Starting phenix.real_space_refine on Sat Sep 12 16:26:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6t9n_10418/09_2026/6t9n_10418.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t9n_10418/09_2026/6t9n_10418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6t9n_10418/09_2026/6t9n_10418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t9n_10418/09_2026/6t9n_10418.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6t9n_10418/09_2026/6t9n_10418.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6t9n_10418/09_2026/6t9n_10418.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6t9n_10418/09_2026/6t9n_10418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t9n_10418/09_2026/6t9n_10418.map" } resolution = 2.96 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 80 5.16 5 C 11232 2.51 5 N 2504 2.21 5 O 3100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16917 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3917 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 10, 'TRANS': 469} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 6, 'TYR:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3917 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 10, 'TRANS': 469} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 6, 'TYR:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3917 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 10, 'TRANS': 469} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 6, 'TYR:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3917 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 10, 'TRANS': 469} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 6, 'TYR:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 319 Unusual residues: {' CA': 1, 'CLR': 1, 'NAG': 2, 'UMQ': 9} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen chiralities: 22 Chain: "B" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 250 Unusual residues: {'CLR': 1, 'NAG': 2, 'UMQ': 7} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen chiralities: 22 Chain: "C" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 284 Unusual residues: {'CLR': 1, 'NAG': 2, 'UMQ': 8} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen chiralities: 22 Chain: "D" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 284 Unusual residues: {'CLR': 1, 'NAG': 2, 'UMQ': 8} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen chiralities: 22 Time building chain proxies: 4.09, per 1000 atoms: 0.24 Number of scatterers: 16917 At special positions: 0 Unit cell: (112.614, 112.614, 108.504, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 80 16.00 O 3100 8.00 N 2504 7.00 C 11232 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 344 " distance=2.04 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 344 " distance=2.04 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 344 " distance=2.04 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 344 " distance=2.04 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A 802 " - " ASN A 328 " " NAG A 803 " - " ASN A 362 " " NAG B 802 " - " ASN B 328 " " NAG B 803 " - " ASN B 362 " " NAG C 802 " - " ASN C 328 " " NAG C 803 " - " ASN C 362 " " NAG D 802 " - " ASN D 328 " " NAG D 803 " - " ASN D 362 " " NAG E 1 " - " ASN A 375 " " NAG F 1 " - " ASN B 375 " " NAG G 1 " - " ASN C 375 " " NAG H 1 " - " ASN D 375 " Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 742.6 milliseconds 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3688 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 12 sheets defined 58.8% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 213 through 242 removed outlier: 3.970A pdb=" N MET A 242 " --> pdb=" O THR A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 258 removed outlier: 4.181A pdb=" N MET A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET A 253 " --> pdb=" O TYR A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 285 Processing helix chain 'A' and resid 285 through 292 Processing helix chain 'A' and resid 334 through 338 removed outlier: 3.836A pdb=" N ARG A 338 " --> pdb=" O GLN A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 412 Processing helix chain 'A' and resid 467 through 496 Processing helix chain 'A' and resid 506 through 528 Processing helix chain 'A' and resid 532 through 539 removed outlier: 3.669A pdb=" N LEU A 536 " --> pdb=" O VAL A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 573 removed outlier: 3.707A pdb=" N LEU A 573 " --> pdb=" O VAL A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 576 No H-bonds generated for 'chain 'A' and resid 574 through 576' Processing helix chain 'A' and resid 580 through 620 removed outlier: 5.009A pdb=" N LYS A 595 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ASP A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 627 Processing helix chain 'A' and resid 628 through 642 Processing helix chain 'A' and resid 645 through 653 removed outlier: 3.728A pdb=" N ILE A 649 " --> pdb=" O ASN A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 668 Processing helix chain 'A' and resid 672 through 698 removed outlier: 4.285A pdb=" N PHE A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 242 removed outlier: 3.970A pdb=" N MET B 242 " --> pdb=" O THR B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 258 removed outlier: 4.181A pdb=" N MET B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET B 253 " --> pdb=" O TYR B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 285 Processing helix chain 'B' and resid 285 through 292 Processing helix chain 'B' and resid 334 through 338 removed outlier: 3.835A pdb=" N ARG B 338 " --> pdb=" O GLN B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 412 Processing helix chain 'B' and resid 467 through 496 Processing helix chain 'B' and resid 506 through 528 Processing helix chain 'B' and resid 532 through 539 removed outlier: 3.669A pdb=" N LEU B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 573 removed outlier: 3.707A pdb=" N LEU B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 576 No H-bonds generated for 'chain 'B' and resid 574 through 576' Processing helix chain 'B' and resid 580 through 620 removed outlier: 5.010A pdb=" N LYS B 595 " --> pdb=" O SER B 591 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ASP B 596 " --> pdb=" O ARG B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 627 Processing helix chain 'B' and resid 628 through 642 Processing helix chain 'B' and resid 645 through 653 removed outlier: 3.728A pdb=" N ILE B 649 " --> pdb=" O ASN B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 668 Processing helix chain 'B' and resid 672 through 698 removed outlier: 4.286A pdb=" N PHE B 676 " --> pdb=" O LEU B 672 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 242 removed outlier: 3.970A pdb=" N MET C 242 " --> pdb=" O THR C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 258 removed outlier: 4.182A pdb=" N MET C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET C 253 " --> pdb=" O TYR C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 285 Processing helix chain 'C' and resid 285 through 292 Processing helix chain 'C' and resid 334 through 338 removed outlier: 3.836A pdb=" N ARG C 338 " --> pdb=" O GLN C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 412 Processing helix chain 'C' and resid 467 through 496 Processing helix chain 'C' and resid 506 through 528 Processing helix chain 'C' and resid 532 through 539 removed outlier: 3.668A pdb=" N LEU C 536 " --> pdb=" O VAL C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 573 removed outlier: 3.707A pdb=" N LEU C 573 " --> pdb=" O VAL C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 576 No H-bonds generated for 'chain 'C' and resid 574 through 576' Processing helix chain 'C' and resid 580 through 620 removed outlier: 5.009A pdb=" N LYS C 595 " --> pdb=" O SER C 591 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ASP C 596 " --> pdb=" O ARG C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 627 Processing helix chain 'C' and resid 628 through 642 Processing helix chain 'C' and resid 645 through 653 removed outlier: 3.728A pdb=" N ILE C 649 " --> pdb=" O ASN C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 668 Processing helix chain 'C' and resid 672 through 698 removed outlier: 4.285A pdb=" N PHE C 676 " --> pdb=" O LEU C 672 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 242 removed outlier: 3.970A pdb=" N MET D 242 " --> pdb=" O THR D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 258 removed outlier: 4.181A pdb=" N MET D 252 " --> pdb=" O TYR D 248 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET D 253 " --> pdb=" O TYR D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 285 Processing helix chain 'D' and resid 285 through 292 Processing helix chain 'D' and resid 334 through 338 removed outlier: 3.836A pdb=" N ARG D 338 " --> pdb=" O GLN D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 412 Processing helix chain 'D' and resid 467 through 496 Processing helix chain 'D' and resid 506 through 528 Processing helix chain 'D' and resid 532 through 539 removed outlier: 3.668A pdb=" N LEU D 536 " --> pdb=" O VAL D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 573 removed outlier: 3.709A pdb=" N LEU D 573 " --> pdb=" O VAL D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 576 No H-bonds generated for 'chain 'D' and resid 574 through 576' Processing helix chain 'D' and resid 580 through 620 removed outlier: 5.010A pdb=" N LYS D 595 " --> pdb=" O SER D 591 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ASP D 596 " --> pdb=" O ARG D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 627 Processing helix chain 'D' and resid 628 through 642 Processing helix chain 'D' and resid 645 through 653 removed outlier: 3.728A pdb=" N ILE D 649 " --> pdb=" O ASN D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 668 Processing helix chain 'D' and resid 672 through 698 removed outlier: 4.285A pdb=" N PHE D 676 " --> pdb=" O LEU D 672 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 308 through 309 removed outlier: 6.522A pdb=" N LEU A 324 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR A 422 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ARG A 322 " --> pdb=" O THR A 422 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE A 424 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ARG A 320 " --> pdb=" O ILE A 424 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 308 through 309 Processing sheet with id=AA3, first strand: chain 'A' and resid 379 through 380 Processing sheet with id=AA4, first strand: chain 'B' and resid 308 through 309 removed outlier: 6.522A pdb=" N LEU B 324 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR B 422 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ARG B 322 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE B 424 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG B 320 " --> pdb=" O ILE B 424 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 308 through 309 Processing sheet with id=AA6, first strand: chain 'B' and resid 379 through 380 Processing sheet with id=AA7, first strand: chain 'C' and resid 308 through 309 removed outlier: 6.521A pdb=" N LEU C 324 " --> pdb=" O ARG C 420 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR C 422 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ARG C 322 " --> pdb=" O THR C 422 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE C 424 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG C 320 " --> pdb=" O ILE C 424 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 308 through 309 Processing sheet with id=AA9, first strand: chain 'C' and resid 379 through 380 Processing sheet with id=AB1, first strand: chain 'D' and resid 308 through 309 removed outlier: 6.522A pdb=" N LEU D 324 " --> pdb=" O ARG D 420 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR D 422 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ARG D 322 " --> pdb=" O THR D 422 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ILE D 424 " --> pdb=" O ARG D 320 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG D 320 " --> pdb=" O ILE D 424 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 308 through 309 Processing sheet with id=AB3, first strand: chain 'D' and resid 379 through 380 965 hydrogen bonds defined for protein. 2787 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: 2.66 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3265 1.33 - 1.45: 4748 1.45 - 1.57: 9206 1.57 - 1.70: 13 1.70 - 1.82: 124 Bond restraints: 17356 Sorted by residual: bond pdb=" C1' UMQ B 809 " pdb=" O5' UMQ B 809 " ideal model delta sigma weight residual 1.405 1.491 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C1' UMQ D 809 " pdb=" O5' UMQ D 809 " ideal model delta sigma weight residual 1.405 1.491 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C1' UMQ C 809 " pdb=" O5' UMQ C 809 " ideal model delta sigma weight residual 1.405 1.490 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C1' UMQ A 809 " pdb=" O5' UMQ A 809 " ideal model delta sigma weight residual 1.405 1.490 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C1' UMQ A 809 " pdb=" C2' UMQ A 809 " ideal model delta sigma weight residual 1.525 1.599 -0.074 2.00e-02 2.50e+03 1.39e+01 ... (remaining 17351 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 22582 2.66 - 5.32: 795 5.32 - 7.98: 119 7.98 - 10.65: 8 10.65 - 13.31: 8 Bond angle restraints: 23512 Sorted by residual: angle pdb=" CA LEU B 374 " pdb=" CB LEU B 374 " pdb=" CG LEU B 374 " ideal model delta sigma weight residual 116.30 129.61 -13.31 3.50e+00 8.16e-02 1.45e+01 angle pdb=" CA LEU A 374 " pdb=" CB LEU A 374 " pdb=" CG LEU A 374 " ideal model delta sigma weight residual 116.30 129.57 -13.27 3.50e+00 8.16e-02 1.44e+01 angle pdb=" CA LEU D 374 " pdb=" CB LEU D 374 " pdb=" CG LEU D 374 " ideal model delta sigma weight residual 116.30 129.56 -13.26 3.50e+00 8.16e-02 1.44e+01 angle pdb=" CA LEU C 374 " pdb=" CB LEU C 374 " pdb=" CG LEU C 374 " ideal model delta sigma weight residual 116.30 129.55 -13.25 3.50e+00 8.16e-02 1.43e+01 angle pdb=" C ARG C 361 " pdb=" N ASN C 362 " pdb=" CA ASN C 362 " ideal model delta sigma weight residual 122.79 117.02 5.77 1.63e+00 3.76e-01 1.25e+01 ... (remaining 23507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.32: 8892 14.32 - 28.64: 532 28.64 - 42.96: 148 42.96 - 57.28: 64 57.28 - 71.60: 16 Dihedral angle restraints: 9652 sinusoidal: 3956 harmonic: 5696 Sorted by residual: dihedral pdb=" CB CYS B 331 " pdb=" SG CYS B 331 " pdb=" SG CYS B 344 " pdb=" CB CYS B 344 " ideal model delta sinusoidal sigma weight residual 93.00 164.60 -71.60 1 1.00e+01 1.00e-02 6.57e+01 dihedral pdb=" CB CYS D 331 " pdb=" SG CYS D 331 " pdb=" SG CYS D 344 " pdb=" CB CYS D 344 " ideal model delta sinusoidal sigma weight residual 93.00 164.55 -71.55 1 1.00e+01 1.00e-02 6.56e+01 dihedral pdb=" CB CYS A 331 " pdb=" SG CYS A 331 " pdb=" SG CYS A 344 " pdb=" CB CYS A 344 " ideal model delta sinusoidal sigma weight residual 93.00 164.53 -71.53 1 1.00e+01 1.00e-02 6.56e+01 ... (remaining 9649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2051 0.068 - 0.135: 530 0.135 - 0.203: 185 0.203 - 0.270: 38 0.270 - 0.338: 8 Chirality restraints: 2812 Sorted by residual: chirality pdb=" C4' UMQ A 811 " pdb=" C3' UMQ A 811 " pdb=" C5' UMQ A 811 " pdb=" O1 UMQ A 811 " both_signs ideal model delta sigma weight residual False -2.54 -2.88 0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" C4' UMQ A 814 " pdb=" C3' UMQ A 814 " pdb=" C5' UMQ A 814 " pdb=" O1 UMQ A 814 " both_signs ideal model delta sigma weight residual False -2.54 -2.88 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" C4' UMQ C 811 " pdb=" C3' UMQ C 811 " pdb=" C5' UMQ C 811 " pdb=" O1 UMQ C 811 " both_signs ideal model delta sigma weight residual False -2.54 -2.88 0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 2809 not shown) Planarity restraints: 2740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 362 " -0.023 2.00e-02 2.50e+03 2.45e-02 7.52e+00 pdb=" CG ASN B 362 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN B 362 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B 362 " 0.038 2.00e-02 2.50e+03 pdb=" C1 NAG B 803 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 362 " -0.023 2.00e-02 2.50e+03 2.43e-02 7.40e+00 pdb=" CG ASN C 362 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN C 362 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN C 362 " 0.037 2.00e-02 2.50e+03 pdb=" C1 NAG C 803 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 362 " 0.023 2.00e-02 2.50e+03 2.43e-02 7.36e+00 pdb=" CG ASN D 362 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN D 362 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN D 362 " -0.037 2.00e-02 2.50e+03 pdb=" C1 NAG D 803 " 0.028 2.00e-02 2.50e+03 ... (remaining 2737 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2674 2.75 - 3.29: 15219 3.29 - 3.83: 28428 3.83 - 4.36: 35538 4.36 - 4.90: 60455 Nonbonded interactions: 142314 Sorted by model distance: nonbonded pdb=" OH TYR C 227 " pdb=" O VAL C 569 " model vdw 2.216 3.040 nonbonded pdb=" O GLU A 340 " pdb=" NH2 ARG D 306 " model vdw 2.217 3.120 nonbonded pdb=" OH TYR D 227 " pdb=" O VAL D 569 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR A 227 " pdb=" O VAL A 569 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR B 227 " pdb=" O VAL B 569 " model vdw 2.217 3.040 ... (remaining 142309 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 213 through 810 or (resid 811 through 812 and (name CA or \ name CB or name CG or name CD or name CH or name C1' or name C2' or name C3' or \ name C4' or name C5' or name C6' or name CC or name CF or name CI or name CJ or \ name CK or name CL or name O1 or name O1' or name O2' or name O3' or name O5' or \ name O6')))) selection = chain 'B' selection = (chain 'C' and (resid 213 through 810 or (resid 811 through 812 and (name CA or \ name CB or name CG or name CD or name CH or name C1' or name C2' or name C3' or \ name C4' or name C5' or name C6' or name CC or name CF or name CI or name CJ or \ name CK or name CL or name O1 or name O1' or name O2' or name O3' or name O5' or \ name O6')))) selection = (chain 'D' and (resid 213 through 810 or (resid 811 through 812 and (name CA or \ name CB or name CG or name CD or name CH or name C1' or name C2' or name C3' or \ name C4' or name C5' or name C6' or name CC or name CF or name CI or name CJ or \ name CK or name CL or name O1 or name O1' or name O2' or name O3' or name O5' or \ name O6')))) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 1.040 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.570 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:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 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 : 0.012 0.090 17376 Z= 0.509 Angle : 1.194 13.308 23568 Z= 0.584 Chirality : 0.074 0.338 2812 Planarity : 0.006 0.064 2728 Dihedral : 11.555 63.081 5952 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.15 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.35 (0.15), residues: 1904 helix: -2.18 (0.11), residues: 1100 sheet: -1.74 (0.33), residues: 200 loop : -2.02 (0.19), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 251 TYR 0.029 0.004 TYR D 249 PHE 0.028 0.004 PHE D 600 TRP 0.042 0.005 TRP D 293 HIS 0.006 0.003 HIS C 501 Details of bonding type rmsd/Z covalent geometry : bond 0.01175 / 0.51 (17356) covalent geometry : angle 1.16503 / 0.58 (23512) SS BOND : bond 0.00513 / 0.26 ( 4) SS BOND : angle 4.65610 / 2.58 ( 8) hydrogen bonds : bond 0.15578 / 9.97 ( 949) hydrogen bonds : angle 7.18127 / 4.96 ( 2787) link_BETA1-4 : bond 0.00160 / 0.08 ( 4) link_BETA1-4 : angle 4.27080 / 2.82 ( 12) link_NAG-ASN : bond 0.01208 / 0.82 ( 12) link_NAG-ASN : angle 6.01513 / 4.20 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 0.564 Fit side-chains REVERT: A 575 LYS cc_start: 0.8603 (mtpt) cc_final: 0.8353 (mtpp) REVERT: B 499 LYS cc_start: 0.7715 (mmmt) cc_final: 0.7020 (mmtt) REVERT: B 575 LYS cc_start: 0.8631 (mtpt) cc_final: 0.8427 (mtpp) REVERT: C 499 LYS cc_start: 0.7743 (mmmt) cc_final: 0.7052 (mmtt) REVERT: D 255 GLN cc_start: 0.8165 (mt0) cc_final: 0.7965 (mt0) REVERT: D 267 LYS cc_start: 0.8241 (mtmm) cc_final: 0.8026 (mtpt) REVERT: D 499 LYS cc_start: 0.7669 (mmmt) cc_final: 0.7012 (mmtt) REVERT: D 575 LYS cc_start: 0.8514 (mtpt) cc_final: 0.8239 (mtpp) outliers start: 0 outliers final: 4 residues processed: 326 average time/residue: 0.4841 time to fit residues: 180.1354 Evaluate side-chains 215 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 211 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 690 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 GLN A 580 ASN A 636 GLN B 313 ASN B 323 GLN B 580 ASN B 636 GLN C 323 GLN C 580 ASN C 636 GLN D 323 GLN D 636 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.136279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.106008 restraints weight = 19508.709| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.56 r_work: 0.2935 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17376 Z= 0.149 Angle : 0.608 8.564 23568 Z= 0.302 Chirality : 0.042 0.312 2812 Planarity : 0.004 0.045 2728 Dihedral : 11.174 56.336 2464 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.05 % Favored : 98.74 % Rotamer: Outliers : 2.08 % Allowed : 8.27 % Favored : 89.64 % 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: -1.01 (0.17), residues: 1904 helix: -0.05 (0.14), residues: 1108 sheet: -1.47 (0.32), residues: 200 loop : -1.33 (0.22), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 306 TYR 0.013 0.002 TYR A 616 PHE 0.023 0.001 PHE D 600 TRP 0.015 0.002 TRP C 554 HIS 0.003 0.001 HIS C 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (17356) covalent geometry : angle 0.58421 / 0.30 (23512) SS BOND : bond 0.00100 / 0.05 ( 4) SS BOND : angle 1.47577 / 0.80 ( 8) hydrogen bonds : bond 0.04945 / 3.19 ( 949) hydrogen bonds : angle 4.88968 / 3.36 ( 2787) link_BETA1-4 : bond 0.00382 / 0.19 ( 4) link_BETA1-4 : angle 1.87852 / 1.26 ( 12) link_NAG-ASN : bond 0.00470 / 0.31 ( 12) link_NAG-ASN : angle 4.14478 / 2.87 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 240 time to evaluate : 0.636 Fit side-chains REVERT: A 559 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.7756 (m-40) REVERT: A 575 LYS cc_start: 0.8732 (mtpt) cc_final: 0.8393 (mtpp) REVERT: A 624 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7768 (p0) REVERT: A 690 ASP cc_start: 0.7531 (t0) cc_final: 0.6970 (m-30) REVERT: B 242 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7440 (mmt) REVERT: B 464 ARG cc_start: 0.8155 (mmm160) cc_final: 0.7937 (mmm-85) REVERT: B 575 LYS cc_start: 0.8736 (mtpt) cc_final: 0.8412 (mtpp) REVERT: B 624 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7715 (p0) REVERT: B 690 ASP cc_start: 0.7580 (t0) cc_final: 0.6998 (m-30) REVERT: C 537 GLN cc_start: 0.8254 (tt0) cc_final: 0.8009 (mt0) REVERT: C 559 ASN cc_start: 0.8348 (OUTLIER) cc_final: 0.7725 (m-40) REVERT: C 575 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8563 (mtpp) REVERT: C 624 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7763 (p0) REVERT: C 690 ASP cc_start: 0.7592 (t0) cc_final: 0.7043 (m-30) REVERT: D 267 LYS cc_start: 0.8361 (mtmm) cc_final: 0.7856 (mtpt) REVERT: D 537 GLN cc_start: 0.8292 (tt0) cc_final: 0.8002 (tt0) REVERT: D 559 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.7727 (m-40) REVERT: D 575 LYS cc_start: 0.8688 (mtpt) cc_final: 0.8349 (mtpp) REVERT: D 624 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7788 (p0) outliers start: 35 outliers final: 10 residues processed: 265 average time/residue: 0.4447 time to fit residues: 136.4298 Evaluate side-chains 215 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 196 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 559 ASN Chi-restraints excluded: chain D residue 624 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 144 optimal weight: 20.0000 chunk 105 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 171 optimal weight: 7.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 636 GLN B 636 GLN C 313 ASN C 636 GLN D 313 ASN D 636 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.138054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.106749 restraints weight = 19520.807| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.66 r_work: 0.2893 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 17376 Z= 0.159 Angle : 0.574 8.198 23568 Z= 0.281 Chirality : 0.041 0.271 2812 Planarity : 0.004 0.042 2728 Dihedral : 10.790 58.556 2456 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.73 % Favored : 98.06 % Rotamer: Outliers : 3.15 % Allowed : 9.11 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.18), residues: 1904 helix: 0.95 (0.15), residues: 1096 sheet: -1.36 (0.32), residues: 200 loop : -0.88 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 251 TYR 0.012 0.002 TYR B 616 PHE 0.022 0.001 PHE D 600 TRP 0.013 0.002 TRP C 554 HIS 0.003 0.001 HIS A 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (17356) covalent geometry : angle 0.55263 / 0.28 (23512) SS BOND : bond 0.00267 / 0.13 ( 4) SS BOND : angle 1.03014 / 0.59 ( 8) hydrogen bonds : bond 0.04606 / 2.98 ( 949) hydrogen bonds : angle 4.50174 / 3.10 ( 2787) link_BETA1-4 : bond 0.00258 / 0.13 ( 4) link_BETA1-4 : angle 1.78546 / 1.17 ( 12) link_NAG-ASN : bond 0.00628 / 0.41 ( 12) link_NAG-ASN : angle 3.90939 / 2.75 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 221 time to evaluate : 0.679 Fit side-chains REVERT: A 559 ASN cc_start: 0.8457 (OUTLIER) cc_final: 0.7910 (m-40) REVERT: A 624 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.8032 (p0) REVERT: B 228 LEU cc_start: 0.8900 (mt) cc_final: 0.8689 (mt) REVERT: B 242 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7502 (mmt) REVERT: B 624 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.7988 (p0) REVERT: C 228 LEU cc_start: 0.8879 (mt) cc_final: 0.8673 (mt) REVERT: C 344 CYS cc_start: 0.7823 (p) cc_final: 0.7322 (t) REVERT: C 537 GLN cc_start: 0.8289 (tt0) cc_final: 0.8082 (mt0) REVERT: C 559 ASN cc_start: 0.8373 (OUTLIER) cc_final: 0.7798 (m-40) REVERT: C 575 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8665 (mtpp) REVERT: C 624 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8000 (p0) REVERT: C 677 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8580 (tt) REVERT: C 681 ASN cc_start: 0.8520 (OUTLIER) cc_final: 0.8209 (m-40) REVERT: D 267 LYS cc_start: 0.8383 (mtmm) cc_final: 0.7898 (mtpt) REVERT: D 337 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7482 (mp) REVERT: D 537 GLN cc_start: 0.8285 (tt0) cc_final: 0.8046 (tt0) REVERT: D 559 ASN cc_start: 0.8367 (OUTLIER) cc_final: 0.7817 (m-40) REVERT: D 624 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.8048 (p0) REVERT: D 681 ASN cc_start: 0.8445 (OUTLIER) cc_final: 0.8109 (m110) REVERT: D 690 ASP cc_start: 0.7900 (m-30) cc_final: 0.7433 (t0) outliers start: 53 outliers final: 14 residues processed: 259 average time/residue: 0.4154 time to fit residues: 125.9574 Evaluate side-chains 232 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 205 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain C residue 681 ASN Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 559 ASN Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 651 GLU Chi-restraints excluded: chain D residue 681 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 34 optimal weight: 0.9980 chunk 176 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 ASN B 636 GLN C 636 GLN D 580 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.137238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.106912 restraints weight = 19424.038| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.56 r_work: 0.2968 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 17376 Z= 0.116 Angle : 0.534 8.688 23568 Z= 0.260 Chirality : 0.040 0.256 2812 Planarity : 0.003 0.040 2728 Dihedral : 10.361 58.982 2456 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.10 % Favored : 98.69 % Rotamer: Outliers : 2.38 % Allowed : 11.01 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.18), residues: 1904 helix: 1.34 (0.15), residues: 1096 sheet: -1.29 (0.32), residues: 200 loop : -0.70 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 361 TYR 0.012 0.001 TYR D 292 PHE 0.021 0.001 PHE D 600 TRP 0.011 0.001 TRP C 554 HIS 0.001 0.001 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (17356) covalent geometry : angle 0.51281 / 0.26 (23512) SS BOND : bond 0.00135 / 0.07 ( 4) SS BOND : angle 0.96960 / 0.54 ( 8) hydrogen bonds : bond 0.04193 / 2.71 ( 949) hydrogen bonds : angle 4.27880 / 2.94 ( 2787) link_BETA1-4 : bond 0.00352 / 0.18 ( 4) link_BETA1-4 : angle 1.61322 / 1.06 ( 12) link_NAG-ASN : bond 0.00481 / 0.32 ( 12) link_NAG-ASN : angle 3.75768 / 2.64 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 238 time to evaluate : 0.618 Fit side-chains REVERT: A 344 CYS cc_start: 0.7706 (p) cc_final: 0.7279 (t) REVERT: A 559 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.7887 (m-40) REVERT: A 643 ASP cc_start: 0.7909 (t70) cc_final: 0.7457 (t0) REVERT: A 690 ASP cc_start: 0.7588 (t0) cc_final: 0.7241 (t0) REVERT: B 228 LEU cc_start: 0.8806 (mt) cc_final: 0.8599 (mt) REVERT: B 344 CYS cc_start: 0.7677 (p) cc_final: 0.7313 (t) REVERT: B 643 ASP cc_start: 0.7929 (t70) cc_final: 0.7469 (t0) REVERT: C 228 LEU cc_start: 0.8783 (mt) cc_final: 0.8570 (mt) REVERT: C 349 SER cc_start: 0.8584 (OUTLIER) cc_final: 0.8236 (p) REVERT: C 559 ASN cc_start: 0.8375 (OUTLIER) cc_final: 0.7807 (m-40) REVERT: C 575 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8624 (mtpp) REVERT: C 643 ASP cc_start: 0.7927 (t70) cc_final: 0.7502 (t0) REVERT: D 344 CYS cc_start: 0.7694 (p) cc_final: 0.7155 (t) REVERT: D 537 GLN cc_start: 0.8198 (tt0) cc_final: 0.7992 (tt0) REVERT: D 559 ASN cc_start: 0.8397 (OUTLIER) cc_final: 0.7842 (m-40) REVERT: D 643 ASP cc_start: 0.8042 (t70) cc_final: 0.7585 (t0) REVERT: D 690 ASP cc_start: 0.7885 (m-30) cc_final: 0.7374 (t0) outliers start: 40 outliers final: 9 residues processed: 268 average time/residue: 0.4162 time to fit residues: 130.0440 Evaluate side-chains 227 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 213 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 559 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 164 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 0.0870 chunk 94 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 53 optimal weight: 0.0470 overall best weight: 1.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 653 ASN A 681 ASN B 636 GLN C 636 GLN C 653 ASN D 580 ASN D 653 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.139653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.109218 restraints weight = 19182.076| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.60 r_work: 0.2941 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 17376 Z= 0.113 Angle : 0.534 8.526 23568 Z= 0.257 Chirality : 0.040 0.280 2812 Planarity : 0.003 0.039 2728 Dihedral : 10.058 59.851 2456 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.68 % Favored : 98.11 % Rotamer: Outliers : 2.20 % Allowed : 12.56 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.19), residues: 1904 helix: 1.53 (0.15), residues: 1096 sheet: -1.25 (0.31), residues: 200 loop : -0.54 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 361 TYR 0.011 0.001 TYR D 292 PHE 0.020 0.001 PHE C 600 TRP 0.010 0.001 TRP C 554 HIS 0.001 0.000 HIS B 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (17356) covalent geometry : angle 0.51233 / 0.25 (23512) SS BOND : bond 0.00202 / 0.10 ( 4) SS BOND : angle 0.78078 / 0.42 ( 8) hydrogen bonds : bond 0.04077 / 2.63 ( 949) hydrogen bonds : angle 4.16191 / 2.86 ( 2787) link_BETA1-4 : bond 0.00329 / 0.17 ( 4) link_BETA1-4 : angle 1.51702 / 1.00 ( 12) link_NAG-ASN : bond 0.00695 / 0.46 ( 12) link_NAG-ASN : angle 3.81058 / 2.66 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 236 time to evaluate : 0.652 Fit side-chains REVERT: A 242 MET cc_start: 0.7788 (tpt) cc_final: 0.7448 (mmt) REVERT: A 411 LYS cc_start: 0.8636 (ttpt) cc_final: 0.8372 (ttpt) REVERT: A 559 ASN cc_start: 0.8498 (OUTLIER) cc_final: 0.7937 (m-40) REVERT: A 643 ASP cc_start: 0.8011 (t70) cc_final: 0.7610 (t0) REVERT: B 228 LEU cc_start: 0.8790 (mt) cc_final: 0.8589 (mt) REVERT: B 344 CYS cc_start: 0.7732 (p) cc_final: 0.7328 (t) REVERT: B 643 ASP cc_start: 0.7913 (t70) cc_final: 0.7500 (t0) REVERT: C 344 CYS cc_start: 0.7708 (p) cc_final: 0.7402 (t) REVERT: C 349 SER cc_start: 0.8528 (OUTLIER) cc_final: 0.8181 (p) REVERT: C 559 ASN cc_start: 0.8384 (OUTLIER) cc_final: 0.7847 (m-40) REVERT: C 575 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8619 (mtpp) REVERT: C 643 ASP cc_start: 0.7960 (t70) cc_final: 0.7569 (t0) REVERT: D 267 LYS cc_start: 0.8374 (mtmm) cc_final: 0.7865 (mtpt) REVERT: D 337 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7472 (mp) REVERT: D 559 ASN cc_start: 0.8420 (OUTLIER) cc_final: 0.7884 (m-40) REVERT: D 643 ASP cc_start: 0.8040 (t70) cc_final: 0.7627 (OUTLIER) REVERT: D 690 ASP cc_start: 0.7933 (m-30) cc_final: 0.7396 (t0) outliers start: 37 outliers final: 14 residues processed: 261 average time/residue: 0.4317 time to fit residues: 131.2015 Evaluate side-chains 225 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 206 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 361 ARG Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 559 ASN Chi-restraints excluded: chain D residue 651 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 63 optimal weight: 0.9980 chunk 175 optimal weight: 20.0000 chunk 72 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 681 ASN B 379 HIS B 636 GLN D 580 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.139810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.109323 restraints weight = 19228.699| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.61 r_work: 0.2979 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17376 Z= 0.113 Angle : 0.544 9.461 23568 Z= 0.260 Chirality : 0.040 0.286 2812 Planarity : 0.003 0.039 2728 Dihedral : 9.777 59.317 2456 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.73 % Favored : 98.06 % Rotamer: Outliers : 2.74 % Allowed : 13.10 % Favored : 84.17 % 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: 1.12 (0.19), residues: 1904 helix: 1.80 (0.15), residues: 1072 sheet: -1.07 (0.31), residues: 200 loop : -0.41 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 361 TYR 0.012 0.001 TYR D 292 PHE 0.019 0.001 PHE D 600 TRP 0.009 0.001 TRP D 554 HIS 0.001 0.000 HIS B 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (17356) covalent geometry : angle 0.52255 / 0.26 (23512) SS BOND : bond 0.00054 / 0.03 ( 4) SS BOND : angle 0.72776 / 0.40 ( 8) hydrogen bonds : bond 0.04026 / 2.60 ( 949) hydrogen bonds : angle 4.10470 / 2.82 ( 2787) link_BETA1-4 : bond 0.00278 / 0.14 ( 4) link_BETA1-4 : angle 1.44187 / 0.95 ( 12) link_NAG-ASN : bond 0.00524 / 0.34 ( 12) link_NAG-ASN : angle 3.78741 / 2.64 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 224 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 LYS cc_start: 0.8643 (ttpt) cc_final: 0.8375 (ttpt) REVERT: A 559 ASN cc_start: 0.8495 (OUTLIER) cc_final: 0.7973 (m-40) REVERT: A 643 ASP cc_start: 0.7922 (t70) cc_final: 0.7545 (t0) REVERT: B 643 ASP cc_start: 0.7921 (t70) cc_final: 0.7559 (t0) REVERT: C 344 CYS cc_start: 0.7730 (p) cc_final: 0.7386 (t) REVERT: C 361 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7733 (mtp85) REVERT: C 559 ASN cc_start: 0.8409 (OUTLIER) cc_final: 0.7887 (m-40) REVERT: C 575 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8565 (mtpp) REVERT: C 643 ASP cc_start: 0.7886 (t70) cc_final: 0.7536 (t0) REVERT: D 337 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7510 (mp) REVERT: D 361 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7555 (mtp85) REVERT: D 559 ASN cc_start: 0.8446 (OUTLIER) cc_final: 0.7908 (m-40) REVERT: D 643 ASP cc_start: 0.7953 (t70) cc_final: 0.7589 (t0) outliers start: 46 outliers final: 14 residues processed: 260 average time/residue: 0.4292 time to fit residues: 130.1628 Evaluate side-chains 228 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 207 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 361 ARG Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 361 ARG Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 559 ASN Chi-restraints excluded: chain D residue 651 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 178 optimal weight: 0.8980 chunk 143 optimal weight: 5.9990 chunk 75 optimal weight: 0.0270 chunk 53 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 147 optimal weight: 0.5980 chunk 32 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 overall best weight: 1.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 653 ASN A 681 ASN B 636 GLN C 636 GLN C 653 ASN D 379 HIS D 580 ASN D 653 ASN D 681 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.139443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.109452 restraints weight = 19365.672| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.57 r_work: 0.2943 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17376 Z= 0.118 Angle : 0.562 8.891 23568 Z= 0.267 Chirality : 0.040 0.273 2812 Planarity : 0.003 0.039 2728 Dihedral : 9.600 59.990 2456 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.89 % Favored : 97.90 % Rotamer: Outliers : 2.32 % Allowed : 13.39 % Favored : 84.29 % 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: 1.24 (0.19), residues: 1904 helix: 1.88 (0.15), residues: 1072 sheet: -0.99 (0.32), residues: 200 loop : -0.33 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 361 TYR 0.018 0.001 TYR A 486 PHE 0.018 0.001 PHE C 600 TRP 0.009 0.001 TRP A 554 HIS 0.001 0.000 HIS B 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (17356) covalent geometry : angle 0.53631 / 0.26 (23512) SS BOND : bond 0.00109 / 0.06 ( 4) SS BOND : angle 3.18633 / 1.69 ( 8) hydrogen bonds : bond 0.04019 / 2.60 ( 949) hydrogen bonds : angle 4.08416 / 2.80 ( 2787) link_BETA1-4 : bond 0.00240 / 0.12 ( 4) link_BETA1-4 : angle 1.40702 / 0.93 ( 12) link_NAG-ASN : bond 0.00306 / 0.20 ( 12) link_NAG-ASN : angle 3.97345 / 2.75 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 213 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 559 ASN cc_start: 0.8477 (OUTLIER) cc_final: 0.7950 (m-40) REVERT: A 643 ASP cc_start: 0.7917 (t70) cc_final: 0.7545 (t0) REVERT: B 643 ASP cc_start: 0.7862 (t70) cc_final: 0.7506 (t0) REVERT: C 349 SER cc_start: 0.8529 (OUTLIER) cc_final: 0.8163 (p) REVERT: C 361 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7463 (mtp85) REVERT: C 559 ASN cc_start: 0.8415 (OUTLIER) cc_final: 0.7883 (m-40) REVERT: C 575 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8568 (mtpp) REVERT: C 643 ASP cc_start: 0.7886 (t70) cc_final: 0.7539 (t0) REVERT: D 337 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7457 (mp) REVERT: D 559 ASN cc_start: 0.8447 (OUTLIER) cc_final: 0.7918 (m-40) REVERT: D 643 ASP cc_start: 0.7906 (t70) cc_final: 0.7566 (t0) outliers start: 39 outliers final: 14 residues processed: 245 average time/residue: 0.4103 time to fit residues: 118.2805 Evaluate side-chains 226 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 205 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 361 ARG Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 559 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 12 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 161 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 175 optimal weight: 20.0000 chunk 184 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 379 HIS B 636 GLN C 379 HIS C 636 GLN D 580 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.134958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.103960 restraints weight = 19602.635| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.62 r_work: 0.2866 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 17376 Z= 0.220 Angle : 0.670 9.461 23568 Z= 0.314 Chirality : 0.043 0.234 2812 Planarity : 0.004 0.041 2728 Dihedral : 10.051 57.239 2456 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.89 % Favored : 97.90 % Rotamer: Outliers : 2.56 % Allowed : 13.51 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.19), residues: 1904 helix: 1.56 (0.15), residues: 1096 sheet: -0.97 (0.32), residues: 200 loop : -0.46 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 361 TYR 0.014 0.002 TYR D 249 PHE 0.020 0.002 PHE C 600 TRP 0.011 0.002 TRP C 554 HIS 0.005 0.001 HIS A 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.22 (17356) covalent geometry : angle 0.64387 / 0.31 (23512) SS BOND : bond 0.00146 / 0.07 ( 4) SS BOND : angle 3.45649 / 1.91 ( 8) hydrogen bonds : bond 0.04637 / 2.99 ( 949) hydrogen bonds : angle 4.35317 / 2.98 ( 2787) link_BETA1-4 : bond 0.00143 / 0.07 ( 4) link_BETA1-4 : angle 1.73876 / 1.15 ( 12) link_NAG-ASN : bond 0.00544 / 0.36 ( 12) link_NAG-ASN : angle 4.40174 / 3.04 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 219 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 361 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7597 (mtp85) REVERT: A 559 ASN cc_start: 0.8524 (OUTLIER) cc_final: 0.7986 (m-40) REVERT: A 643 ASP cc_start: 0.8079 (t70) cc_final: 0.7676 (t0) REVERT: A 656 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8774 (mp) REVERT: B 361 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7590 (mtp85) REVERT: B 643 ASP cc_start: 0.8008 (t70) cc_final: 0.7626 (t0) REVERT: C 361 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7685 (mtp85) REVERT: C 559 ASN cc_start: 0.8450 (OUTLIER) cc_final: 0.7901 (m-40) REVERT: C 575 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8672 (mtpp) REVERT: C 643 ASP cc_start: 0.8029 (t70) cc_final: 0.7640 (t0) REVERT: D 267 LYS cc_start: 0.8449 (mtmm) cc_final: 0.7919 (mtpt) REVERT: D 337 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7453 (mp) REVERT: D 361 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7536 (mtp85) REVERT: D 559 ASN cc_start: 0.8469 (OUTLIER) cc_final: 0.7910 (m-40) REVERT: D 643 ASP cc_start: 0.8079 (t70) cc_final: 0.7684 (t0) REVERT: D 656 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8775 (mp) REVERT: D 690 ASP cc_start: 0.7954 (m-30) cc_final: 0.7447 (t0) outliers start: 43 outliers final: 14 residues processed: 251 average time/residue: 0.4592 time to fit residues: 133.2572 Evaluate side-chains 235 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 210 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 361 ARG Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 361 ARG Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 361 ARG Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 361 ARG Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 547 ASN Chi-restraints excluded: chain D residue 559 ASN Chi-restraints excluded: chain D residue 656 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 135 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 636 GLN B 636 GLN C 636 GLN D 580 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.137692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.107906 restraints weight = 19373.747| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.54 r_work: 0.2938 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17376 Z= 0.124 Angle : 0.598 10.278 23568 Z= 0.282 Chirality : 0.040 0.290 2812 Planarity : 0.003 0.039 2728 Dihedral : 9.734 58.733 2456 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.94 % Favored : 97.85 % Rotamer: Outliers : 1.73 % Allowed : 14.40 % Favored : 83.87 % 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: 1.28 (0.19), residues: 1904 helix: 1.90 (0.15), residues: 1072 sheet: -0.96 (0.32), residues: 200 loop : -0.28 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 338 TYR 0.011 0.001 TYR D 292 PHE 0.020 0.001 PHE C 600 TRP 0.010 0.001 TRP D 554 HIS 0.001 0.000 HIS A 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (17356) covalent geometry : angle 0.56711 / 0.27 (23512) SS BOND : bond 0.00196 / 0.10 ( 4) SS BOND : angle 3.49640 / 1.94 ( 8) hydrogen bonds : bond 0.04125 / 2.67 ( 949) hydrogen bonds : angle 4.19522 / 2.87 ( 2787) link_BETA1-4 : bond 0.00229 / 0.11 ( 4) link_BETA1-4 : angle 1.47230 / 0.98 ( 12) link_NAG-ASN : bond 0.00398 / 0.26 ( 12) link_NAG-ASN : angle 4.58140 / 3.15 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 216 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 559 ASN cc_start: 0.8427 (OUTLIER) cc_final: 0.7834 (m-40) REVERT: A 643 ASP cc_start: 0.7889 (t70) cc_final: 0.7455 (t0) REVERT: B 643 ASP cc_start: 0.7886 (t70) cc_final: 0.7465 (t0) REVERT: C 361 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7223 (mtp85) REVERT: C 559 ASN cc_start: 0.8369 (OUTLIER) cc_final: 0.7791 (m-40) REVERT: C 575 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8581 (mtpp) REVERT: C 643 ASP cc_start: 0.7856 (t70) cc_final: 0.7450 (t0) REVERT: D 267 LYS cc_start: 0.8420 (mtmm) cc_final: 0.7868 (mtpt) REVERT: D 337 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7241 (mp) REVERT: D 361 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7135 (mtp85) REVERT: D 559 ASN cc_start: 0.8424 (OUTLIER) cc_final: 0.7832 (m-40) REVERT: D 643 ASP cc_start: 0.7933 (t70) cc_final: 0.7523 (t0) REVERT: D 690 ASP cc_start: 0.7879 (m-30) cc_final: 0.7321 (t0) outliers start: 29 outliers final: 15 residues processed: 238 average time/residue: 0.4609 time to fit residues: 126.9394 Evaluate side-chains 228 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 361 ARG Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 361 ARG Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 559 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 125 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 177 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 636 GLN A 681 ASN B 636 GLN C 636 GLN C 681 ASN D 580 ASN D 681 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.133975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.103793 restraints weight = 19519.603| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.55 r_work: 0.2881 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 17376 Z= 0.244 Angle : 0.699 10.916 23568 Z= 0.326 Chirality : 0.044 0.258 2812 Planarity : 0.004 0.040 2728 Dihedral : 10.127 59.983 2456 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.89 % Favored : 97.90 % Rotamer: Outliers : 1.79 % Allowed : 14.23 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.19), residues: 1904 helix: 1.57 (0.15), residues: 1096 sheet: -0.93 (0.32), residues: 200 loop : -0.42 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 338 TYR 0.016 0.002 TYR D 249 PHE 0.019 0.002 PHE A 600 TRP 0.009 0.002 TRP C 554 HIS 0.005 0.001 HIS B 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.24 (17356) covalent geometry : angle 0.66778 / 0.32 (23512) SS BOND : bond 0.00039 / 0.02 ( 4) SS BOND : angle 3.35199 / 1.86 ( 8) hydrogen bonds : bond 0.04708 / 3.04 ( 949) hydrogen bonds : angle 4.37951 / 3.00 ( 2787) link_BETA1-4 : bond 0.00044 / 0.02 ( 4) link_BETA1-4 : angle 1.77562 / 1.18 ( 12) link_NAG-ASN : bond 0.00467 / 0.31 ( 12) link_NAG-ASN : angle 5.04515 / 3.51 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 221 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.7798 (tpt) cc_final: 0.7526 (mmt) REVERT: A 559 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.7876 (m-40) REVERT: A 643 ASP cc_start: 0.7993 (t70) cc_final: 0.7525 (t0) REVERT: B 643 ASP cc_start: 0.7995 (t70) cc_final: 0.7547 (t0) REVERT: C 559 ASN cc_start: 0.8410 (OUTLIER) cc_final: 0.7797 (m-40) REVERT: C 575 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8605 (mtpp) REVERT: C 643 ASP cc_start: 0.8011 (t70) cc_final: 0.7559 (t0) REVERT: D 267 LYS cc_start: 0.8420 (mtmm) cc_final: 0.7876 (mtpt) REVERT: D 361 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7772 (mtt90) REVERT: D 559 ASN cc_start: 0.8424 (OUTLIER) cc_final: 0.7801 (m-40) REVERT: D 643 ASP cc_start: 0.8024 (t70) cc_final: 0.7570 (t0) REVERT: D 690 ASP cc_start: 0.7886 (m-30) cc_final: 0.7352 (t0) outliers start: 30 outliers final: 18 residues processed: 237 average time/residue: 0.4604 time to fit residues: 125.8048 Evaluate side-chains 233 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 210 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 547 ASN Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 361 ARG Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 559 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 153 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 95 optimal weight: 30.0000 chunk 165 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 15 optimal weight: 20.0000 chunk 9 optimal weight: 0.4980 chunk 110 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 636 GLN B 681 ASN C 636 GLN C 681 ASN D 681 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.136271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.106203 restraints weight = 19398.442| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.56 r_work: 0.2910 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17376 Z= 0.145 Angle : 0.622 11.064 23568 Z= 0.292 Chirality : 0.041 0.283 2812 Planarity : 0.004 0.049 2728 Dihedral : 9.890 59.836 2456 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.79 % Favored : 98.00 % Rotamer: Outliers : 1.43 % Allowed : 14.70 % Favored : 83.87 % 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: 1.26 (0.19), residues: 1904 helix: 1.86 (0.15), residues: 1072 sheet: -0.95 (0.32), residues: 200 loop : -0.24 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 306 TYR 0.011 0.001 TYR D 292 PHE 0.020 0.001 PHE A 600 TRP 0.010 0.001 TRP C 554 HIS 0.002 0.001 HIS C 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (17356) covalent geometry : angle 0.59187 / 0.28 (23512) SS BOND : bond 0.00164 / 0.08 ( 4) SS BOND : angle 3.48864 / 1.93 ( 8) hydrogen bonds : bond 0.04248 / 2.75 ( 949) hydrogen bonds : angle 4.24863 / 2.91 ( 2787) link_BETA1-4 : bond 0.00188 / 0.09 ( 4) link_BETA1-4 : angle 1.55528 / 1.04 ( 12) link_NAG-ASN : bond 0.00491 / 0.32 ( 12) link_NAG-ASN : angle 4.56086 / 3.18 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5004.52 seconds wall clock time: 86 minutes 25.72 seconds (5185.72 seconds total)