Starting phenix.real_space_refine on Sat Oct 11 07:51:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v49_42969/10_2025/8v49_42969.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v49_42969/10_2025/8v49_42969.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8v49_42969/10_2025/8v49_42969.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v49_42969/10_2025/8v49_42969.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v49_42969/10_2025/8v49_42969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v49_42969/10_2025/8v49_42969.map" } resolution = 3.62 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 48 5.16 5 C 8197 2.51 5 N 2155 2.21 5 O 2431 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12834 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3236 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 390} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 3148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3148 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 9, 'TRANS': 380} Chain breaks: 6 Chain: "D" Number of atoms: 3236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3236 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 390} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3183 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 10, 'TRANS': 383} Chain breaks: 6 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.29, per 1000 atoms: 0.26 Number of scatterers: 12834 At special positions: 0 Unit cell: (99.11, 126.225, 169.235, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 3 15.00 O 2431 8.00 N 2155 7.00 C 8197 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.02 Conformation dependent library (CDL) restraints added in 580.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3024 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 12 sheets defined 55.2% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 39 through 51 Processing helix chain 'A' and resid 53 through 60 removed outlier: 3.539A pdb=" N ARG A 56 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA A 58 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A 60 " --> pdb=" O PHE A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 102 through 110 removed outlier: 3.812A pdb=" N ARG A 110 " --> pdb=" O MET A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 138 Processing helix chain 'A' and resid 151 through 159 removed outlier: 3.741A pdb=" N ALA A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 189 Processing helix chain 'A' and resid 199 through 237 Processing helix chain 'A' and resid 249 through 264 Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 273 through 287 Processing helix chain 'A' and resid 296 through 319 Processing helix chain 'A' and resid 319 through 331 Processing helix chain 'A' and resid 362 through 366 Processing helix chain 'A' and resid 367 through 380 removed outlier: 3.627A pdb=" N LEU A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.670A pdb=" N ASP A 405 " --> pdb=" O ASP A 401 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LEU A 407 " --> pdb=" O GLN A 403 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LYS A 408 " --> pdb=" O GLU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 430 removed outlier: 4.108A pdb=" N ALA A 429 " --> pdb=" O SER A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'B' and resid 13 through 17 removed outlier: 3.729A pdb=" N ARG B 17 " --> pdb=" O ILE B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 51 Processing helix chain 'B' and resid 53 through 60 removed outlier: 3.636A pdb=" N ARG B 56 " --> pdb=" O ASP B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 110 removed outlier: 3.706A pdb=" N ALA B 107 " --> pdb=" O GLY B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 139 Processing helix chain 'B' and resid 151 through 161 Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 199 through 239 removed outlier: 3.621A pdb=" N PHE B 238 " --> pdb=" O PHE B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 264 Processing helix chain 'B' and resid 273 through 288 Processing helix chain 'B' and resid 294 through 319 Processing helix chain 'B' and resid 322 through 331 Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 370 through 380 Processing helix chain 'B' and resid 399 through 413 removed outlier: 4.888A pdb=" N LEU B 407 " --> pdb=" O GLN B 403 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LYS B 408 " --> pdb=" O GLU B 404 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 409 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 51 Processing helix chain 'D' and resid 53 through 60 removed outlier: 3.548A pdb=" N ARG D 56 " --> pdb=" O ASP D 53 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA D 58 " --> pdb=" O ILE D 55 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU D 60 " --> pdb=" O PHE D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 Processing helix chain 'D' and resid 102 through 110 removed outlier: 3.815A pdb=" N ARG D 110 " --> pdb=" O MET D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 138 Processing helix chain 'D' and resid 151 through 159 removed outlier: 3.547A pdb=" N ALA D 157 " --> pdb=" O THR D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 189 Processing helix chain 'D' and resid 199 through 237 Processing helix chain 'D' and resid 249 through 264 Processing helix chain 'D' and resid 265 through 269 Processing helix chain 'D' and resid 273 through 287 Processing helix chain 'D' and resid 296 through 319 Processing helix chain 'D' and resid 319 through 331 Processing helix chain 'D' and resid 362 through 366 Processing helix chain 'D' and resid 367 through 380 removed outlier: 3.580A pdb=" N LEU D 373 " --> pdb=" O GLY D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.691A pdb=" N ASP D 405 " --> pdb=" O ASP D 401 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LEU D 407 " --> pdb=" O GLN D 403 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LYS D 408 " --> pdb=" O GLU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 430 removed outlier: 4.068A pdb=" N ALA D 429 " --> pdb=" O SER D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 434 No H-bonds generated for 'chain 'D' and resid 432 through 434' Processing helix chain 'C' and resid 39 through 51 Processing helix chain 'C' and resid 53 through 60 removed outlier: 3.565A pdb=" N ARG C 56 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA C 58 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU C 60 " --> pdb=" O PHE C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 110 removed outlier: 3.884A pdb=" N ARG C 110 " --> pdb=" O MET C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 138 Processing helix chain 'C' and resid 151 through 159 removed outlier: 3.721A pdb=" N ALA C 157 " --> pdb=" O THR C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'C' and resid 199 through 237 Processing helix chain 'C' and resid 250 through 264 Processing helix chain 'C' and resid 273 through 287 Processing helix chain 'C' and resid 294 through 319 removed outlier: 3.637A pdb=" N SER C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 331 Processing helix chain 'C' and resid 362 through 366 Processing helix chain 'C' and resid 367 through 380 Processing helix chain 'C' and resid 399 through 413 removed outlier: 3.553A pdb=" N ASP C 405 " --> pdb=" O ASP C 401 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LEU C 407 " --> pdb=" O GLN C 403 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LYS C 408 " --> pdb=" O GLU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 430 removed outlier: 4.023A pdb=" N ALA C 429 " --> pdb=" O SER C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 434 No H-bonds generated for 'chain 'C' and resid 432 through 434' Processing sheet with id=AA1, first strand: chain 'A' and resid 98 through 101 removed outlier: 4.025A pdb=" N VAL A 90 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 100 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLU A 64 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU A 11 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LYS A 66 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ILE A 9 " --> pdb=" O LYS A 66 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N THR A 68 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU A 20 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N TYR A 18 " --> pdb=" O LYS A 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 146 through 148 removed outlier: 3.764A pdb=" N CYS A 422 " --> pdb=" O ILE A 391 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 337 through 340 Processing sheet with id=AA4, first strand: chain 'B' and resid 20 through 23 removed outlier: 3.863A pdb=" N ILE B 9 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU B 64 " --> pdb=" O SER B 12 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.589A pdb=" N VAL B 389 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N CYS B 422 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ILE B 391 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N PHE B 148 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 338 through 341 Processing sheet with id=AA7, first strand: chain 'D' and resid 98 through 101 removed outlier: 4.317A pdb=" N VAL D 90 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE D 100 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLU D 64 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LEU D 11 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LYS D 66 " --> pdb=" O ILE D 9 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ILE D 9 " --> pdb=" O LYS D 66 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N THR D 68 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU D 20 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS D 13 " --> pdb=" O TYR D 18 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N TYR D 18 " --> pdb=" O LYS D 13 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 146 through 148 removed outlier: 4.012A pdb=" N CYS D 422 " --> pdb=" O ILE D 391 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE D 437 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL D 30 " --> pdb=" O ILE D 437 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 337 through 340 removed outlier: 3.788A pdb=" N ALA D 339 " --> pdb=" O GLY D 352 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY D 352 " --> pdb=" O ALA D 339 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 98 through 101 removed outlier: 3.634A pdb=" N PHE C 100 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C 88 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLU C 64 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU C 11 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LYS C 66 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ILE C 9 " --> pdb=" O LYS C 66 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR C 68 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU C 20 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS C 13 " --> pdb=" O TYR C 18 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N TYR C 18 " --> pdb=" O LYS C 13 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 144 through 148 removed outlier: 4.069A pdb=" N GLN C 418 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE C 391 " --> pdb=" O ILE C 420 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N CYS C 422 " --> pdb=" O ILE C 391 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ASN C 29 " --> pdb=" O VAL C 421 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL C 30 " --> pdb=" O ILE C 437 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 337 through 341 713 hydrogen bonds defined for protein. 2007 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: 2.11 Time building geometry restraints manager: 1.38 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: 3806 1.34 - 1.46: 2087 1.46 - 1.57: 7076 1.57 - 1.69: 5 1.69 - 1.81: 92 Bond restraints: 13066 Sorted by residual: bond pdb=" C PHE B 355 " pdb=" N PRO B 356 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.28e-02 6.10e+03 2.20e+00 bond pdb=" CB ILE C 439 " pdb=" CG1 ILE C 439 " ideal model delta sigma weight residual 1.530 1.556 -0.026 2.00e-02 2.50e+03 1.73e+00 bond pdb=" CA ILE C 439 " pdb=" CB ILE C 439 " ideal model delta sigma weight residual 1.535 1.550 -0.015 1.18e-02 7.18e+03 1.67e+00 bond pdb=" CA LYS D 142 " pdb=" CB LYS D 142 " ideal model delta sigma weight residual 1.532 1.549 -0.017 1.33e-02 5.65e+03 1.63e+00 bond pdb=" CA LYS A 142 " pdb=" CB LYS A 142 " ideal model delta sigma weight residual 1.537 1.553 -0.016 1.31e-02 5.83e+03 1.58e+00 ... (remaining 13061 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 17246 2.35 - 4.69: 293 4.69 - 7.04: 33 7.04 - 9.38: 7 9.38 - 11.73: 2 Bond angle restraints: 17581 Sorted by residual: angle pdb=" CA ILE C 439 " pdb=" CB ILE C 439 " pdb=" CG1 ILE C 439 " ideal model delta sigma weight residual 110.40 118.76 -8.36 1.70e+00 3.46e-01 2.42e+01 angle pdb=" CA LYS A 142 " pdb=" CB LYS A 142 " pdb=" CG LYS A 142 " ideal model delta sigma weight residual 114.10 122.29 -8.19 2.00e+00 2.50e-01 1.68e+01 angle pdb=" CA LYS D 142 " pdb=" CB LYS D 142 " pdb=" CG LYS D 142 " ideal model delta sigma weight residual 114.10 121.76 -7.66 2.00e+00 2.50e-01 1.47e+01 angle pdb=" C LYS D 347 " pdb=" N TYR D 348 " pdb=" CA TYR D 348 " ideal model delta sigma weight residual 121.80 131.08 -9.28 2.44e+00 1.68e-01 1.45e+01 angle pdb=" CA GLU A 84 " pdb=" CB GLU A 84 " pdb=" CG GLU A 84 " ideal model delta sigma weight residual 114.10 121.38 -7.28 2.00e+00 2.50e-01 1.32e+01 ... (remaining 17576 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 7334 17.86 - 35.72: 454 35.72 - 53.59: 108 53.59 - 71.45: 21 71.45 - 89.31: 7 Dihedral angle restraints: 7924 sinusoidal: 3266 harmonic: 4658 Sorted by residual: dihedral pdb=" CA PHE D 342 " pdb=" C PHE D 342 " pdb=" N ASP D 343 " pdb=" CA ASP D 343 " ideal model delta harmonic sigma weight residual 180.00 -163.48 -16.52 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ALA C 236 " pdb=" C ALA C 236 " pdb=" N LEU C 237 " pdb=" CA LEU C 237 " ideal model delta harmonic sigma weight residual 180.00 164.56 15.44 0 5.00e+00 4.00e-02 9.53e+00 dihedral pdb=" CA LYS B 99 " pdb=" CB LYS B 99 " pdb=" CG LYS B 99 " pdb=" CD LYS B 99 " ideal model delta sinusoidal sigma weight residual 60.00 117.29 -57.29 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 7921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1519 0.058 - 0.116: 349 0.116 - 0.173: 55 0.173 - 0.231: 8 0.231 - 0.289: 2 Chirality restraints: 1933 Sorted by residual: chirality pdb=" CG LEU A 11 " pdb=" CB LEU A 11 " pdb=" CD1 LEU A 11 " pdb=" CD2 LEU A 11 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CG LEU D 11 " pdb=" CB LEU D 11 " pdb=" CD1 LEU D 11 " pdb=" CD2 LEU D 11 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB VAL B 30 " pdb=" CA VAL B 30 " pdb=" CG1 VAL B 30 " pdb=" CG2 VAL B 30 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1930 not shown) Planarity restraints: 2242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 439 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.21e+00 pdb=" C ILE C 439 " 0.039 2.00e-02 2.50e+03 pdb=" O ILE C 439 " -0.015 2.00e-02 2.50e+03 pdb=" N SER C 440 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 142 " 0.012 2.00e-02 2.50e+03 2.28e-02 5.18e+00 pdb=" C LYS A 142 " -0.039 2.00e-02 2.50e+03 pdb=" O LYS A 142 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL A 143 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 141 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.48e+00 pdb=" C GLN A 141 " -0.032 2.00e-02 2.50e+03 pdb=" O GLN A 141 " 0.012 2.00e-02 2.50e+03 pdb=" N LYS A 142 " 0.011 2.00e-02 2.50e+03 ... (remaining 2239 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 3657 2.82 - 3.34: 11785 3.34 - 3.86: 20568 3.86 - 4.38: 22740 4.38 - 4.90: 40035 Nonbonded interactions: 98785 Sorted by model distance: nonbonded pdb=" O GLN A 262 " pdb=" OG SER A 265 " model vdw 2.306 3.040 nonbonded pdb=" O GLN D 262 " pdb=" OG SER D 265 " model vdw 2.309 3.040 nonbonded pdb=" O GLN C 262 " pdb=" OG SER C 265 " model vdw 2.320 3.040 nonbonded pdb=" O TYR C 221 " pdb=" OG1 THR C 225 " model vdw 2.323 3.040 nonbonded pdb=" O TYR A 378 " pdb=" OG SER A 381 " model vdw 2.329 3.040 ... (remaining 98780 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 3 through 33 or resid 38 through 160 or resid 173 through \ 238 or resid 249 through 342 or resid 348 through 440)) selection = (chain 'B' and (resid 3 through 238 or resid 249 through 288 or resid 295 throug \ h 440)) selection = (chain 'C' and (resid 3 through 238 or resid 249 through 288 or resid 295 throug \ h 440)) selection = (chain 'D' and (resid 3 through 33 or resid 38 through 160 or resid 173 through \ 238 or resid 249 through 342 or resid 348 through 440)) } 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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.010 Find NCS groups from input model: 0.290 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 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 : 0.003 0.037 13066 Z= 0.185 Angle : 0.795 11.730 17581 Z= 0.473 Chirality : 0.050 0.289 1933 Planarity : 0.005 0.046 2242 Dihedral : 12.614 89.308 4900 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.08 % Allowed : 8.45 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.22), residues: 1538 helix: 1.58 (0.18), residues: 786 sheet: -2.04 (0.30), residues: 271 loop : -1.09 (0.30), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 185 TYR 0.014 0.002 TYR B 378 PHE 0.022 0.002 PHE B 59 TRP 0.017 0.002 TRP B 158 HIS 0.008 0.001 HIS D 32 Details of bonding type rmsd covalent geometry : bond 0.00335 (13066) covalent geometry : angle 0.79502 (17581) hydrogen bonds : bond 0.22224 ( 713) hydrogen bonds : angle 6.69593 ( 2007) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 263 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ILE cc_start: 0.9068 (tt) cc_final: 0.8614 (tp) REVERT: A 56 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7762 (mmm160) REVERT: A 209 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8021 (tp30) REVERT: A 277 VAL cc_start: 0.9265 (m) cc_final: 0.8937 (m) REVERT: A 341 ASP cc_start: 0.7615 (t0) cc_final: 0.7103 (t0) REVERT: B 87 PHE cc_start: 0.9337 (m-80) cc_final: 0.8419 (m-80) REVERT: B 228 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8447 (tm-30) REVERT: B 335 ASP cc_start: 0.8348 (m-30) cc_final: 0.8001 (t0) REVERT: B 338 MET cc_start: 0.8837 (ttt) cc_final: 0.8500 (ttt) REVERT: B 403 GLN cc_start: 0.9119 (mt0) cc_final: 0.8861 (mt0) REVERT: D 56 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8422 (mmm160) REVERT: D 90 VAL cc_start: 0.8418 (OUTLIER) cc_final: 0.7561 (p) REVERT: D 222 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8045 (tp30) REVERT: C 201 MET cc_start: 0.9009 (mmt) cc_final: 0.8724 (mmm) REVERT: C 225 THR cc_start: 0.9259 (OUTLIER) cc_final: 0.8966 (p) REVERT: C 338 MET cc_start: 0.8504 (ttp) cc_final: 0.7025 (ttp) REVERT: C 375 THR cc_start: 0.9586 (p) cc_final: 0.9333 (t) REVERT: C 414 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9032 (mm) outliers start: 43 outliers final: 8 residues processed: 300 average time/residue: 0.1273 time to fit residues: 54.2213 Evaluate side-chains 144 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 346 ARG Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 439 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 30.0000 chunk 149 optimal weight: 9.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 138 ASN A 262 GLN A 312 GLN A 315 GLN A 399 HIS A 418 GLN B 15 HIS B 29 ASN B 48 ASN B 85 GLN B 424 HIS D 138 ASN D 262 GLN D 312 GLN D 315 GLN D 418 GLN C 15 HIS C 29 ASN ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.072655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.051835 restraints weight = 71773.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.053177 restraints weight = 39713.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.053256 restraints weight = 24857.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.053490 restraints weight = 24363.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.053546 restraints weight = 21483.323| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 13066 Z= 0.287 Angle : 0.690 7.728 17581 Z= 0.369 Chirality : 0.044 0.163 1933 Planarity : 0.004 0.036 2242 Dihedral : 7.513 73.011 1799 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.23 % Allowed : 13.11 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.22), residues: 1538 helix: 1.93 (0.18), residues: 772 sheet: -1.61 (0.29), residues: 298 loop : -0.53 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 152 TYR 0.021 0.002 TYR A 278 PHE 0.021 0.002 PHE B 332 TRP 0.019 0.002 TRP A 360 HIS 0.009 0.001 HIS D 15 Details of bonding type rmsd covalent geometry : bond 0.00625 (13066) covalent geometry : angle 0.68959 (17581) hydrogen bonds : bond 0.04837 ( 713) hydrogen bonds : angle 5.08839 ( 2007) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 135 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7826 (mmm160) REVERT: A 209 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8266 (tp30) REVERT: A 326 MET cc_start: 0.9154 (mmt) cc_final: 0.8286 (mmm) REVERT: A 338 MET cc_start: 0.8080 (ttp) cc_final: 0.7698 (ttm) REVERT: A 341 ASP cc_start: 0.8246 (t0) cc_final: 0.7671 (t0) REVERT: B 87 PHE cc_start: 0.9197 (m-80) cc_final: 0.8903 (m-80) REVERT: B 228 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8507 (tm-30) REVERT: D 23 ASP cc_start: 0.8449 (p0) cc_final: 0.8014 (t0) REVERT: D 147 TYR cc_start: 0.9067 (t80) cc_final: 0.8807 (t80) REVERT: D 154 MET cc_start: 0.8927 (tmm) cc_final: 0.7612 (mtt) REVERT: D 222 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8622 (tp30) REVERT: D 383 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8571 (mmm) REVERT: D 436 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.6978 (mmm) REVERT: C 326 MET cc_start: 0.9134 (mmm) cc_final: 0.8473 (mmm) REVERT: C 338 MET cc_start: 0.8420 (ttp) cc_final: 0.8037 (ttp) REVERT: C 406 LEU cc_start: 0.9690 (tp) cc_final: 0.9133 (tp) REVERT: C 410 MET cc_start: 0.9285 (mtm) cc_final: 0.8760 (mtm) REVERT: C 414 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9164 (mm) outliers start: 59 outliers final: 20 residues processed: 186 average time/residue: 0.1182 time to fit residues: 32.3614 Evaluate side-chains 130 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain D residue 8 LYS Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 346 ARG Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 439 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 107 optimal weight: 10.0000 chunk 134 optimal weight: 0.0470 chunk 109 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 144 optimal weight: 8.9990 chunk 4 optimal weight: 0.6980 chunk 104 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 73 optimal weight: 0.0980 chunk 151 optimal weight: 4.9990 overall best weight: 1.3480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN ** B 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN C 32 HIS C 48 ASN ** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.073991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.052464 restraints weight = 71670.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.054145 restraints weight = 39873.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.055000 restraints weight = 22458.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.055173 restraints weight = 19941.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.055262 restraints weight = 18649.192| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13066 Z= 0.131 Angle : 0.563 10.719 17581 Z= 0.295 Chirality : 0.041 0.163 1933 Planarity : 0.003 0.030 2242 Dihedral : 6.315 81.576 1794 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.01 % Allowed : 15.76 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.22), residues: 1538 helix: 2.08 (0.18), residues: 797 sheet: -1.28 (0.31), residues: 286 loop : -0.35 (0.32), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 364 TYR 0.024 0.001 TYR A 378 PHE 0.017 0.001 PHE A 230 TRP 0.023 0.001 TRP A 360 HIS 0.005 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00282 (13066) covalent geometry : angle 0.56289 (17581) hydrogen bonds : bond 0.04155 ( 713) hydrogen bonds : angle 4.56390 ( 2007) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7778 (mmm160) REVERT: A 154 MET cc_start: 0.9034 (mtp) cc_final: 0.8392 (mtm) REVERT: A 209 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8308 (tp30) REVERT: A 326 MET cc_start: 0.9169 (mmt) cc_final: 0.8283 (mmm) REVERT: A 338 MET cc_start: 0.8171 (ttp) cc_final: 0.7915 (ttm) REVERT: A 341 ASP cc_start: 0.8032 (t0) cc_final: 0.7467 (t0) REVERT: B 11 LEU cc_start: 0.9226 (mp) cc_final: 0.8859 (pp) REVERT: B 87 PHE cc_start: 0.9266 (m-80) cc_final: 0.8973 (m-80) REVERT: B 151 PHE cc_start: 0.8682 (OUTLIER) cc_final: 0.7890 (p90) REVERT: B 228 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8427 (tm-30) REVERT: B 335 ASP cc_start: 0.8209 (m-30) cc_final: 0.7906 (t0) REVERT: B 338 MET cc_start: 0.8585 (ttt) cc_final: 0.8270 (ttt) REVERT: D 23 ASP cc_start: 0.8394 (p0) cc_final: 0.7940 (t0) REVERT: D 222 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8673 (tp30) REVERT: D 383 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8505 (mmm) REVERT: D 436 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.7083 (mmm) REVERT: C 326 MET cc_start: 0.9153 (mmm) cc_final: 0.8488 (mmm) REVERT: C 406 LEU cc_start: 0.9613 (tp) cc_final: 0.9074 (tp) REVERT: C 410 MET cc_start: 0.9251 (mtm) cc_final: 0.8739 (mtm) REVERT: C 414 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9159 (mm) outliers start: 28 outliers final: 12 residues processed: 136 average time/residue: 0.1175 time to fit residues: 23.8908 Evaluate side-chains 121 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain D residue 8 LYS Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 346 ARG Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain C residue 18 TYR Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 439 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 143 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 130 optimal weight: 20.0000 chunk 125 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 262 GLN ** B 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN ** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.072155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.049945 restraints weight = 72046.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.051807 restraints weight = 34600.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.052907 restraints weight = 22462.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.053549 restraints weight = 17492.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.053921 restraints weight = 15143.256| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13066 Z= 0.187 Angle : 0.570 8.306 17581 Z= 0.302 Chirality : 0.041 0.161 1933 Planarity : 0.003 0.027 2242 Dihedral : 5.756 79.267 1789 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.87 % Allowed : 14.97 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.22), residues: 1538 helix: 2.24 (0.18), residues: 781 sheet: -1.11 (0.32), residues: 279 loop : -0.14 (0.31), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 282 TYR 0.020 0.001 TYR A 278 PHE 0.014 0.002 PHE C 226 TRP 0.024 0.002 TRP A 360 HIS 0.005 0.001 HIS D 15 Details of bonding type rmsd covalent geometry : bond 0.00407 (13066) covalent geometry : angle 0.57045 (17581) hydrogen bonds : bond 0.04004 ( 713) hydrogen bonds : angle 4.57833 ( 2007) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 104 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7702 (mmm160) REVERT: A 154 MET cc_start: 0.9190 (mtp) cc_final: 0.8931 (mtm) REVERT: A 209 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8274 (tp30) REVERT: A 341 ASP cc_start: 0.8250 (t0) cc_final: 0.7640 (t0) REVERT: A 436 MET cc_start: 0.9017 (mmt) cc_final: 0.8807 (mmt) REVERT: B 11 LEU cc_start: 0.9252 (mp) cc_final: 0.8928 (pp) REVERT: B 87 PHE cc_start: 0.9186 (m-80) cc_final: 0.8917 (m-80) REVERT: B 151 PHE cc_start: 0.8823 (OUTLIER) cc_final: 0.8004 (p90) REVERT: D 147 TYR cc_start: 0.8991 (t80) cc_final: 0.8657 (t80) REVERT: D 192 LEU cc_start: 0.9325 (mm) cc_final: 0.9115 (mp) REVERT: D 222 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8617 (tp30) REVERT: D 234 PHE cc_start: 0.9211 (t80) cc_final: 0.8972 (m-80) REVERT: D 383 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8566 (mmm) REVERT: D 436 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.6942 (mmm) REVERT: C 326 MET cc_start: 0.9187 (mmm) cc_final: 0.8977 (mmm) REVERT: C 376 MET cc_start: 0.9661 (mtm) cc_final: 0.9167 (mtp) REVERT: C 414 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9271 (mm) outliers start: 40 outliers final: 22 residues processed: 132 average time/residue: 0.1144 time to fit residues: 22.2950 Evaluate side-chains 123 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 152 ARG Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain D residue 8 LYS Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 346 ARG Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain C residue 18 TYR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 439 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 0.3980 chunk 111 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 141 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 HIS D 262 GLN D 413 GLN ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.070997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.048754 restraints weight = 74425.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.050533 restraints weight = 35387.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.051616 restraints weight = 23228.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.052256 restraints weight = 18208.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.052572 restraints weight = 15782.242| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 13066 Z= 0.272 Angle : 0.656 10.149 17581 Z= 0.346 Chirality : 0.043 0.162 1933 Planarity : 0.004 0.033 2242 Dihedral : 6.203 82.010 1789 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.80 % Allowed : 14.68 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.22), residues: 1538 helix: 1.96 (0.18), residues: 768 sheet: -1.20 (0.31), residues: 279 loop : -0.10 (0.30), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 152 TYR 0.021 0.002 TYR A 278 PHE 0.016 0.002 PHE C 226 TRP 0.025 0.002 TRP A 360 HIS 0.004 0.001 HIS D 15 Details of bonding type rmsd covalent geometry : bond 0.00591 (13066) covalent geometry : angle 0.65597 (17581) hydrogen bonds : bond 0.04386 ( 713) hydrogen bonds : angle 4.89183 ( 2007) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 93 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8078 (mmm160) REVERT: A 209 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8305 (tp30) REVERT: A 256 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8389 (mt-10) REVERT: A 305 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8289 (tmm-80) REVERT: A 336 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7633 (pmtt) REVERT: A 341 ASP cc_start: 0.8358 (t0) cc_final: 0.7966 (t0) REVERT: A 413 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8310 (tt0) REVERT: B 11 LEU cc_start: 0.9180 (mp) cc_final: 0.8930 (pp) REVERT: B 151 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.7919 (p90) REVERT: D 222 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8644 (tt0) REVERT: D 234 PHE cc_start: 0.9253 (t80) cc_final: 0.9034 (m-80) REVERT: D 304 TYR cc_start: 0.9322 (t80) cc_final: 0.9121 (t80) REVERT: D 383 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8582 (mmm) REVERT: D 436 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.6758 (mmm) REVERT: C 326 MET cc_start: 0.9183 (mmm) cc_final: 0.8955 (mmm) outliers start: 53 outliers final: 28 residues processed: 139 average time/residue: 0.1233 time to fit residues: 25.1781 Evaluate side-chains 124 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 87 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 305 ARG Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 152 ARG Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain D residue 8 LYS Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 346 ARG Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain C residue 18 TYR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 439 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 144 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 GLN D 424 HIS ** C 190 GLN ** 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 = 0.3847 r_free = 0.3847 target = 0.072550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.050694 restraints weight = 70829.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.052543 restraints weight = 33315.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.053678 restraints weight = 21686.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.054306 restraints weight = 16809.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.054697 restraints weight = 14532.726| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13066 Z= 0.118 Angle : 0.538 10.539 17581 Z= 0.282 Chirality : 0.041 0.161 1933 Planarity : 0.003 0.029 2242 Dihedral : 5.693 75.338 1787 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.36 % Allowed : 16.62 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.22), residues: 1538 helix: 2.17 (0.18), residues: 781 sheet: -1.04 (0.31), residues: 289 loop : 0.03 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 208 TYR 0.018 0.001 TYR A 278 PHE 0.013 0.001 PHE B 134 TRP 0.017 0.001 TRP A 360 HIS 0.002 0.000 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00254 (13066) covalent geometry : angle 0.53812 (17581) hydrogen bonds : bond 0.03825 ( 713) hydrogen bonds : angle 4.47332 ( 2007) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7800 (mmm160) REVERT: A 209 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8273 (tp30) REVERT: A 256 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8675 (mt-10) REVERT: A 341 ASP cc_start: 0.8304 (t0) cc_final: 0.7759 (t0) REVERT: B 151 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.7945 (p90) REVERT: B 230 PHE cc_start: 0.9079 (m-80) cc_final: 0.8802 (t80) REVERT: B 383 MET cc_start: 0.8764 (ptm) cc_final: 0.8460 (ptp) REVERT: D 192 LEU cc_start: 0.9361 (mm) cc_final: 0.9149 (mp) REVERT: D 222 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8608 (tp30) REVERT: D 383 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8672 (mmm) REVERT: D 436 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.6950 (mmm) REVERT: C 187 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8944 (mt) REVERT: C 338 MET cc_start: 0.8807 (ptm) cc_final: 0.8458 (ptm) REVERT: C 376 MET cc_start: 0.9563 (mtp) cc_final: 0.9298 (mtp) outliers start: 33 outliers final: 20 residues processed: 127 average time/residue: 0.1127 time to fit residues: 21.5149 Evaluate side-chains 120 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 346 ARG Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 18 TYR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 439 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 152 optimal weight: 0.2980 chunk 142 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN D 262 GLN ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 GLN ** 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 = 0.3810 r_free = 0.3810 target = 0.071069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.048882 restraints weight = 72905.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.050689 restraints weight = 34544.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.051797 restraints weight = 22611.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.052444 restraints weight = 17622.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.052814 restraints weight = 15289.528| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.5628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13066 Z= 0.210 Angle : 0.595 10.636 17581 Z= 0.314 Chirality : 0.042 0.192 1933 Planarity : 0.003 0.028 2242 Dihedral : 6.225 80.309 1787 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.94 % Allowed : 16.91 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.22), residues: 1538 helix: 2.02 (0.18), residues: 781 sheet: -1.09 (0.31), residues: 279 loop : 0.03 (0.31), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 152 TYR 0.026 0.002 TYR D 304 PHE 0.019 0.002 PHE A 230 TRP 0.017 0.001 TRP A 360 HIS 0.005 0.001 HIS B 15 Details of bonding type rmsd covalent geometry : bond 0.00457 (13066) covalent geometry : angle 0.59498 (17581) hydrogen bonds : bond 0.04089 ( 713) hydrogen bonds : angle 4.68115 ( 2007) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 92 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.8016 (mmm160) REVERT: A 209 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8282 (tp30) REVERT: A 341 ASP cc_start: 0.8530 (t0) cc_final: 0.7974 (t0) REVERT: B 151 PHE cc_start: 0.8738 (OUTLIER) cc_final: 0.8138 (p90) REVERT: D 222 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8716 (tp30) REVERT: D 383 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8639 (mmm) REVERT: D 436 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.6819 (mmm) REVERT: C 187 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9077 (mt) outliers start: 41 outliers final: 29 residues processed: 124 average time/residue: 0.1204 time to fit residues: 22.0188 Evaluate side-chains 124 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 89 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 152 ARG Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain D residue 8 LYS Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 346 ARG Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 18 TYR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 439 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 154 optimal weight: 0.4980 chunk 88 optimal weight: 7.9990 chunk 150 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 64 optimal weight: 20.0000 chunk 109 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 119 optimal weight: 20.0000 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 GLN ** 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 = 0.3810 r_free = 0.3810 target = 0.071051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.048974 restraints weight = 72574.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.050819 restraints weight = 34318.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.051914 restraints weight = 22381.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.052527 restraints weight = 17486.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.052809 restraints weight = 15175.445| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.5795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13066 Z= 0.196 Angle : 0.596 11.514 17581 Z= 0.312 Chirality : 0.042 0.186 1933 Planarity : 0.003 0.028 2242 Dihedral : 6.164 77.845 1787 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.22 % Allowed : 17.62 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.22), residues: 1538 helix: 1.98 (0.18), residues: 781 sheet: -1.02 (0.32), residues: 273 loop : 0.12 (0.32), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 152 TYR 0.029 0.002 TYR D 304 PHE 0.014 0.001 PHE C 226 TRP 0.014 0.001 TRP A 360 HIS 0.003 0.001 HIS A 399 Details of bonding type rmsd covalent geometry : bond 0.00426 (13066) covalent geometry : angle 0.59627 (17581) hydrogen bonds : bond 0.04040 ( 713) hydrogen bonds : angle 4.66513 ( 2007) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 93 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7999 (mmm160) REVERT: A 209 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8276 (tp30) REVERT: A 222 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7929 (tp30) REVERT: A 341 ASP cc_start: 0.8545 (t0) cc_final: 0.8022 (t0) REVERT: B 151 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.7734 (p90) REVERT: D 106 MET cc_start: 0.9165 (tpt) cc_final: 0.8549 (ttt) REVERT: D 190 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8780 (tp-100) REVERT: D 222 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8671 (tp30) REVERT: D 326 MET cc_start: 0.9381 (mtm) cc_final: 0.8973 (mpp) REVERT: D 383 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8676 (mmm) REVERT: D 424 HIS cc_start: 0.4894 (OUTLIER) cc_final: 0.4259 (t-170) REVERT: D 436 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.6920 (mmm) REVERT: C 376 MET cc_start: 0.9555 (mtp) cc_final: 0.9129 (mtt) outliers start: 45 outliers final: 32 residues processed: 127 average time/residue: 0.1132 time to fit residues: 21.7881 Evaluate side-chains 130 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 90 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain D residue 8 LYS Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 346 ARG Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 424 HIS Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 18 TYR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 439 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 36 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 154 optimal weight: 0.9980 chunk 79 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 152 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 HIS ** C 190 GLN ** 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 = 0.3843 r_free = 0.3843 target = 0.072512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.050532 restraints weight = 72779.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.052383 restraints weight = 34373.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.053531 restraints weight = 22319.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.054185 restraints weight = 17361.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.054568 restraints weight = 15029.096| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.5759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13066 Z= 0.118 Angle : 0.567 13.571 17581 Z= 0.290 Chirality : 0.041 0.179 1933 Planarity : 0.003 0.028 2242 Dihedral : 5.923 74.915 1787 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.65 % Allowed : 18.27 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.23), residues: 1538 helix: 2.19 (0.18), residues: 777 sheet: -0.87 (0.30), residues: 298 loop : 0.31 (0.32), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 152 TYR 0.022 0.001 TYR D 304 PHE 0.013 0.001 PHE C 226 TRP 0.015 0.001 TRP A 360 HIS 0.003 0.000 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00255 (13066) covalent geometry : angle 0.56711 (17581) hydrogen bonds : bond 0.03721 ( 713) hydrogen bonds : angle 4.42652 ( 2007) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 95 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7760 (mmm160) REVERT: A 209 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8303 (tp30) REVERT: A 341 ASP cc_start: 0.8412 (t0) cc_final: 0.7863 (t0) REVERT: B 151 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8187 (p90) REVERT: B 230 PHE cc_start: 0.9026 (OUTLIER) cc_final: 0.8817 (t80) REVERT: D 106 MET cc_start: 0.9185 (tpt) cc_final: 0.8572 (ttt) REVERT: D 190 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8667 (tp-100) REVERT: D 222 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8598 (tp30) REVERT: D 383 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8708 (mmm) REVERT: D 436 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.6772 (mmm) REVERT: C 11 LEU cc_start: 0.9611 (pt) cc_final: 0.9031 (tt) REVERT: C 338 MET cc_start: 0.8725 (ptm) cc_final: 0.8382 (ptm) REVERT: C 376 MET cc_start: 0.9544 (mtp) cc_final: 0.9274 (mtp) outliers start: 37 outliers final: 24 residues processed: 124 average time/residue: 0.1138 time to fit residues: 21.2820 Evaluate side-chains 119 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 88 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 346 ARG Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 18 TYR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 439 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 148 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 35 optimal weight: 0.0670 chunk 30 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 overall best weight: 2.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 ASN ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 GLN ** 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 = 0.3814 r_free = 0.3814 target = 0.071321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.049181 restraints weight = 73217.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.051016 restraints weight = 34656.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.052131 restraints weight = 22636.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.052777 restraints weight = 17634.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.053121 restraints weight = 15269.874| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.5950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13066 Z= 0.196 Angle : 0.618 12.351 17581 Z= 0.321 Chirality : 0.042 0.180 1933 Planarity : 0.003 0.028 2242 Dihedral : 6.158 80.807 1787 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.72 % Allowed : 18.12 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.22), residues: 1538 helix: 2.02 (0.18), residues: 784 sheet: -0.73 (0.32), residues: 272 loop : 0.23 (0.32), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 152 TYR 0.023 0.002 TYR D 304 PHE 0.014 0.002 PHE C 226 TRP 0.041 0.002 TRP A 360 HIS 0.003 0.001 HIS A 399 Details of bonding type rmsd covalent geometry : bond 0.00427 (13066) covalent geometry : angle 0.61821 (17581) hydrogen bonds : bond 0.03964 ( 713) hydrogen bonds : angle 4.65053 ( 2007) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 88 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7952 (mmm160) REVERT: A 154 MET cc_start: 0.8915 (ptm) cc_final: 0.8453 (ppp) REVERT: A 209 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8281 (tp30) REVERT: A 341 ASP cc_start: 0.8509 (t0) cc_final: 0.8093 (t0) REVERT: B 151 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8064 (p90) REVERT: B 230 PHE cc_start: 0.9087 (m-80) cc_final: 0.8842 (t80) REVERT: D 190 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8706 (tp-100) REVERT: D 222 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8698 (tp30) REVERT: D 326 MET cc_start: 0.9416 (mtm) cc_final: 0.9148 (mtm) REVERT: D 383 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8634 (mmm) REVERT: D 424 HIS cc_start: 0.5100 (OUTLIER) cc_final: 0.4384 (t-170) REVERT: D 436 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.6842 (mmm) REVERT: C 11 LEU cc_start: 0.9680 (pt) cc_final: 0.9125 (tt) REVERT: C 376 MET cc_start: 0.9556 (mtp) cc_final: 0.9117 (mtt) outliers start: 38 outliers final: 29 residues processed: 118 average time/residue: 0.1020 time to fit residues: 17.9596 Evaluate side-chains 121 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 85 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 152 ARG Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 346 ARG Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 424 HIS Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 18 TYR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 439 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 47 optimal weight: 8.9990 chunk 142 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 144 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 GLN ** 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 = 0.3797 r_free = 0.3797 target = 0.070869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.048504 restraints weight = 72548.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.050303 restraints weight = 34780.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.051389 restraints weight = 22880.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.052020 restraints weight = 17924.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.052391 restraints weight = 15566.376| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.6134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13066 Z= 0.206 Angle : 0.626 12.098 17581 Z= 0.327 Chirality : 0.042 0.206 1933 Planarity : 0.003 0.030 2242 Dihedral : 6.082 79.655 1787 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.15 % Allowed : 18.12 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.22), residues: 1538 helix: 1.88 (0.18), residues: 778 sheet: -0.85 (0.32), residues: 272 loop : 0.32 (0.32), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 152 TYR 0.023 0.002 TYR D 304 PHE 0.014 0.002 PHE B 134 TRP 0.032 0.002 TRP A 360 HIS 0.003 0.001 HIS A 399 Details of bonding type rmsd covalent geometry : bond 0.00449 (13066) covalent geometry : angle 0.62572 (17581) hydrogen bonds : bond 0.04085 ( 713) hydrogen bonds : angle 4.78309 ( 2007) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2924.78 seconds wall clock time: 51 minutes 2.99 seconds (3062.99 seconds total)