Starting phenix.real_space_refine on Sat Aug 23 17:28:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eyr_28693/08_2025/8eyr_28693.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eyr_28693/08_2025/8eyr_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/cci-nas-00/data/ceres_data/8eyr_28693/08_2025/8eyr_28693.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eyr_28693/08_2025/8eyr_28693.map" model { file = "/net/cci-nas-00/data/ceres_data/8eyr_28693/08_2025/8eyr_28693.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eyr_28693/08_2025/8eyr_28693.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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, 'ASP:plan': 1, 'ASN:plan1': 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, 'ASP:plan': 1, 'ASN:plan1': 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: 2.66, per 1000 atoms: 0.20 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: 0.86 Conformation dependent library (CDL) restraints added in 389.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.34 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: 2.27 Time building geometry restraints manager: 1.11 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: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.470 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.850 ------------------------------------------------------------------------------- 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 13985 Z= 0.227 Angle : 0.756 13.437 18987 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.007 0.001 ARG A 762 TYR 0.017 0.002 TYR B 488 PHE 0.020 0.001 PHE A 752 TRP 0.032 0.002 TRP A 403 HIS 0.006 0.001 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00526 (13953) covalent geometry : angle 0.75459 (18923) SS BOND : bond 0.00361 ( 32) SS BOND : angle 1.08219 ( 64) hydrogen bonds : bond 0.18840 ( 306) hydrogen bonds : angle 8.96608 ( 795) *********************** 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 : 0.535 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: 0.1039 time to fit residues: 14.8161 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 : 0.340 ------------------------------------------------------------------------------- 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 98 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 overall best weight: 1.6582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.100199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.067519 restraints weight = 45240.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.066296 restraints weight = 35240.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.066301 restraints weight = 32726.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.066690 restraints weight = 28645.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.066847 restraints weight = 25812.263| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13985 Z= 0.163 Angle : 0.642 10.139 18987 Z= 0.329 Chirality : 0.046 0.153 2041 Planarity : 0.005 0.066 2459 Dihedral : 5.401 35.893 1892 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.03 % Favored : 89.79 % Rotamer: Outliers : 4.75 % Allowed : 29.38 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.44 (0.20), residues: 1665 helix: -0.92 (0.37), residues: 195 sheet: -1.61 (0.30), residues: 324 loop : -1.84 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 762 TYR 0.010 0.001 TYR A 551 PHE 0.015 0.001 PHE B 697 TRP 0.009 0.001 TRP B 520 HIS 0.007 0.001 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00377 (13953) covalent geometry : angle 0.64149 (18923) SS BOND : bond 0.00371 ( 32) SS BOND : angle 0.85062 ( 64) hydrogen bonds : bond 0.04245 ( 306) hydrogen bonds : angle 6.88965 ( 795) *********************** 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 173 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 102 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 274 MET cc_start: 0.8272 (pmm) cc_final: 0.7305 (pmm) REVERT: B 599 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.8982 (tp) REVERT: B 628 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8330 (mt) REVERT: B 690 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7918 (tp30) REVERT: A 180 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8084 (ttm110) REVERT: A 752 PHE cc_start: 0.9414 (OUTLIER) cc_final: 0.9168 (t80) REVERT: C 46 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8418 (tm-30) outliers start: 71 outliers final: 30 residues processed: 161 average time/residue: 0.0900 time to fit residues: 22.3531 Evaluate side-chains 127 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 91 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 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 175 CYS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 309 THR 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 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 A residue 577 THR Chi-restraints excluded: chain A residue 752 PHE 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 64 optimal weight: 6.9990 chunk 66 optimal weight: 20.0000 chunk 165 optimal weight: 4.9990 chunk 158 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 139 optimal weight: 0.3980 chunk 77 optimal weight: 30.0000 chunk 58 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.099773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.066741 restraints weight = 45609.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.065436 restraints weight = 40190.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.065945 restraints weight = 31702.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.066368 restraints weight = 27749.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.066535 restraints weight = 24476.718| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13985 Z= 0.167 Angle : 0.642 9.291 18987 Z= 0.323 Chirality : 0.046 0.158 2041 Planarity : 0.005 0.056 2459 Dihedral : 5.289 38.540 1890 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.61 % Favored : 90.21 % Rotamer: Outliers : 6.49 % Allowed : 28.45 % Favored : 65.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.40 (0.20), residues: 1665 helix: -0.96 (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 ARG 0.005 0.000 ARG B 799 TYR 0.011 0.001 TYR A 551 PHE 0.016 0.001 PHE B 697 TRP 0.008 0.001 TRP B 520 HIS 0.006 0.001 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00385 (13953) covalent geometry : angle 0.64111 (18923) SS BOND : bond 0.00310 ( 32) SS BOND : angle 0.77212 ( 64) hydrogen bonds : bond 0.04043 ( 306) hydrogen bonds : angle 6.56365 ( 795) *********************** 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 195 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 98 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 272 GLU cc_start: 0.6021 (OUTLIER) cc_final: 0.4833 (mm-30) REVERT: B 274 MET cc_start: 0.8348 (pmm) cc_final: 0.7427 (pmm) REVERT: B 488 TYR cc_start: 0.8905 (OUTLIER) cc_final: 0.8686 (p90) REVERT: B 599 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.8945 (tp) REVERT: B 628 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8325 (mt) REVERT: B 690 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7795 (tp30) REVERT: A 180 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8159 (ttm110) REVERT: A 274 MET cc_start: 0.8274 (pmm) cc_final: 0.7427 (pmm) REVERT: A 618 ARG cc_start: 0.9381 (OUTLIER) cc_final: 0.8527 (ptp90) REVERT: A 752 PHE cc_start: 0.9419 (OUTLIER) cc_final: 0.9041 (t80) REVERT: C 46 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8684 (tm-30) outliers start: 97 outliers final: 52 residues processed: 183 average time/residue: 0.0853 time to fit residues: 24.3978 Evaluate side-chains 152 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 91 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 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 488 TYR Chi-restraints excluded: chain B residue 491 LEU 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 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 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 320 MET Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 422 ASN 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 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 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 2 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 163 optimal weight: 0.0980 chunk 65 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 117 optimal weight: 4.9990 chunk 160 optimal weight: 0.1980 chunk 66 optimal weight: 40.0000 overall best weight: 0.4982 ------------------------------------------------------------------------------- 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 481 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.102003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.069627 restraints weight = 45360.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.067954 restraints weight = 31399.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.068377 restraints weight = 28284.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.068616 restraints weight = 25848.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.068852 restraints weight = 23696.315| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 13985 Z= 0.107 Angle : 0.635 11.735 18987 Z= 0.313 Chirality : 0.046 0.269 2041 Planarity : 0.004 0.056 2459 Dihedral : 5.100 42.980 1887 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.71 % Favored : 91.11 % Rotamer: Outliers : 5.35 % Allowed : 29.18 % Favored : 65.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.28 (0.20), residues: 1665 helix: -0.80 (0.37), residues: 196 sheet: -1.55 (0.29), residues: 338 loop : -1.71 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 489 TYR 0.012 0.001 TYR A 224 PHE 0.019 0.001 PHE B 697 TRP 0.007 0.001 TRP B 520 HIS 0.004 0.001 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00245 (13953) covalent geometry : angle 0.63245 (18923) SS BOND : bond 0.00439 ( 32) SS BOND : angle 1.21830 ( 64) hydrogen bonds : bond 0.03600 ( 306) hydrogen bonds : angle 6.18594 ( 795) *********************** 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 191 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 111 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 272 GLU cc_start: 0.5964 (OUTLIER) cc_final: 0.4875 (mm-30) REVERT: B 274 MET cc_start: 0.8364 (pmm) cc_final: 0.7511 (pmm) REVERT: B 434 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7404 (tm-30) REVERT: B 488 TYR cc_start: 0.8837 (OUTLIER) cc_final: 0.8598 (p90) REVERT: B 599 ILE cc_start: 0.9264 (OUTLIER) cc_final: 0.8905 (tp) REVERT: B 628 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8320 (mt) REVERT: B 690 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7716 (tp30) REVERT: A 274 MET cc_start: 0.8191 (pmm) cc_final: 0.7460 (pmm) REVERT: A 314 SER cc_start: 0.9427 (OUTLIER) cc_final: 0.9046 (t) REVERT: A 403 TRP cc_start: 0.8650 (OUTLIER) cc_final: 0.8213 (p90) REVERT: A 752 PHE cc_start: 0.9439 (OUTLIER) cc_final: 0.9098 (t80) REVERT: C 46 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8690 (tm-30) REVERT: D 45 ASP cc_start: 0.8255 (p0) cc_final: 0.8009 (p0) outliers start: 80 outliers final: 40 residues processed: 181 average time/residue: 0.0825 time to fit residues: 23.2593 Evaluate side-chains 147 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 97 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 LYS Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 60 VAL 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 244 TRP Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 403 TRP Chi-restraints excluded: chain B residue 427 VAL 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 488 TYR 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 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 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 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 403 TRP Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 559 MET 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 163 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 78 optimal weight: 20.0000 chunk 113 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 159 optimal weight: 0.6980 chunk 102 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 564 HIS ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.100378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.066775 restraints weight = 45503.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.065811 restraints weight = 34710.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.066001 restraints weight = 29886.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.066392 restraints weight = 26918.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.066507 restraints weight = 23583.906| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13985 Z= 0.152 Angle : 0.641 9.279 18987 Z= 0.316 Chirality : 0.046 0.216 2041 Planarity : 0.004 0.054 2459 Dihedral : 5.105 36.683 1887 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.95 % Favored : 90.87 % Rotamer: Outliers : 6.16 % Allowed : 28.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.25 (0.20), residues: 1665 helix: -0.61 (0.38), residues: 183 sheet: -1.44 (0.30), residues: 328 loop : -1.75 (0.18), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 756 TYR 0.010 0.001 TYR B 392 PHE 0.017 0.001 PHE B 348 TRP 0.006 0.001 TRP B 520 HIS 0.007 0.001 HIS B 564 Details of bonding type rmsd covalent geometry : bond 0.00353 (13953) covalent geometry : angle 0.63669 (18923) SS BOND : bond 0.00374 ( 32) SS BOND : angle 1.48845 ( 64) hydrogen bonds : bond 0.03766 ( 306) hydrogen bonds : angle 6.20977 ( 795) *********************** 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 188 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 96 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8896 (pp) REVERT: B 272 GLU cc_start: 0.5896 (OUTLIER) cc_final: 0.4779 (mm-30) REVERT: B 274 MET cc_start: 0.8359 (pmm) cc_final: 0.7548 (pmm) REVERT: B 599 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.8998 (tp) REVERT: B 628 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8404 (mt) REVERT: B 690 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7741 (tp30) REVERT: B 771 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.8651 (t80) REVERT: A 180 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8014 (ttm110) REVERT: A 274 MET cc_start: 0.8344 (pmm) cc_final: 0.7731 (pmm) REVERT: A 314 SER cc_start: 0.9436 (OUTLIER) cc_final: 0.9079 (t) REVERT: A 403 TRP cc_start: 0.8663 (OUTLIER) cc_final: 0.8186 (p90) REVERT: A 618 ARG cc_start: 0.9425 (OUTLIER) cc_final: 0.8565 (ptp90) REVERT: A 752 PHE cc_start: 0.9507 (OUTLIER) cc_final: 0.9162 (t80) REVERT: C 46 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8762 (tm-30) outliers start: 92 outliers final: 56 residues processed: 178 average time/residue: 0.0818 time to fit residues: 22.6276 Evaluate side-chains 161 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 93 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 98 ILE 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 272 GLU Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 354 VAL 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 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 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 244 TRP 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 163 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 139 optimal weight: 30.0000 chunk 69 optimal weight: 30.0000 chunk 74 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 154 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.098728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.065243 restraints weight = 45718.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.064258 restraints weight = 41301.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.064571 restraints weight = 30926.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.065349 restraints weight = 27293.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.065344 restraints weight = 23926.986| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13985 Z= 0.221 Angle : 0.673 12.469 18987 Z= 0.337 Chirality : 0.047 0.205 2041 Planarity : 0.004 0.052 2459 Dihedral : 5.291 36.675 1887 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.91 % Favored : 89.91 % Rotamer: Outliers : 6.22 % Allowed : 28.78 % Favored : 64.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.32 (0.20), residues: 1665 helix: -0.95 (0.36), residues: 201 sheet: -1.46 (0.30), residues: 329 loop : -1.76 (0.18), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 336 TYR 0.014 0.001 TYR A 551 PHE 0.020 0.002 PHE B 241 TRP 0.009 0.001 TRP A 403 HIS 0.006 0.001 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00506 (13953) covalent geometry : angle 0.67057 (18923) SS BOND : bond 0.00407 ( 32) SS BOND : angle 1.27118 ( 64) hydrogen bonds : bond 0.03967 ( 306) hydrogen bonds : angle 6.41354 ( 795) *********************** 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 181 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 88 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8966 (pp) REVERT: B 272 GLU cc_start: 0.5876 (OUTLIER) cc_final: 0.4566 (mm-30) REVERT: B 274 MET cc_start: 0.8410 (pmm) cc_final: 0.7644 (pmm) REVERT: B 559 MET cc_start: 0.8202 (tpp) cc_final: 0.7932 (tpp) REVERT: B 628 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8298 (mt) REVERT: B 690 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7775 (tm-30) REVERT: B 771 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.8499 (t80) REVERT: A 180 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8163 (ttm110) REVERT: A 274 MET cc_start: 0.8257 (pmm) cc_final: 0.7560 (pmm) REVERT: A 314 SER cc_start: 0.9369 (OUTLIER) cc_final: 0.9022 (t) REVERT: A 618 ARG cc_start: 0.9364 (OUTLIER) cc_final: 0.8406 (ptp90) REVERT: A 752 PHE cc_start: 0.9436 (OUTLIER) cc_final: 0.9004 (t80) REVERT: C 46 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8726 (tm-30) outliers start: 93 outliers final: 68 residues processed: 170 average time/residue: 0.0889 time to fit residues: 23.3531 Evaluate side-chains 166 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 88 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 60 VAL Chi-restraints excluded: chain B residue 69 LEU 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 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 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 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 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 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 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 50 ARG 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 141 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 140 optimal weight: 0.0570 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 129 optimal weight: 0.0970 overall best weight: 0.4896 ------------------------------------------------------------------------------- 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 834 ASN A 334 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.101771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.068315 restraints weight = 45155.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.067415 restraints weight = 33262.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.067628 restraints weight = 29062.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.067992 restraints weight = 25501.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.068264 restraints weight = 22635.068| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13985 Z= 0.105 Angle : 0.632 13.109 18987 Z= 0.311 Chirality : 0.045 0.185 2041 Planarity : 0.004 0.052 2459 Dihedral : 4.994 36.827 1887 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.59 % Favored : 91.23 % Rotamer: Outliers : 5.29 % Allowed : 29.38 % Favored : 65.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.17 (0.20), residues: 1665 helix: -0.65 (0.37), residues: 190 sheet: -1.26 (0.31), residues: 313 loop : -1.73 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 337 TYR 0.014 0.001 TYR B 13 PHE 0.022 0.001 PHE B 348 TRP 0.010 0.001 TRP B 602 HIS 0.004 0.001 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00239 (13953) covalent geometry : angle 0.63068 (18923) SS BOND : bond 0.00279 ( 32) SS BOND : angle 0.99191 ( 64) hydrogen bonds : bond 0.03521 ( 306) hydrogen bonds : angle 6.01823 ( 795) *********************** 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 182 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 103 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8784 (pp) REVERT: B 272 GLU cc_start: 0.5880 (OUTLIER) cc_final: 0.4750 (mm-30) REVERT: B 274 MET cc_start: 0.8398 (pmm) cc_final: 0.7623 (pmm) REVERT: B 403 TRP cc_start: 0.8547 (OUTLIER) cc_final: 0.8265 (p90) REVERT: B 599 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.8946 (tp) REVERT: B 628 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8439 (mt) REVERT: B 690 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7701 (tm-30) REVERT: B 771 PHE cc_start: 0.8880 (OUTLIER) cc_final: 0.8542 (t80) REVERT: A 180 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7769 (ptp-170) REVERT: A 274 MET cc_start: 0.8252 (pmm) cc_final: 0.7644 (pmm) REVERT: A 314 SER cc_start: 0.9506 (OUTLIER) cc_final: 0.9164 (t) REVERT: A 403 TRP cc_start: 0.8606 (OUTLIER) cc_final: 0.8277 (p90) REVERT: A 618 ARG cc_start: 0.9458 (OUTLIER) cc_final: 0.8578 (ptp90) REVERT: A 752 PHE cc_start: 0.9513 (OUTLIER) cc_final: 0.9126 (t80) outliers start: 79 outliers final: 51 residues processed: 174 average time/residue: 0.1033 time to fit residues: 28.7208 Evaluate side-chains 156 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 93 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 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 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 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 244 TRP 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 335 ILE 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 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 44 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 58 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 50 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 166 optimal weight: 0.9990 chunk 70 optimal weight: 0.0470 chunk 78 optimal weight: 0.0170 chunk 143 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.4122 ------------------------------------------------------------------------------- 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** ** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN ** 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 = 0.3965 r_free = 0.3965 target = 0.100538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.067465 restraints weight = 45650.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.065623 restraints weight = 38480.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.065955 restraints weight = 33187.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.066320 restraints weight = 28437.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.066614 restraints weight = 25333.287| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13985 Z= 0.144 Angle : 0.639 10.682 18987 Z= 0.317 Chirality : 0.046 0.181 2041 Planarity : 0.004 0.051 2459 Dihedral : 5.020 36.871 1887 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.19 % Favored : 90.63 % Rotamer: Outliers : 5.49 % Allowed : 29.59 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.17 (0.20), residues: 1665 helix: -0.53 (0.39), residues: 183 sheet: -1.28 (0.30), residues: 324 loop : -1.73 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 756 TYR 0.020 0.001 TYR B 13 PHE 0.019 0.001 PHE C 23 TRP 0.009 0.001 TRP A 827 HIS 0.004 0.001 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00335 (13953) covalent geometry : angle 0.63655 (18923) SS BOND : bond 0.00299 ( 32) SS BOND : angle 1.11325 ( 64) hydrogen bonds : bond 0.03614 ( 306) hydrogen bonds : angle 6.04954 ( 795) *********************** 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 176 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 94 time to evaluate : 0.572 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: 0.9042 (OUTLIER) cc_final: 0.8774 (pp) REVERT: B 272 GLU cc_start: 0.5812 (OUTLIER) cc_final: 0.4727 (mm-30) REVERT: B 274 MET cc_start: 0.8426 (pmm) cc_final: 0.7651 (pmm) REVERT: B 599 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.8965 (tp) REVERT: B 628 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8431 (mt) REVERT: B 690 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: B 771 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.8571 (t80) REVERT: A 180 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8042 (ttm110) REVERT: A 274 MET cc_start: 0.8305 (pmm) cc_final: 0.7754 (pmm) REVERT: A 618 ARG cc_start: 0.9461 (OUTLIER) cc_final: 0.8605 (ptp90) REVERT: A 752 PHE cc_start: 0.9527 (OUTLIER) cc_final: 0.9154 (t80) outliers start: 82 outliers final: 57 residues processed: 168 average time/residue: 0.1032 time to fit residues: 27.3501 Evaluate side-chains 159 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 93 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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 98 ILE 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 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 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 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 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 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 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 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 796 VAL Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 44 VAL 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 76 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 105 optimal weight: 0.0270 chunk 52 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 overall best weight: 0.8642 ------------------------------------------------------------------------------- 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** ** A 443 GLN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.101445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.068219 restraints weight = 45416.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.067715 restraints weight = 33881.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.067634 restraints weight = 30000.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.068101 restraints weight = 26623.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.068519 restraints weight = 23584.139| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13985 Z= 0.116 Angle : 0.648 10.302 18987 Z= 0.317 Chirality : 0.045 0.219 2041 Planarity : 0.004 0.051 2459 Dihedral : 4.951 37.046 1887 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.35 % Favored : 91.47 % Rotamer: Outliers : 5.35 % Allowed : 29.72 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.14 (0.20), residues: 1665 helix: -0.53 (0.38), residues: 183 sheet: -1.25 (0.30), residues: 324 loop : -1.71 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 174 TYR 0.009 0.001 TYR B 418 PHE 0.024 0.001 PHE B 348 TRP 0.007 0.001 TRP B 520 HIS 0.004 0.001 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00269 (13953) covalent geometry : angle 0.64293 (18923) SS BOND : bond 0.00386 ( 32) SS BOND : angle 1.55008 ( 64) hydrogen bonds : bond 0.03494 ( 306) hydrogen bonds : angle 5.99259 ( 795) *********************** 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 179 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 99 time to evaluate : 0.631 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: 0.9008 (OUTLIER) cc_final: 0.8722 (pp) REVERT: B 172 ASN cc_start: 0.9228 (OUTLIER) cc_final: 0.8681 (p0) REVERT: B 272 GLU cc_start: 0.5810 (OUTLIER) cc_final: 0.4778 (mm-30) REVERT: B 274 MET cc_start: 0.8396 (pmm) cc_final: 0.7703 (pmm) REVERT: B 599 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.8928 (tp) REVERT: B 628 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8347 (mt) REVERT: B 690 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7640 (tm-30) REVERT: B 771 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.8520 (t80) REVERT: A 180 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7741 (ptp-170) REVERT: A 274 MET cc_start: 0.8257 (pmm) cc_final: 0.7727 (pmm) REVERT: A 403 TRP cc_start: 0.8647 (OUTLIER) cc_final: 0.8289 (p90) REVERT: A 618 ARG cc_start: 0.9432 (OUTLIER) cc_final: 0.8615 (ptp90) REVERT: A 752 PHE cc_start: 0.9505 (OUTLIER) cc_final: 0.9099 (t80) outliers start: 80 outliers final: 58 residues processed: 171 average time/residue: 0.1047 time to fit residues: 28.2528 Evaluate side-chains 162 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 93 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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 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 44 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 153 optimal weight: 6.9990 chunk 128 optimal weight: 8.9990 chunk 156 optimal weight: 9.9990 chunk 64 optimal weight: 0.5980 chunk 141 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 17 optimal weight: 10.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 564 HIS ** B 703 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.101940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.068740 restraints weight = 45367.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.068098 restraints weight = 33700.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.067980 restraints weight = 29220.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.068385 restraints weight = 26555.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.068648 restraints weight = 23690.119| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13985 Z= 0.110 Angle : 0.651 14.005 18987 Z= 0.315 Chirality : 0.045 0.203 2041 Planarity : 0.004 0.051 2459 Dihedral : 4.856 36.906 1887 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.05 % Favored : 91.77 % Rotamer: Outliers : 4.69 % Allowed : 30.59 % Favored : 64.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.12 (0.20), residues: 1665 helix: -0.58 (0.38), residues: 189 sheet: -1.20 (0.31), residues: 324 loop : -1.71 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 174 TYR 0.020 0.001 TYR B 13 PHE 0.017 0.001 PHE B 348 TRP 0.007 0.001 TRP B 619 HIS 0.010 0.001 HIS B 564 Details of bonding type rmsd covalent geometry : bond 0.00256 (13953) covalent geometry : angle 0.64705 (18923) SS BOND : bond 0.00333 ( 32) SS BOND : angle 1.45393 ( 64) hydrogen bonds : bond 0.03395 ( 306) hydrogen bonds : angle 5.85292 ( 795) ********************** 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 164 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 94 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8706 (pp) REVERT: B 172 ASN cc_start: 0.9220 (OUTLIER) cc_final: 0.8701 (p0) REVERT: B 272 GLU cc_start: 0.5784 (OUTLIER) cc_final: 0.4664 (mm-30) REVERT: B 274 MET cc_start: 0.8411 (pmm) cc_final: 0.7704 (pmm) REVERT: B 599 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.8933 (tp) REVERT: B 628 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8322 (mt) REVERT: B 690 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7612 (tm-30) REVERT: B 771 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8517 (t80) REVERT: A 180 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7764 (ptp-170) REVERT: A 274 MET cc_start: 0.8278 (pmm) cc_final: 0.7758 (pmm) REVERT: A 403 TRP cc_start: 0.8645 (OUTLIER) cc_final: 0.8326 (p90) REVERT: A 618 ARG cc_start: 0.9433 (OUTLIER) cc_final: 0.8678 (ptp90) REVERT: A 752 PHE cc_start: 0.9521 (OUTLIER) cc_final: 0.9112 (t80) outliers start: 70 outliers final: 54 residues processed: 157 average time/residue: 0.1029 time to fit residues: 25.4404 Evaluate side-chains 155 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 90 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 98 ILE 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 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 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 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 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 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 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 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 44 VAL 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 34 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 chunk 144 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 chunk 33 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 125 optimal weight: 0.0050 chunk 35 optimal weight: 0.9990 chunk 135 optimal weight: 30.0000 overall best weight: 0.6998 ------------------------------------------------------------------------------- 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 564 HIS ** B 703 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.102232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.069298 restraints weight = 45489.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.068750 restraints weight = 34942.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.068500 restraints weight = 30588.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.069061 restraints weight = 26923.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.069293 restraints weight = 23724.430| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13985 Z= 0.111 Angle : 0.646 12.074 18987 Z= 0.314 Chirality : 0.045 0.207 2041 Planarity : 0.004 0.050 2459 Dihedral : 4.817 37.249 1887 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.99 % Favored : 91.83 % Rotamer: Outliers : 4.62 % Allowed : 30.46 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.20), residues: 1665 helix: -0.67 (0.37), residues: 196 sheet: -1.17 (0.31), residues: 324 loop : -1.74 (0.18), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 174 TYR 0.009 0.001 TYR A 488 PHE 0.016 0.001 PHE B 348 TRP 0.024 0.001 TRP B 403 HIS 0.013 0.001 HIS B 564 Details of bonding type rmsd covalent geometry : bond 0.00257 (13953) covalent geometry : angle 0.64253 (18923) SS BOND : bond 0.00316 ( 32) SS BOND : angle 1.37941 ( 64) hydrogen bonds : bond 0.03478 ( 306) hydrogen bonds : angle 5.79245 ( 795) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2125.59 seconds wall clock time: 37 minutes 46.62 seconds (2266.62 seconds total)