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN C 564 " --> pdb=" O VAL C 527 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU C 524 " --> pdb=" O VAL C 537 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL C 537 " --> pdb=" O LEU C 524 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL C 526 " --> pdb=" O PHE C 535 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 224 through 225 Processing sheet with id=AB2, first strand: chain 'D' and resid 496 through 498 Processing sheet with id=AB3, first strand: chain 'D' and resid 505 through 507 removed outlier: 6.455A pdb=" N TYR D 505 " --> pdb=" O SER D 567 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N SER D 567 " --> pdb=" O TYR D 505 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS D 507 " --> pdb=" O ILE D 565 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN D 564 " --> pdb=" O VAL D 527 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL D 536 " --> pdb=" O VAL D 526 " (cutoff:3.500A) 909 hydrogen bonds defined for protein. 2616 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: 1.87 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2436 1.31 - 1.44: 4400 1.44 - 1.57: 9471 1.57 - 1.70: 76 1.70 - 1.82: 140 Bond restraints: 16523 Sorted by residual: bond pdb=" C2' PCG D 703 " pdb=" C3' PCG D 703 " ideal model delta sigma weight residual 1.514 1.195 0.319 2.00e-02 2.50e+03 2.55e+02 bond pdb=" C2' PCG C 702 " pdb=" C3' PCG C 702 " ideal model delta sigma weight residual 1.514 1.195 0.319 2.00e-02 2.50e+03 2.54e+02 bond pdb=" C2' PCG A 701 " pdb=" C3' PCG A 701 " ideal model delta sigma weight residual 1.514 1.195 0.319 2.00e-02 2.50e+03 2.54e+02 bond pdb=" C2' PCG B 702 " pdb=" C3' PCG B 702 " ideal model delta sigma weight residual 1.514 1.196 0.318 2.00e-02 2.50e+03 2.53e+02 bond pdb=" C3' PCG A 701 " pdb=" C4' PCG A 701 " ideal model delta sigma weight residual 1.519 1.813 -0.294 2.00e-02 2.50e+03 2.16e+02 ... (remaining 16518 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 21846 2.43 - 4.86: 216 4.86 - 7.29: 94 7.29 - 9.72: 48 9.72 - 12.15: 17 Bond angle restraints: 22221 Sorted by residual: angle pdb=" CB ARG D 478 " pdb=" CG ARG D 478 " pdb=" CD ARG D 478 " ideal model delta sigma weight residual 111.30 121.82 -10.52 2.30e+00 1.89e-01 2.09e+01 angle pdb=" CB MET C 582 " pdb=" CG MET C 582 " pdb=" SD MET C 582 " ideal model delta sigma weight residual 112.70 124.85 -12.15 3.00e+00 1.11e-01 1.64e+01 angle pdb=" CA MET D 594 " pdb=" CB MET D 594 " pdb=" CG MET D 594 " ideal model delta sigma weight residual 114.10 122.13 -8.03 2.00e+00 2.50e-01 1.61e+01 angle pdb=" O1 PIO B 708 " pdb=" P1 PIO B 708 " pdb=" O13 PIO B 708 " ideal model delta sigma weight residual 97.64 109.62 -11.98 3.00e+00 1.11e-01 1.59e+01 angle pdb=" O1 PIO C 709 " pdb=" P1 PIO C 709 " pdb=" O13 PIO C 709 " ideal model delta sigma weight residual 97.64 109.59 -11.95 3.00e+00 1.11e-01 1.59e+01 ... (remaining 22216 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.90: 9379 25.90 - 51.81: 762 51.81 - 77.71: 130 77.71 - 103.62: 21 103.62 - 129.52: 2 Dihedral angle restraints: 10294 sinusoidal: 4982 harmonic: 5312 Sorted by residual: dihedral pdb=" N PCW A 707 " pdb=" C4 PCW A 707 " pdb=" C5 PCW A 707 " pdb=" O4P PCW A 707 " ideal model delta sinusoidal sigma weight residual -66.66 62.86 -129.52 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" C2 PCW C 704 " pdb=" C31 PCW C 704 " pdb=" O2 PCW C 704 " pdb=" C32 PCW C 704 " ideal model delta sinusoidal sigma weight residual 175.43 70.90 104.53 1 3.00e+01 1.11e-03 1.33e+01 dihedral pdb=" C33 PCW A 704 " pdb=" C31 PCW A 704 " pdb=" C32 PCW A 704 " pdb=" O2 PCW A 704 " ideal model delta sinusoidal sigma weight residual 191.83 90.06 101.77 1 3.00e+01 1.11e-03 1.28e+01 ... (remaining 10291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 2341 0.104 - 0.208: 45 0.208 - 0.312: 0 0.312 - 0.416: 8 0.416 - 0.519: 4 Chirality restraints: 2398 Sorted by residual: chirality pdb=" PA PCG C 702 " pdb=" O2A PCG C 702 " pdb=" O3' PCG C 702 " pdb=" O5' PCG C 702 " both_signs ideal model delta sigma weight residual True 2.70 3.22 -0.52 2.00e-01 2.50e+01 6.74e+00 chirality pdb=" PA PCG D 703 " pdb=" O2A PCG D 703 " pdb=" O3' PCG D 703 " pdb=" O5' PCG D 703 " both_signs ideal model delta sigma weight residual True 2.70 3.22 -0.52 2.00e-01 2.50e+01 6.74e+00 chirality pdb=" PA PCG A 701 " pdb=" O2A PCG A 701 " pdb=" O3' PCG A 701 " pdb=" O5' PCG A 701 " both_signs ideal model delta sigma weight residual True 2.70 3.21 -0.51 2.00e-01 2.50e+01 6.61e+00 ... (remaining 2395 not shown) Planarity restraints: 2635 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 234 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.08e+00 pdb=" C LEU A 234 " -0.052 2.00e-02 2.50e+03 pdb=" O LEU A 234 " 0.019 2.00e-02 2.50e+03 pdb=" N LYS A 235 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET D 594 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.04e+00 pdb=" C MET D 594 " -0.030 2.00e-02 2.50e+03 pdb=" O MET D 594 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU D 595 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 366 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO C 367 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 367 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 367 " -0.017 5.00e-02 4.00e+02 ... (remaining 2632 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.79: 3756 2.79 - 3.38: 17925 3.38 - 3.97: 31904 3.97 - 4.55: 45065 4.55 - 5.14: 65081 Nonbonded interactions: 163731 Sorted by model distance: nonbonded pdb=" N GLN C 601 " pdb=" OE1 GLN C 601 " model vdw 2.206 3.120 nonbonded pdb=" O GLU B 583 " pdb=" OG1 THR B 586 " model vdw 2.217 3.040 nonbonded pdb=" O THR A 357 " pdb=" OG1 THR A 361 " model vdw 2.233 3.040 nonbonded pdb=" OG SER B 427 " pdb=" OD1 ASP B 429 " model vdw 2.234 3.040 nonbonded pdb=" O THR B 357 " pdb=" OG1 THR B 361 " model vdw 2.254 3.040 ... (remaining 163726 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 156 through 604 or (resid 705 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C2 or name C3 or name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C36 or name C37 or name O11 or name O \ 1P or name O2 or name O2P or name O3 or name O31 or name O3P or name O4P or name \ P )) or (resid 706 and (name C1 or name C11 or name C12 or name C13 or name C14 \ or name C2 or name C3 or name C31 or name C32 or name C33 or name C34 or name C \ 35)) or (resid 707 and (name C1 or name C11 or name C12 or name C13 or name C14 \ or name C2 or name C3 or name C31 or name C32 or name C33 or name C34 or name C3 \ 5 or name C36 or name C37 or name O2 or name O3 or name O31 or name O3P)))) selection = (chain 'B' and (resid 156 through 604 or (resid 705 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C2 or name C3 or name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C36 or name C37 or name O11 or name O \ 1P or name O2 or name O2P or name O3 or name O31 or name O3P or name O4P or name \ P )) or (resid 706 and (name C1 or name C11 or name C12 or name C13 or name C14 \ or name C2 or name C3 or name C31 or name C32 or name C33 or name C34 or name C \ 35)) or (resid 707 and (name C1 or name C11 or name C12 or name C13 or name C14 \ or name C2 or name C3 or name C31 or name C32 or name C33 or name C34 or name C3 \ 5 or name C36 or name C37 or name O2 or name O3 or name O31 or name O3P)))) selection = (chain 'C' and (resid 156 through 604 or (resid 705 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C2 or name C3 or name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C36 or name C37 or name O11 or name O \ 1P or name O2 or name O2P or name O3 or name O31 or name O3P or name O4P or name \ P )) or (resid 706 and (name C1 or name C11 or name C12 or name C13 or name C14 \ or name C2 or name C3 or name C31 or name C32 or name C33 or name C34 or name C \ 35)) or (resid 707 and (name C1 or name C11 or name C12 or name C13 or name C14 \ or name C2 or name C3 or name C31 or name C32 or name C33 or name C34 or name C3 \ 5 or name C36 or name C37 or name O2 or name O3 or name O31 or name O3P)))) selection = (chain 'D' and (resid 156 through 604 or (resid 705 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C2 or name C3 or name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C36 or name C37 or name O11 or name O \ 1P or name O2 or name O2P or name O3 or name O31 or name O3P or name O4P or name \ P )) or (resid 706 and (name C1 or name C11 or name C12 or name C13 or name C14 \ or name C2 or name C3 or name C31 or name C32 or name C33 or name C34 or name C \ 35)) or (resid 707 and (name C1 or name C11 or name C12 or name C13 or name C14 \ or name C2 or name C3 or name C31 or name C32 or name C33 or name C34 or name C3 \ 5 or name C36 or name C37 or name O2 or name O3 or name O31 or name O3P)))) } 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: 2.550 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.370 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 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:5.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9146 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 0.319 16523 Z= 0.543 Angle : 0.803 12.153 22221 Z= 0.320 Chirality : 0.048 0.519 2398 Planarity : 0.003 0.031 2635 Dihedral : 18.054 129.524 6886 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.36 % Allowed : 24.32 % 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: 2.49 (0.21), residues: 1788 helix: 2.30 (0.15), residues: 1216 sheet: 1.01 (0.79), residues: 48 loop : 0.22 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 514 TYR 0.015 0.001 TYR D 588 PHE 0.005 0.001 PHE D 410 TRP 0.017 0.001 TRP A 168 HIS 0.003 0.001 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.01089 / 0.54 (16523) covalent geometry : angle 0.80306 / 0.32 (22221) hydrogen bonds : bond 0.10760 / 6.75 ( 909) hydrogen bonds : angle 4.38517 / 3.06 ( 2616) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: D 514 ARG cc_start: 0.9116 (ttm-80) cc_final: 0.8669 (mtt90) REVERT: D 515 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7745 (pm20) outliers start: 22 outliers final: 12 residues processed: 126 average time/residue: 0.5218 time to fit residues: 72.6299 Evaluate side-chains 115 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 549 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 494 LYS Chi-restraints excluded: chain D residue 515 GLU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 595 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 496 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.105606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.068124 restraints weight = 26787.304| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.84 r_work: 0.2775 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9188 moved from start: 0.0617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 16523 Z= 0.127 Angle : 0.480 10.106 22221 Z= 0.243 Chirality : 0.039 0.197 2398 Planarity : 0.003 0.030 2635 Dihedral : 13.600 129.731 3349 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.72 % Allowed : 21.98 % Favored : 75.31 % 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: 2.68 (0.20), residues: 1788 helix: 2.51 (0.15), residues: 1164 sheet: 0.90 (0.70), residues: 48 loop : 0.37 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 514 TYR 0.011 0.001 TYR A 349 PHE 0.007 0.001 PHE B 438 TRP 0.015 0.001 TRP A 168 HIS 0.002 0.001 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (16523) covalent geometry : angle 0.47966 / 0.24 (22221) hydrogen bonds : bond 0.03769 / 2.45 ( 909) hydrogen bonds : angle 3.65611 / 2.57 ( 2616) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 116 time to evaluate : 0.644 Fit side-chains REVERT: A 415 ASP cc_start: 0.8828 (m-30) cc_final: 0.8461 (m-30) REVERT: A 536 VAL cc_start: 0.9521 (OUTLIER) cc_final: 0.9308 (p) REVERT: A 579 ASP cc_start: 0.9118 (OUTLIER) cc_final: 0.8822 (p0) REVERT: B 415 ASP cc_start: 0.8871 (m-30) cc_final: 0.8529 (m-30) REVERT: C 415 ASP cc_start: 0.8849 (m-30) cc_final: 0.8500 (m-30) REVERT: C 476 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8895 (mmpt) REVERT: D 441 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8962 (mp) REVERT: D 452 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8392 (mp0) REVERT: D 514 ARG cc_start: 0.9119 (ttm-80) cc_final: 0.8704 (mtt90) REVERT: D 515 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7668 (pm20) outliers start: 44 outliers final: 11 residues processed: 158 average time/residue: 0.5576 time to fit residues: 97.8095 Evaluate side-chains 127 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 548 SER Chi-restraints excluded: chain C residue 549 ILE Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 494 LYS Chi-restraints excluded: chain D residue 515 GLU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 603 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 84 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.103114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.065591 restraints weight = 27129.417| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.83 r_work: 0.2720 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9226 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 16523 Z= 0.238 Angle : 0.545 11.881 22221 Z= 0.276 Chirality : 0.043 0.192 2398 Planarity : 0.004 0.030 2635 Dihedral : 14.511 127.875 3339 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.77 % Allowed : 20.74 % Favored : 75.49 % 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: 2.37 (0.20), residues: 1788 helix: 2.28 (0.15), residues: 1160 sheet: 0.63 (0.63), residues: 48 loop : 0.25 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 514 TYR 0.016 0.002 TYR D 351 PHE 0.011 0.001 PHE B 298 TRP 0.017 0.002 TRP D 168 HIS 0.005 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.24 (16523) covalent geometry : angle 0.54467 / 0.28 (22221) hydrogen bonds : bond 0.04662 / 3.03 ( 909) hydrogen bonds : angle 3.87973 / 2.72 ( 2616) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 108 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: B 409 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8362 (tm-30) REVERT: B 441 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8971 (mp) REVERT: B 478 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8040 (tpm170) REVERT: B 594 MET cc_start: 0.8757 (mpt) cc_final: 0.8374 (mmt) REVERT: C 441 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8980 (mp) REVERT: C 476 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8882 (mmpt) REVERT: C 494 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8128 (mtpp) REVERT: D 441 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8987 (mp) REVERT: D 452 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8433 (mp0) REVERT: D 515 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8060 (pt0) outliers start: 61 outliers final: 24 residues processed: 168 average time/residue: 0.5028 time to fit residues: 93.8193 Evaluate side-chains 137 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 478 ARG Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 494 LYS Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 548 SER Chi-restraints excluded: chain C residue 549 ILE Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 478 ARG Chi-restraints excluded: chain D residue 494 LYS Chi-restraints excluded: chain D residue 515 GLU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 595 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 72 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 170 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3726 r_free = 0.3726 target = 0.105558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.068110 restraints weight = 26861.884| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.84 r_work: 0.2778 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9184 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16523 Z= 0.107 Angle : 0.479 10.611 22221 Z= 0.238 Chirality : 0.039 0.204 2398 Planarity : 0.003 0.030 2635 Dihedral : 13.650 129.448 3337 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.65 % Allowed : 21.98 % Favored : 75.37 % 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: 2.57 (0.20), residues: 1788 helix: 2.44 (0.15), residues: 1160 sheet: 0.81 (0.65), residues: 48 loop : 0.32 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 514 TYR 0.014 0.001 TYR D 588 PHE 0.011 0.001 PHE D 480 TRP 0.016 0.001 TRP A 168 HIS 0.002 0.001 HIS D 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (16523) covalent geometry : angle 0.47939 / 0.24 (22221) hydrogen bonds : bond 0.03587 / 2.34 ( 909) hydrogen bonds : angle 3.56585 / 2.50 ( 2616) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 112 time to evaluate : 0.638 Fit side-chains REVERT: A 415 ASP cc_start: 0.8831 (m-30) cc_final: 0.8453 (m-30) REVERT: B 415 ASP cc_start: 0.8881 (m-30) cc_final: 0.8526 (m-30) REVERT: B 478 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8105 (tpm170) REVERT: C 415 ASP cc_start: 0.8820 (m-30) cc_final: 0.8458 (m-30) REVERT: C 476 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8878 (mmpt) REVERT: C 494 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8114 (mtpp) REVERT: D 452 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8382 (mp0) REVERT: D 483 CYS cc_start: 0.7102 (m) cc_final: 0.6754 (m) REVERT: D 515 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8115 (pt0) outliers start: 43 outliers final: 17 residues processed: 153 average time/residue: 0.5321 time to fit residues: 89.9352 Evaluate side-chains 131 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 478 ARG Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 494 LYS Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 549 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 494 LYS Chi-restraints excluded: chain D residue 515 GLU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 603 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 130 optimal weight: 9.9990 chunk 163 optimal weight: 9.9990 chunk 146 optimal weight: 0.7980 chunk 156 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 154 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.105269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.067706 restraints weight = 26936.684| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.85 r_work: 0.2770 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9192 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16523 Z= 0.122 Angle : 0.480 10.194 22221 Z= 0.240 Chirality : 0.039 0.214 2398 Planarity : 0.003 0.030 2635 Dihedral : 13.531 129.544 3336 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.72 % Allowed : 22.22 % Favored : 75.06 % 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: 2.58 (0.20), residues: 1788 helix: 2.45 (0.15), residues: 1160 sheet: 0.76 (0.64), residues: 48 loop : 0.34 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 413 TYR 0.013 0.001 TYR C 588 PHE 0.007 0.001 PHE A 298 TRP 0.015 0.001 TRP A 168 HIS 0.003 0.001 HIS D 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (16523) covalent geometry : angle 0.48025 / 0.24 (22221) hydrogen bonds : bond 0.03697 / 2.41 ( 909) hydrogen bonds : angle 3.55232 / 2.49 ( 2616) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 110 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 415 ASP cc_start: 0.8843 (m-30) cc_final: 0.8488 (m-30) REVERT: B 415 ASP cc_start: 0.8873 (m-30) cc_final: 0.8517 (m-30) REVERT: C 415 ASP cc_start: 0.8825 (m-30) cc_final: 0.8457 (m-30) REVERT: C 476 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8877 (mmpt) REVERT: C 494 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8102 (mtpp) REVERT: D 441 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8961 (mp) REVERT: D 452 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8387 (mp0) REVERT: D 515 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8243 (pt0) outliers start: 44 outliers final: 18 residues processed: 154 average time/residue: 0.5256 time to fit residues: 90.0311 Evaluate side-chains 131 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 494 LYS Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 548 SER Chi-restraints excluded: chain C residue 549 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 494 LYS Chi-restraints excluded: chain D residue 515 GLU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 595 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 22 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 159 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 158 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 145 optimal weight: 0.0770 chunk 124 optimal weight: 3.9990 overall best weight: 2.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 551 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.103408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.066067 restraints weight = 26959.792| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 1.82 r_work: 0.2733 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9217 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 16523 Z= 0.208 Angle : 0.542 12.853 22221 Z= 0.270 Chirality : 0.042 0.241 2398 Planarity : 0.003 0.030 2635 Dihedral : 14.173 128.282 3336 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.84 % Allowed : 22.10 % Favored : 75.06 % 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: 2.40 (0.20), residues: 1788 helix: 2.30 (0.15), residues: 1160 sheet: 0.63 (0.61), residues: 48 loop : 0.28 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 478 TYR 0.015 0.001 TYR A 351 PHE 0.011 0.001 PHE D 298 TRP 0.016 0.001 TRP B 168 HIS 0.004 0.001 HIS D 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.21 (16523) covalent geometry : angle 0.54175 / 0.27 (22221) hydrogen bonds : bond 0.04372 / 2.85 ( 909) hydrogen bonds : angle 3.76089 / 2.64 ( 2616) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 107 time to evaluate : 0.507 Fit side-chains REVERT: B 478 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.7999 (tpm170) REVERT: C 415 ASP cc_start: 0.8893 (m-30) cc_final: 0.8571 (m-30) REVERT: C 476 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8887 (mmpt) REVERT: C 494 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8169 (mtpp) REVERT: D 441 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8953 (mp) REVERT: D 452 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8364 (mp0) REVERT: D 483 CYS cc_start: 0.7246 (m) cc_final: 0.6883 (m) REVERT: D 515 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8305 (pt0) outliers start: 46 outliers final: 21 residues processed: 152 average time/residue: 0.5250 time to fit residues: 88.8393 Evaluate side-chains 132 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 478 ARG Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 494 LYS Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 548 SER Chi-restraints excluded: chain C residue 549 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 494 LYS Chi-restraints excluded: chain D residue 515 GLU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 603 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 113 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 100 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 chunk 131 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.106071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.068875 restraints weight = 26928.779| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.84 r_work: 0.2799 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9168 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16523 Z= 0.097 Angle : 0.489 12.338 22221 Z= 0.238 Chirality : 0.039 0.265 2398 Planarity : 0.003 0.030 2635 Dihedral : 13.325 130.294 3336 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.98 % Allowed : 23.09 % Favored : 74.94 % 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: 2.66 (0.20), residues: 1788 helix: 2.50 (0.15), residues: 1160 sheet: 0.87 (0.63), residues: 48 loop : 0.38 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 514 TYR 0.015 0.001 TYR C 588 PHE 0.005 0.001 PHE D 170 TRP 0.017 0.001 TRP A 168 HIS 0.001 0.000 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (16523) covalent geometry : angle 0.48868 / 0.24 (22221) hydrogen bonds : bond 0.03322 / 2.17 ( 909) hydrogen bonds : angle 3.47282 / 2.43 ( 2616) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 ASP cc_start: 0.8836 (m-30) cc_final: 0.8468 (m-30) REVERT: B 415 ASP cc_start: 0.8856 (m-30) cc_final: 0.8473 (m-30) REVERT: B 478 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8049 (tpm170) REVERT: C 415 ASP cc_start: 0.8833 (m-30) cc_final: 0.8457 (m-30) REVERT: C 476 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8872 (mmpt) REVERT: C 494 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8111 (mtpp) REVERT: D 452 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8328 (mp0) REVERT: D 483 CYS cc_start: 0.7197 (m) cc_final: 0.6816 (m) REVERT: D 515 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8243 (pt0) outliers start: 32 outliers final: 17 residues processed: 144 average time/residue: 0.6203 time to fit residues: 98.7399 Evaluate side-chains 127 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 478 ARG Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 598 LYS Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 494 LYS Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 549 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 494 LYS Chi-restraints excluded: chain D residue 515 GLU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 595 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 124 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 152 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.104353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.066797 restraints weight = 26918.781| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.84 r_work: 0.2742 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9192 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16523 Z= 0.156 Angle : 0.529 12.108 22221 Z= 0.259 Chirality : 0.040 0.254 2398 Planarity : 0.003 0.030 2635 Dihedral : 13.668 129.455 3336 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.28 % Allowed : 23.02 % Favored : 74.69 % 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: 2.56 (0.20), residues: 1788 helix: 2.41 (0.15), residues: 1160 sheet: 0.75 (0.62), residues: 48 loop : 0.38 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 514 TYR 0.016 0.001 TYR C 588 PHE 0.008 0.001 PHE A 298 TRP 0.014 0.001 TRP B 168 HIS 0.003 0.001 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (16523) covalent geometry : angle 0.52898 / 0.26 (22221) hydrogen bonds : bond 0.03958 / 2.58 ( 909) hydrogen bonds : angle 3.60654 / 2.52 ( 2616) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 106 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 415 ASP cc_start: 0.8836 (m-30) cc_final: 0.8504 (m-30) REVERT: B 415 ASP cc_start: 0.8878 (m-30) cc_final: 0.8511 (m-30) REVERT: B 478 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7993 (tpm170) REVERT: C 415 ASP cc_start: 0.8819 (m-30) cc_final: 0.8487 (m-30) REVERT: C 476 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8887 (mmpt) REVERT: C 494 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8173 (mtpp) REVERT: D 452 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8355 (mp0) REVERT: D 483 CYS cc_start: 0.7123 (m) cc_final: 0.6760 (m) outliers start: 37 outliers final: 16 residues processed: 143 average time/residue: 0.6262 time to fit residues: 99.4042 Evaluate side-chains 122 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 478 ARG Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 494 LYS Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 549 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 494 LYS Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 595 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 70 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 162 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.105425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.068070 restraints weight = 26869.712| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.84 r_work: 0.2772 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9170 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16523 Z= 0.113 Angle : 0.519 11.943 22221 Z= 0.250 Chirality : 0.039 0.294 2398 Planarity : 0.003 0.030 2635 Dihedral : 13.331 130.111 3333 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.91 % Allowed : 23.21 % Favored : 74.88 % 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: 2.63 (0.20), residues: 1788 helix: 2.45 (0.15), residues: 1160 sheet: 0.96 (0.63), residues: 48 loop : 0.41 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 514 TYR 0.015 0.001 TYR C 588 PHE 0.006 0.001 PHE C 438 TRP 0.016 0.001 TRP A 168 HIS 0.002 0.001 HIS D 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (16523) covalent geometry : angle 0.51891 / 0.25 (22221) hydrogen bonds : bond 0.03519 / 2.29 ( 909) hydrogen bonds : angle 3.50038 / 2.44 ( 2616) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 415 ASP cc_start: 0.8806 (m-30) cc_final: 0.8438 (m-30) REVERT: B 415 ASP cc_start: 0.8859 (m-30) cc_final: 0.8483 (m-30) REVERT: B 478 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8021 (tpm170) REVERT: C 415 ASP cc_start: 0.8822 (m-30) cc_final: 0.8458 (m-30) REVERT: C 476 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8897 (mmpt) REVERT: C 494 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8171 (mtpp) REVERT: D 441 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8935 (mp) REVERT: D 452 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8353 (mp0) REVERT: D 483 CYS cc_start: 0.7131 (m) cc_final: 0.6766 (m) outliers start: 31 outliers final: 19 residues processed: 136 average time/residue: 0.6168 time to fit residues: 93.1484 Evaluate side-chains 126 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 478 ARG Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 494 LYS Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 548 SER Chi-restraints excluded: chain C residue 549 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 494 LYS Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 595 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 31 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 127 optimal weight: 0.4980 chunk 152 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.105575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.068283 restraints weight = 26961.117| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.84 r_work: 0.2777 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9169 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16523 Z= 0.109 Angle : 0.531 13.562 22221 Z= 0.253 Chirality : 0.039 0.294 2398 Planarity : 0.003 0.030 2635 Dihedral : 13.165 130.322 3333 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.54 % Allowed : 23.70 % Favored : 74.75 % 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: 2.68 (0.20), residues: 1788 helix: 2.49 (0.15), residues: 1156 sheet: 1.07 (0.64), residues: 48 loop : 0.45 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 514 TYR 0.017 0.001 TYR C 588 PHE 0.006 0.001 PHE A 298 TRP 0.016 0.001 TRP A 168 HIS 0.002 0.001 HIS D 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (16523) covalent geometry : angle 0.53073 / 0.25 (22221) hydrogen bonds : bond 0.03478 / 2.27 ( 909) hydrogen bonds : angle 3.45471 / 2.41 ( 2616) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: A 415 ASP cc_start: 0.8825 (m-30) cc_final: 0.8452 (m-30) REVERT: A 582 MET cc_start: 0.9267 (mmm) cc_final: 0.9064 (mpm) REVERT: B 415 ASP cc_start: 0.8856 (m-30) cc_final: 0.8461 (m-30) REVERT: B 582 MET cc_start: 0.9224 (mmm) cc_final: 0.8971 (mpm) REVERT: C 415 ASP cc_start: 0.8821 (m-30) cc_final: 0.8441 (m-30) REVERT: C 476 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8895 (mmpt) REVERT: C 494 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8183 (mtpp) REVERT: D 452 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8357 (mp0) REVERT: D 483 CYS cc_start: 0.7266 (m) cc_final: 0.6950 (m) outliers start: 25 outliers final: 19 residues processed: 131 average time/residue: 0.6075 time to fit residues: 88.1244 Evaluate side-chains 126 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 494 LYS Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 548 SER Chi-restraints excluded: chain C residue 549 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 494 LYS Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 595 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 166 optimal weight: 0.0060 chunk 134 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 chunk 119 optimal weight: 4.9990 chunk 34 optimal weight: 0.2980 chunk 160 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 551 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.106621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.069498 restraints weight = 26813.471| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 1.84 r_work: 0.2807 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9148 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16523 Z= 0.093 Angle : 0.516 13.532 22221 Z= 0.246 Chirality : 0.039 0.283 2398 Planarity : 0.003 0.030 2635 Dihedral : 12.856 130.745 3333 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.42 % Allowed : 23.83 % Favored : 74.75 % 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: 3.04 (0.20), residues: 1788 helix: 2.99 (0.15), residues: 1092 sheet: 1.22 (0.64), residues: 48 loop : 0.38 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 478 TYR 0.017 0.001 TYR C 588 PHE 0.005 0.001 PHE D 544 TRP 0.017 0.001 TRP A 168 HIS 0.001 0.000 HIS D 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 (16523) covalent geometry : angle 0.51624 / 0.25 (22221) hydrogen bonds : bond 0.03199 / 2.09 ( 909) hydrogen bonds : angle 3.37767 / 2.36 ( 2616) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6208.76 seconds wall clock time: 106 minutes 16.48 seconds (6376.48 seconds total)