Starting phenix.real_space_refine on Wed Mar 4 22:40:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t9n_10418/03_2026/6t9n_10418.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t9n_10418/03_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_10418/03_2026/6t9n_10418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t9n_10418/03_2026/6t9n_10418.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6t9n_10418/03_2026/6t9n_10418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t9n_10418/03_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-dev-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 110 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 dihedrals: 110 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 dihedrals: 110 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 dihedrals: 110 Unresolved non-hydrogen chiralities: 22 Time building chain proxies: 3.86, per 1000 atoms: 0.23 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: 1.04 Conformation dependent library (CDL) restraints added in 611.4 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: 0.48 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: 2.34 Time building geometry restraints manager: 1.42 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 - 27.32: 10924 27.32 - 54.65: 395 54.65 - 81.97: 45 81.97 - 109.29: 24 109.29 - 136.62: 8 Dihedral angle restraints: 11396 sinusoidal: 5700 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 11393 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: 0.640 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: 0.030 Set scattering table: 0.020 Process input model: 14.400 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.030 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:6.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 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 : 14.614 136.616 7696 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 covalent geometry : bond 0.01175 (17356) covalent geometry : angle 1.16503 (23512) SS BOND : bond 0.00513 ( 4) SS BOND : angle 4.65610 ( 8) hydrogen bonds : bond 0.15578 ( 949) hydrogen bonds : angle 7.18127 ( 2787) link_BETA1-4 : bond 0.00160 ( 4) link_BETA1-4 : angle 4.27080 ( 12) link_NAG-ASN : bond 0.01208 ( 12) link_NAG-ASN : angle 6.01513 ( 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 : 0.599 Fit side-chains REVERT: A 575 LYS cc_start: 0.8603 (mtpt) cc_final: 0.8352 (mtpp) REVERT: B 499 LYS cc_start: 0.7715 (mmmt) cc_final: 0.7021 (mmtt) REVERT: B 575 LYS cc_start: 0.8631 (mtpt) cc_final: 0.8428 (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: 0.8027 (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: 0.8238 (mtpp) outliers start: 0 outliers final: 4 residues processed: 326 average time/residue: 0.4891 time to fit residues: 180.7813 Evaluate side-chains 214 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 210 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3502 r_free = 0.3502 target = 0.136508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.106223 restraints weight = 19479.246| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.56 r_work: 0.2956 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1428 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= 0.155 Angle : 0.644 9.023 23568 Z= 0.313 Chirality : 0.043 0.318 2812 Planarity : 0.005 0.045 2728 Dihedral : 14.021 119.558 4208 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.26 % Favored : 98.53 % Rotamer: Outliers : 2.08 % Allowed : 8.45 % Favored : 89.46 % 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: -1.08 (0.17), residues: 1904 helix: -0.10 (0.14), residues: 1108 sheet: -1.48 (0.32), residues: 200 loop : -1.35 (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 B 498 Details of bonding type rmsd covalent geometry : bond 0.00338 (17356) covalent geometry : angle 0.61997 (23512) SS BOND : bond 0.00120 ( 4) SS BOND : angle 1.63231 ( 8) hydrogen bonds : bond 0.05106 ( 949) hydrogen bonds : angle 4.95499 ( 2787) link_BETA1-4 : bond 0.00195 ( 4) link_BETA1-4 : angle 2.10944 ( 12) link_NAG-ASN : bond 0.00420 ( 12) link_NAG-ASN : angle 4.30203 ( 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 271 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 236 time to evaluate : 0.535 Fit side-chains REVERT: A 559 ASN cc_start: 0.8389 (OUTLIER) cc_final: 0.7802 (m-40) REVERT: A 575 LYS cc_start: 0.8781 (mtpt) cc_final: 0.8466 (mtpp) REVERT: A 624 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7839 (p0) REVERT: A 690 ASP cc_start: 0.7644 (t0) cc_final: 0.7071 (m-30) REVERT: B 464 ARG cc_start: 0.8159 (mmm160) cc_final: 0.7940 (mmm-85) REVERT: B 575 LYS cc_start: 0.8786 (mtpt) cc_final: 0.8479 (mtpp) REVERT: B 624 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7816 (p0) REVERT: B 690 ASP cc_start: 0.7635 (t0) cc_final: 0.7090 (m-30) REVERT: C 537 GLN cc_start: 0.8303 (tt0) cc_final: 0.8080 (tt0) REVERT: C 559 ASN cc_start: 0.8377 (OUTLIER) cc_final: 0.7838 (m-40) REVERT: C 575 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8618 (mtpp) REVERT: C 624 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7813 (p0) REVERT: C 690 ASP cc_start: 0.7701 (t0) cc_final: 0.7231 (m-30) REVERT: D 267 LYS cc_start: 0.8390 (mtmm) cc_final: 0.7899 (mtpt) REVERT: D 537 GLN cc_start: 0.8335 (tt0) cc_final: 0.8054 (tt0) REVERT: D 559 ASN cc_start: 0.8346 (OUTLIER) cc_final: 0.7774 (m-40) REVERT: D 575 LYS cc_start: 0.8739 (mtpt) cc_final: 0.8413 (mtpp) REVERT: D 624 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7838 (p0) outliers start: 35 outliers final: 10 residues processed: 262 average time/residue: 0.4684 time to fit residues: 140.4922 Evaluate side-chains 215 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 130 optimal weight: 1.9990 chunk 144 optimal weight: 20.0000 chunk 105 optimal weight: 0.9980 chunk 176 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 171 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 GLN B 636 GLN C 636 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.135286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.104679 restraints weight = 19643.437| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.57 r_work: 0.2907 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 17376 Z= 0.197 Angle : 0.636 8.889 23568 Z= 0.304 Chirality : 0.044 0.268 2812 Planarity : 0.004 0.044 2728 Dihedral : 13.125 113.993 4200 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.94 % Favored : 97.85 % Rotamer: Outliers : 3.10 % Allowed : 8.99 % Favored : 87.92 % 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: -0.12 (0.18), residues: 1904 helix: 0.73 (0.15), residues: 1108 sheet: -1.41 (0.32), residues: 200 loop : -0.96 (0.23), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 251 TYR 0.013 0.002 TYR B 249 PHE 0.023 0.002 PHE D 600 TRP 0.014 0.002 TRP C 554 HIS 0.004 0.001 HIS D 550 Details of bonding type rmsd covalent geometry : bond 0.00458 (17356) covalent geometry : angle 0.61374 (23512) SS BOND : bond 0.00697 ( 4) SS BOND : angle 0.92061 ( 8) hydrogen bonds : bond 0.04818 ( 949) hydrogen bonds : angle 4.59639 ( 2787) link_BETA1-4 : bond 0.00121 ( 4) link_BETA1-4 : angle 2.02440 ( 12) link_NAG-ASN : bond 0.00511 ( 12) link_NAG-ASN : angle 4.12656 ( 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 273 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 221 time to evaluate : 0.610 Fit side-chains REVERT: A 559 ASN cc_start: 0.8359 (OUTLIER) cc_final: 0.7734 (m-40) REVERT: A 624 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7810 (p0) REVERT: B 624 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7746 (p0) REVERT: C 537 GLN cc_start: 0.8242 (tt0) cc_final: 0.8014 (tt0) REVERT: C 559 ASN cc_start: 0.8354 (OUTLIER) cc_final: 0.7714 (m-40) REVERT: C 575 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8556 (mtpp) REVERT: C 624 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7742 (p0) REVERT: C 677 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8362 (tt) REVERT: C 681 ASN cc_start: 0.8593 (OUTLIER) cc_final: 0.8052 (m-40) REVERT: C 690 ASP cc_start: 0.7554 (t0) cc_final: 0.7067 (m-30) REVERT: D 267 LYS cc_start: 0.8390 (mtmm) cc_final: 0.7870 (mtpt) REVERT: D 337 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7330 (mp) REVERT: D 559 ASN cc_start: 0.8330 (OUTLIER) cc_final: 0.7716 (m-40) REVERT: D 575 LYS cc_start: 0.8686 (mtpt) cc_final: 0.8353 (mtpp) REVERT: D 624 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7781 (p0) REVERT: D 681 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.8094 (m110) outliers start: 52 outliers final: 11 residues processed: 259 average time/residue: 0.4173 time to fit residues: 125.2885 Evaluate side-chains 227 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 204 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 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 349 SER Chi-restraints excluded: chain B residue 547 ASN 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 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 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: 0.8980 chunk 176 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN A 636 GLN B 636 GLN C 313 ASN C 636 GLN D 313 ASN D 580 ASN D 636 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.138262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.107023 restraints weight = 19337.457| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.64 r_work: 0.2904 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17376 Z= 0.144 Angle : 0.584 8.489 23568 Z= 0.278 Chirality : 0.042 0.265 2812 Planarity : 0.004 0.042 2728 Dihedral : 12.621 110.232 4200 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.47 % Favored : 98.32 % Rotamer: Outliers : 3.10 % Allowed : 10.24 % Favored : 86.67 % 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: 0.45 (0.18), residues: 1904 helix: 1.22 (0.15), residues: 1096 sheet: -1.30 (0.32), residues: 200 loop : -0.71 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 361 TYR 0.013 0.001 TYR D 292 PHE 0.022 0.001 PHE D 600 TRP 0.013 0.001 TRP C 554 HIS 0.002 0.001 HIS D 550 Details of bonding type rmsd covalent geometry : bond 0.00322 (17356) covalent geometry : angle 0.56319 (23512) SS BOND : bond 0.00717 ( 4) SS BOND : angle 0.76366 ( 8) hydrogen bonds : bond 0.04400 ( 949) hydrogen bonds : angle 4.36866 ( 2787) link_BETA1-4 : bond 0.00211 ( 4) link_BETA1-4 : angle 1.86248 ( 12) link_NAG-ASN : bond 0.00392 ( 12) link_NAG-ASN : angle 3.87556 ( 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 283 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 231 time to evaluate : 0.536 Fit side-chains REVERT: A 337 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7617 (mp) REVERT: A 559 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.7895 (m-40) REVERT: A 624 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.8018 (p0) REVERT: A 681 ASN cc_start: 0.8376 (t0) cc_final: 0.8019 (m-40) REVERT: B 228 LEU cc_start: 0.8888 (mt) cc_final: 0.8682 (mt) REVERT: B 344 CYS cc_start: 0.7816 (p) cc_final: 0.7403 (t) REVERT: C 228 LEU cc_start: 0.8879 (mt) cc_final: 0.8668 (mt) REVERT: C 344 CYS cc_start: 0.7856 (p) cc_final: 0.7455 (t) REVERT: C 349 SER cc_start: 0.8616 (OUTLIER) cc_final: 0.8303 (p) REVERT: C 559 ASN cc_start: 0.8426 (OUTLIER) cc_final: 0.7873 (m-40) REVERT: C 575 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8664 (mtpp) REVERT: C 624 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.8065 (p0) REVERT: C 677 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8605 (tt) REVERT: C 681 ASN cc_start: 0.8593 (OUTLIER) cc_final: 0.8333 (m-40) REVERT: D 537 GLN cc_start: 0.8264 (tt0) cc_final: 0.8043 (tt0) REVERT: D 559 ASN cc_start: 0.8394 (OUTLIER) cc_final: 0.7846 (m-40) REVERT: D 643 ASP cc_start: 0.8060 (t70) cc_final: 0.7581 (t0) REVERT: D 677 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8418 (tt) REVERT: D 681 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.8070 (m-40) REVERT: D 690 ASP cc_start: 0.7925 (m-30) cc_final: 0.7439 (t0) outliers start: 52 outliers final: 8 residues processed: 268 average time/residue: 0.4160 time to fit residues: 129.6169 Evaluate side-chains 236 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 216 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 349 SER 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 349 SER 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 C residue 603 MET 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 451 VAL Chi-restraints excluded: chain D residue 559 ASN Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 681 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 164 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 0.0020 chunk 94 optimal weight: 0.9990 chunk 158 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 GLN C 636 GLN D 580 ASN D 636 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.137444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.107196 restraints weight = 19269.235| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.54 r_work: 0.2952 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17376 Z= 0.133 Angle : 0.579 8.835 23568 Z= 0.274 Chirality : 0.042 0.262 2812 Planarity : 0.003 0.041 2728 Dihedral : 12.187 107.253 4200 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.21 % Favored : 97.58 % Rotamer: Outliers : 3.04 % Allowed : 11.61 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.19), residues: 1904 helix: 1.41 (0.15), residues: 1096 sheet: -1.20 (0.32), residues: 200 loop : -0.53 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 338 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 0.002 0.001 HIS B 550 Details of bonding type rmsd covalent geometry : bond 0.00294 (17356) covalent geometry : angle 0.55627 (23512) SS BOND : bond 0.00137 ( 4) SS BOND : angle 0.85727 ( 8) hydrogen bonds : bond 0.04259 ( 949) hydrogen bonds : angle 4.25771 ( 2787) link_BETA1-4 : bond 0.00305 ( 4) link_BETA1-4 : angle 1.74189 ( 12) link_NAG-ASN : bond 0.00579 ( 12) link_NAG-ASN : angle 4.01088 ( 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 280 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 229 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: A 337 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7465 (mp) REVERT: A 338 ARG cc_start: 0.7698 (ttm110) cc_final: 0.7415 (mtm-85) REVERT: A 344 CYS cc_start: 0.7691 (p) cc_final: 0.7293 (t) REVERT: A 559 ASN cc_start: 0.8418 (OUTLIER) cc_final: 0.7818 (m-40) REVERT: A 643 ASP cc_start: 0.7906 (t70) cc_final: 0.7441 (t0) REVERT: B 344 CYS cc_start: 0.7700 (p) cc_final: 0.7268 (t) REVERT: B 411 LYS cc_start: 0.8530 (ttpt) cc_final: 0.8232 (ttpm) REVERT: B 643 ASP cc_start: 0.7868 (t70) cc_final: 0.7373 (t0) REVERT: C 228 LEU cc_start: 0.8699 (mt) cc_final: 0.8493 (mt) REVERT: C 277 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7753 (pt0) REVERT: C 344 CYS cc_start: 0.7706 (p) cc_final: 0.7312 (t) REVERT: C 349 SER cc_start: 0.8495 (OUTLIER) cc_final: 0.8098 (p) REVERT: C 559 ASN cc_start: 0.8390 (OUTLIER) cc_final: 0.7786 (m-40) REVERT: C 575 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8575 (mtpp) REVERT: C 643 ASP cc_start: 0.7901 (t70) cc_final: 0.7449 (t0) REVERT: D 337 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7414 (mp) REVERT: D 537 GLN cc_start: 0.8192 (tt0) cc_final: 0.7967 (tt0) REVERT: D 559 ASN cc_start: 0.8417 (OUTLIER) cc_final: 0.7830 (m-40) REVERT: D 643 ASP cc_start: 0.7973 (t70) cc_final: 0.7511 (t0) REVERT: D 681 ASN cc_start: 0.8302 (OUTLIER) cc_final: 0.7927 (m-40) REVERT: D 690 ASP cc_start: 0.7838 (m-30) cc_final: 0.7310 (t0) outliers start: 51 outliers final: 14 residues processed: 265 average time/residue: 0.4026 time to fit residues: 124.4429 Evaluate side-chains 236 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 214 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 LEU 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 233 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 603 MET 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 454 SER Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain D residue 233 VAL 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 547 ASN Chi-restraints excluded: chain D residue 559 ASN Chi-restraints excluded: chain D residue 651 GLU Chi-restraints excluded: chain D residue 681 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 63 optimal weight: 8.9990 chunk 175 optimal weight: 20.0000 chunk 72 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 HIS B 379 HIS C 379 HIS D 379 HIS D 580 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.135469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.104802 restraints weight = 19434.378| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.57 r_work: 0.2916 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 17376 Z= 0.155 Angle : 0.603 8.685 23568 Z= 0.282 Chirality : 0.043 0.275 2812 Planarity : 0.004 0.041 2728 Dihedral : 11.944 105.306 4200 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.79 % Favored : 98.00 % Rotamer: Outliers : 2.68 % Allowed : 12.68 % Favored : 84.64 % 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: 0.84 (0.19), residues: 1904 helix: 1.48 (0.15), residues: 1096 sheet: -1.08 (0.32), residues: 200 loop : -0.46 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 251 TYR 0.012 0.001 TYR D 292 PHE 0.020 0.001 PHE A 600 TRP 0.011 0.001 TRP C 554 HIS 0.003 0.001 HIS B 550 Details of bonding type rmsd covalent geometry : bond 0.00352 (17356) covalent geometry : angle 0.58035 (23512) SS BOND : bond 0.00096 ( 4) SS BOND : angle 0.77321 ( 8) hydrogen bonds : bond 0.04336 ( 949) hydrogen bonds : angle 4.25390 ( 2787) link_BETA1-4 : bond 0.00084 ( 4) link_BETA1-4 : angle 1.77156 ( 12) link_NAG-ASN : bond 0.00346 ( 12) link_NAG-ASN : angle 4.08957 ( 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 273 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 228 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 337 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7435 (mp) REVERT: A 338 ARG cc_start: 0.7746 (ttm110) cc_final: 0.7517 (mtm-85) REVERT: A 344 CYS cc_start: 0.7742 (p) cc_final: 0.7325 (t) REVERT: A 559 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.7846 (m-40) REVERT: A 643 ASP cc_start: 0.8030 (t70) cc_final: 0.7580 (t0) REVERT: B 411 LYS cc_start: 0.8554 (ttpt) cc_final: 0.8275 (ttpt) REVERT: B 643 ASP cc_start: 0.7967 (t70) cc_final: 0.7526 (t0) REVERT: C 277 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7762 (pt0) REVERT: C 344 CYS cc_start: 0.7739 (p) cc_final: 0.7334 (t) REVERT: C 349 SER cc_start: 0.8480 (OUTLIER) cc_final: 0.8082 (p) REVERT: C 559 ASN cc_start: 0.8403 (OUTLIER) cc_final: 0.7818 (m-40) REVERT: C 575 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8571 (mtpp) REVERT: C 643 ASP cc_start: 0.8034 (t70) cc_final: 0.7588 (t0) REVERT: D 337 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7382 (mp) REVERT: D 559 ASN cc_start: 0.8448 (OUTLIER) cc_final: 0.7857 (m-40) REVERT: D 643 ASP cc_start: 0.8037 (t70) cc_final: 0.7583 (t0) REVERT: D 681 ASN cc_start: 0.8383 (OUTLIER) cc_final: 0.7933 (m-40) REVERT: D 690 ASP cc_start: 0.7867 (m-30) cc_final: 0.7335 (t0) outliers start: 45 outliers final: 16 residues processed: 261 average time/residue: 0.4055 time to fit residues: 122.8325 Evaluate side-chains 242 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 218 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 337 LEU 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 A residue 603 MET Chi-restraints excluded: chain B residue 233 VAL 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 233 VAL 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 C residue 603 MET Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 337 LEU 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 651 GLU Chi-restraints excluded: chain D residue 681 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 75 optimal weight: 20.0000 chunk 53 optimal weight: 0.5980 chunk 2 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 147 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 580 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.135927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.105355 restraints weight = 19427.926| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.56 r_work: 0.2907 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 17376 Z= 0.158 Angle : 0.613 8.887 23568 Z= 0.284 Chirality : 0.043 0.265 2812 Planarity : 0.004 0.041 2728 Dihedral : 11.694 102.604 4200 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.05 % Favored : 97.74 % Rotamer: Outliers : 2.80 % Allowed : 12.68 % Favored : 84.52 % 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: -1.04 (0.32), residues: 200 loop : -0.43 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 251 TYR 0.012 0.001 TYR C 292 PHE 0.020 0.001 PHE D 600 TRP 0.011 0.001 TRP C 554 HIS 0.003 0.001 HIS B 550 Details of bonding type rmsd covalent geometry : bond 0.00361 (17356) covalent geometry : angle 0.58852 (23512) SS BOND : bond 0.00301 ( 4) SS BOND : angle 0.79386 ( 8) hydrogen bonds : bond 0.04327 ( 949) hydrogen bonds : angle 4.23645 ( 2787) link_BETA1-4 : bond 0.00150 ( 4) link_BETA1-4 : angle 1.76242 ( 12) link_NAG-ASN : bond 0.00467 ( 12) link_NAG-ASN : angle 4.27545 ( 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 279 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 232 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 337 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7410 (mp) REVERT: A 338 ARG cc_start: 0.7710 (ttm110) cc_final: 0.7437 (ttm-80) REVERT: A 559 ASN cc_start: 0.8441 (OUTLIER) cc_final: 0.7861 (m-40) REVERT: A 643 ASP cc_start: 0.8029 (t70) cc_final: 0.7582 (t0) REVERT: B 643 ASP cc_start: 0.7977 (t70) cc_final: 0.7546 (t0) REVERT: B 656 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8735 (mp) REVERT: C 277 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7765 (pt0) REVERT: C 349 SER cc_start: 0.8494 (OUTLIER) cc_final: 0.8089 (p) REVERT: C 559 ASN cc_start: 0.8410 (OUTLIER) cc_final: 0.7820 (m-40) REVERT: C 575 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8571 (mtpp) REVERT: C 643 ASP cc_start: 0.8034 (t70) cc_final: 0.7591 (t0) REVERT: D 337 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7367 (mp) REVERT: D 559 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.7854 (m-40) REVERT: D 643 ASP cc_start: 0.8015 (t70) cc_final: 0.7577 (t0) REVERT: D 690 ASP cc_start: 0.7857 (m-30) cc_final: 0.7340 (t0) outliers start: 47 outliers final: 20 residues processed: 268 average time/residue: 0.3959 time to fit residues: 123.6795 Evaluate side-chains 249 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 221 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 373 ASP 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 651 GLU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 236 ILE 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 B residue 656 LEU Chi-restraints excluded: chain C residue 233 VAL 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 559 ASN Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 547 ASN 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: 0.9990 chunk 10 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 161 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 95 optimal weight: 20.0000 chunk 175 optimal weight: 20.0000 chunk 184 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 653 ASN C 653 ASN D 653 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.137041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.106774 restraints weight = 19474.757| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.56 r_work: 0.2931 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17376 Z= 0.137 Angle : 0.612 9.726 23568 Z= 0.283 Chirality : 0.042 0.281 2812 Planarity : 0.003 0.040 2728 Dihedral : 11.334 98.486 4200 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.10 % Favored : 97.69 % Rotamer: Outliers : 2.02 % Allowed : 14.40 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.19), residues: 1904 helix: 1.65 (0.15), residues: 1096 sheet: -0.96 (0.32), residues: 200 loop : -0.39 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 338 TYR 0.012 0.001 TYR D 292 PHE 0.020 0.001 PHE C 600 TRP 0.011 0.001 TRP D 554 HIS 0.002 0.001 HIS B 550 Details of bonding type rmsd covalent geometry : bond 0.00306 (17356) covalent geometry : angle 0.58574 (23512) SS BOND : bond 0.00058 ( 4) SS BOND : angle 0.78882 ( 8) hydrogen bonds : bond 0.04214 ( 949) hydrogen bonds : angle 4.17757 ( 2787) link_BETA1-4 : bond 0.00171 ( 4) link_BETA1-4 : angle 1.67448 ( 12) link_NAG-ASN : bond 0.00394 ( 12) link_NAG-ASN : angle 4.45475 ( 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 272 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 238 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.7737 (tpt) cc_final: 0.7288 (mmt) REVERT: A 337 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7372 (mp) REVERT: A 338 ARG cc_start: 0.7691 (ttm110) cc_final: 0.7434 (ttm-80) REVERT: A 559 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.7818 (m-40) REVERT: A 643 ASP cc_start: 0.7961 (t70) cc_final: 0.7520 (t0) REVERT: B 643 ASP cc_start: 0.7943 (t70) cc_final: 0.7509 (t0) REVERT: C 277 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7718 (pt0) REVERT: C 349 SER cc_start: 0.8433 (OUTLIER) cc_final: 0.8002 (p) REVERT: C 559 ASN cc_start: 0.8372 (OUTLIER) cc_final: 0.7777 (m-40) REVERT: C 575 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8552 (mtpp) REVERT: C 643 ASP cc_start: 0.7960 (t70) cc_final: 0.7522 (OUTLIER) REVERT: D 337 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7280 (mp) REVERT: D 559 ASN cc_start: 0.8423 (OUTLIER) cc_final: 0.7820 (m-40) REVERT: D 643 ASP cc_start: 0.8002 (t70) cc_final: 0.7560 (t0) REVERT: D 690 ASP cc_start: 0.7858 (m-30) cc_final: 0.7323 (t0) outliers start: 34 outliers final: 19 residues processed: 262 average time/residue: 0.4210 time to fit residues: 127.4872 Evaluate side-chains 247 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 222 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 337 LEU 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 A residue 651 GLU 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 B residue 454 SER Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain C residue 233 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 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 451 VAL Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 559 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 681 ASN C 653 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.137448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.107592 restraints weight = 19364.500| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.53 r_work: 0.2961 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2564 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= 0.140 Angle : 0.631 9.988 23568 Z= 0.289 Chirality : 0.042 0.305 2812 Planarity : 0.003 0.041 2728 Dihedral : 11.088 94.930 4200 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.10 % Favored : 97.69 % Rotamer: Outliers : 1.79 % Allowed : 14.88 % Favored : 83.33 % 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: 1.10 (0.19), residues: 1904 helix: 1.69 (0.15), residues: 1096 sheet: -0.94 (0.32), residues: 200 loop : -0.35 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 338 TYR 0.012 0.001 TYR C 292 PHE 0.020 0.001 PHE D 600 TRP 0.011 0.001 TRP D 554 HIS 0.002 0.001 HIS B 550 Details of bonding type rmsd covalent geometry : bond 0.00313 (17356) covalent geometry : angle 0.59883 (23512) SS BOND : bond 0.00070 ( 4) SS BOND : angle 0.79351 ( 8) hydrogen bonds : bond 0.04210 ( 949) hydrogen bonds : angle 4.17847 ( 2787) link_BETA1-4 : bond 0.00150 ( 4) link_BETA1-4 : angle 1.66567 ( 12) link_NAG-ASN : bond 0.00527 ( 12) link_NAG-ASN : angle 5.00151 ( 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 261 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 231 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7357 (mp) REVERT: A 338 ARG cc_start: 0.7691 (ttm110) cc_final: 0.7457 (ttm-80) REVERT: A 349 SER cc_start: 0.8434 (OUTLIER) cc_final: 0.8010 (p) REVERT: A 559 ASN cc_start: 0.8411 (OUTLIER) cc_final: 0.7829 (m-40) REVERT: A 643 ASP cc_start: 0.7983 (t70) cc_final: 0.7569 (t0) REVERT: B 643 ASP cc_start: 0.7949 (t70) cc_final: 0.7538 (t0) REVERT: C 277 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7741 (pt0) REVERT: C 349 SER cc_start: 0.8462 (OUTLIER) cc_final: 0.8040 (p) REVERT: C 559 ASN cc_start: 0.8379 (OUTLIER) cc_final: 0.7809 (m-40) REVERT: C 575 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8573 (mtpp) REVERT: C 643 ASP cc_start: 0.7961 (t70) cc_final: 0.7551 (t0) REVERT: D 337 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7294 (mp) REVERT: D 559 ASN cc_start: 0.8431 (OUTLIER) cc_final: 0.7834 (m-40) REVERT: D 643 ASP cc_start: 0.7971 (t70) cc_final: 0.7562 (t0) REVERT: D 690 ASP cc_start: 0.7886 (m-30) cc_final: 0.7346 (t0) outliers start: 30 outliers final: 14 residues processed: 254 average time/residue: 0.4022 time to fit residues: 118.5078 Evaluate side-chains 245 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 223 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain C residue 233 VAL 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 559 ASN Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 337 LEU 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: 5.9990 chunk 117 optimal weight: 8.9990 chunk 177 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 20.0000 chunk 66 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 653 ASN D 653 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.136773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.105945 restraints weight = 19329.796| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.61 r_work: 0.2890 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17376 Z= 0.173 Angle : 0.664 10.194 23568 Z= 0.303 Chirality : 0.044 0.354 2812 Planarity : 0.004 0.041 2728 Dihedral : 10.951 90.351 4200 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.05 % Favored : 97.74 % Rotamer: Outliers : 1.85 % Allowed : 14.88 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.19), residues: 1904 helix: 1.65 (0.15), residues: 1096 sheet: -0.93 (0.32), residues: 200 loop : -0.32 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 338 TYR 0.012 0.002 TYR D 292 PHE 0.021 0.001 PHE D 600 TRP 0.011 0.001 TRP C 554 HIS 0.003 0.001 HIS D 550 Details of bonding type rmsd covalent geometry : bond 0.00401 (17356) covalent geometry : angle 0.63495 (23512) SS BOND : bond 0.00065 ( 4) SS BOND : angle 0.73041 ( 8) hydrogen bonds : bond 0.04408 ( 949) hydrogen bonds : angle 4.25295 ( 2787) link_BETA1-4 : bond 0.00052 ( 4) link_BETA1-4 : angle 1.79502 ( 12) link_NAG-ASN : bond 0.00571 ( 12) link_NAG-ASN : angle 4.91556 ( 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 259 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 228 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7440 (mp) REVERT: A 349 SER cc_start: 0.8512 (OUTLIER) cc_final: 0.8139 (p) REVERT: A 559 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.7908 (m-40) REVERT: A 643 ASP cc_start: 0.8063 (t70) cc_final: 0.7671 (t0) REVERT: B 643 ASP cc_start: 0.8030 (t70) cc_final: 0.7648 (t0) REVERT: C 349 SER cc_start: 0.8541 (OUTLIER) cc_final: 0.8167 (p) REVERT: C 559 ASN cc_start: 0.8459 (OUTLIER) cc_final: 0.7909 (m-40) REVERT: C 575 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8648 (mtpp) REVERT: C 643 ASP cc_start: 0.8037 (t70) cc_final: 0.7642 (t0) REVERT: D 337 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7395 (mp) REVERT: D 559 ASN cc_start: 0.8500 (OUTLIER) cc_final: 0.7938 (m-40) REVERT: D 643 ASP cc_start: 0.8054 (t70) cc_final: 0.7656 (t0) REVERT: D 690 ASP cc_start: 0.7969 (m-30) cc_final: 0.7454 (t0) outliers start: 31 outliers final: 14 residues processed: 250 average time/residue: 0.3889 time to fit residues: 113.8116 Evaluate side-chains 247 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 225 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 337 LEU 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 233 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain C residue 233 VAL 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 559 ASN Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 337 LEU 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: 0.0040 chunk 128 optimal weight: 5.9990 chunk 161 optimal weight: 7.9990 chunk 95 optimal weight: 30.0000 chunk 165 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 15 optimal weight: 20.0000 chunk 9 optimal weight: 0.0270 chunk 110 optimal weight: 0.0470 chunk 130 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.6152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 653 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.140333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.110858 restraints weight = 19270.313| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.53 r_work: 0.3043 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17376 Z= 0.107 Angle : 0.599 10.161 23568 Z= 0.275 Chirality : 0.042 0.397 2812 Planarity : 0.003 0.039 2728 Dihedral : 10.048 75.763 4200 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.94 % Favored : 97.85 % Rotamer: Outliers : 1.01 % Allowed : 15.71 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.19), residues: 1904 helix: 1.85 (0.15), residues: 1096 sheet: -0.78 (0.33), residues: 200 loop : -0.21 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 338 TYR 0.010 0.001 TYR D 292 PHE 0.019 0.001 PHE C 600 TRP 0.009 0.001 TRP D 554 HIS 0.002 0.001 HIS D 379 Details of bonding type rmsd covalent geometry : bond 0.00221 (17356) covalent geometry : angle 0.57675 (23512) SS BOND : bond 0.00094 ( 4) SS BOND : angle 0.97071 ( 8) hydrogen bonds : bond 0.03878 ( 949) hydrogen bonds : angle 4.05569 ( 2787) link_BETA1-4 : bond 0.00446 ( 4) link_BETA1-4 : angle 1.42033 ( 12) link_NAG-ASN : bond 0.00628 ( 12) link_NAG-ASN : angle 4.08731 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4623.25 seconds wall clock time: 79 minutes 50.63 seconds (4790.63 seconds total)