Starting phenix.real_space_refine on Fri Jul 3 23:12:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zq1_74540/07_2026/9zq1_74540.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zq1_74540/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9zq1_74540/07_2026/9zq1_74540.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zq1_74540/07_2026/9zq1_74540.map" model { file = "/net/cci-nas-00/data/ceres_data/9zq1_74540/07_2026/9zq1_74540.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zq1_74540/07_2026/9zq1_74540.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 407 Ad-hoc single atom residues: {' K': 4} Unusual residues: {'CLR': 1, 'PCG': 1, 'PCW': 8, 'PIO': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain breaks: 4 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, 329 Ad-hoc single atom residues: {' K': 1} Unusual residues: {'CLR': 1, 'PCG': 1, 'PCW': 6, 'PIO': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain breaks: 1 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: 3.72, per 1000 atoms: 0.23 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: 1.46 Conformation dependent library (CDL) restraints added in 664.8 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: 0.56 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: 2.84 Time building geometry restraints manager: 1.92 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: 3.440 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.850 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.410 ------------------------------------------------------------------------------- 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 : 0.716 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: 0.6329 time to fit residues: 87.9656 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 : 0.446 ------------------------------------------------------------------------------- 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 = 0.105599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.068169 restraints weight = 26783.120| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.84 r_work: 0.2775 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9188 moved from start: 0.0611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 16523 Z= 0.127 Angle : 0.480 10.069 22221 Z= 0.243 Chirality : 0.039 0.197 2398 Planarity : 0.003 0.030 2635 Dihedral : 13.594 129.691 3349 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.65 % Allowed : 22.04 % 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 A 438 TRP 0.015 0.001 TRP D 168 HIS 0.003 0.001 HIS D 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (16523) covalent geometry : angle 0.47983 / 0.24 (22221) hydrogen bonds : bond 0.03766 / 2.45 ( 909) hydrogen bonds : angle 3.65661 / 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 159 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 116 time to evaluate : 0.659 Fit side-chains REVERT: A 415 ASP cc_start: 0.8826 (m-30) cc_final: 0.8458 (m-30) REVERT: A 579 ASP cc_start: 0.9119 (OUTLIER) cc_final: 0.8814 (p0) REVERT: B 415 ASP cc_start: 0.8867 (m-30) cc_final: 0.8525 (m-30) REVERT: C 415 ASP cc_start: 0.8844 (m-30) cc_final: 0.8488 (m-30) REVERT: C 476 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8893 (mmpt) REVERT: D 441 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8963 (mp) REVERT: D 452 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8391 (mp0) REVERT: D 514 ARG cc_start: 0.9119 (ttm-80) cc_final: 0.8703 (mtt90) REVERT: D 515 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7664 (pm20) outliers start: 43 outliers final: 11 residues processed: 157 average time/residue: 0.6327 time to fit residues: 110.0347 Evaluate side-chains 127 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU 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: 2.9990 chunk 26 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.102762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.065238 restraints weight = 27173.763| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 1.83 r_work: 0.2712 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9231 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 16523 Z= 0.271 Angle : 0.563 12.008 22221 Z= 0.285 Chirality : 0.044 0.191 2398 Planarity : 0.004 0.030 2635 Dihedral : 14.789 127.587 3338 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.83 % Allowed : 20.37 % Favored : 75.80 % 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: 2.29 (0.20), residues: 1788 helix: 2.22 (0.15), residues: 1160 sheet: 0.55 (0.62), residues: 48 loop : 0.22 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 514 TYR 0.017 0.002 TYR C 351 PHE 0.012 0.002 PHE B 298 TRP 0.017 0.002 TRP D 168 HIS 0.005 0.002 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00639 / 0.27 (16523) covalent geometry : angle 0.56263 / 0.29 (22221) hydrogen bonds : bond 0.04846 / 3.15 ( 909) hydrogen bonds : angle 3.94721 / 2.77 ( 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: 62 poor density : 107 time to evaluate : 0.631 Fit side-chains REVERT: B 305 MET cc_start: 0.9016 (ttm) cc_final: 0.8775 (ttp) REVERT: B 409 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8351 (tm-30) REVERT: B 441 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8971 (mp) REVERT: B 594 MET cc_start: 0.8768 (mpt) cc_final: 0.8376 (mmt) REVERT: C 305 MET cc_start: 0.9022 (ttm) cc_final: 0.8780 (ttp) REVERT: C 441 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9012 (mp) REVERT: C 476 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8872 (mmpt) REVERT: C 494 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8139 (mtpp) REVERT: D 441 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8988 (mp) REVERT: D 452 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8420 (mp0) REVERT: D 483 CYS cc_start: 0.7327 (m) cc_final: 0.6952 (m) REVERT: D 515 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8112 (pt0) outliers start: 62 outliers final: 24 residues processed: 168 average time/residue: 0.6328 time to fit residues: 118.1830 Evaluate side-chains 134 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 234 LEU 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 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 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: 0.9980 chunk 69 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 170 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN C 551 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.105356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.067980 restraints weight = 26920.467| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.83 r_work: 0.2776 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9184 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16523 Z= 0.111 Angle : 0.480 10.761 22221 Z= 0.239 Chirality : 0.039 0.140 2398 Planarity : 0.003 0.030 2635 Dihedral : 13.760 129.515 3338 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.53 % Allowed : 21.98 % 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: 2.56 (0.20), residues: 1788 helix: 2.43 (0.15), residues: 1160 sheet: 0.79 (0.64), 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 0.012 0.001 TYR C 588 PHE 0.006 0.001 PHE B 438 TRP 0.016 0.001 TRP A 168 HIS 0.002 0.001 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (16523) covalent geometry : angle 0.48045 / 0.24 (22221) hydrogen bonds : bond 0.03598 / 2.34 ( 909) hydrogen bonds : angle 3.58115 / 2.51 ( 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 153 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 112 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: A 415 ASP cc_start: 0.8823 (m-30) cc_final: 0.8444 (m-30) REVERT: A 536 VAL cc_start: 0.9542 (OUTLIER) cc_final: 0.9341 (p) REVERT: B 415 ASP cc_start: 0.8852 (m-30) cc_final: 0.8482 (m-30) REVERT: C 415 ASP cc_start: 0.8821 (m-30) cc_final: 0.8458 (m-30) REVERT: C 476 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8875 (mmpt) REVERT: C 494 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8146 (mtpp) REVERT: D 452 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8375 (mp0) REVERT: D 483 CYS cc_start: 0.7082 (m) cc_final: 0.6622 (m) REVERT: D 515 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8117 (pt0) outliers start: 41 outliers final: 18 residues processed: 151 average time/residue: 0.6336 time to fit residues: 106.1251 Evaluate side-chains 132 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 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 479 ILE 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 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 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: 5.9990 chunk 163 optimal weight: 9.9990 chunk 146 optimal weight: 0.7980 chunk 156 optimal weight: 0.5980 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: 0.8980 chunk 132 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3722 r_free = 0.3722 target = 0.105237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.067990 restraints weight = 26871.650| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.83 r_work: 0.2776 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9190 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 0.023 16523 Z= 0.118 Angle : 0.479 10.135 22221 Z= 0.239 Chirality : 0.039 0.140 2398 Planarity : 0.003 0.030 2635 Dihedral : 13.561 129.712 3338 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.84 % Allowed : 21.79 % 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: 2.60 (0.20), residues: 1788 helix: 2.46 (0.15), residues: 1160 sheet: 0.74 (0.63), residues: 48 loop : 0.34 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 514 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 A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (16523) covalent geometry : angle 0.47911 / 0.24 (22221) hydrogen bonds : bond 0.03650 / 2.38 ( 909) hydrogen bonds : angle 3.53779 / 2.47 ( 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 156 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 110 time to evaluate : 0.643 Fit side-chains REVERT: A 415 ASP cc_start: 0.8820 (m-30) cc_final: 0.8470 (m-30) REVERT: B 415 ASP cc_start: 0.8869 (m-30) cc_final: 0.8496 (m-30) REVERT: C 415 ASP cc_start: 0.8823 (m-30) cc_final: 0.8456 (m-30) REVERT: C 476 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8877 (mmpt) REVERT: C 494 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8141 (mtpp) REVERT: D 452 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8386 (mp0) REVERT: D 515 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8249 (pt0) outliers start: 46 outliers final: 15 residues processed: 155 average time/residue: 0.6113 time to fit residues: 105.4592 Evaluate side-chains 126 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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 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 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 603 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: 3.9990 chunk 75 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 145 optimal weight: 0.3980 chunk 124 optimal weight: 3.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.103116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.065758 restraints weight = 27035.663| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 1.82 r_work: 0.2727 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2583 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9222 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 16523 Z= 0.230 Angle : 0.550 9.873 22221 Z= 0.276 Chirality : 0.042 0.175 2398 Planarity : 0.003 0.030 2635 Dihedral : 14.349 128.132 3334 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % 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: 2.35 (0.20), residues: 1788 helix: 2.26 (0.15), residues: 1160 sheet: 0.56 (0.60), residues: 48 loop : 0.26 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 514 TYR 0.016 0.002 TYR A 351 PHE 0.011 0.001 PHE B 298 TRP 0.016 0.002 TRP B 168 HIS 0.005 0.001 HIS D 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.23 (16523) covalent geometry : angle 0.55019 / 0.28 (22221) hydrogen bonds : bond 0.04531 / 2.95 ( 909) hydrogen bonds : angle 3.81628 / 2.68 ( 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 149 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 105 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 476 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8882 (mmpt) REVERT: C 494 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8170 (mtpp) REVERT: D 441 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8994 (mp) REVERT: D 452 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8361 (mp0) REVERT: D 483 CYS cc_start: 0.7268 (m) cc_final: 0.6892 (m) REVERT: D 515 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8245 (pt0) outliers start: 44 outliers final: 20 residues processed: 148 average time/residue: 0.6143 time to fit residues: 101.1510 Evaluate side-chains 128 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 320 SER Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 451 LYS 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 113 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 131 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.105431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.068051 restraints weight = 26900.681| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.84 r_work: 0.2779 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9185 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16523 Z= 0.107 Angle : 0.490 10.438 22221 Z= 0.241 Chirality : 0.039 0.145 2398 Planarity : 0.003 0.030 2635 Dihedral : 13.578 129.924 3334 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.16 % Allowed : 22.96 % 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: 2.60 (0.20), residues: 1788 helix: 2.45 (0.15), residues: 1160 sheet: 0.85 (0.62), residues: 48 loop : 0.36 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 478 TYR 0.014 0.001 TYR C 588 PHE 0.006 0.001 PHE A 438 TRP 0.017 0.001 TRP A 168 HIS 0.002 0.001 HIS D 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (16523) covalent geometry : angle 0.48991 / 0.24 (22221) hydrogen bonds : bond 0.03551 / 2.32 ( 909) hydrogen bonds : angle 3.54195 / 2.48 ( 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: 35 poor density : 109 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 ASP cc_start: 0.8806 (m-30) cc_final: 0.8441 (m-30) REVERT: B 415 ASP cc_start: 0.8872 (m-30) cc_final: 0.8521 (m-30) REVERT: C 415 ASP cc_start: 0.8817 (m-30) cc_final: 0.8459 (m-30) REVERT: C 476 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8870 (mmpt) REVERT: C 494 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8149 (mtpp) REVERT: D 441 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8958 (mp) REVERT: D 452 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8334 (mp0) REVERT: D 483 CYS cc_start: 0.7205 (m) cc_final: 0.6885 (m) REVERT: D 515 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8290 (pt0) outliers start: 35 outliers final: 17 residues processed: 144 average time/residue: 0.6319 time to fit residues: 101.0763 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 : 0.596 ------------------------------------------------------------------------------- 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 320 SER Chi-restraints excluded: chain B residue 451 LYS 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 124 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 83 optimal weight: 9.9990 chunk 152 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN A 419 GLN C 551 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.103725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.066462 restraints weight = 26950.888| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.82 r_work: 0.2743 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9213 moved from start: 0.1108 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= 0.189 Angle : 0.542 13.156 22221 Z= 0.266 Chirality : 0.041 0.157 2398 Planarity : 0.003 0.030 2635 Dihedral : 14.000 129.001 3334 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.41 % Allowed : 22.84 % 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: 2.46 (0.20), residues: 1788 helix: 2.34 (0.15), residues: 1160 sheet: 0.76 (0.61), 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 0.016 0.001 TYR C 588 PHE 0.010 0.001 PHE B 298 TRP 0.015 0.001 TRP B 168 HIS 0.004 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (16523) covalent geometry : angle 0.54169 / 0.27 (22221) hydrogen bonds : bond 0.04211 / 2.74 ( 909) hydrogen bonds : angle 3.69657 / 2.59 ( 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 145 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 106 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: C 415 ASP cc_start: 0.8845 (m-30) cc_final: 0.8540 (m-30) REVERT: C 476 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8880 (mmpt) REVERT: C 494 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8175 (mtpp) REVERT: D 441 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8968 (mp) REVERT: D 452 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8347 (mp0) REVERT: D 478 ARG cc_start: 0.8409 (tmm160) cc_final: 0.8163 (ttp80) REVERT: D 483 CYS cc_start: 0.6983 (m) cc_final: 0.6709 (m) outliers start: 39 outliers final: 21 residues processed: 145 average time/residue: 0.6079 time to fit residues: 97.7292 Evaluate side-chains 128 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 401 SER Chi-restraints excluded: chain B residue 451 LYS 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 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 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: 6.9990 chunk 22 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.104173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.066883 restraints weight = 26913.563| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.83 r_work: 0.2753 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9205 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16523 Z= 0.158 Angle : 0.542 12.937 22221 Z= 0.266 Chirality : 0.040 0.147 2398 Planarity : 0.003 0.030 2635 Dihedral : 13.885 129.510 3331 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.73 % Allowed : 23.70 % Favored : 74.57 % 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 (0.20), residues: 1788 helix: 2.36 (0.15), residues: 1160 sheet: 0.81 (0.61), residues: 48 loop : 0.33 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 514 TYR 0.017 0.001 TYR C 588 PHE 0.008 0.001 PHE A 298 TRP 0.016 0.001 TRP D 168 HIS 0.004 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (16523) covalent geometry : angle 0.54162 / 0.27 (22221) hydrogen bonds : bond 0.03993 / 2.60 ( 909) hydrogen bonds : angle 3.65516 / 2.56 ( 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 133 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 415 ASP cc_start: 0.8831 (m-30) cc_final: 0.8504 (m-30) REVERT: B 582 MET cc_start: 0.9236 (mmm) cc_final: 0.9034 (mpm) REVERT: C 415 ASP cc_start: 0.8839 (m-30) cc_final: 0.8505 (m-30) REVERT: C 476 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8875 (mmpt) REVERT: C 494 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8165 (mtpp) REVERT: D 441 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8959 (mp) REVERT: D 452 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8341 (mp0) REVERT: D 483 CYS cc_start: 0.7171 (m) cc_final: 0.6802 (m) outliers start: 28 outliers final: 18 residues processed: 133 average time/residue: 0.6394 time to fit residues: 94.3573 Evaluate side-chains 124 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 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 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 279 SER 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 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: 10.0000 chunk 28 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 57 optimal weight: 0.2980 chunk 101 optimal weight: 0.8980 chunk 127 optimal weight: 0.0980 chunk 152 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 419 GLN ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.106017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.068887 restraints weight = 26925.822| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.84 r_work: 0.2790 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9157 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16523 Z= 0.099 Angle : 0.519 12.647 22221 Z= 0.248 Chirality : 0.039 0.144 2398 Planarity : 0.003 0.031 2635 Dihedral : 13.216 130.764 3331 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.54 % Allowed : 23.77 % 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: 2.97 (0.20), residues: 1788 helix: 2.83 (0.15), residues: 1112 sheet: 1.03 (0.63), residues: 48 loop : 0.52 (0.26), residues: 628 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 0.005 0.001 PHE A 438 TRP 0.018 0.001 TRP A 168 HIS 0.001 0.000 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (16523) covalent geometry : angle 0.51852 / 0.25 (22221) hydrogen bonds : bond 0.03299 / 2.16 ( 909) hydrogen bonds : angle 3.44160 / 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 130 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 415 ASP cc_start: 0.8825 (m-30) cc_final: 0.8436 (m-30) REVERT: B 415 ASP cc_start: 0.8842 (m-30) cc_final: 0.8458 (m-30) REVERT: C 415 ASP cc_start: 0.8836 (m-30) cc_final: 0.8460 (m-30) REVERT: C 476 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8883 (mmpt) REVERT: C 494 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8168 (mtpp) REVERT: D 441 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8920 (mp) REVERT: D 483 CYS cc_start: 0.7319 (m) cc_final: 0.6940 (m) outliers start: 25 outliers final: 16 residues processed: 130 average time/residue: 0.5971 time to fit residues: 86.1081 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 : 0.647 ------------------------------------------------------------------------------- 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 451 LYS 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 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 279 SER Chi-restraints excluded: chain D residue 441 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: 2.9990 chunk 134 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 58 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 160 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 = 0.3732 r_free = 0.3732 target = 0.105559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.068254 restraints weight = 26806.247| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.83 r_work: 0.2777 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9170 moved from start: 0.0971 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= 0.112 Angle : 0.515 15.455 22221 Z= 0.250 Chirality : 0.039 0.160 2398 Planarity : 0.003 0.030 2635 Dihedral : 13.216 130.707 3331 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.48 % Allowed : 24.01 % Favored : 74.51 % 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: 2.67 (0.20), residues: 1788 helix: 2.49 (0.15), residues: 1160 sheet: 1.07 (0.63), residues: 48 loop : 0.41 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 478 TYR 0.016 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 A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (16523) covalent geometry : angle 0.51515 / 0.25 (22221) hydrogen bonds : bond 0.03502 / 2.29 ( 909) hydrogen bonds : angle 3.45579 / 2.42 ( 2616) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7228.50 seconds wall clock time: 123 minutes 42.98 seconds (7422.98 seconds total)