Starting phenix.real_space_refine on Sat Jan 18 22:36:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v49_42969/01_2025/8v49_42969.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v49_42969/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8v49_42969/01_2025/8v49_42969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v49_42969/01_2025/8v49_42969.map" model { file = "/net/cci-nas-00/data/ceres_data/8v49_42969/01_2025/8v49_42969.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v49_42969/01_2025/8v49_42969.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 8.08, per 1000 atoms: 0.63 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: 3.25 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.35 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: 4.15 Time building geometry restraints manager: 3.66 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: 2.660 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: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 30.540 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.600 ------------------------------------------------------------------------------- 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= 0.215 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.017 0.002 TRP B 158 HIS 0.008 0.001 HIS D 32 PHE 0.022 0.002 PHE B 59 TYR 0.014 0.002 TYR B 378 ARG 0.009 0.001 ARG A 185 *********************** 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 : 1.731 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: symmetry clash REVERT: A 55 ILE cc_start: 0.9068 (tt) cc_final: 0.8615 (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: 0.8000 (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: 0.7560 (p) REVERT: D 222 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8044 (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: 0.9334 (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: 0.2720 time to fit residues: 114.2253 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 : 1.489 ------------------------------------------------------------------------------- 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 133 optimal weight: 20.0000 chunk 119 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 123 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 143 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 312 GLN A 315 GLN A 399 HIS A 418 GLN B 15 HIS B 29 ASN ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN B 424 HIS D 138 ASN 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.072213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.049914 restraints weight = 71810.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.051614 restraints weight = 35289.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.052727 restraints weight = 23405.680| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 13066 Z= 0.435 Angle : 0.718 8.317 17581 Z= 0.384 Chirality : 0.044 0.165 1933 Planarity : 0.005 0.037 2242 Dihedral : 7.670 74.181 1799 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.51 % Allowed : 13.04 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.22), residues: 1538 helix: 1.81 (0.18), residues: 773 sheet: -1.64 (0.29), residues: 298 loop : -0.54 (0.31), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 360 HIS 0.007 0.002 HIS D 15 PHE 0.023 0.002 PHE B 332 TYR 0.021 0.002 TYR A 278 ARG 0.008 0.001 ARG B 152 *********************** 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 191 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 128 time to evaluate : 1.526 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: A 56 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7846 (mmm160) REVERT: A 154 MET cc_start: 0.9248 (mtp) cc_final: 0.8630 (mtm) REVERT: A 209 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8260 (tp30) REVERT: A 256 GLU cc_start: 0.9076 (tt0) cc_final: 0.8854 (mt-10) REVERT: A 326 MET cc_start: 0.9212 (mmt) cc_final: 0.8764 (mmm) REVERT: A 341 ASP cc_start: 0.8401 (t0) cc_final: 0.7800 (t0) REVERT: B 87 PHE cc_start: 0.9185 (m-80) cc_final: 0.8893 (m-80) REVERT: B 228 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8542 (tm-30) REVERT: D 23 ASP cc_start: 0.8521 (p0) cc_final: 0.8070 (t0) REVERT: D 147 TYR cc_start: 0.9164 (t80) cc_final: 0.8953 (t80) REVERT: D 154 MET cc_start: 0.8959 (tmm) cc_final: 0.7701 (mtt) REVERT: D 383 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8626 (mmm) REVERT: D 436 MET cc_start: 0.8501 (tpt) cc_final: 0.7031 (mmm) REVERT: C 326 MET cc_start: 0.9183 (mmm) cc_final: 0.8683 (mmm) REVERT: C 410 MET cc_start: 0.9350 (mtm) cc_final: 0.9143 (mtm) REVERT: C 414 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9207 (mm) outliers start: 63 outliers final: 26 residues processed: 184 average time/residue: 0.2527 time to fit residues: 67.3813 Evaluate side-chains 125 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 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 104 GLU Chi-restraints excluded: chain A residue 203 ILE 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 428 ILE 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 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 C residue 14 ILE Chi-restraints excluded: chain C residue 18 TYR 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 373 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 153 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 149 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 129 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN B 48 ASN B 288 ASN D 262 GLN C 32 HIS ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.072997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.052894 restraints weight = 72097.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.053429 restraints weight = 32468.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.053941 restraints weight = 23886.894| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13066 Z= 0.229 Angle : 0.581 10.761 17581 Z= 0.305 Chirality : 0.041 0.162 1933 Planarity : 0.003 0.031 2242 Dihedral : 6.426 80.600 1794 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.44 % Allowed : 15.62 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.22), residues: 1538 helix: 2.09 (0.18), residues: 783 sheet: -1.34 (0.31), residues: 284 loop : -0.32 (0.31), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 360 HIS 0.007 0.001 HIS C 32 PHE 0.018 0.002 PHE A 230 TYR 0.029 0.001 TYR D 304 ARG 0.006 0.000 ARG A 364 *********************** 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 147 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 113 time to evaluate : 1.491 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: A 56 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7685 (mmm160) REVERT: A 154 MET cc_start: 0.8910 (mtp) cc_final: 0.8544 (mtp) REVERT: A 209 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8245 (tp30) REVERT: A 326 MET cc_start: 0.9167 (mmt) cc_final: 0.8580 (mmm) REVERT: A 341 ASP cc_start: 0.8188 (t0) cc_final: 0.7602 (t0) REVERT: A 399 HIS cc_start: 0.8677 (OUTLIER) cc_final: 0.8458 (m90) REVERT: B 87 PHE cc_start: 0.9270 (m-80) cc_final: 0.8988 (m-80) REVERT: B 151 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.7911 (p90) REVERT: D 23 ASP cc_start: 0.8549 (p0) cc_final: 0.8077 (t0) REVERT: D 187 LEU cc_start: 0.9633 (tp) cc_final: 0.9430 (mm) REVERT: D 383 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8627 (mmm) REVERT: D 436 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.7260 (mmm) REVERT: C 30 VAL cc_start: 0.9748 (t) cc_final: 0.9459 (m) REVERT: C 201 MET cc_start: 0.9128 (mmp) cc_final: 0.8871 (mmp) REVERT: C 326 MET cc_start: 0.9162 (mmm) cc_final: 0.8942 (mmm) REVERT: C 414 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9229 (mm) outliers start: 34 outliers final: 13 residues processed: 139 average time/residue: 0.2708 time to fit residues: 55.4676 Evaluate side-chains 120 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 399 HIS 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 D residue 8 LYS Chi-restraints excluded: chain D residue 56 ARG 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 155 LEU Chi-restraints excluded: chain C residue 396 ILE 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 73 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 60 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 107 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN ** D 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN D 424 HIS ** C 48 ASN ** 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 = 0.3826 r_free = 0.3826 target = 0.072012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.050024 restraints weight = 70522.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.051799 restraints weight = 33793.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.052905 restraints weight = 22077.608| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13066 Z= 0.254 Angle : 0.559 8.575 17581 Z= 0.296 Chirality : 0.041 0.160 1933 Planarity : 0.003 0.027 2242 Dihedral : 5.785 76.781 1789 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.22 % Allowed : 15.19 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.22), residues: 1538 helix: 2.12 (0.18), residues: 783 sheet: -1.16 (0.32), residues: 279 loop : -0.16 (0.31), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 360 HIS 0.006 0.001 HIS D 15 PHE 0.014 0.002 PHE C 226 TYR 0.021 0.001 TYR D 304 ARG 0.005 0.000 ARG B 152 *********************** 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 148 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 103 time to evaluate : 1.576 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: 0.8274 (OUTLIER) cc_final: 0.7869 (mmm160) REVERT: A 154 MET cc_start: 0.9005 (mtp) cc_final: 0.8795 (mtp) REVERT: A 209 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8288 (tp30) REVERT: A 256 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8563 (mt-10) REVERT: A 341 ASP cc_start: 0.8199 (t0) cc_final: 0.7787 (t0) REVERT: B 11 LEU cc_start: 0.9381 (mt) cc_final: 0.8714 (pp) REVERT: B 151 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.8057 (p90) REVERT: D 147 TYR cc_start: 0.8944 (t80) cc_final: 0.8627 (t80) REVERT: D 192 LEU cc_start: 0.9339 (mm) cc_final: 0.9121 (mp) REVERT: D 383 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8669 (mmm) REVERT: D 436 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.6920 (mmm) REVERT: C 187 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8990 (mt) REVERT: C 201 MET cc_start: 0.9096 (mmp) cc_final: 0.8832 (mmm) REVERT: C 376 MET cc_start: 0.9649 (mtm) cc_final: 0.8976 (mtt) REVERT: C 414 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9295 (mm) outliers start: 45 outliers final: 24 residues processed: 140 average time/residue: 0.2670 time to fit residues: 54.2394 Evaluate side-chains 125 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 1.517 ------------------------------------------------------------------------------- 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 282 ARG 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 428 ILE 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 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 187 LEU Chi-restraints excluded: chain C residue 336 LYS Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 396 ILE 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 137 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 135 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 15 HIS D 413 GLN ** C 48 ASN ** 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 = 0.3800 r_free = 0.3800 target = 0.070831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.048786 restraints weight = 71969.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.050535 restraints weight = 34654.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.051601 restraints weight = 22745.590| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13066 Z= 0.336 Angle : 0.612 8.878 17581 Z= 0.326 Chirality : 0.042 0.159 1933 Planarity : 0.003 0.027 2242 Dihedral : 6.058 81.350 1789 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.65 % Allowed : 15.40 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.22), residues: 1538 helix: 1.94 (0.18), residues: 776 sheet: -1.18 (0.31), residues: 279 loop : -0.09 (0.31), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 360 HIS 0.005 0.001 HIS D 15 PHE 0.022 0.002 PHE A 230 TYR 0.014 0.002 TYR D 432 ARG 0.007 0.001 ARG B 152 *********************** 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 144 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 93 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.8034 (mmm160) REVERT: A 209 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8303 (tp30) REVERT: A 256 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8592 (mt-10) REVERT: A 304 TYR cc_start: 0.9117 (t80) cc_final: 0.8799 (t80) REVERT: A 341 ASP cc_start: 0.8488 (t0) cc_final: 0.7990 (t0) REVERT: B 11 LEU cc_start: 0.9383 (mt) cc_final: 0.8693 (pp) REVERT: B 151 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8082 (p90) REVERT: D 230 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.8431 (m-80) REVERT: D 383 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8624 (mmm) REVERT: D 436 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.6833 (mmm) REVERT: C 187 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9052 (mt) REVERT: C 338 MET cc_start: 0.8806 (ttm) cc_final: 0.8460 (ttm) REVERT: C 376 MET cc_start: 0.9677 (mtm) cc_final: 0.9220 (mtp) outliers start: 51 outliers final: 30 residues processed: 136 average time/residue: 0.2384 time to fit residues: 48.7862 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 : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 9 ILE 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 104 GLU Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 326 MET 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 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 230 PHE 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 11 LEU Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 18 TYR Chi-restraints excluded: chain C residue 49 ILE 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 374 LEU Chi-restraints excluded: chain C residue 396 ILE 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 4 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 101 optimal weight: 20.0000 chunk 156 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 22 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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** ** C 48 ASN ** 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 = 0.3823 r_free = 0.3823 target = 0.071874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.049885 restraints weight = 71754.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.051730 restraints weight = 34259.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.052851 restraints weight = 22250.082| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13066 Z= 0.191 Angle : 0.546 10.617 17581 Z= 0.288 Chirality : 0.041 0.160 1933 Planarity : 0.003 0.029 2242 Dihedral : 5.693 74.636 1787 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.87 % Allowed : 16.83 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.22), residues: 1538 helix: 2.08 (0.18), residues: 781 sheet: -0.99 (0.31), residues: 279 loop : 0.02 (0.31), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 360 HIS 0.002 0.001 HIS C 44 PHE 0.013 0.001 PHE C 226 TYR 0.015 0.001 TYR C 432 ARG 0.005 0.000 ARG B 152 *********************** 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 136 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 96 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7781 (mmm160) REVERT: A 209 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8262 (tp30) REVERT: A 256 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8654 (mp0) REVERT: A 305 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8264 (tmm-80) REVERT: A 338 MET cc_start: 0.8796 (ptm) cc_final: 0.8295 (ptm) REVERT: A 341 ASP cc_start: 0.8483 (t0) cc_final: 0.7928 (t0) REVERT: B 11 LEU cc_start: 0.9377 (mt) cc_final: 0.8787 (pp) REVERT: B 151 PHE cc_start: 0.8855 (OUTLIER) cc_final: 0.8160 (p90) REVERT: B 154 MET cc_start: 0.8407 (ttp) cc_final: 0.8175 (ttp) REVERT: D 383 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.8734 (mmm) REVERT: D 436 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.6860 (mmm) REVERT: C 187 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9019 (mt) REVERT: C 201 MET cc_start: 0.9129 (mmp) cc_final: 0.8864 (mmm) REVERT: C 338 MET cc_start: 0.8716 (ttm) cc_final: 0.8515 (ttm) REVERT: C 376 MET cc_start: 0.9734 (mtm) cc_final: 0.8941 (mtt) REVERT: C 436 MET cc_start: 0.9145 (mpp) cc_final: 0.8880 (mpp) outliers start: 40 outliers final: 25 residues processed: 132 average time/residue: 0.2720 time to fit residues: 52.7821 Evaluate side-chains 123 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 1.554 ------------------------------------------------------------------------------- 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 282 ARG Chi-restraints excluded: chain A residue 305 ARG 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 56 ARG Chi-restraints excluded: chain D residue 178 ARG 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 18 TYR Chi-restraints excluded: chain C residue 49 ILE 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 396 ILE 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 74 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 34 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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** ** C 44 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.072315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.050361 restraints weight = 70539.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.052208 restraints weight = 33726.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.053352 restraints weight = 21996.081| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.5465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13066 Z= 0.162 Angle : 0.530 11.435 17581 Z= 0.279 Chirality : 0.041 0.160 1933 Planarity : 0.003 0.032 2242 Dihedral : 5.631 74.866 1787 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.79 % Allowed : 17.34 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.22), residues: 1538 helix: 2.14 (0.18), residues: 781 sheet: -0.84 (0.33), residues: 252 loop : 0.05 (0.30), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 360 HIS 0.003 0.000 HIS C 44 PHE 0.013 0.001 PHE C 226 TYR 0.015 0.001 TYR D 197 ARG 0.005 0.000 ARG B 152 *********************** 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 136 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 97 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7693 (mmm160) REVERT: A 209 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8214 (tp30) REVERT: A 256 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8585 (mt-10) REVERT: A 341 ASP cc_start: 0.8288 (t0) cc_final: 0.7896 (t0) REVERT: B 11 LEU cc_start: 0.9392 (mt) cc_final: 0.8802 (pp) REVERT: B 151 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.8006 (p90) REVERT: B 230 PHE cc_start: 0.9132 (m-80) cc_final: 0.8887 (t80) REVERT: D 106 MET cc_start: 0.9127 (tpt) cc_final: 0.8520 (ttt) REVERT: D 383 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8652 (mmm) REVERT: D 424 HIS cc_start: 0.5410 (OUTLIER) cc_final: 0.4643 (t-170) REVERT: D 436 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.6879 (mmm) REVERT: C 11 LEU cc_start: 0.9686 (pt) cc_final: 0.9126 (tt) REVERT: C 187 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9003 (mt) REVERT: C 201 MET cc_start: 0.9126 (mmp) cc_final: 0.8897 (mmp) REVERT: C 338 MET cc_start: 0.8705 (ttm) cc_final: 0.8363 (ttm) REVERT: C 376 MET cc_start: 0.9726 (mtm) cc_final: 0.8944 (mtt) outliers start: 39 outliers final: 26 residues processed: 128 average time/residue: 0.2478 time to fit residues: 46.6765 Evaluate side-chains 121 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 1.471 ------------------------------------------------------------------------------- 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 226 PHE Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 28 LEU 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 439 ILE Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 178 ARG 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 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 396 ILE Chi-restraints excluded: chain C residue 407 LEU 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 119 optimal weight: 20.0000 chunk 57 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 104 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 110 optimal weight: 0.0370 chunk 59 optimal weight: 10.0000 overall best weight: 2.2066 ------------------------------------------------------------------------------- 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** ** C 44 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.071527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.049475 restraints weight = 71627.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.051277 restraints weight = 34383.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.052345 restraints weight = 22479.881| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.5639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13066 Z= 0.227 Angle : 0.572 11.577 17581 Z= 0.298 Chirality : 0.041 0.160 1933 Planarity : 0.003 0.029 2242 Dihedral : 5.900 77.208 1787 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.08 % Allowed : 17.41 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.22), residues: 1538 helix: 2.09 (0.18), residues: 781 sheet: -0.82 (0.33), residues: 252 loop : 0.07 (0.30), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 360 HIS 0.003 0.001 HIS B 32 PHE 0.014 0.001 PHE C 226 TYR 0.015 0.001 TYR A 278 ARG 0.006 0.000 ARG B 152 *********************** 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 132 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 89 time to evaluate : 1.497 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: A 56 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7846 (mmm160) REVERT: A 154 MET cc_start: 0.9017 (ttm) cc_final: 0.8761 (ptp) REVERT: A 209 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8261 (tp30) REVERT: A 256 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8649 (mp0) REVERT: A 341 ASP cc_start: 0.8394 (t0) cc_final: 0.8000 (t0) REVERT: B 11 LEU cc_start: 0.9389 (mt) cc_final: 0.8772 (pp) REVERT: B 151 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.7912 (p90) REVERT: B 230 PHE cc_start: 0.9122 (m-80) cc_final: 0.8875 (t80) REVERT: D 190 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8671 (tp-100) REVERT: D 326 MET cc_start: 0.9376 (mtm) cc_final: 0.8965 (mpp) REVERT: D 383 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8678 (mmm) REVERT: D 424 HIS cc_start: 0.5205 (OUTLIER) cc_final: 0.4642 (t-170) REVERT: D 436 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.6865 (mmm) REVERT: C 11 LEU cc_start: 0.9685 (pt) cc_final: 0.9131 (tt) REVERT: C 187 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9046 (mt) REVERT: C 326 MET cc_start: 0.9083 (mmm) cc_final: 0.8852 (mmm) REVERT: C 376 MET cc_start: 0.9716 (mtm) cc_final: 0.8910 (mtt) REVERT: C 436 MET cc_start: 0.8604 (mpp) cc_final: 0.7985 (mpp) outliers start: 43 outliers final: 31 residues processed: 123 average time/residue: 0.2418 time to fit residues: 44.5643 Evaluate side-chains 126 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 87 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 9 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 226 PHE Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 28 LEU 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 190 GLN 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 43 ILE 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 396 ILE Chi-restraints excluded: chain C residue 407 LEU 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 18 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 150 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 156 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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** ** C 44 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.072086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.050132 restraints weight = 70519.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.051951 restraints weight = 33904.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.053069 restraints weight = 22115.135| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.5692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13066 Z= 0.177 Angle : 0.554 12.506 17581 Z= 0.288 Chirality : 0.041 0.177 1933 Planarity : 0.003 0.028 2242 Dihedral : 5.865 75.550 1787 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.01 % Allowed : 17.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.22), residues: 1538 helix: 2.14 (0.18), residues: 781 sheet: -0.67 (0.33), residues: 267 loop : 0.15 (0.31), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 360 HIS 0.003 0.001 HIS B 32 PHE 0.013 0.001 PHE C 226 TYR 0.019 0.001 TYR A 278 ARG 0.005 0.000 ARG B 152 *********************** 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 135 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 93 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7679 (mmm160) REVERT: A 209 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8142 (tp30) REVERT: A 256 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8612 (mp0) REVERT: A 341 ASP cc_start: 0.8414 (t0) cc_final: 0.8060 (t0) REVERT: B 11 LEU cc_start: 0.9396 (mt) cc_final: 0.8804 (pp) REVERT: B 151 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.7973 (p90) REVERT: B 230 PHE cc_start: 0.9132 (OUTLIER) cc_final: 0.8900 (t80) REVERT: D 106 MET cc_start: 0.9190 (tpt) cc_final: 0.8605 (ttt) REVERT: D 190 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8629 (tp-100) REVERT: D 383 MET cc_start: 0.9229 (OUTLIER) cc_final: 0.8705 (mmm) REVERT: D 424 HIS cc_start: 0.5288 (OUTLIER) cc_final: 0.4608 (t-170) REVERT: D 436 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.6860 (mmm) REVERT: C 11 LEU cc_start: 0.9650 (pt) cc_final: 0.9078 (tt) REVERT: C 187 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8985 (mt) REVERT: C 376 MET cc_start: 0.9734 (mtm) cc_final: 0.8909 (mtt) outliers start: 42 outliers final: 29 residues processed: 125 average time/residue: 0.2569 time to fit residues: 47.6540 Evaluate side-chains 124 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 86 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 9 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 226 PHE Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 436 MET 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 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 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 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 187 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 396 ILE 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 69 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 125 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 155 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 113 optimal weight: 20.0000 chunk 99 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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** ** C 44 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.071343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.049520 restraints weight = 70091.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.051216 restraints weight = 33550.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.052302 restraints weight = 22078.918| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.5850 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= 0.225 Angle : 0.578 12.433 17581 Z= 0.302 Chirality : 0.042 0.199 1933 Planarity : 0.003 0.028 2242 Dihedral : 6.101 78.371 1787 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.87 % Allowed : 18.12 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.22), residues: 1538 helix: 2.08 (0.18), residues: 781 sheet: -0.73 (0.32), residues: 272 loop : 0.21 (0.31), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 360 HIS 0.005 0.001 HIS B 32 PHE 0.014 0.001 PHE B 134 TYR 0.021 0.001 TYR A 278 ARG 0.006 0.000 ARG B 152 ********************** 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 128 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 88 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7824 (mmm160) REVERT: A 209 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8267 (tp30) REVERT: A 256 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8623 (mp0) REVERT: A 341 ASP cc_start: 0.8427 (t0) cc_final: 0.8067 (t0) REVERT: B 11 LEU cc_start: 0.9381 (mt) cc_final: 0.8772 (pp) REVERT: B 151 PHE cc_start: 0.8663 (OUTLIER) cc_final: 0.7915 (p90) REVERT: B 230 PHE cc_start: 0.9118 (OUTLIER) cc_final: 0.8885 (t80) REVERT: D 190 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8675 (tp-100) REVERT: D 383 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8615 (mmm) REVERT: D 424 HIS cc_start: 0.4949 (OUTLIER) cc_final: 0.4363 (t-170) REVERT: D 436 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.6782 (mmm) REVERT: C 11 LEU cc_start: 0.9639 (pt) cc_final: 0.9070 (tt) REVERT: C 187 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9025 (mt) REVERT: C 326 MET cc_start: 0.9095 (mmm) cc_final: 0.8880 (mmp) REVERT: C 376 MET cc_start: 0.9714 (mtm) cc_final: 0.9135 (mtp) REVERT: C 436 MET cc_start: 0.8526 (mpp) cc_final: 0.7945 (mpp) outliers start: 40 outliers final: 28 residues processed: 118 average time/residue: 0.2507 time to fit residues: 44.1121 Evaluate side-chains 122 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 85 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 9 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 226 PHE Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 436 MET 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 190 GLN 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 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 187 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 396 ILE 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 114 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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** ** C 44 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.071438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.049564 restraints weight = 69708.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.051346 restraints weight = 33606.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.052430 restraints weight = 22001.420| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.5913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13066 Z= 0.209 Angle : 0.590 12.423 17581 Z= 0.305 Chirality : 0.042 0.175 1933 Planarity : 0.003 0.028 2242 Dihedral : 6.077 78.082 1787 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.87 % Allowed : 18.27 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.23), residues: 1538 helix: 2.07 (0.18), residues: 785 sheet: -0.67 (0.32), residues: 272 loop : 0.27 (0.32), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 360 HIS 0.002 0.001 HIS A 399 PHE 0.013 0.001 PHE B 134 TYR 0.020 0.001 TYR A 278 ARG 0.005 0.000 ARG B 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4573.33 seconds wall clock time: 82 minutes 43.01 seconds (4963.01 seconds total)