Starting phenix.real_space_refine on Sun Aug 24 04:25:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t9n_10418/08_2025/6t9n_10418.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t9n_10418/08_2025/6t9n_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_10418/08_2025/6t9n_10418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t9n_10418/08_2025/6t9n_10418.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6t9n_10418/08_2025/6t9n_10418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t9n_10418/08_2025/6t9n_10418.map" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 80 5.16 5 C 11232 2.51 5 N 2504 2.21 5 O 3100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16917 Number of models: 1 Model: "" Number of chains: 5 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: "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: "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 Restraints were copied for chains: C, D, F, G, H Time building chain proxies: 4.92, per 1000 atoms: 0.29 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: 1.57 Conformation dependent library (CDL) restraints added in 720.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.50 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: 2.86 Time building geometry restraints manager: 2.05 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: 0.760 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.590 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 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:6.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.260 ------------------------------------------------------------------------------- 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 aren 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 : 0.559 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: 0.8513 (mtpt) cc_final: 0.8238 (mtpp) outliers start: 0 outliers final: 4 residues processed: 326 average time/residue: 0.5083 time to fit residues: 188.3943 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 : 0.663 ------------------------------------------------------------------------------- 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 = 47)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.106246 restraints weight = 19479.246| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.56 r_work: 0.2950 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 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 aren 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 : 0.675 Fit side-chains REVERT: A 559 ASN cc_start: 0.8387 (OUTLIER) cc_final: 0.7801 (m-40) REVERT: A 575 LYS cc_start: 0.8778 (mtpt) cc_final: 0.8461 (mtpp) REVERT: A 624 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7829 (p0) REVERT: A 690 ASP cc_start: 0.7640 (t0) cc_final: 0.7065 (m-30) REVERT: B 464 ARG cc_start: 0.8157 (mmm160) cc_final: 0.7939 (mmm-85) REVERT: B 575 LYS cc_start: 0.8781 (mtpt) cc_final: 0.8474 (mtpp) REVERT: B 624 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7806 (p0) REVERT: B 690 ASP cc_start: 0.7631 (t0) cc_final: 0.7083 (m-30) REVERT: C 537 GLN cc_start: 0.8305 (tt0) cc_final: 0.8080 (tt0) REVERT: C 559 ASN cc_start: 0.8375 (OUTLIER) cc_final: 0.7836 (m-40) REVERT: C 575 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8615 (mtpp) REVERT: C 624 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7804 (p0) REVERT: C 690 ASP cc_start: 0.7696 (t0) cc_final: 0.7223 (m-30) REVERT: D 267 LYS cc_start: 0.8385 (mtmm) cc_final: 0.7896 (mtpt) REVERT: D 537 GLN cc_start: 0.8337 (tt0) cc_final: 0.8055 (tt0) REVERT: D 559 ASN cc_start: 0.8345 (OUTLIER) cc_final: 0.7772 (m-40) REVERT: D 575 LYS cc_start: 0.8736 (mtpt) cc_final: 0.8409 (mtpp) REVERT: D 624 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7830 (p0) outliers start: 35 outliers final: 10 residues processed: 262 average time/residue: 0.4937 time to fit residues: 148.9313 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 : 0.647 ------------------------------------------------------------------------------- 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: 6.9990 chunk 103 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 171 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 D 255 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.133784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.103042 restraints weight = 19688.468| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.56 r_work: 0.2903 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 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 0.036 17376 Z= 0.224 Angle : 0.658 9.002 23568 Z= 0.314 Chirality : 0.045 0.265 2812 Planarity : 0.004 0.044 2728 Dihedral : 13.204 114.118 4200 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.94 % Favored : 97.85 % Rotamer: Outliers : 3.15 % Allowed : 8.93 % 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 aren not related in a simple way. whole: -0.18 (0.18), residues: 1904 helix: 0.67 (0.15), residues: 1108 sheet: -1.41 (0.32), residues: 200 loop : -0.97 (0.23), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 251 TYR 0.014 0.002 TYR B 249 PHE 0.023 0.002 PHE D 600 TRP 0.015 0.002 TRP C 554 HIS 0.004 0.001 HIS D 550 Details of bonding type rmsd covalent geometry : bond 0.00533 (17356) covalent geometry : angle 0.63535 (23512) SS BOND : bond 0.00391 ( 4) SS BOND : angle 1.11228 ( 8) hydrogen bonds : bond 0.04966 ( 949) hydrogen bonds : angle 4.65081 ( 2787) link_BETA1-4 : bond 0.00031 ( 4) link_BETA1-4 : angle 2.08307 ( 12) link_NAG-ASN : bond 0.00518 ( 12) link_NAG-ASN : angle 4.21599 ( 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 276 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 223 time to evaluate : 0.705 Fit side-chains REVERT: A 559 ASN cc_start: 0.8366 (OUTLIER) cc_final: 0.7747 (m-40) REVERT: A 624 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7834 (p0) REVERT: B 624 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7760 (p0) REVERT: C 559 ASN cc_start: 0.8375 (OUTLIER) cc_final: 0.7739 (m-40) REVERT: C 575 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8595 (mtpp) REVERT: C 624 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7802 (p0) REVERT: C 677 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8486 (tt) REVERT: C 681 ASN cc_start: 0.8631 (OUTLIER) cc_final: 0.8115 (m-40) REVERT: C 690 ASP cc_start: 0.7581 (t0) cc_final: 0.7117 (m-30) REVERT: D 255 GLN cc_start: 0.8683 (mt0) cc_final: 0.8459 (mt0) REVERT: D 267 LYS cc_start: 0.8406 (mtmm) cc_final: 0.7908 (mtpt) REVERT: D 337 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7387 (mp) REVERT: D 559 ASN cc_start: 0.8357 (OUTLIER) cc_final: 0.7751 (m-40) REVERT: D 575 LYS cc_start: 0.8701 (mtpt) cc_final: 0.8386 (mtpp) REVERT: D 624 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7831 (p0) REVERT: D 677 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8396 (tt) REVERT: D 681 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.8059 (m-40) outliers start: 53 outliers final: 12 residues processed: 260 average time/residue: 0.4607 time to fit residues: 139.2020 Evaluate side-chains 227 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 202 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 547 ASN 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 677 LEU 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: 0.9990 chunk 176 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN C 313 ASN D 313 ASN D 580 ASN D 636 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.136208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.105784 restraints weight = 19444.455| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.55 r_work: 0.2953 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2072 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= 0.128 Angle : 0.573 8.651 23568 Z= 0.273 Chirality : 0.042 0.267 2812 Planarity : 0.004 0.041 2728 Dihedral : 12.608 109.844 4200 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.31 % Favored : 98.48 % Rotamer: Outliers : 2.62 % Allowed : 10.77 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.18), residues: 1904 helix: 1.22 (0.15), residues: 1096 sheet: -1.26 (0.32), residues: 200 loop : -0.72 (0.23), 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 0.001 0.000 HIS D 550 Details of bonding type rmsd covalent geometry : bond 0.00277 (17356) covalent geometry : angle 0.55065 (23512) SS BOND : bond 0.00092 ( 4) SS BOND : angle 0.97384 ( 8) hydrogen bonds : bond 0.04322 ( 949) hydrogen bonds : angle 4.35245 ( 2787) link_BETA1-4 : bond 0.00229 ( 4) link_BETA1-4 : angle 1.77004 ( 12) link_NAG-ASN : bond 0.00374 ( 12) link_NAG-ASN : angle 3.91492 ( 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 276 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 232 time to evaluate : 0.642 Fit side-chains REVERT: A 277 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7737 (pt0) REVERT: A 337 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7518 (mp) REVERT: A 559 ASN cc_start: 0.8389 (OUTLIER) cc_final: 0.7785 (m-40) REVERT: B 228 LEU cc_start: 0.8732 (mt) cc_final: 0.8525 (mt) REVERT: B 277 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7772 (pt0) REVERT: B 344 CYS cc_start: 0.7670 (p) cc_final: 0.7293 (t) REVERT: B 681 ASN cc_start: 0.8380 (t0) cc_final: 0.7940 (m-40) REVERT: C 228 LEU cc_start: 0.8728 (mt) cc_final: 0.8514 (mt) REVERT: C 344 CYS cc_start: 0.7703 (p) cc_final: 0.7355 (t) REVERT: C 349 SER cc_start: 0.8529 (OUTLIER) cc_final: 0.8151 (p) REVERT: C 559 ASN cc_start: 0.8375 (OUTLIER) cc_final: 0.7748 (m-40) REVERT: C 575 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8556 (mtpp) REVERT: C 624 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7924 (p0) REVERT: D 255 GLN cc_start: 0.8649 (mt0) cc_final: 0.8394 (mt0) REVERT: D 537 GLN cc_start: 0.8204 (tt0) cc_final: 0.7970 (tt0) REVERT: D 559 ASN cc_start: 0.8344 (OUTLIER) cc_final: 0.7743 (m-40) REVERT: D 643 ASP cc_start: 0.7979 (t70) cc_final: 0.7487 (t0) REVERT: D 681 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.7910 (m-40) REVERT: D 690 ASP cc_start: 0.7822 (m-30) cc_final: 0.7319 (t0) outliers start: 44 outliers final: 10 residues processed: 260 average time/residue: 0.4596 time to fit residues: 138.5763 Evaluate side-chains 228 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 451 VAL Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 559 ASN 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: 10.0000 chunk 41 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 5 optimal weight: 0.0170 chunk 94 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.5622 ------------------------------------------------------------------------------- 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 D 580 ASN D 636 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.136598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.106045 restraints weight = 19313.270| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.56 r_work: 0.2943 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17376 Z= 0.131 Angle : 0.579 8.556 23568 Z= 0.273 Chirality : 0.042 0.254 2812 Planarity : 0.004 0.041 2728 Dihedral : 12.221 107.523 4200 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.94 % Favored : 97.85 % Rotamer: Outliers : 3.04 % Allowed : 11.73 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.18), residues: 1904 helix: 1.40 (0.15), residues: 1096 sheet: -1.20 (0.32), residues: 200 loop : -0.54 (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 D 554 HIS 0.002 0.001 HIS C 550 Details of bonding type rmsd covalent geometry : bond 0.00289 (17356) covalent geometry : angle 0.55659 (23512) SS BOND : bond 0.00529 ( 4) SS BOND : angle 0.92112 ( 8) hydrogen bonds : bond 0.04253 ( 949) hydrogen bonds : angle 4.25317 ( 2787) link_BETA1-4 : bond 0.00230 ( 4) link_BETA1-4 : angle 1.72158 ( 12) link_NAG-ASN : bond 0.00610 ( 12) link_NAG-ASN : angle 4.03146 ( 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 274 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 223 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: A 242 MET cc_start: 0.7818 (tpt) cc_final: 0.7571 (mmt) REVERT: A 277 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7740 (pt0) REVERT: A 337 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7415 (mp) REVERT: A 338 ARG cc_start: 0.7715 (ttm110) cc_final: 0.7407 (mtm-85) REVERT: A 344 CYS cc_start: 0.7706 (p) cc_final: 0.7326 (t) REVERT: A 559 ASN cc_start: 0.8416 (OUTLIER) cc_final: 0.7812 (m-40) REVERT: A 643 ASP cc_start: 0.7914 (t70) cc_final: 0.7437 (t0) REVERT: B 228 LEU cc_start: 0.8689 (mt) cc_final: 0.8476 (mt) REVERT: B 277 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7776 (pt0) REVERT: B 411 LYS cc_start: 0.8525 (ttpt) cc_final: 0.8249 (ttpt) REVERT: B 643 ASP cc_start: 0.7882 (t70) cc_final: 0.7398 (t0) REVERT: C 228 LEU cc_start: 0.8701 (mt) cc_final: 0.8499 (mt) REVERT: C 344 CYS cc_start: 0.7696 (p) cc_final: 0.7308 (t) REVERT: C 349 SER cc_start: 0.8493 (OUTLIER) cc_final: 0.8095 (p) REVERT: C 559 ASN cc_start: 0.8389 (OUTLIER) cc_final: 0.7774 (m-40) REVERT: C 575 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8572 (mtpp) REVERT: C 643 ASP cc_start: 0.7928 (t70) cc_final: 0.7471 (t0) REVERT: D 337 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7417 (mp) REVERT: D 537 GLN cc_start: 0.8155 (tt0) cc_final: 0.7932 (tt0) REVERT: D 559 ASN cc_start: 0.8411 (OUTLIER) cc_final: 0.7812 (m-40) REVERT: D 643 ASP cc_start: 0.7993 (t70) cc_final: 0.7526 (t0) REVERT: D 681 ASN cc_start: 0.8355 (OUTLIER) cc_final: 0.7942 (m-40) REVERT: D 690 ASP cc_start: 0.7849 (m-30) cc_final: 0.7320 (t0) outliers start: 51 outliers final: 16 residues processed: 262 average time/residue: 0.4712 time to fit residues: 143.1151 Evaluate side-chains 237 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 451 VAL Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 603 MET 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 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: 0.8980 chunk 175 optimal weight: 20.0000 chunk 72 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 B 653 ASN C 636 GLN D 379 HIS D 580 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.138016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.107732 restraints weight = 19325.009| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.56 r_work: 0.2958 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2381 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= 0.120 Angle : 0.575 8.970 23568 Z= 0.269 Chirality : 0.041 0.244 2812 Planarity : 0.003 0.040 2728 Dihedral : 11.760 104.164 4200 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.00 % Favored : 97.79 % Rotamer: Outliers : 2.38 % Allowed : 12.80 % Favored : 84.82 % 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 aren not related in a simple way. whole: 0.93 (0.19), residues: 1904 helix: 1.57 (0.15), residues: 1096 sheet: -1.06 (0.32), residues: 200 loop : -0.46 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 361 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 0.001 0.001 HIS B 550 Details of bonding type rmsd covalent geometry : bond 0.00260 (17356) covalent geometry : angle 0.55112 (23512) SS BOND : bond 0.00142 ( 4) SS BOND : angle 0.80861 ( 8) hydrogen bonds : bond 0.04126 ( 949) hydrogen bonds : angle 4.17817 ( 2787) link_BETA1-4 : bond 0.00203 ( 4) link_BETA1-4 : angle 1.63148 ( 12) link_NAG-ASN : bond 0.00462 ( 12) link_NAG-ASN : angle 4.09797 ( 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: 40 poor density : 233 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: A 242 MET cc_start: 0.7800 (tpt) cc_final: 0.7541 (mmt) REVERT: A 337 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7525 (mp) REVERT: A 338 ARG cc_start: 0.7729 (ttm110) cc_final: 0.7526 (mtm-85) REVERT: A 344 CYS cc_start: 0.7727 (p) cc_final: 0.7299 (t) REVERT: A 559 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.7876 (m-40) REVERT: A 643 ASP cc_start: 0.7979 (t70) cc_final: 0.7546 (t0) REVERT: B 411 LYS cc_start: 0.8556 (ttpt) cc_final: 0.8283 (ttpt) REVERT: B 643 ASP cc_start: 0.7980 (t70) cc_final: 0.7564 (t0) REVERT: C 228 LEU cc_start: 0.8769 (mt) cc_final: 0.8567 (mt) REVERT: C 277 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7839 (pt0) REVERT: C 349 SER cc_start: 0.8501 (OUTLIER) cc_final: 0.8127 (p) REVERT: C 559 ASN cc_start: 0.8377 (OUTLIER) cc_final: 0.7814 (m-40) REVERT: C 575 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8600 (mtpp) REVERT: C 643 ASP cc_start: 0.7990 (t70) cc_final: 0.7579 (t0) REVERT: D 337 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7437 (mp) REVERT: D 344 CYS cc_start: 0.7704 (p) cc_final: 0.7290 (t) REVERT: D 537 GLN cc_start: 0.8204 (tt0) cc_final: 0.7983 (tt0) REVERT: D 559 ASN cc_start: 0.8423 (OUTLIER) cc_final: 0.7847 (m-40) REVERT: D 643 ASP cc_start: 0.7974 (t70) cc_final: 0.7563 (t0) REVERT: D 681 ASN cc_start: 0.8329 (OUTLIER) cc_final: 0.7946 (m-40) REVERT: D 690 ASP cc_start: 0.7895 (m-30) cc_final: 0.7367 (t0) outliers start: 40 outliers final: 14 residues processed: 264 average time/residue: 0.4649 time to fit residues: 142.5301 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 : 0.666 ------------------------------------------------------------------------------- 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 451 VAL Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 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 547 ASN Chi-restraints excluded: chain D residue 559 ASN Chi-restraints excluded: chain D residue 603 MET 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: 1.9990 chunk 118 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 143 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 147 optimal weight: 0.0020 chunk 32 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 HIS A 636 GLN A 681 ASN B 379 HIS B 636 GLN B 653 ASN C 379 HIS D 580 ASN D 636 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.136210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.105791 restraints weight = 19439.420| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.55 r_work: 0.2929 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2433 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= 0.155 Angle : 0.614 10.391 23568 Z= 0.285 Chirality : 0.042 0.262 2812 Planarity : 0.004 0.040 2728 Dihedral : 11.568 101.980 4200 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.94 % Favored : 97.85 % Rotamer: Outliers : 2.62 % Allowed : 13.04 % Favored : 84.35 % 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 aren not related in a simple way. whole: 0.98 (0.19), residues: 1904 helix: 1.60 (0.15), residues: 1096 sheet: -0.99 (0.32), residues: 200 loop : -0.41 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 338 TYR 0.019 0.001 TYR D 486 PHE 0.020 0.001 PHE D 600 TRP 0.011 0.001 TRP D 554 HIS 0.003 0.001 HIS C 550 Details of bonding type rmsd covalent geometry : bond 0.00353 (17356) covalent geometry : angle 0.58748 (23512) SS BOND : bond 0.00118 ( 4) SS BOND : angle 0.73431 ( 8) hydrogen bonds : bond 0.04293 ( 949) hydrogen bonds : angle 4.20053 ( 2787) link_BETA1-4 : bond 0.00117 ( 4) link_BETA1-4 : angle 1.73110 ( 12) link_NAG-ASN : bond 0.00412 ( 12) link_NAG-ASN : angle 4.50606 ( 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 269 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 225 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.7781 (tpt) cc_final: 0.7510 (mmt) REVERT: A 337 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7379 (mp) REVERT: A 338 ARG cc_start: 0.7697 (ttm110) cc_final: 0.7478 (mtm-85) REVERT: A 559 ASN cc_start: 0.8446 (OUTLIER) cc_final: 0.7848 (m-40) REVERT: A 643 ASP cc_start: 0.7955 (t70) cc_final: 0.7511 (OUTLIER) REVERT: B 411 LYS cc_start: 0.8586 (ttpt) cc_final: 0.8296 (ttpt) REVERT: B 643 ASP cc_start: 0.7928 (t70) cc_final: 0.7493 (t0) REVERT: C 349 SER cc_start: 0.8456 (OUTLIER) cc_final: 0.8034 (p) REVERT: C 559 ASN cc_start: 0.8395 (OUTLIER) cc_final: 0.7788 (m-40) REVERT: C 575 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8558 (mtpp) REVERT: C 643 ASP cc_start: 0.7944 (t70) cc_final: 0.7519 (OUTLIER) REVERT: D 337 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7342 (mp) REVERT: D 559 ASN cc_start: 0.8439 (OUTLIER) cc_final: 0.7836 (m-40) REVERT: D 643 ASP cc_start: 0.7999 (t70) cc_final: 0.7582 (t0) REVERT: D 681 ASN cc_start: 0.8383 (OUTLIER) cc_final: 0.7986 (m110) REVERT: D 690 ASP cc_start: 0.7862 (m-30) cc_final: 0.7318 (t0) outliers start: 44 outliers final: 16 residues processed: 258 average time/residue: 0.4564 time to fit residues: 136.8589 Evaluate side-chains 243 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 221 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 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 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 C residue 349 SER Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 547 ASN Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 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 603 MET Chi-restraints excluded: chain D residue 681 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 12 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 175 optimal weight: 5.9990 chunk 184 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 GLN A 653 ASN A 681 ASN B 636 GLN D 580 ASN D 653 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.135594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.104945 restraints weight = 19564.336| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.57 r_work: 0.2906 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17376 Z= 0.159 Angle : 0.629 10.095 23568 Z= 0.291 Chirality : 0.043 0.288 2812 Planarity : 0.004 0.040 2728 Dihedral : 11.348 98.564 4200 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.89 % Favored : 97.90 % Rotamer: Outliers : 1.85 % Allowed : 14.23 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.19), residues: 1904 helix: 1.64 (0.15), residues: 1096 sheet: -0.94 (0.32), residues: 200 loop : -0.40 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 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 0.003 0.001 HIS C 550 Details of bonding type rmsd covalent geometry : bond 0.00364 (17356) covalent geometry : angle 0.60245 (23512) SS BOND : bond 0.00134 ( 4) SS BOND : angle 0.73682 ( 8) hydrogen bonds : bond 0.04311 ( 949) hydrogen bonds : angle 4.21373 ( 2787) link_BETA1-4 : bond 0.00207 ( 4) link_BETA1-4 : angle 1.75591 ( 12) link_NAG-ASN : bond 0.00497 ( 12) link_NAG-ASN : angle 4.60681 ( 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 259 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 228 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.7787 (tpt) cc_final: 0.7516 (mmt) REVERT: A 337 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7372 (mp) REVERT: A 338 ARG cc_start: 0.7719 (ttm110) cc_final: 0.7451 (ttm-80) REVERT: A 559 ASN cc_start: 0.8462 (OUTLIER) cc_final: 0.7873 (m-40) REVERT: A 643 ASP cc_start: 0.7967 (t70) cc_final: 0.7531 (t0) REVERT: B 643 ASP cc_start: 0.7960 (t70) cc_final: 0.7534 (t0) REVERT: C 349 SER cc_start: 0.8467 (OUTLIER) cc_final: 0.8035 (p) REVERT: C 559 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.7808 (m-40) REVERT: C 575 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8562 (mtpp) REVERT: C 643 ASP cc_start: 0.7995 (t70) cc_final: 0.7566 (t0) REVERT: D 337 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7308 (mp) REVERT: D 559 ASN cc_start: 0.8459 (OUTLIER) cc_final: 0.7866 (m-40) REVERT: D 643 ASP cc_start: 0.8027 (t70) cc_final: 0.7610 (t0) REVERT: D 681 ASN cc_start: 0.8411 (OUTLIER) cc_final: 0.7993 (m-40) REVERT: D 690 ASP cc_start: 0.7844 (m-30) cc_final: 0.7316 (t0) outliers start: 31 outliers final: 15 residues processed: 248 average time/residue: 0.4538 time to fit residues: 130.2018 Evaluate side-chains 242 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 219 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 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 454 SER Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 547 ASN Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 559 ASN Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 681 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: 5.9990 chunk 187 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 653 ASN D 580 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.137227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.106946 restraints weight = 19340.585| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.56 r_work: 0.2939 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17376 Z= 0.123 Angle : 0.614 10.164 23568 Z= 0.282 Chirality : 0.042 0.308 2812 Planarity : 0.003 0.040 2728 Dihedral : 10.925 92.946 4200 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.00 % Favored : 97.79 % Rotamer: Outliers : 1.07 % Allowed : 15.36 % 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 aren not related in a simple way. whole: 1.19 (0.19), residues: 1904 helix: 1.77 (0.15), residues: 1096 sheet: -0.91 (0.32), residues: 200 loop : -0.34 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 338 TYR 0.012 0.001 TYR D 292 PHE 0.020 0.001 PHE D 600 TRP 0.011 0.001 TRP C 554 HIS 0.001 0.001 HIS C 550 Details of bonding type rmsd covalent geometry : bond 0.00267 (17356) covalent geometry : angle 0.58192 (23512) SS BOND : bond 0.00070 ( 4) SS BOND : angle 0.80711 ( 8) hydrogen bonds : bond 0.04085 ( 949) hydrogen bonds : angle 4.12642 ( 2787) link_BETA1-4 : bond 0.00221 ( 4) link_BETA1-4 : angle 1.59704 ( 12) link_NAG-ASN : bond 0.00537 ( 12) link_NAG-ASN : angle 4.96084 ( 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 241 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 223 time to evaluate : 0.641 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 236 ILE cc_start: 0.8943 (mt) cc_final: 0.8741 (mp) REVERT: A 242 MET cc_start: 0.7790 (tpt) cc_final: 0.7466 (mmt) REVERT: A 337 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7354 (mp) REVERT: A 338 ARG cc_start: 0.7698 (ttm110) cc_final: 0.7470 (ttm-80) REVERT: A 559 ASN cc_start: 0.8440 (OUTLIER) cc_final: 0.7869 (m-40) REVERT: A 643 ASP cc_start: 0.7943 (t70) cc_final: 0.7541 (t0) REVERT: B 411 LYS cc_start: 0.8613 (ttpt) cc_final: 0.8330 (ttpt) REVERT: B 643 ASP cc_start: 0.7935 (t70) cc_final: 0.7532 (OUTLIER) REVERT: C 277 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7779 (pt0) REVERT: C 349 SER cc_start: 0.8456 (OUTLIER) cc_final: 0.8035 (p) REVERT: C 559 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.7809 (m-40) REVERT: C 575 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8573 (mtpp) REVERT: C 643 ASP cc_start: 0.7932 (t70) cc_final: 0.7543 (t0) REVERT: D 277 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7670 (pt0) REVERT: D 337 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7291 (mp) REVERT: D 537 GLN cc_start: 0.8150 (tt0) cc_final: 0.7939 (tt0) REVERT: D 559 ASN cc_start: 0.8417 (OUTLIER) cc_final: 0.7816 (m-40) REVERT: D 643 ASP cc_start: 0.7915 (t70) cc_final: 0.7527 (t0) REVERT: D 681 ASN cc_start: 0.8351 (OUTLIER) cc_final: 0.8015 (m-40) REVERT: D 690 ASP cc_start: 0.7892 (m-30) cc_final: 0.7340 (t0) outliers start: 18 outliers final: 7 residues processed: 235 average time/residue: 0.4001 time to fit residues: 109.4295 Evaluate side-chains 233 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 219 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 373 ASP Chi-restraints excluded: chain A residue 559 ASN 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 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 559 ASN Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 681 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 125 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 177 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 GLN A 653 ASN B 636 GLN C 653 ASN D 580 ASN D 653 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.133724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.103088 restraints weight = 19475.556| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.57 r_work: 0.2876 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 17376 Z= 0.233 Angle : 0.701 10.848 23568 Z= 0.321 Chirality : 0.045 0.360 2812 Planarity : 0.004 0.041 2728 Dihedral : 11.169 92.185 4200 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.89 % Favored : 97.90 % Rotamer: Outliers : 1.73 % Allowed : 14.23 % Favored : 84.05 % 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 aren not related in a simple way. whole: 1.01 (0.19), residues: 1904 helix: 1.57 (0.15), residues: 1096 sheet: -0.91 (0.32), residues: 200 loop : -0.34 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 338 TYR 0.015 0.002 TYR D 249 PHE 0.020 0.002 PHE D 600 TRP 0.011 0.002 TRP C 554 HIS 0.004 0.001 HIS B 550 Details of bonding type rmsd covalent geometry : bond 0.00545 (17356) covalent geometry : angle 0.67460 (23512) SS BOND : bond 0.00059 ( 4) SS BOND : angle 0.69790 ( 8) hydrogen bonds : bond 0.04682 ( 949) hydrogen bonds : angle 4.35086 ( 2787) link_BETA1-4 : bond 0.00097 ( 4) link_BETA1-4 : angle 1.93570 ( 12) link_NAG-ASN : bond 0.00463 ( 12) link_NAG-ASN : angle 4.84685 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 222 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.7902 (tpt) cc_final: 0.7539 (mmt) REVERT: A 559 ASN cc_start: 0.8486 (OUTLIER) cc_final: 0.7912 (m-40) REVERT: A 643 ASP cc_start: 0.8027 (t70) cc_final: 0.7583 (t0) REVERT: B 643 ASP cc_start: 0.8051 (t70) cc_final: 0.7612 (OUTLIER) REVERT: C 349 SER cc_start: 0.8502 (OUTLIER) cc_final: 0.8092 (p) REVERT: C 559 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.7830 (m-40) REVERT: C 575 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8605 (mtpp) REVERT: C 643 ASP cc_start: 0.8059 (t70) cc_final: 0.7625 (t0) REVERT: D 559 ASN cc_start: 0.8448 (OUTLIER) cc_final: 0.7842 (m-40) REVERT: D 643 ASP cc_start: 0.8049 (t70) cc_final: 0.7614 (t0) REVERT: D 681 ASN cc_start: 0.8602 (OUTLIER) cc_final: 0.8148 (m-40) REVERT: D 690 ASP cc_start: 0.7892 (m-30) cc_final: 0.7374 (t0) outliers start: 29 outliers final: 16 residues processed: 239 average time/residue: 0.4328 time to fit residues: 120.3727 Evaluate side-chains 237 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 216 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 547 ASN Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 559 ASN Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 681 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 153 optimal weight: 0.9980 chunk 128 optimal weight: 7.9990 chunk 161 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 15 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 110 optimal weight: 0.0970 chunk 130 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 255 GLN D 580 ASN D 653 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.138570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.108612 restraints weight = 19280.583| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.55 r_work: 0.3024 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17376 Z= 0.107 Angle : 0.615 11.250 23568 Z= 0.283 Chirality : 0.042 0.373 2812 Planarity : 0.003 0.040 2728 Dihedral : 10.456 82.007 4200 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.89 % Favored : 97.90 % Rotamer: Outliers : 1.13 % Allowed : 15.42 % Favored : 83.45 % 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 aren not related in a simple way. whole: 1.30 (0.19), residues: 1904 helix: 1.82 (0.15), residues: 1096 sheet: -0.85 (0.32), residues: 200 loop : -0.21 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 338 TYR 0.011 0.001 TYR D 292 PHE 0.021 0.001 PHE D 600 TRP 0.011 0.001 TRP A 554 HIS 0.001 0.000 HIS C 379 Details of bonding type rmsd covalent geometry : bond 0.00220 (17356) covalent geometry : angle 0.58738 (23512) SS BOND : bond 0.00072 ( 4) SS BOND : angle 0.90419 ( 8) hydrogen bonds : bond 0.03976 ( 949) hydrogen bonds : angle 4.13765 ( 2787) link_BETA1-4 : bond 0.00348 ( 4) link_BETA1-4 : angle 1.51084 ( 12) link_NAG-ASN : bond 0.00595 ( 12) link_NAG-ASN : angle 4.62333 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5091.38 seconds wall clock time: 88 minutes 3.09 seconds (5283.09 seconds total)