Starting phenix.real_space_refine on Sun Nov 17 11:52:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyr_28693/11_2024/8eyr_28693.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyr_28693/11_2024/8eyr_28693.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyr_28693/11_2024/8eyr_28693.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyr_28693/11_2024/8eyr_28693.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyr_28693/11_2024/8eyr_28693.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyr_28693/11_2024/8eyr_28693.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 106 5.16 5 C 8625 2.51 5 N 2367 2.21 5 O 2537 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 13635 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 6382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 794, 6382 Classifications: {'peptide': 794} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 749} Chain breaks: 7 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 6387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 6387 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 750} Chain breaks: 7 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 433 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 433 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 9.66, per 1000 atoms: 0.71 Number of scatterers: 13635 At special positions: 0 Unit cell: (126.99, 122.01, 166, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 106 16.00 O 2537 8.00 N 2367 7.00 C 8625 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 22 " distance=2.03 Simple disulfide: pdb=" SG CYS B 120 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 181 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 200 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS B 218 " distance=2.03 Simple disulfide: pdb=" SG CYS B 221 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 234 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 252 " - pdb=" SG CYS B 273 " distance=2.04 Simple disulfide: pdb=" SG CYS B 302 " - pdb=" SG CYS B 324 " distance=2.03 Simple disulfide: pdb=" SG CYS B 781 " - pdb=" SG CYS B 790 " distance=2.03 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 22 " distance=2.03 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 148 " distance=2.03 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 175 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 181 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 200 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 205 " - pdb=" SG CYS A 218 " distance=2.03 Simple disulfide: pdb=" SG CYS A 221 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 252 " - pdb=" SG CYS A 273 " distance=2.04 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 324 " distance=2.03 Simple disulfide: pdb=" SG CYS A 781 " - pdb=" SG CYS A 790 " distance=2.03 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 48 " distance=2.02 Simple disulfide: pdb=" SG CYS C 18 " - pdb=" SG CYS C 61 " distance=2.03 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 52 " distance=2.03 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 48 " distance=2.03 Simple disulfide: pdb=" SG CYS D 18 " - pdb=" SG CYS D 61 " distance=2.03 Simple disulfide: pdb=" SG CYS D 47 " - pdb=" SG CYS D 52 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.40 Conformation dependent library (CDL) restraints added in 1.9 seconds 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3202 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 32 sheets defined 15.2% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'B' and resid 12 through 20 Processing helix chain 'B' and resid 133 through 137 removed outlier: 3.915A pdb=" N ASN B 136 " --> pdb=" O ALA B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 149 Processing helix chain 'B' and resid 248 through 254 removed outlier: 3.519A pdb=" N CYS B 252 " --> pdb=" O ASP B 248 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASN B 254 " --> pdb=" O ASP B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 320 Processing helix chain 'B' and resid 341 through 350 Processing helix chain 'B' and resid 426 through 438 Processing helix chain 'B' and resid 439 through 443 removed outlier: 3.627A pdb=" N GLN B 443 " --> pdb=" O LYS B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 631 Processing helix chain 'B' and resid 680 through 706 Processing helix chain 'B' and resid 856 through 863 Processing helix chain 'A' and resid 12 through 20 Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 314 through 320 removed outlier: 3.974A pdb=" N MET A 320 " --> pdb=" O THR A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 350 removed outlier: 3.871A pdb=" N ASN A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 438 Processing helix chain 'A' and resid 439 through 443 removed outlier: 3.689A pdb=" N GLN A 443 " --> pdb=" O LYS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 631 Processing helix chain 'A' and resid 680 through 706 removed outlier: 3.673A pdb=" N PHE A 706 " --> pdb=" O HIS A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 863 Processing helix chain 'C' and resid 7 through 19 removed outlier: 3.908A pdb=" N VAL C 11 " --> pdb=" O GLY C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 22 No H-bonds generated for 'chain 'C' and resid 20 through 22' Processing helix chain 'C' and resid 43 through 48 Processing helix chain 'C' and resid 53 through 58 Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'D' and resid 7 through 19 Processing helix chain 'D' and resid 43 through 48 Processing helix chain 'D' and resid 53 through 58 Processing helix chain 'D' and resid 59 through 61 No H-bonds generated for 'chain 'D' and resid 59 through 61' Processing sheet with id=AA1, first strand: chain 'B' and resid 2 through 3 removed outlier: 3.617A pdb=" N ILE B 25 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 51 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 7 through 10 removed outlier: 6.479A pdb=" N ILE B 7 " --> pdb=" O HIS B 30 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N LEU B 32 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ILE B 9 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ILE B 34 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL B 60 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU B 55 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N PHE B 90 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU B 57 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ALA B 110 " --> pdb=" O TYR B 85 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU B 87 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL B 140 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 115 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN B 142 " --> pdb=" O LYS B 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 164 through 166 Processing sheet with id=AA4, first strand: chain 'B' and resid 239 through 241 Processing sheet with id=AA5, first strand: chain 'B' and resid 267 through 269 Processing sheet with id=AA6, first strand: chain 'B' and resid 281 through 284 removed outlier: 5.901A pdb=" N TYR B 290 " --> pdb=" O ASN B 284 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 310 through 312 removed outlier: 3.873A pdb=" N LEU B 332 " --> pdb=" O LYS B 310 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 326 through 327 removed outlier: 9.131A pdb=" N LEU B 327 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 10.590A pdb=" N VAL B 354 " --> pdb=" O LEU B 380 " (cutoff:3.500A) removed outlier: 9.784A pdb=" N GLU B 382 " --> pdb=" O VAL B 354 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N THR B 356 " --> pdb=" O GLU B 382 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 462 through 464 removed outlier: 5.466A pdb=" N ASP B 462 " --> pdb=" O LYS B 569 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA B 568 " --> pdb=" O ALA B 554 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N VAL B 552 " --> pdb=" O SER B 570 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE B 494 " --> pdb=" O VAL B 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 462 through 464 removed outlier: 5.466A pdb=" N ASP B 462 " --> pdb=" O LYS B 569 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA B 568 " --> pdb=" O ALA B 554 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N VAL B 552 " --> pdb=" O SER B 570 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 466 through 471 Processing sheet with id=AB3, first strand: chain 'B' and resid 589 through 594 removed outlier: 3.782A pdb=" N ASN B 593 " --> pdb=" O GLN B 597 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLN B 597 " --> pdb=" O ASN B 593 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 752 through 756 Processing sheet with id=AB5, first strand: chain 'B' and resid 814 through 816 Processing sheet with id=AB6, first strand: chain 'B' and resid 841 through 844 Processing sheet with id=AB7, first strand: chain 'B' and resid 881 through 884 removed outlier: 6.173A pdb=" N SER B 884 " --> pdb=" O ASN B 888 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ASN B 888 " --> pdb=" O SER B 884 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 2 through 3 removed outlier: 3.607A pdb=" N ILE A 51 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 6 through 10 removed outlier: 6.491A pdb=" N ILE A 7 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LEU A 32 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE A 9 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ILE A 34 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL A 60 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU A 55 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N PHE A 90 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU A 57 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ALA A 110 " --> pdb=" O TYR A 85 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU A 87 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 112 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 140 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A 115 " --> pdb=" O VAL A 140 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASN A 142 " --> pdb=" O LYS A 115 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 239 through 241 Processing sheet with id=AC2, first strand: chain 'A' and resid 267 through 269 Processing sheet with id=AC3, first strand: chain 'A' and resid 281 through 284 removed outlier: 5.817A pdb=" N TYR A 290 " --> pdb=" O ASN A 284 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 309 through 312 removed outlier: 3.800A pdb=" N LEU A 332 " --> pdb=" O LYS A 310 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL A 359 " --> pdb=" O TYR A 392 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N LEU A 394 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE A 361 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 326 through 327 Processing sheet with id=AC6, first strand: chain 'A' and resid 462 through 464 removed outlier: 5.588A pdb=" N ASP A 462 " --> pdb=" O LYS A 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'A' and resid 466 through 471 Processing sheet with id=AC8, first strand: chain 'A' and resid 522 through 525 removed outlier: 3.743A pdb=" N PHE A 494 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 589 through 594 removed outlier: 6.833A pdb=" N GLN A 597 " --> pdb=" O ASN A 593 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 752 through 756 removed outlier: 7.121A pdb=" N CYS A 781 " --> pdb=" O SER A 613 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 776 through 777 Processing sheet with id=AD3, first strand: chain 'A' and resid 814 through 816 Processing sheet with id=AD4, first strand: chain 'A' and resid 841 through 844 removed outlier: 3.891A pdb=" N ILE A 842 " --> pdb=" O GLU A 853 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 881 through 884 removed outlier: 5.688A pdb=" N ALA A 882 " --> pdb=" O GLY A 889 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY A 889 " --> pdb=" O ALA A 882 " (cutoff:3.500A) 308 hydrogen bonds defined for protein. 795 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: 4.91 Time building geometry restraints manager: 3.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4487 1.34 - 1.46: 3219 1.46 - 1.58: 6113 1.58 - 1.70: 2 1.70 - 1.82: 132 Bond restraints: 13953 Sorted by residual: bond pdb=" CB PRO B 894 " pdb=" CG PRO B 894 " ideal model delta sigma weight residual 1.492 1.666 -0.174 5.00e-02 4.00e+02 1.20e+01 bond pdb=" CB PRO A 894 " pdb=" CG PRO A 894 " ideal model delta sigma weight residual 1.492 1.606 -0.114 5.00e-02 4.00e+02 5.17e+00 bond pdb=" N PRO B 894 " pdb=" CA PRO B 894 " ideal model delta sigma weight residual 1.469 1.444 0.025 1.28e-02 6.10e+03 3.79e+00 bond pdb=" CG GLU B 386 " pdb=" CD GLU B 386 " ideal model delta sigma weight residual 1.516 1.474 0.042 2.50e-02 1.60e+03 2.79e+00 bond pdb=" CB ARG D 55 " pdb=" CG ARG D 55 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.94e+00 ... (remaining 13948 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 18704 2.69 - 5.37: 182 5.37 - 8.06: 28 8.06 - 10.75: 6 10.75 - 13.44: 3 Bond angle restraints: 18923 Sorted by residual: angle pdb=" CA PRO B 894 " pdb=" N PRO B 894 " pdb=" CD PRO B 894 " ideal model delta sigma weight residual 112.00 98.56 13.44 1.40e+00 5.10e-01 9.21e+01 angle pdb=" C HIS A 564 " pdb=" CA HIS A 564 " pdb=" CB HIS A 564 " ideal model delta sigma weight residual 115.79 109.61 6.18 1.19e+00 7.06e-01 2.70e+01 angle pdb=" CA PRO A 894 " pdb=" N PRO A 894 " pdb=" CD PRO A 894 " ideal model delta sigma weight residual 112.00 105.51 6.49 1.40e+00 5.10e-01 2.15e+01 angle pdb=" N PRO B 894 " pdb=" CD PRO B 894 " pdb=" CG PRO B 894 " ideal model delta sigma weight residual 103.20 96.33 6.87 1.50e+00 4.44e-01 2.10e+01 angle pdb=" CA ARG D 55 " pdb=" CB ARG D 55 " pdb=" CG ARG D 55 " ideal model delta sigma weight residual 114.10 123.04 -8.94 2.00e+00 2.50e-01 2.00e+01 ... (remaining 18918 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 7027 16.84 - 33.68: 1019 33.68 - 50.52: 314 50.52 - 67.36: 64 67.36 - 84.20: 25 Dihedral angle restraints: 8449 sinusoidal: 3470 harmonic: 4979 Sorted by residual: dihedral pdb=" CB CYS D 18 " pdb=" SG CYS D 18 " pdb=" SG CYS D 61 " pdb=" CB CYS D 61 " ideal model delta sinusoidal sigma weight residual 93.00 175.61 -82.61 1 1.00e+01 1.00e-02 8.37e+01 dihedral pdb=" CB CYS C 18 " pdb=" SG CYS C 18 " pdb=" SG CYS C 61 " pdb=" CB CYS C 61 " ideal model delta sinusoidal sigma weight residual 93.00 173.15 -80.15 1 1.00e+01 1.00e-02 7.96e+01 dihedral pdb=" CB CYS B 162 " pdb=" SG CYS B 162 " pdb=" SG CYS B 181 " pdb=" CB CYS B 181 " ideal model delta sinusoidal sigma weight residual 93.00 16.25 76.75 1 1.00e+01 1.00e-02 7.40e+01 ... (remaining 8446 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1299 0.038 - 0.075: 507 0.075 - 0.113: 190 0.113 - 0.151: 40 0.151 - 0.188: 5 Chirality restraints: 2041 Sorted by residual: chirality pdb=" CG LEU A 32 " pdb=" CB LEU A 32 " pdb=" CD1 LEU A 32 " pdb=" CD2 LEU A 32 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.85e-01 chirality pdb=" CB ILE A 448 " pdb=" CA ILE A 448 " pdb=" CG1 ILE A 448 " pdb=" CG2 ILE A 448 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.99e-01 chirality pdb=" CA VAL A 899 " pdb=" N VAL A 899 " pdb=" C VAL A 899 " pdb=" CB VAL A 899 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.41e-01 ... (remaining 2038 not shown) Planarity restraints: 2459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 893 " 0.098 5.00e-02 4.00e+02 1.38e-01 3.05e+01 pdb=" N PRO B 894 " -0.238 5.00e-02 4.00e+02 pdb=" CA PRO B 894 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO B 894 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 893 " -0.068 5.00e-02 4.00e+02 9.94e-02 1.58e+01 pdb=" N PRO A 894 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO A 894 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 894 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 403 " 0.000 2.00e-02 2.50e+03 1.39e-02 4.85e+00 pdb=" CG TRP A 403 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP A 403 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A 403 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 403 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 403 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 403 " 0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 403 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 403 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 403 " -0.003 2.00e-02 2.50e+03 ... (remaining 2456 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 407 2.66 - 3.22: 14008 3.22 - 3.78: 22603 3.78 - 4.34: 29630 4.34 - 4.90: 46281 Nonbonded interactions: 112929 Sorted by model distance: nonbonded pdb=" OD1 ASP A 313 " pdb=" OG SER A 317 " model vdw 2.099 3.040 nonbonded pdb=" OD1 ASP B 313 " pdb=" OG SER B 317 " model vdw 2.101 3.040 nonbonded pdb=" OE2 GLU B 690 " pdb=" OH TYR A 138 " model vdw 2.151 3.040 nonbonded pdb=" O ARG B 77 " pdb=" OG1 THR B 107 " model vdw 2.153 3.040 nonbonded pdb=" OG SER A 461 " pdb=" O ARG A 566 " model vdw 2.194 3.040 ... (remaining 112924 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 1 through 294 or resid 301 through 901)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.380 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: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 34.940 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 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 : 0.005 0.174 13953 Z= 0.358 Angle : 0.755 13.437 18923 Z= 0.398 Chirality : 0.046 0.188 2041 Planarity : 0.006 0.138 2459 Dihedral : 17.459 84.202 5151 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 23.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.47 % Favored : 88.35 % Rotamer: Outliers : 0.27 % Allowed : 33.20 % Favored : 66.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.20), residues: 1665 helix: -1.38 (0.36), residues: 190 sheet: -1.70 (0.29), residues: 333 loop : -1.91 (0.18), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 403 HIS 0.006 0.001 HIS B 269 PHE 0.020 0.001 PHE A 752 TYR 0.017 0.002 TYR B 488 ARG 0.007 0.001 ARG A 762 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 558 THR cc_start: 0.9215 (p) cc_final: 0.8948 (t) REVERT: A 320 MET cc_start: 0.8508 (ptm) cc_final: 0.8182 (ptt) outliers start: 4 outliers final: 2 residues processed: 93 average time/residue: 0.2524 time to fit residues: 36.0465 Evaluate side-chains 86 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 84 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 522 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 43 optimal weight: 0.1980 chunk 85 optimal weight: 0.9980 chunk 68 optimal weight: 8.9990 chunk 131 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 152 optimal weight: 50.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 14 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13953 Z= 0.220 Angle : 0.633 10.590 18923 Z= 0.324 Chirality : 0.045 0.154 2041 Planarity : 0.005 0.066 2459 Dihedral : 5.332 35.903 1892 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.55 % Favored : 90.27 % Rotamer: Outliers : 4.28 % Allowed : 29.59 % Favored : 66.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.20), residues: 1665 helix: -0.90 (0.38), residues: 195 sheet: -1.58 (0.30), residues: 323 loop : -1.85 (0.18), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 815 HIS 0.007 0.001 HIS B 269 PHE 0.017 0.001 PHE B 697 TYR 0.010 0.001 TYR B 13 ARG 0.004 0.000 ARG A 762 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 104 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 274 MET cc_start: 0.8338 (pmm) cc_final: 0.7394 (pmm) REVERT: B 559 MET cc_start: 0.8345 (tpp) cc_final: 0.8127 (tpp) REVERT: B 599 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.8987 (tp) REVERT: B 628 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8497 (mt) REVERT: B 690 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7931 (tp30) REVERT: A 180 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8110 (ttm110) REVERT: C 46 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.8488 (tm-30) outliers start: 64 outliers final: 27 residues processed: 158 average time/residue: 0.2375 time to fit residues: 57.1261 Evaluate side-chains 125 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 175 CYS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 417 MET Chi-restraints excluded: chain B residue 434 GLU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain D residue 10 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 152 optimal weight: 40.0000 chunk 165 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 151 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13953 Z= 0.279 Angle : 0.639 9.375 18923 Z= 0.325 Chirality : 0.046 0.162 2041 Planarity : 0.005 0.056 2459 Dihedral : 5.321 37.823 1890 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.09 % Favored : 89.73 % Rotamer: Outliers : 6.49 % Allowed : 28.38 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.20), residues: 1665 helix: -0.98 (0.36), residues: 201 sheet: -1.66 (0.29), residues: 340 loop : -1.77 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 520 HIS 0.006 0.001 HIS B 269 PHE 0.015 0.001 PHE B 348 TYR 0.012 0.001 TYR A 551 ARG 0.008 0.000 ARG A 618 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 96 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 272 GLU cc_start: 0.5976 (OUTLIER) cc_final: 0.4818 (mm-30) REVERT: B 274 MET cc_start: 0.8423 (pmm) cc_final: 0.7511 (pmm) REVERT: B 628 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8412 (mt) REVERT: B 690 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7860 (tm-30) REVERT: A 180 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8221 (ttm110) REVERT: A 274 MET cc_start: 0.8352 (pmm) cc_final: 0.7535 (pmm) REVERT: A 314 SER cc_start: 0.9378 (OUTLIER) cc_final: 0.9122 (t) REVERT: C 46 GLU cc_start: 0.9128 (OUTLIER) cc_final: 0.8859 (tm-30) outliers start: 97 outliers final: 49 residues processed: 181 average time/residue: 0.2435 time to fit residues: 68.4025 Evaluate side-chains 143 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 88 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 175 CYS Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 434 GLU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 795 PHE Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 244 TRP Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 618 ARG Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 58 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 72 optimal weight: 30.0000 chunk 102 optimal weight: 0.9980 chunk 153 optimal weight: 40.0000 chunk 162 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 43 optimal weight: 0.4980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 347 ASN ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13953 Z= 0.290 Angle : 0.669 11.455 18923 Z= 0.334 Chirality : 0.047 0.292 2041 Planarity : 0.005 0.055 2459 Dihedral : 5.383 43.341 1887 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.21 % Favored : 89.61 % Rotamer: Outliers : 6.43 % Allowed : 28.45 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.20), residues: 1665 helix: -0.95 (0.36), residues: 201 sheet: -1.62 (0.29), residues: 339 loop : -1.75 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 403 HIS 0.006 0.001 HIS B 269 PHE 0.024 0.001 PHE B 241 TYR 0.013 0.001 TYR A 224 ARG 0.003 0.000 ARG B 756 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 96 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 272 GLU cc_start: 0.6000 (OUTLIER) cc_final: 0.4780 (mm-30) REVERT: B 274 MET cc_start: 0.8417 (pmm) cc_final: 0.7552 (pmm) REVERT: B 403 TRP cc_start: 0.8461 (OUTLIER) cc_final: 0.8182 (p90) REVERT: B 599 ILE cc_start: 0.9327 (OUTLIER) cc_final: 0.8982 (tp) REVERT: B 628 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8426 (mt) REVERT: B 690 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7866 (tm-30) REVERT: B 771 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.8656 (t80) REVERT: A 180 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8225 (ttm110) REVERT: A 274 MET cc_start: 0.8328 (pmm) cc_final: 0.7578 (pmm) REVERT: A 314 SER cc_start: 0.9379 (OUTLIER) cc_final: 0.9083 (t) REVERT: A 618 ARG cc_start: 0.9490 (OUTLIER) cc_final: 0.8766 (ptp90) REVERT: A 752 PHE cc_start: 0.9602 (OUTLIER) cc_final: 0.9273 (t80) REVERT: C 46 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8804 (tm-30) outliers start: 96 outliers final: 61 residues processed: 184 average time/residue: 0.2269 time to fit residues: 64.9388 Evaluate side-chains 162 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 90 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 175 CYS Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 403 TRP Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 434 GLU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain B residue 771 PHE Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 795 PHE Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 244 TRP Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 540 HIS Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 618 ARG Chi-restraints excluded: chain A residue 752 PHE Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 54 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 30.0000 chunk 92 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 120 optimal weight: 0.0170 chunk 67 optimal weight: 8.9990 chunk 138 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 0 optimal weight: 0.9990 chunk 82 optimal weight: 0.0770 chunk 145 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 347 ASN ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13953 Z= 0.189 Angle : 0.633 12.183 18923 Z= 0.313 Chirality : 0.046 0.213 2041 Planarity : 0.004 0.054 2459 Dihedral : 5.142 36.574 1887 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.71 % Favored : 91.11 % Rotamer: Outliers : 6.29 % Allowed : 28.71 % Favored : 64.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.20), residues: 1665 helix: -0.75 (0.37), residues: 195 sheet: -1.41 (0.30), residues: 323 loop : -1.74 (0.18), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 520 HIS 0.005 0.001 HIS B 269 PHE 0.022 0.001 PHE B 348 TYR 0.010 0.001 TYR B 418 ARG 0.003 0.000 ARG A 857 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 103 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8776 (pp) REVERT: B 272 GLU cc_start: 0.5917 (OUTLIER) cc_final: 0.4832 (mm-30) REVERT: B 274 MET cc_start: 0.8478 (pmm) cc_final: 0.7669 (pmm) REVERT: B 559 MET cc_start: 0.8489 (tpp) cc_final: 0.8227 (tpp) REVERT: B 599 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.8942 (tp) REVERT: B 628 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8428 (mt) REVERT: B 690 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7758 (tp30) REVERT: B 771 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.8589 (t80) REVERT: A 180 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7879 (ptp-170) REVERT: A 274 MET cc_start: 0.8311 (pmm) cc_final: 0.7583 (pmm) REVERT: A 618 ARG cc_start: 0.9439 (OUTLIER) cc_final: 0.8917 (ptp90) REVERT: A 752 PHE cc_start: 0.9597 (OUTLIER) cc_final: 0.9271 (t80) REVERT: C 46 GLU cc_start: 0.9138 (OUTLIER) cc_final: 0.8817 (tm-30) outliers start: 94 outliers final: 54 residues processed: 187 average time/residue: 0.2106 time to fit residues: 61.8696 Evaluate side-chains 160 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 96 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 LYS Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 175 CYS Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 540 HIS Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain B residue 771 PHE Chi-restraints excluded: chain B residue 795 PHE Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 244 TRP Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 403 TRP Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 540 HIS Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 618 ARG Chi-restraints excluded: chain A residue 752 PHE Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 58 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 134 optimal weight: 0.3980 chunk 75 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 53 optimal weight: 0.3980 chunk 85 optimal weight: 9.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN ** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13953 Z= 0.272 Angle : 0.653 10.218 18923 Z= 0.324 Chirality : 0.046 0.183 2041 Planarity : 0.004 0.052 2459 Dihedral : 5.200 36.619 1887 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.79 % Favored : 90.03 % Rotamer: Outliers : 6.22 % Allowed : 29.05 % Favored : 64.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.20), residues: 1665 helix: -0.91 (0.36), residues: 201 sheet: -1.44 (0.30), residues: 330 loop : -1.72 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 520 HIS 0.005 0.001 HIS B 269 PHE 0.023 0.001 PHE B 348 TYR 0.014 0.001 TYR B 13 ARG 0.004 0.000 ARG B 337 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 98 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8818 (pp) REVERT: B 272 GLU cc_start: 0.5900 (OUTLIER) cc_final: 0.4782 (mm-30) REVERT: B 274 MET cc_start: 0.8434 (pmm) cc_final: 0.7618 (pmm) REVERT: B 559 MET cc_start: 0.8602 (tpp) cc_final: 0.8375 (tpp) REVERT: B 599 ILE cc_start: 0.9310 (OUTLIER) cc_final: 0.8959 (tp) REVERT: B 628 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8406 (mt) REVERT: B 690 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7804 (tm-30) REVERT: B 771 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8569 (t80) REVERT: A 180 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8179 (ttm110) REVERT: A 274 MET cc_start: 0.8355 (pmm) cc_final: 0.7680 (pmm) REVERT: A 314 SER cc_start: 0.9422 (OUTLIER) cc_final: 0.9099 (t) REVERT: A 618 ARG cc_start: 0.9431 (OUTLIER) cc_final: 0.8880 (ptp90) REVERT: A 752 PHE cc_start: 0.9602 (OUTLIER) cc_final: 0.9282 (t80) REVERT: C 46 GLU cc_start: 0.9170 (OUTLIER) cc_final: 0.8798 (tm-30) outliers start: 93 outliers final: 67 residues processed: 182 average time/residue: 0.2096 time to fit residues: 60.2158 Evaluate side-chains 170 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 92 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 17 LYS Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 175 CYS Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 540 HIS Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain B residue 771 PHE Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 795 PHE Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 403 TRP Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 540 HIS Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 618 ARG Chi-restraints excluded: chain A residue 752 PHE Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 58 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 136 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN ** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13953 Z= 0.384 Angle : 0.704 11.804 18923 Z= 0.354 Chirality : 0.048 0.203 2041 Planarity : 0.005 0.051 2459 Dihedral : 5.449 37.142 1887 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.57 % Favored : 89.25 % Rotamer: Outliers : 7.10 % Allowed : 28.11 % Favored : 64.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.20), residues: 1665 helix: -0.83 (0.37), residues: 189 sheet: -1.50 (0.29), residues: 332 loop : -1.74 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 403 HIS 0.005 0.001 HIS B 269 PHE 0.024 0.002 PHE B 348 TYR 0.016 0.002 TYR A 551 ARG 0.004 0.001 ARG B 756 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 92 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8832 (pp) REVERT: B 272 GLU cc_start: 0.5942 (OUTLIER) cc_final: 0.4715 (mm-30) REVERT: B 274 MET cc_start: 0.8509 (pmm) cc_final: 0.7747 (pmm) REVERT: B 559 MET cc_start: 0.8532 (tpp) cc_final: 0.8253 (mmt) REVERT: B 599 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.8983 (tp) REVERT: B 628 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8425 (mt) REVERT: B 690 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7861 (tm-30) REVERT: B 771 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.8598 (t80) REVERT: A 180 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8285 (ttm110) REVERT: A 274 MET cc_start: 0.8360 (pmm) cc_final: 0.7684 (pmm) REVERT: A 314 SER cc_start: 0.9407 (OUTLIER) cc_final: 0.9104 (t) REVERT: A 752 PHE cc_start: 0.9604 (OUTLIER) cc_final: 0.9284 (t80) REVERT: C 46 GLU cc_start: 0.9192 (OUTLIER) cc_final: 0.8783 (tm-30) outliers start: 106 outliers final: 76 residues processed: 187 average time/residue: 0.2164 time to fit residues: 63.7433 Evaluate side-chains 173 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 87 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 17 LYS Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 175 CYS Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 348 PHE Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 426 CYS Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 540 HIS Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain B residue 771 PHE Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 795 PHE Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 403 TRP Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 540 HIS Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 752 PHE Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 800 THR Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 54 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.4980 chunk 64 optimal weight: 9.9990 chunk 96 optimal weight: 0.0970 chunk 48 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 15 optimal weight: 0.0030 chunk 127 optimal weight: 4.9990 chunk 147 optimal weight: 9.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 881 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13953 Z= 0.172 Angle : 0.661 12.407 18923 Z= 0.322 Chirality : 0.046 0.187 2041 Planarity : 0.004 0.053 2459 Dihedral : 5.084 36.691 1887 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.77 % Favored : 91.05 % Rotamer: Outliers : 5.02 % Allowed : 30.32 % Favored : 64.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.20), residues: 1665 helix: -0.47 (0.38), residues: 177 sheet: -1.29 (0.31), residues: 313 loop : -1.65 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 520 HIS 0.004 0.001 HIS B 269 PHE 0.026 0.001 PHE B 348 TYR 0.020 0.001 TYR B 13 ARG 0.004 0.000 ARG B 337 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 108 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 LEU cc_start: 0.9149 (tp) cc_final: 0.8909 (tp) REVERT: B 32 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8721 (pp) REVERT: B 272 GLU cc_start: 0.6006 (OUTLIER) cc_final: 0.4884 (mm-30) REVERT: B 274 MET cc_start: 0.8542 (pmm) cc_final: 0.7806 (pmm) REVERT: B 403 TRP cc_start: 0.8493 (OUTLIER) cc_final: 0.8229 (p90) REVERT: B 559 MET cc_start: 0.8577 (tpp) cc_final: 0.8344 (tpp) REVERT: B 599 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8874 (tp) REVERT: B 628 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8422 (mt) REVERT: B 690 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7750 (tm-30) REVERT: B 771 PHE cc_start: 0.8947 (OUTLIER) cc_final: 0.8549 (t80) REVERT: A 274 MET cc_start: 0.8353 (pmm) cc_final: 0.7781 (pmm) REVERT: A 403 TRP cc_start: 0.8559 (OUTLIER) cc_final: 0.8230 (p90) REVERT: A 752 PHE cc_start: 0.9595 (OUTLIER) cc_final: 0.9253 (t80) REVERT: C 46 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8814 (tm-30) outliers start: 75 outliers final: 51 residues processed: 176 average time/residue: 0.2091 time to fit residues: 58.6496 Evaluate side-chains 153 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 92 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 LYS Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 175 CYS Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 403 TRP Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 488 TYR Chi-restraints excluded: chain B residue 540 HIS Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain B residue 771 PHE Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 795 PHE Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 244 TRP Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 403 TRP Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 540 HIS Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 752 PHE Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 800 THR Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 58 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 30.0000 chunk 141 optimal weight: 0.8980 chunk 150 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 142 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13953 Z= 0.356 Angle : 0.706 11.944 18923 Z= 0.353 Chirality : 0.048 0.195 2041 Planarity : 0.005 0.051 2459 Dihedral : 5.315 37.313 1887 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.97 % Favored : 89.85 % Rotamer: Outliers : 5.02 % Allowed : 30.99 % Favored : 63.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.20), residues: 1665 helix: -0.70 (0.38), residues: 183 sheet: -1.33 (0.30), residues: 324 loop : -1.75 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 403 HIS 0.005 0.001 HIS B 269 PHE 0.018 0.002 PHE B 241 TYR 0.021 0.002 TYR B 13 ARG 0.004 0.000 ARG B 756 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 87 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8753 (pp) REVERT: B 172 ASN cc_start: 0.9241 (OUTLIER) cc_final: 0.8636 (p0) REVERT: B 272 GLU cc_start: 0.5839 (OUTLIER) cc_final: 0.4615 (mm-30) REVERT: B 274 MET cc_start: 0.8551 (pmm) cc_final: 0.7801 (pmm) REVERT: B 559 MET cc_start: 0.8597 (tpp) cc_final: 0.8301 (mmt) REVERT: B 599 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.8927 (tp) REVERT: B 628 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8439 (mt) REVERT: B 690 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7841 (tm-30) REVERT: B 771 PHE cc_start: 0.8995 (OUTLIER) cc_final: 0.8576 (t80) REVERT: A 180 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8260 (ttm110) REVERT: A 274 MET cc_start: 0.8344 (pmm) cc_final: 0.7669 (pmm) REVERT: A 314 SER cc_start: 0.9319 (OUTLIER) cc_final: 0.9106 (t) REVERT: A 403 TRP cc_start: 0.8537 (OUTLIER) cc_final: 0.8178 (p90) REVERT: A 752 PHE cc_start: 0.9592 (OUTLIER) cc_final: 0.9252 (t80) REVERT: C 46 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8846 (tm-30) outliers start: 75 outliers final: 59 residues processed: 157 average time/residue: 0.2091 time to fit residues: 52.4486 Evaluate side-chains 157 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 86 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 175 CYS Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 426 CYS Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 540 HIS Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain B residue 771 PHE Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 795 PHE Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 403 TRP Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 540 HIS Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 752 PHE Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 800 THR Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 58 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 6.9990 chunk 75 optimal weight: 0.0980 chunk 110 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 154 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 chunk 13 optimal weight: 0.0770 chunk 102 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 834 ASN ** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13953 Z= 0.182 Angle : 0.664 11.489 18923 Z= 0.325 Chirality : 0.046 0.172 2041 Planarity : 0.004 0.051 2459 Dihedral : 5.043 37.020 1887 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.53 % Favored : 91.29 % Rotamer: Outliers : 4.42 % Allowed : 31.26 % Favored : 64.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.20), residues: 1665 helix: -0.47 (0.38), residues: 177 sheet: -1.31 (0.30), residues: 327 loop : -1.70 (0.18), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 520 HIS 0.004 0.001 HIS B 269 PHE 0.020 0.001 PHE B 348 TYR 0.010 0.001 TYR B 418 ARG 0.003 0.000 ARG B 709 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 96 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 272 GLU cc_start: 0.5935 (OUTLIER) cc_final: 0.4809 (mm-30) REVERT: B 274 MET cc_start: 0.8560 (pmm) cc_final: 0.7804 (pmm) REVERT: B 559 MET cc_start: 0.8560 (tpp) cc_final: 0.8213 (mmt) REVERT: B 599 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8882 (tp) REVERT: B 628 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8458 (mt) REVERT: B 690 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7792 (tm-30) REVERT: B 771 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8482 (t80) REVERT: A 180 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8103 (ttm110) REVERT: A 274 MET cc_start: 0.8385 (pmm) cc_final: 0.7809 (pmm) REVERT: A 403 TRP cc_start: 0.8559 (OUTLIER) cc_final: 0.8207 (p90) REVERT: A 752 PHE cc_start: 0.9586 (OUTLIER) cc_final: 0.9230 (t80) REVERT: C 46 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8743 (tm-30) outliers start: 66 outliers final: 51 residues processed: 156 average time/residue: 0.2144 time to fit residues: 53.6377 Evaluate side-chains 153 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 93 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 175 CYS Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 488 TYR Chi-restraints excluded: chain B residue 540 HIS Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain B residue 771 PHE Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 795 PHE Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 403 TRP Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 540 HIS Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 752 PHE Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 800 THR Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 58 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 37 optimal weight: 0.2980 chunk 133 optimal weight: 0.9980 chunk 55 optimal weight: 9.9990 chunk 137 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 24 optimal weight: 10.0000 chunk 117 optimal weight: 0.5980 chunk 7 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 ASN ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.101680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.067846 restraints weight = 45018.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.067732 restraints weight = 31857.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.067810 restraints weight = 26580.468| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13953 Z= 0.168 Angle : 0.648 11.003 18923 Z= 0.315 Chirality : 0.045 0.171 2041 Planarity : 0.004 0.051 2459 Dihedral : 4.836 37.070 1887 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.05 % Favored : 91.77 % Rotamer: Outliers : 4.08 % Allowed : 31.86 % Favored : 64.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.20), residues: 1665 helix: -0.53 (0.38), residues: 183 sheet: -1.19 (0.30), residues: 327 loop : -1.69 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 520 HIS 0.003 0.001 HIS B 269 PHE 0.020 0.001 PHE B 348 TYR 0.009 0.001 TYR A 431 ARG 0.003 0.000 ARG B 174 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2578.01 seconds wall clock time: 48 minutes 22.92 seconds (2902.92 seconds total)