Starting phenix.real_space_refine on Wed Jun 11 14:51:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v49_42969/06_2025/8v49_42969.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v49_42969/06_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_42969/06_2025/8v49_42969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v49_42969/06_2025/8v49_42969.map" model { file = "/net/cci-nas-00/data/ceres_data/8v49_42969/06_2025/8v49_42969.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v49_42969/06_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-5710/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: 2.86 Conformation dependent library (CDL) restraints added in 1.6 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: 1.49 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: 3.70 Time building geometry restraints manager: 3.42 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: 2.590 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: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.280 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13066 Z= 0.185 Angle : 0.795 11.730 17581 Z= 0.473 Chirality : 0.050 0.289 1933 Planarity : 0.005 0.046 2242 Dihedral : 12.614 89.308 4900 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.08 % Allowed : 8.45 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.22224 ( 713) hydrogen bonds : angle 6.69593 ( 2007) covalent geometry : bond 0.00335 (13066) covalent geometry : angle 0.79502 (17581) *********************** 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 : 1.461 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: 0.2632 time to fit residues: 110.9812 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 : 1.568 ------------------------------------------------------------------------------- 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 = 49)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.049915 restraints weight = 71810.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.051656 restraints weight = 35286.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.052735 restraints weight = 23366.880| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- 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= 0.311 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 Details of bonding type rmsd hydrogen bonds : bond 0.04888 ( 713) hydrogen bonds : angle 5.13374 ( 2007) covalent geometry : bond 0.00677 (13066) covalent geometry : angle 0.71791 (17581) *********************** 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 : 1.431 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: 0.7847 (mmm160) REVERT: A 154 MET cc_start: 0.9247 (mtp) cc_final: 0.8630 (mtm) REVERT: A 209 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8262 (tp30) REVERT: A 256 GLU cc_start: 0.9075 (tt0) cc_final: 0.8852 (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: 0.7801 (t0) REVERT: B 87 PHE cc_start: 0.9192 (m-80) cc_final: 0.8900 (m-80) REVERT: B 228 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8542 (tm-30) REVERT: D 23 ASP cc_start: 0.8519 (p0) cc_final: 0.8067 (t0) REVERT: D 147 TYR cc_start: 0.9162 (t80) cc_final: 0.8952 (t80) REVERT: D 154 MET cc_start: 0.8958 (tmm) cc_final: 0.7700 (mtt) REVERT: D 383 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8625 (mmm) REVERT: D 436 MET cc_start: 0.8498 (tpt) cc_final: 0.7029 (mmm) REVERT: C 326 MET cc_start: 0.9182 (mmm) cc_final: 0.8682 (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: 0.2414 time to fit residues: 64.5049 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 : 1.393 ------------------------------------------------------------------------------- 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: 9.9990 chunk 29 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 129 optimal weight: 0.0870 chunk 28 optimal weight: 0.7980 chunk 123 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.7762 ------------------------------------------------------------------------------- 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 = 0.3861 r_free = 0.3861 target = 0.073385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.052105 restraints weight = 71918.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.053893 restraints weight = 39650.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.054435 restraints weight = 22462.331| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4307 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= 0.147 Angle : 0.570 9.846 17581 Z= 0.299 Chirality : 0.041 0.162 1933 Planarity : 0.003 0.031 2242 Dihedral : 6.306 79.365 1794 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.29 % Allowed : 15.76 % 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: 1.06 (0.22), residues: 1538 helix: 2.13 (0.18), residues: 783 sheet: -1.32 (0.31), residues: 284 loop : -0.33 (0.31), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 360 HIS 0.006 0.001 HIS C 32 PHE 0.020 0.001 PHE A 230 TYR 0.022 0.001 TYR D 304 ARG 0.006 0.000 ARG A 364 Details of bonding type rmsd hydrogen bonds : bond 0.04245 ( 713) hydrogen bonds : angle 4.63935 ( 2007) covalent geometry : bond 0.00317 (13066) covalent geometry : angle 0.56957 (17581) *********************** 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: 32 poor density : 115 time to evaluate : 1.484 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: 0.8293 (OUTLIER) cc_final: 0.7692 (mmm160) REVERT: A 154 MET cc_start: 0.8813 (mtp) cc_final: 0.8449 (mtp) REVERT: A 209 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8308 (tp30) REVERT: A 326 MET cc_start: 0.9135 (mmt) cc_final: 0.8469 (mmm) REVERT: A 341 ASP cc_start: 0.8131 (t0) cc_final: 0.7567 (t0) REVERT: B 11 LEU cc_start: 0.9407 (mt) cc_final: 0.8757 (pp) REVERT: B 87 PHE cc_start: 0.9262 (m-80) cc_final: 0.8969 (m-80) REVERT: B 151 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.7943 (p90) REVERT: B 228 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8456 (tm-30) REVERT: D 147 TYR cc_start: 0.9113 (t80) cc_final: 0.8887 (t80) REVERT: D 187 LEU cc_start: 0.9619 (tp) cc_final: 0.9418 (mm) REVERT: D 383 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8667 (mmm) REVERT: D 436 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.7157 (mmm) REVERT: C 30 VAL cc_start: 0.9726 (t) cc_final: 0.9460 (m) REVERT: C 201 MET cc_start: 0.9132 (mmp) cc_final: 0.8874 (mmp) REVERT: C 414 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9227 (mm) outliers start: 32 outliers final: 12 residues processed: 140 average time/residue: 0.2391 time to fit residues: 49.3982 Evaluate side-chains 119 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 1.382 ------------------------------------------------------------------------------- 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 439 ILE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 423 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 383 MET Chi-restraints excluded: chain D residue 436 MET 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: 3.9990 chunk 19 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 60 optimal weight: 9.9990 chunk 87 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 424 HIS C 48 ASN ** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.072688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.050750 restraints weight = 69981.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.052608 restraints weight = 33396.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.053716 restraints weight = 21705.355| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13066 Z= 0.140 Angle : 0.533 8.921 17581 Z= 0.282 Chirality : 0.041 0.161 1933 Planarity : 0.003 0.028 2242 Dihedral : 5.636 76.383 1789 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.51 % Allowed : 15.83 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.28 (0.22), residues: 1538 helix: 2.22 (0.18), residues: 783 sheet: -1.09 (0.32), residues: 279 loop : -0.13 (0.31), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 360 HIS 0.006 0.001 HIS D 15 PHE 0.013 0.001 PHE C 435 TYR 0.018 0.001 TYR D 304 ARG 0.004 0.000 ARG B 152 Details of bonding type rmsd hydrogen bonds : bond 0.03848 ( 713) hydrogen bonds : angle 4.46713 ( 2007) covalent geometry : bond 0.00304 (13066) covalent geometry : angle 0.53298 (17581) *********************** 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 139 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 104 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: 0.8165 (OUTLIER) cc_final: 0.7723 (mmm160) REVERT: A 209 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8256 (tp30) REVERT: A 256 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8566 (mt-10) REVERT: A 338 MET cc_start: 0.8518 (ttm) cc_final: 0.7964 (ptm) REVERT: A 341 ASP cc_start: 0.8186 (t0) cc_final: 0.7662 (t0) REVERT: B 11 LEU cc_start: 0.9401 (mt) cc_final: 0.8760 (pp) REVERT: B 151 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8022 (p90) REVERT: B 338 MET cc_start: 0.8805 (ttt) cc_final: 0.8395 (ttt) REVERT: D 147 TYR cc_start: 0.9031 (t80) cc_final: 0.8748 (t80) REVERT: D 234 PHE cc_start: 0.9235 (t80) cc_final: 0.9010 (m-80) REVERT: D 383 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8692 (mmm) REVERT: D 436 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.6914 (mmm) REVERT: C 187 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8942 (mt) REVERT: C 201 MET cc_start: 0.9145 (mmp) cc_final: 0.8870 (mmm) REVERT: C 376 MET cc_start: 0.9653 (mtm) cc_final: 0.9039 (mtt) REVERT: C 414 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9244 (mm) REVERT: C 436 MET cc_start: 0.8948 (mpp) cc_final: 0.8451 (mpp) outliers start: 35 outliers final: 17 residues processed: 130 average time/residue: 0.2649 time to fit residues: 50.2395 Evaluate side-chains 122 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 1.575 ------------------------------------------------------------------------------- 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 256 GLU Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain D residue 8 LYS Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 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 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 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: 3.9990 chunk 65 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 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: 20.0000 chunk 135 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 94 ASN D 262 GLN D 413 GLN ** 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 = 0.3779 r_free = 0.3779 target = 0.069965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.047898 restraints weight = 72691.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.049566 restraints weight = 35342.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.050613 restraints weight = 23424.666| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.5540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 13066 Z= 0.319 Angle : 0.700 9.695 17581 Z= 0.373 Chirality : 0.044 0.163 1933 Planarity : 0.004 0.036 2242 Dihedral : 6.592 85.236 1789 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.80 % Allowed : 15.69 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.74 (0.22), residues: 1538 helix: 1.64 (0.18), residues: 778 sheet: -1.24 (0.32), residues: 253 loop : -0.24 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 360 HIS 0.006 0.001 HIS A 399 PHE 0.025 0.002 PHE A 230 TYR 0.017 0.002 TYR D 432 ARG 0.010 0.001 ARG B 152 Details of bonding type rmsd hydrogen bonds : bond 0.04641 ( 713) hydrogen bonds : angle 5.10300 ( 2007) covalent geometry : bond 0.00689 (13066) covalent geometry : angle 0.70015 (17581) *********************** 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 147 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 94 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7950 (mmm160) REVERT: A 209 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8310 (tp30) REVERT: A 256 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8608 (mt-10) REVERT: A 304 TYR cc_start: 0.9109 (t80) cc_final: 0.8875 (t80) REVERT: A 305 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8313 (tmm-80) REVERT: A 341 ASP cc_start: 0.8512 (t0) cc_final: 0.8088 (t0) REVERT: B 11 LEU cc_start: 0.9404 (mt) cc_final: 0.8634 (pp) REVERT: B 151 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.8102 (p90) REVERT: B 338 MET cc_start: 0.8680 (ttt) cc_final: 0.8404 (ttt) REVERT: D 234 PHE cc_start: 0.9289 (t80) cc_final: 0.9069 (m-80) REVERT: D 383 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8668 (mmm) REVERT: C 187 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9048 (mt) REVERT: C 376 MET cc_start: 0.9720 (mtm) cc_final: 0.8952 (mtt) REVERT: C 436 MET cc_start: 0.8954 (mpp) cc_final: 0.8593 (mpp) outliers start: 53 outliers final: 32 residues processed: 139 average time/residue: 0.2382 time to fit residues: 49.3454 Evaluate side-chains 123 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 85 time to evaluate : 1.485 ------------------------------------------------------------------------------- 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 65 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 305 ARG Chi-restraints excluded: chain A residue 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 423 THR Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain D residue 8 LYS Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 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 C residue 11 LEU Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 16 ASN 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 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: 0.6980 chunk 120 optimal weight: 3.9990 chunk 101 optimal weight: 20.0000 chunk 156 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 109 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 GLN ** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.072218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.050322 restraints weight = 71083.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.052182 restraints weight = 33575.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.053294 restraints weight = 21747.851| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13066 Z= 0.111 Angle : 0.551 11.066 17581 Z= 0.286 Chirality : 0.041 0.160 1933 Planarity : 0.003 0.030 2242 Dihedral : 5.889 73.698 1787 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.22 % Allowed : 17.05 % Favored : 80.73 % 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: 1.23 (0.22), residues: 1538 helix: 2.04 (0.18), residues: 785 sheet: -0.93 (0.32), residues: 279 loop : -0.02 (0.31), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 360 HIS 0.004 0.001 HIS C 44 PHE 0.013 0.001 PHE C 226 TYR 0.016 0.001 TYR A 378 ARG 0.006 0.000 ARG B 152 Details of bonding type rmsd hydrogen bonds : bond 0.03826 ( 713) hydrogen bonds : angle 4.51086 ( 2007) covalent geometry : bond 0.00232 (13066) covalent geometry : angle 0.55090 (17581) *********************** 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 128 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7694 (mmm160) REVERT: A 209 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8256 (tp30) REVERT: A 256 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8572 (mt-10) REVERT: A 338 MET cc_start: 0.8516 (ttm) cc_final: 0.8178 (ptm) REVERT: A 341 ASP cc_start: 0.8405 (t0) cc_final: 0.7917 (t0) REVERT: B 11 LEU cc_start: 0.9374 (mt) cc_final: 0.8804 (pp) REVERT: B 151 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8295 (p90) REVERT: B 230 PHE cc_start: 0.9159 (m-80) cc_final: 0.8880 (t80) REVERT: B 338 MET cc_start: 0.8695 (ttt) cc_final: 0.8457 (ttt) REVERT: D 383 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8671 (mmm) REVERT: D 436 MET cc_start: 0.8341 (tpt) cc_final: 0.6823 (mmm) REVERT: C 187 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8994 (mt) REVERT: C 201 MET cc_start: 0.9110 (mmp) cc_final: 0.8851 (mmp) REVERT: C 376 MET cc_start: 0.9726 (mtm) cc_final: 0.8938 (mtt) outliers start: 31 outliers final: 19 residues processed: 125 average time/residue: 0.2381 time to fit residues: 44.2087 Evaluate side-chains 112 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 138 ASN 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 151 PHE Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 74 optimal weight: 5.9990 chunk 116 optimal weight: 0.0980 chunk 23 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 69 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.071586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.049596 restraints weight = 70969.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.051427 restraints weight = 33959.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.052530 restraints weight = 22166.807| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.5509 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= 0.149 Angle : 0.566 12.415 17581 Z= 0.296 Chirality : 0.041 0.164 1933 Planarity : 0.003 0.029 2242 Dihedral : 6.018 77.474 1787 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.08 % Allowed : 16.83 % Favored : 80.09 % 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: 1.32 (0.22), residues: 1538 helix: 2.08 (0.18), residues: 783 sheet: -0.85 (0.32), residues: 284 loop : 0.08 (0.32), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 360 HIS 0.002 0.001 HIS A 399 PHE 0.014 0.001 PHE C 226 TYR 0.015 0.001 TYR D 304 ARG 0.006 0.000 ARG B 152 Details of bonding type rmsd hydrogen bonds : bond 0.03820 ( 713) hydrogen bonds : angle 4.50765 ( 2007) covalent geometry : bond 0.00323 (13066) covalent geometry : angle 0.56633 (17581) *********************** 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 130 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 87 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7845 (mmm160) REVERT: A 209 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8237 (tp30) REVERT: A 256 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8608 (mp0) REVERT: A 338 MET cc_start: 0.8482 (ttm) cc_final: 0.8173 (ptm) REVERT: A 341 ASP cc_start: 0.8255 (t0) cc_final: 0.7876 (t0) REVERT: B 11 LEU cc_start: 0.9371 (mt) cc_final: 0.8766 (pp) REVERT: B 151 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8080 (p90) REVERT: D 106 MET cc_start: 0.9125 (tpt) cc_final: 0.8526 (ttt) REVERT: D 190 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8639 (tp-100) REVERT: D 383 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8744 (mmm) REVERT: D 424 HIS cc_start: 0.5078 (OUTLIER) cc_final: 0.4522 (t-170) REVERT: D 436 MET cc_start: 0.8378 (tpt) cc_final: 0.6820 (mmm) REVERT: C 187 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9028 (mt) REVERT: C 201 MET cc_start: 0.9060 (mmp) cc_final: 0.8839 (mmp) REVERT: C 376 MET cc_start: 0.9719 (mtm) cc_final: 0.9176 (mtp) outliers start: 43 outliers final: 28 residues processed: 123 average time/residue: 0.2449 time to fit residues: 44.7830 Evaluate side-chains 118 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 83 time to evaluate : 1.492 ------------------------------------------------------------------------------- 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 104 GLU Chi-restraints excluded: chain A residue 138 ASN 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 326 MET Chi-restraints excluded: chain A residue 336 LYS 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 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 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 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: 3.9990 chunk 149 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 262 GLN ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.069501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.047569 restraints weight = 72374.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.049252 restraints weight = 35090.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.050278 restraints weight = 23153.205| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.6018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 13066 Z= 0.290 Angle : 0.682 11.015 17581 Z= 0.360 Chirality : 0.043 0.167 1933 Planarity : 0.004 0.037 2242 Dihedral : 6.450 82.484 1787 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.58 % Allowed : 17.48 % Favored : 78.94 % 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: 0.92 (0.22), residues: 1538 helix: 1.69 (0.18), residues: 771 sheet: -1.08 (0.33), residues: 255 loop : 0.01 (0.31), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 360 HIS 0.004 0.001 HIS A 399 PHE 0.016 0.002 PHE D 230 TYR 0.019 0.002 TYR C 432 ARG 0.005 0.001 ARG B 152 Details of bonding type rmsd hydrogen bonds : bond 0.04466 ( 713) hydrogen bonds : angle 4.98206 ( 2007) covalent geometry : bond 0.00627 (13066) covalent geometry : angle 0.68155 (17581) *********************** 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 136 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 86 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8057 (mmm160) REVERT: A 209 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8299 (tp30) REVERT: A 256 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8650 (mt-10) REVERT: A 305 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8208 (tmm-80) REVERT: A 341 ASP cc_start: 0.8661 (t0) cc_final: 0.8316 (t0) REVERT: B 11 LEU cc_start: 0.9404 (mt) cc_final: 0.8670 (pp) REVERT: B 151 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.8031 (p90) REVERT: D 190 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8796 (tp-100) REVERT: D 383 MET cc_start: 0.9200 (mpp) cc_final: 0.8735 (mmm) REVERT: D 424 HIS cc_start: 0.4840 (OUTLIER) cc_final: 0.3874 (t-170) REVERT: C 187 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9044 (mt) REVERT: C 376 MET cc_start: 0.9742 (mtm) cc_final: 0.9181 (mtp) outliers start: 50 outliers final: 35 residues processed: 129 average time/residue: 0.2600 time to fit residues: 49.0204 Evaluate side-chains 124 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 82 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 65 ILE 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 282 ARG Chi-restraints excluded: chain A residue 305 ARG Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 407 LEU 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 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 354 LYS Chi-restraints excluded: chain D residue 424 HIS Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 18 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 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: 6.9990 chunk 123 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 47 optimal weight: 0.0570 chunk 122 optimal weight: 4.9990 chunk 155 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 156 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 ASN ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.071464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.049539 restraints weight = 69999.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.051364 restraints weight = 33512.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.052456 restraints weight = 21917.474| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.5872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13066 Z= 0.123 Angle : 0.564 12.524 17581 Z= 0.295 Chirality : 0.042 0.168 1933 Planarity : 0.003 0.029 2242 Dihedral : 6.022 74.015 1787 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.94 % Allowed : 18.41 % Favored : 78.65 % 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: 1.38 (0.23), residues: 1538 helix: 2.08 (0.18), residues: 769 sheet: -0.85 (0.32), residues: 272 loop : 0.25 (0.32), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 360 HIS 0.004 0.001 HIS B 32 PHE 0.016 0.001 PHE D 183 TYR 0.025 0.001 TYR D 278 ARG 0.003 0.000 ARG B 152 Details of bonding type rmsd hydrogen bonds : bond 0.03870 ( 713) hydrogen bonds : angle 4.54300 ( 2007) covalent geometry : bond 0.00263 (13066) covalent geometry : angle 0.56377 (17581) *********************** 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 129 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 88 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7736 (mmm160) REVERT: A 209 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8206 (tp30) REVERT: A 256 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8700 (mp0) REVERT: A 341 ASP cc_start: 0.8414 (t0) cc_final: 0.7662 (t0) REVERT: B 11 LEU cc_start: 0.9381 (mt) cc_final: 0.8786 (pp) REVERT: B 151 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.7995 (p90) REVERT: B 230 PHE cc_start: 0.9176 (OUTLIER) cc_final: 0.8932 (t80) REVERT: D 190 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8673 (tp-100) REVERT: D 326 MET cc_start: 0.9405 (mtm) cc_final: 0.9015 (mpp) REVERT: D 383 MET cc_start: 0.9203 (OUTLIER) cc_final: 0.8759 (mmm) REVERT: D 424 HIS cc_start: 0.4748 (OUTLIER) cc_final: 0.3890 (t-170) REVERT: D 436 MET cc_start: 0.8426 (tpt) cc_final: 0.6943 (mmm) REVERT: C 11 LEU cc_start: 0.9678 (pt) cc_final: 0.9136 (tt) REVERT: C 187 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9039 (mt) REVERT: C 376 MET cc_start: 0.9749 (mtm) cc_final: 0.8941 (mtt) outliers start: 41 outliers final: 28 residues processed: 121 average time/residue: 0.2410 time to fit residues: 42.9191 Evaluate side-chains 117 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 81 time to evaluate : 1.443 ------------------------------------------------------------------------------- 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 256 GLU Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 336 LYS 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 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 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 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 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: 3.9990 chunk 22 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 113 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.070476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.048522 restraints weight = 71164.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.050288 restraints weight = 34195.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.051343 restraints weight = 22512.430| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.6036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13066 Z= 0.207 Angle : 0.616 12.146 17581 Z= 0.322 Chirality : 0.042 0.193 1933 Planarity : 0.003 0.030 2242 Dihedral : 6.188 80.456 1787 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.58 % Allowed : 18.98 % Favored : 78.44 % 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: 1.31 (0.22), residues: 1538 helix: 2.00 (0.18), residues: 769 sheet: -0.80 (0.32), residues: 267 loop : 0.18 (0.31), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 360 HIS 0.006 0.001 HIS B 32 PHE 0.022 0.002 PHE D 183 TYR 0.019 0.002 TYR D 278 ARG 0.007 0.000 ARG B 152 Details of bonding type rmsd hydrogen bonds : bond 0.04082 ( 713) hydrogen bonds : angle 4.69254 ( 2007) covalent geometry : bond 0.00450 (13066) covalent geometry : angle 0.61578 (17581) ********************** 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 120 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 84 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7939 (mmm160) REVERT: A 209 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8240 (tp30) REVERT: A 222 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8071 (tp30) REVERT: A 256 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8681 (mp0) REVERT: A 341 ASP cc_start: 0.8488 (t0) cc_final: 0.8112 (t0) REVERT: B 11 LEU cc_start: 0.9356 (mt) cc_final: 0.8718 (pp) REVERT: B 151 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.8052 (p90) REVERT: B 230 PHE cc_start: 0.9146 (OUTLIER) cc_final: 0.8878 (t80) REVERT: D 106 MET cc_start: 0.9074 (tpt) cc_final: 0.8478 (ttt) REVERT: D 190 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8724 (tp-100) REVERT: D 326 MET cc_start: 0.9359 (mtm) cc_final: 0.8967 (mpp) REVERT: D 383 MET cc_start: 0.9181 (mpp) cc_final: 0.8733 (mmm) REVERT: D 424 HIS cc_start: 0.4850 (OUTLIER) cc_final: 0.4271 (t-170) REVERT: D 436 MET cc_start: 0.8424 (tpt) cc_final: 0.6921 (mmm) REVERT: C 187 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9021 (mt) REVERT: C 376 MET cc_start: 0.9740 (mtm) cc_final: 0.9179 (mtp) outliers start: 36 outliers final: 27 residues processed: 112 average time/residue: 0.2429 time to fit residues: 40.7637 Evaluate side-chains 117 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 82 time to evaluate : 1.392 ------------------------------------------------------------------------------- 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 65 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 336 LYS 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 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 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 424 HIS 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 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 114 optimal weight: 0.0270 chunk 111 optimal weight: 0.0570 chunk 31 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 47 optimal weight: 0.0060 chunk 21 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 ASN ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.072829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.051058 restraints weight = 69456.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.052940 restraints weight = 33114.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.054081 restraints weight = 21423.583| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.5900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13066 Z= 0.106 Angle : 0.573 12.503 17581 Z= 0.295 Chirality : 0.042 0.186 1933 Planarity : 0.003 0.030 2242 Dihedral : 5.487 70.977 1787 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.15 % Allowed : 19.41 % Favored : 78.44 % 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: 1.66 (0.23), residues: 1538 helix: 2.29 (0.18), residues: 769 sheet: -0.46 (0.32), residues: 288 loop : 0.29 (0.32), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 360 HIS 0.003 0.000 HIS B 32 PHE 0.019 0.001 PHE D 183 TYR 0.018 0.001 TYR A 378 ARG 0.005 0.000 ARG B 152 Details of bonding type rmsd hydrogen bonds : bond 0.03673 ( 713) hydrogen bonds : angle 4.38000 ( 2007) covalent geometry : bond 0.00215 (13066) covalent geometry : angle 0.57347 (17581) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5100.60 seconds wall clock time: 88 minutes 57.74 seconds (5337.74 seconds total)