Starting phenix.real_space_refine on Fri Jul 3 02:51:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7pim_13442/07_2026/7pim_13442.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pim_13442/07_2026/7pim_13442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pim_13442/07_2026/7pim_13442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pim_13442/07_2026/7pim_13442.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pim_13442/07_2026/7pim_13442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pim_13442/07_2026/7pim_13442.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7pim_13442/07_2026/7pim_13442.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7pim_13442/07_2026/7pim_13442.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 S 36 5.16 5 C 7192 2.51 5 N 1932 2.21 5 O 2156 1.98 5 H 524 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11844 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2688 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 316} Chain: "G" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 261 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "A" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2688 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 316} Chain: "C" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 261 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "D" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2688 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 316} Chain: "E" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 261 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "F" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2688 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 316} Chain: "H" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 261 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' FE': 1, 'LDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' FE': 1, 'LDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' FE': 1, 'LDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' FE': 1, 'LDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.65, per 1000 atoms: 0.22 Number of scatterers: 11844 At special positions: 0 Unit cell: (103.984, 91.12, 121.136, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 36 16.00 O 2156 8.00 N 1932 7.00 C 7192 6.00 H 524 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 632.2 milliseconds 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2688 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 12 sheets defined 62.3% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'B' and resid 169 through 181 removed outlier: 3.558A pdb=" N THR B 181 " --> pdb=" O HIS B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 213 removed outlier: 3.583A pdb=" N ARG B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 243 Processing helix chain 'B' and resid 248 through 262 removed outlier: 3.593A pdb=" N GLU B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 284 Processing helix chain 'B' and resid 295 through 305 removed outlier: 3.680A pdb=" N PHE B 299 " --> pdb=" O SER B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 335 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 341 through 356 Processing helix chain 'B' and resid 359 through 374 removed outlier: 3.523A pdb=" N TYR B 370 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 395 Processing helix chain 'B' and resid 395 through 404 removed outlier: 3.911A pdb=" N LEU B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 420 Processing helix chain 'B' and resid 436 through 451 removed outlier: 3.525A pdb=" N ALA B 440 " --> pdb=" O SER B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 496 removed outlier: 3.540A pdb=" N GLY B 481 " --> pdb=" O ARG B 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 57 removed outlier: 3.939A pdb=" N ALA G 55 " --> pdb=" O ALA G 51 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 181 removed outlier: 3.558A pdb=" N THR A 181 " --> pdb=" O HIS A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 213 removed outlier: 3.583A pdb=" N ARG A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 243 Processing helix chain 'A' and resid 248 through 262 removed outlier: 3.592A pdb=" N GLU A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 284 Processing helix chain 'A' and resid 295 through 305 removed outlier: 3.681A pdb=" N PHE A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 335 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 341 through 356 Processing helix chain 'A' and resid 359 through 374 removed outlier: 3.523A pdb=" N TYR A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 395 Processing helix chain 'A' and resid 395 through 404 removed outlier: 3.912A pdb=" N LEU A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 420 Processing helix chain 'A' and resid 436 through 451 removed outlier: 3.525A pdb=" N ALA A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 496 removed outlier: 3.541A pdb=" N GLY A 481 " --> pdb=" O ARG A 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 57 removed outlier: 3.938A pdb=" N ALA C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 181 removed outlier: 3.558A pdb=" N THR D 181 " --> pdb=" O HIS D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 213 removed outlier: 3.584A pdb=" N ARG D 200 " --> pdb=" O ASP D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 243 Processing helix chain 'D' and resid 248 through 262 removed outlier: 3.592A pdb=" N GLU D 253 " --> pdb=" O GLY D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 284 Processing helix chain 'D' and resid 295 through 305 removed outlier: 3.680A pdb=" N PHE D 299 " --> pdb=" O SER D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 335 Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 341 through 356 Processing helix chain 'D' and resid 359 through 374 removed outlier: 3.523A pdb=" N TYR D 370 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 395 Processing helix chain 'D' and resid 395 through 404 removed outlier: 3.912A pdb=" N LEU D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 420 Processing helix chain 'D' and resid 436 through 451 removed outlier: 3.526A pdb=" N ALA D 440 " --> pdb=" O SER D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 496 removed outlier: 3.541A pdb=" N GLY D 481 " --> pdb=" O ARG D 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 57 removed outlier: 3.938A pdb=" N ALA E 55 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA E 56 " --> pdb=" O ALA E 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 181 removed outlier: 3.558A pdb=" N THR F 181 " --> pdb=" O HIS F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 213 removed outlier: 3.583A pdb=" N ARG F 200 " --> pdb=" O ASP F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 243 Processing helix chain 'F' and resid 248 through 262 removed outlier: 3.593A pdb=" N GLU F 253 " --> pdb=" O GLY F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 284 Processing helix chain 'F' and resid 295 through 305 removed outlier: 3.681A pdb=" N PHE F 299 " --> pdb=" O SER F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 335 Processing helix chain 'F' and resid 335 through 340 Processing helix chain 'F' and resid 341 through 356 Processing helix chain 'F' and resid 359 through 374 removed outlier: 3.524A pdb=" N TYR F 370 " --> pdb=" O LEU F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 395 Processing helix chain 'F' and resid 395 through 404 removed outlier: 3.912A pdb=" N LEU F 403 " --> pdb=" O LEU F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 420 Processing helix chain 'F' and resid 436 through 451 removed outlier: 3.525A pdb=" N ALA F 440 " --> pdb=" O SER F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 471 through 496 removed outlier: 3.541A pdb=" N GLY F 481 " --> pdb=" O ARG F 477 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 57 removed outlier: 3.938A pdb=" N ALA H 55 " --> pdb=" O ALA H 51 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 286 through 289 removed outlier: 6.500A pdb=" N GLN B 286 " --> pdb=" O PHE B 308 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N CYS B 310 " --> pdb=" O GLN B 286 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ARG B 288 " --> pdb=" O CYS B 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 384 through 387 removed outlier: 6.231A pdb=" N LEU B 378 " --> pdb=" O SER B 434 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 456 through 460 Processing sheet with id=AA4, first strand: chain 'A' and resid 286 through 289 removed outlier: 6.500A pdb=" N GLN A 286 " --> pdb=" O PHE A 308 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N CYS A 310 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ARG A 288 " --> pdb=" O CYS A 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 384 through 387 removed outlier: 6.232A pdb=" N LEU A 378 " --> pdb=" O SER A 434 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 456 through 460 Processing sheet with id=AA7, first strand: chain 'D' and resid 286 through 289 removed outlier: 6.500A pdb=" N GLN D 286 " --> pdb=" O PHE D 308 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N CYS D 310 " --> pdb=" O GLN D 286 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ARG D 288 " --> pdb=" O CYS D 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 384 through 387 removed outlier: 6.232A pdb=" N LEU D 378 " --> pdb=" O SER D 434 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 456 through 460 Processing sheet with id=AB1, first strand: chain 'F' and resid 286 through 289 removed outlier: 6.500A pdb=" N GLN F 286 " --> pdb=" O PHE F 308 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N CYS F 310 " --> pdb=" O GLN F 286 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ARG F 288 " --> pdb=" O CYS F 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'F' and resid 384 through 387 removed outlier: 6.231A pdb=" N LEU F 378 " --> pdb=" O SER F 434 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 456 through 460 636 hydrogen bonds defined for protein. 1872 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: 1.96 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 524 1.03 - 1.23: 0 1.23 - 1.42: 5068 1.42 - 1.62: 6480 1.62 - 1.81: 44 Bond restraints: 12116 Sorted by residual: bond pdb=" C3 LDP D 501 " pdb=" O1 LDP D 501 " ideal model delta sigma weight residual 1.353 1.401 -0.048 2.00e-02 2.50e+03 5.84e+00 bond pdb=" C3 LDP B 501 " pdb=" O1 LDP B 501 " ideal model delta sigma weight residual 1.353 1.401 -0.048 2.00e-02 2.50e+03 5.75e+00 bond pdb=" C3 LDP A 501 " pdb=" O1 LDP A 501 " ideal model delta sigma weight residual 1.353 1.400 -0.047 2.00e-02 2.50e+03 5.63e+00 bond pdb=" C3 LDP F 501 " pdb=" O1 LDP F 501 " ideal model delta sigma weight residual 1.353 1.400 -0.047 2.00e-02 2.50e+03 5.58e+00 bond pdb=" C4 LDP A 501 " pdb=" O2 LDP A 501 " ideal model delta sigma weight residual 1.355 1.402 -0.047 2.00e-02 2.50e+03 5.43e+00 ... (remaining 12111 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.95: 16856 5.95 - 11.89: 0 11.89 - 17.84: 0 17.84 - 23.79: 16 23.79 - 29.73: 32 Bond angle restraints: 16904 Sorted by residual: angle pdb=" CA ALA C 52 " pdb=" CB ALA C 52 " pdb=" HB3 ALA C 52 " ideal model delta sigma weight residual 109.00 79.27 29.73 3.00e+00 1.11e-01 9.82e+01 angle pdb=" CA ALA H 52 " pdb=" CB ALA H 52 " pdb=" HB3 ALA H 52 " ideal model delta sigma weight residual 109.00 79.31 29.69 3.00e+00 1.11e-01 9.79e+01 angle pdb=" CA ALA G 52 " pdb=" CB ALA G 52 " pdb=" HB3 ALA G 52 " ideal model delta sigma weight residual 109.00 79.33 29.67 3.00e+00 1.11e-01 9.78e+01 angle pdb=" CA ALA E 52 " pdb=" CB ALA E 52 " pdb=" HB3 ALA E 52 " ideal model delta sigma weight residual 109.00 79.37 29.63 3.00e+00 1.11e-01 9.75e+01 angle pdb=" CA ALA G 52 " pdb=" CB ALA G 52 " pdb=" HB1 ALA G 52 " ideal model delta sigma weight residual 109.00 79.60 29.40 3.00e+00 1.11e-01 9.60e+01 ... (remaining 16899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.80: 6728 13.80 - 27.61: 272 27.61 - 41.41: 52 41.41 - 55.22: 16 55.22 - 69.02: 8 Dihedral angle restraints: 7076 sinusoidal: 2924 harmonic: 4152 Sorted by residual: dihedral pdb=" CA ILE G 42 " pdb=" CB ILE G 42 " pdb=" CG1 ILE G 42 " pdb=" CD1 ILE G 42 " ideal model delta sinusoidal sigma weight residual 60.00 113.79 -53.79 3 1.50e+01 4.44e-03 9.23e+00 dihedral pdb=" CA ILE C 42 " pdb=" CB ILE C 42 " pdb=" CG1 ILE C 42 " pdb=" CD1 ILE C 42 " ideal model delta sinusoidal sigma weight residual 60.00 113.75 -53.75 3 1.50e+01 4.44e-03 9.23e+00 dihedral pdb=" CA ILE H 42 " pdb=" CB ILE H 42 " pdb=" CG1 ILE H 42 " pdb=" CD1 ILE H 42 " ideal model delta sinusoidal sigma weight residual 60.00 113.75 -53.75 3 1.50e+01 4.44e-03 9.23e+00 ... (remaining 7073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 1096 0.022 - 0.045: 341 0.045 - 0.067: 143 0.067 - 0.089: 52 0.089 - 0.112: 52 Chirality restraints: 1684 Sorted by residual: chirality pdb=" CA ILE B 409 " pdb=" N ILE B 409 " pdb=" C ILE B 409 " pdb=" CB ILE B 409 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.12e-01 chirality pdb=" CA ILE D 409 " pdb=" N ILE D 409 " pdb=" C ILE D 409 " pdb=" CB ILE D 409 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 3.11e-01 chirality pdb=" CA ILE A 466 " pdb=" N ILE A 466 " pdb=" C ILE A 466 " pdb=" CB ILE A 466 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 3.05e-01 ... (remaining 1681 not shown) Planarity restraints: 2136 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE F 166 " -0.015 5.00e-02 4.00e+02 2.31e-02 8.56e-01 pdb=" N PRO F 167 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO F 167 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO F 167 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 166 " 0.015 5.00e-02 4.00e+02 2.30e-02 8.46e-01 pdb=" N PRO B 167 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO B 167 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 167 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 166 " 0.015 5.00e-02 4.00e+02 2.29e-02 8.42e-01 pdb=" N PRO A 167 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO A 167 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 167 " 0.013 5.00e-02 4.00e+02 ... (remaining 2133 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.25: 196 2.25 - 2.84: 6144 2.84 - 3.43: 17764 3.43 - 4.01: 24627 4.01 - 4.60: 35671 Nonbonded interactions: 84402 Sorted by model distance: nonbonded pdb="HG13 ILE E 42 " pdb="HD12 ILE E 42 " model vdw 1.666 1.952 nonbonded pdb="HG13 ILE H 42 " pdb="HD12 ILE H 42 " model vdw 1.667 1.952 nonbonded pdb="HG13 ILE C 42 " pdb="HD12 ILE C 42 " model vdw 1.667 1.952 nonbonded pdb="HG13 ILE G 42 " pdb="HD12 ILE G 42 " model vdw 1.668 1.952 nonbonded pdb="HG12 ILE E 42 " pdb="HD11 ILE E 42 " model vdw 1.676 1.952 ... (remaining 84397 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: 0.02 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'C' selection = chain 'E' selection = chain 'H' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'D' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'G' selection = chain 'C' selection = chain 'E' selection = chain 'H' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.95 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: 0.400 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: 0.080 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.330 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 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 : 0.002 0.048 11592 Z= 0.101 Angle : 0.406 3.557 15712 Z= 0.230 Chirality : 0.032 0.112 1684 Planarity : 0.002 0.023 2068 Dihedral : 8.305 69.020 4252 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 45.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.67 % Allowed : 6.02 % Favored : 93.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.24), residues: 1396 helix: 2.56 (0.20), residues: 760 sheet: -0.61 (0.47), residues: 136 loop : 0.49 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 453 TYR 0.004 0.001 TYR A 313 PHE 0.003 0.000 PHE A 285 TRP 0.004 0.000 TRP F 371 HIS 0.001 0.000 HIS F 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.10 (11592) covalent geometry : angle 0.40593 / 0.23 (15712) hydrogen bonds : bond 0.22780 / 15.11 ( 636) hydrogen bonds : angle 7.95411 / 5.85 ( 1872) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.105 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: B 197 GLN cc_start: 0.9472 (tp40) cc_final: 0.9260 (tp-100) REVERT: B 198 VAL cc_start: 0.9426 (m) cc_final: 0.9199 (p) REVERT: B 233 LYS cc_start: 0.9508 (ttpp) cc_final: 0.9226 (ttpp) REVERT: B 251 HIS cc_start: 0.9069 (t-90) cc_final: 0.8855 (t70) REVERT: B 264 TYR cc_start: 0.7754 (m-10) cc_final: 0.7297 (m-10) REVERT: B 266 GLU cc_start: 0.9245 (pm20) cc_final: 0.8981 (pm20) REVERT: B 268 ASN cc_start: 0.8900 (t0) cc_final: 0.8596 (p0) REVERT: B 308 PHE cc_start: 0.8456 (t80) cc_final: 0.7860 (t80) REVERT: B 339 LEU cc_start: 0.9189 (mm) cc_final: 0.8922 (mm) REVERT: B 344 PHE cc_start: 0.9382 (t80) cc_final: 0.8734 (t80) REVERT: B 362 GLU cc_start: 0.9397 (mp0) cc_final: 0.9159 (mp0) REVERT: B 441 LYS cc_start: 0.9204 (ttmm) cc_final: 0.8763 (mtpt) REVERT: B 491 HIS cc_start: 0.9172 (m170) cc_final: 0.8507 (t-170) outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.0690 time to fit residues: 8.7007 Evaluate side-chains 82 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.100 Evaluate side-chains 7 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 6 time to evaluate : 0.008 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 6 average time/residue: 0.3376 time to fit residues: 2.0462 Evaluate side-chains 1 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 0.0770 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.0870 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.0060 overall best weight: 0.2332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.094955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.072323 restraints weight = 10362.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.074835 restraints weight = 7192.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.076653 restraints weight = 5471.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.078015 restraints weight = 4451.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.079000 restraints weight = 3795.060| |-----------------------------------------------------------------------------| r_work (final): 0.3431 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.180831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.160430 restraints weight = 609.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.164180 restraints weight = 287.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.166918 restraints weight = 165.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.169218 restraints weight = 112.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.170571 restraints weight = 84.720| |-----------------------------------------------------------------------------| r_work (final): 0.4850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11592 Z= 0.133 Angle : 0.525 6.210 15712 Z= 0.277 Chirality : 0.039 0.183 1684 Planarity : 0.004 0.032 2068 Dihedral : 4.036 43.216 1568 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 52.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.22), residues: 1396 helix: 1.01 (0.18), residues: 812 sheet: -0.49 (0.46), residues: 136 loop : 0.72 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 49 TYR 0.021 0.001 TYR D 422 PHE 0.023 0.001 PHE A 255 TRP 0.002 0.000 TRP B 232 HIS 0.003 0.001 HIS F 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (11592) covalent geometry : angle 0.52530 / 0.28 (15712) hydrogen bonds : bond 0.04795 / 3.21 ( 636) hydrogen bonds : angle 6.39361 / 4.63 ( 1872) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 233 LYS cc_start: 0.9596 (ttpp) cc_final: 0.9244 (ttpp) REVERT: F 251 HIS cc_start: 0.9108 (t-90) cc_final: 0.8812 (t70) REVERT: F 264 TYR cc_start: 0.7427 (m-10) cc_final: 0.7225 (m-10) REVERT: F 266 GLU cc_start: 0.9069 (pm20) cc_final: 0.8768 (pm20) REVERT: F 268 ASN cc_start: 0.8519 (t0) cc_final: 0.8280 (p0) REVERT: F 286 GLN cc_start: 0.8705 (pm20) cc_final: 0.7679 (pm20) REVERT: F 308 PHE cc_start: 0.8557 (t80) cc_final: 0.7813 (t80) REVERT: F 321 MET cc_start: 0.7925 (tpt) cc_final: 0.7678 (tpt) REVERT: F 339 LEU cc_start: 0.9276 (mm) cc_final: 0.8989 (mm) REVERT: F 344 PHE cc_start: 0.9452 (t80) cc_final: 0.8758 (t80) REVERT: F 346 GLN cc_start: 0.8378 (tm-30) cc_final: 0.8025 (tm-30) REVERT: F 350 ASP cc_start: 0.7929 (m-30) cc_final: 0.7295 (m-30) REVERT: F 362 GLU cc_start: 0.9352 (mp0) cc_final: 0.9125 (mp0) REVERT: F 369 LEU cc_start: 0.9674 (tp) cc_final: 0.9468 (mt) REVERT: F 396 TYR cc_start: 0.9175 (t80) cc_final: 0.8941 (t80) REVERT: F 466 ILE cc_start: 0.8687 (mm) cc_final: 0.8392 (mm) REVERT: F 473 GLN cc_start: 0.9318 (mp10) cc_final: 0.9071 (mp10) REVERT: F 491 HIS cc_start: 0.9219 (m170) cc_final: 0.8468 (t-170) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0675 time to fit residues: 6.7953 Evaluate side-chains 72 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.096 Evaluate side-chains 3 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.3690 time to fit residues: 1.1225 Evaluate side-chains 2 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 127 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 90 optimal weight: 0.0170 chunk 22 optimal weight: 0.0060 chunk 110 optimal weight: 30.0000 chunk 29 optimal weight: 0.7980 chunk 6 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 3 optimal weight: 30.0000 chunk 69 optimal weight: 4.9990 chunk 53 optimal weight: 0.0370 overall best weight: 1.1714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.092943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.069198 restraints weight = 10700.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.071597 restraints weight = 7579.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.073357 restraints weight = 5851.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.074713 restraints weight = 4805.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.075510 restraints weight = 4126.426| |-----------------------------------------------------------------------------| r_work (final): 0.3377 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.207267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.182053 restraints weight = 575.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.188512 restraints weight = 254.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.194296 restraints weight = 129.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.199144 restraints weight = 71.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.201900 restraints weight = 39.411| |-----------------------------------------------------------------------------| r_work (final): 0.4943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11592 Z= 0.124 Angle : 0.465 5.346 15712 Z= 0.246 Chirality : 0.036 0.148 1684 Planarity : 0.005 0.064 2068 Dihedral : 3.903 35.161 1568 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 54.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.22), residues: 1396 helix: 1.04 (0.18), residues: 796 sheet: -0.51 (0.47), residues: 136 loop : 0.62 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 476 TYR 0.013 0.001 TYR F 422 PHE 0.015 0.001 PHE F 255 TRP 0.004 0.001 TRP F 165 HIS 0.003 0.001 HIS F 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (11592) covalent geometry : angle 0.46533 / 0.25 (15712) hydrogen bonds : bond 0.03877 / 2.61 ( 636) hydrogen bonds : angle 6.11930 / 4.45 ( 1872) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.102 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: B 197 GLN cc_start: 0.9709 (tp-100) cc_final: 0.9495 (tp-100) REVERT: B 233 LYS cc_start: 0.9617 (ttpp) cc_final: 0.9254 (ttpp) REVERT: B 251 HIS cc_start: 0.9189 (t-90) cc_final: 0.8973 (t70) REVERT: B 258 LEU cc_start: 0.9364 (mt) cc_final: 0.9140 (mm) REVERT: B 266 GLU cc_start: 0.9208 (pm20) cc_final: 0.8849 (pm20) REVERT: B 268 ASN cc_start: 0.8707 (t0) cc_final: 0.8310 (p0) REVERT: B 280 LYS cc_start: 0.9100 (mmmm) cc_final: 0.8726 (mmmt) REVERT: B 308 PHE cc_start: 0.8559 (t80) cc_final: 0.7826 (t80) REVERT: B 321 MET cc_start: 0.8036 (tpt) cc_final: 0.7824 (tpt) REVERT: B 339 LEU cc_start: 0.9255 (mm) cc_final: 0.8951 (mm) REVERT: B 344 PHE cc_start: 0.9419 (t80) cc_final: 0.8729 (t80) REVERT: B 350 ASP cc_start: 0.8043 (m-30) cc_final: 0.7762 (m-30) REVERT: B 362 GLU cc_start: 0.9352 (mp0) cc_final: 0.9136 (mp0) REVERT: B 410 ARG cc_start: 0.8739 (ptp-170) cc_final: 0.7867 (ptp-170) REVERT: B 466 ILE cc_start: 0.8795 (mm) cc_final: 0.8473 (mm) REVERT: B 491 HIS cc_start: 0.9217 (m170) cc_final: 0.8342 (t-170) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0748 time to fit residues: 7.1742 Evaluate side-chains 67 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.127 Evaluate side-chains 2 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.009 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.6522 time to fit residues: 1.3228 Evaluate side-chains 2 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 124 optimal weight: 0.4980 chunk 126 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 31 optimal weight: 0.0970 chunk 129 optimal weight: 5.9990 overall best weight: 4.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.086232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.064620 restraints weight = 11149.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.066698 restraints weight = 7901.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.068231 restraints weight = 6151.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.069328 restraints weight = 5086.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.070261 restraints weight = 4422.906| |-----------------------------------------------------------------------------| r_work (final): 0.3251 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.210070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.180893 restraints weight = 585.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.191042 restraints weight = 244.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.197349 restraints weight = 127.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.202166 restraints weight = 76.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.205560 restraints weight = 49.829| |-----------------------------------------------------------------------------| r_work (final): 0.4939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11592 Z= 0.186 Angle : 0.538 5.910 15712 Z= 0.285 Chirality : 0.035 0.122 1684 Planarity : 0.004 0.031 2068 Dihedral : 4.017 26.301 1568 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 68.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.22), residues: 1396 helix: 0.71 (0.18), residues: 800 sheet: -0.89 (0.44), residues: 136 loop : 0.57 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 445 TYR 0.012 0.002 TYR B 264 PHE 0.016 0.002 PHE A 412 TRP 0.009 0.001 TRP F 165 HIS 0.004 0.001 HIS D 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.19 (11592) covalent geometry : angle 0.53824 / 0.29 (15712) hydrogen bonds : bond 0.03748 / 2.52 ( 636) hydrogen bonds : angle 6.16078 / 4.47 ( 1872) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.064 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: B 251 HIS cc_start: 0.9263 (t-90) cc_final: 0.8428 (t70) REVERT: B 255 PHE cc_start: 0.8803 (p90) cc_final: 0.8435 (p90) REVERT: B 266 GLU cc_start: 0.9208 (pm20) cc_final: 0.8612 (pm20) REVERT: B 308 PHE cc_start: 0.8633 (t80) cc_final: 0.8043 (t80) REVERT: B 338 MET cc_start: 0.8881 (mmp) cc_final: 0.8556 (mmp) REVERT: B 344 PHE cc_start: 0.9290 (t80) cc_final: 0.8634 (t80) REVERT: B 350 ASP cc_start: 0.8052 (m-30) cc_final: 0.7763 (m-30) REVERT: B 362 GLU cc_start: 0.9363 (mp0) cc_final: 0.8997 (mp0) REVERT: B 445 ARG cc_start: 0.8477 (ttt180) cc_final: 0.7722 (ttm110) REVERT: B 457 VAL cc_start: 0.9329 (m) cc_final: 0.9112 (m) REVERT: B 479 LEU cc_start: 0.9495 (mt) cc_final: 0.9275 (mt) REVERT: B 491 HIS cc_start: 0.9321 (m170) cc_final: 0.8386 (t-170) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.0722 time to fit residues: 7.1987 Evaluate side-chains 69 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.104 Evaluate side-chains 2 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.008 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.4691 time to fit residues: 0.9524 Evaluate side-chains 2 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 85 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 107 optimal weight: 0.0670 chunk 93 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 overall best weight: 1.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.088451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.065979 restraints weight = 10402.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.068190 restraints weight = 7304.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.069790 restraints weight = 5637.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.071010 restraints weight = 4627.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.071965 restraints weight = 3972.101| |-----------------------------------------------------------------------------| r_work (final): 0.3309 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.211380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.174998 restraints weight = 667.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.185249 restraints weight = 310.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.192357 restraints weight = 170.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.197208 restraints weight = 110.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.198750 restraints weight = 83.549| |-----------------------------------------------------------------------------| r_work (final): 0.4894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11592 Z= 0.122 Angle : 0.468 4.377 15712 Z= 0.252 Chirality : 0.036 0.130 1684 Planarity : 0.004 0.055 2068 Dihedral : 3.906 20.765 1568 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 64.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.22), residues: 1396 helix: 0.90 (0.18), residues: 820 sheet: -0.74 (0.45), residues: 136 loop : 0.64 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 445 TYR 0.006 0.001 TYR F 422 PHE 0.015 0.001 PHE F 255 TRP 0.004 0.001 TRP B 232 HIS 0.003 0.001 HIS B 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (11592) covalent geometry : angle 0.46760 / 0.25 (15712) hydrogen bonds : bond 0.03384 / 2.30 ( 636) hydrogen bonds : angle 6.05779 / 4.40 ( 1872) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.103 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: B 251 HIS cc_start: 0.9171 (t-90) cc_final: 0.8393 (t70) REVERT: B 255 PHE cc_start: 0.8781 (p90) cc_final: 0.8454 (p90) REVERT: B 308 PHE cc_start: 0.8616 (t80) cc_final: 0.8053 (t80) REVERT: B 338 MET cc_start: 0.8855 (mmp) cc_final: 0.8532 (mmp) REVERT: B 339 LEU cc_start: 0.9287 (mm) cc_final: 0.9027 (mm) REVERT: B 341 ASP cc_start: 0.9128 (t0) cc_final: 0.8885 (t0) REVERT: B 344 PHE cc_start: 0.9291 (t80) cc_final: 0.8585 (t80) REVERT: B 439 ASP cc_start: 0.8401 (t70) cc_final: 0.8194 (t0) REVERT: B 445 ARG cc_start: 0.8114 (ttt180) cc_final: 0.7236 (ttm110) REVERT: B 455 PHE cc_start: 0.8405 (p90) cc_final: 0.8128 (p90) REVERT: B 457 VAL cc_start: 0.9227 (m) cc_final: 0.8986 (m) REVERT: B 479 LEU cc_start: 0.9519 (mt) cc_final: 0.9303 (mt) REVERT: B 491 HIS cc_start: 0.9356 (m170) cc_final: 0.8401 (t-170) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0750 time to fit residues: 7.1627 Evaluate side-chains 63 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.104 Evaluate side-chains 2 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.008 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.5065 time to fit residues: 1.0288 Evaluate side-chains 2 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 75 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 76 optimal weight: 20.0000 chunk 56 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 48 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.087331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.064941 restraints weight = 10662.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.067115 restraints weight = 7571.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.068692 restraints weight = 5899.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.069868 restraints weight = 4894.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.070767 restraints weight = 4239.858| |-----------------------------------------------------------------------------| r_work (final): 0.3295 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.212493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.175417 restraints weight = 659.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.184870 restraints weight = 301.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.191643 restraints weight = 171.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.196451 restraints weight = 114.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.198429 restraints weight = 84.047| |-----------------------------------------------------------------------------| r_work (final): 0.4906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11592 Z= 0.128 Angle : 0.469 4.744 15712 Z= 0.249 Chirality : 0.036 0.130 1684 Planarity : 0.003 0.046 2068 Dihedral : 3.853 21.607 1568 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 67.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.22), residues: 1396 helix: 0.98 (0.18), residues: 820 sheet: -0.75 (0.44), residues: 136 loop : 0.64 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 445 TYR 0.006 0.001 TYR F 243 PHE 0.012 0.001 PHE D 255 TRP 0.004 0.001 TRP A 165 HIS 0.003 0.001 HIS B 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (11592) covalent geometry : angle 0.46919 / 0.25 (15712) hydrogen bonds : bond 0.03221 / 2.18 ( 636) hydrogen bonds : angle 5.84205 / 4.24 ( 1872) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.092 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: B 251 HIS cc_start: 0.9194 (t-90) cc_final: 0.8515 (t70) REVERT: B 255 PHE cc_start: 0.8795 (p90) cc_final: 0.8425 (p90) REVERT: B 308 PHE cc_start: 0.8638 (t80) cc_final: 0.8099 (t80) REVERT: B 338 MET cc_start: 0.8840 (mmp) cc_final: 0.8496 (mmp) REVERT: B 341 ASP cc_start: 0.9110 (t0) cc_final: 0.8894 (t0) REVERT: B 344 PHE cc_start: 0.9352 (t80) cc_final: 0.8682 (t80) REVERT: B 356 LEU cc_start: 0.9591 (tt) cc_final: 0.9344 (tt) REVERT: B 362 GLU cc_start: 0.9188 (mp0) cc_final: 0.8864 (mp0) REVERT: B 455 PHE cc_start: 0.8462 (p90) cc_final: 0.8147 (p90) REVERT: B 457 VAL cc_start: 0.9298 (m) cc_final: 0.8925 (m) REVERT: B 479 LEU cc_start: 0.9524 (mt) cc_final: 0.9294 (mt) REVERT: B 491 HIS cc_start: 0.9428 (m170) cc_final: 0.8588 (t-170) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0746 time to fit residues: 6.7936 Evaluate side-chains 64 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.082 Evaluate side-chains 2 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.005 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.4437 time to fit residues: 0.8965 Evaluate side-chains 2 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 126 optimal weight: 0.4980 chunk 129 optimal weight: 0.2980 chunk 86 optimal weight: 9.9990 chunk 118 optimal weight: 0.7980 chunk 95 optimal weight: 0.0870 chunk 81 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 0.0070 chunk 53 optimal weight: 0.0060 chunk 84 optimal weight: 0.9990 overall best weight: 0.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.090034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.067328 restraints weight = 10775.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.069589 restraints weight = 7670.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.071271 restraints weight = 5954.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.072565 restraints weight = 4902.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.073527 restraints weight = 4212.808| |-----------------------------------------------------------------------------| r_work (final): 0.3324 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.210918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.175675 restraints weight = 668.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.185239 restraints weight = 308.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.191443 restraints weight = 172.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.195710 restraints weight = 116.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.197638 restraints weight = 86.631| |-----------------------------------------------------------------------------| r_work (final): 0.4928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.5531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11592 Z= 0.115 Angle : 0.475 7.669 15712 Z= 0.253 Chirality : 0.036 0.123 1684 Planarity : 0.004 0.051 2068 Dihedral : 3.785 23.513 1568 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 59.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.22), residues: 1396 helix: 1.05 (0.18), residues: 820 sheet: -0.58 (0.46), residues: 136 loop : 0.70 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG F 476 TYR 0.004 0.001 TYR A 313 PHE 0.013 0.001 PHE A 255 TRP 0.004 0.001 TRP B 371 HIS 0.003 0.001 HIS A 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (11592) covalent geometry : angle 0.47457 / 0.25 (15712) hydrogen bonds : bond 0.03212 / 2.23 ( 636) hydrogen bonds : angle 5.77328 / 4.18 ( 1872) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.103 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: B 251 HIS cc_start: 0.9088 (t-90) cc_final: 0.8402 (t70) REVERT: B 255 PHE cc_start: 0.8711 (p90) cc_final: 0.8384 (p90) REVERT: B 264 TYR cc_start: 0.7595 (m-80) cc_final: 0.6748 (m-80) REVERT: B 308 PHE cc_start: 0.8552 (t80) cc_final: 0.8007 (t80) REVERT: B 338 MET cc_start: 0.8666 (mmp) cc_final: 0.8428 (mmp) REVERT: B 339 LEU cc_start: 0.9308 (mm) cc_final: 0.9005 (mm) REVERT: B 344 PHE cc_start: 0.9316 (t80) cc_final: 0.8640 (t80) REVERT: B 362 GLU cc_start: 0.9204 (mp0) cc_final: 0.8817 (mp0) REVERT: B 441 LYS cc_start: 0.9406 (tmtt) cc_final: 0.8699 (ttmt) REVERT: B 445 ARG cc_start: 0.8211 (ttt180) cc_final: 0.7962 (ptm160) REVERT: B 455 PHE cc_start: 0.8331 (p90) cc_final: 0.7993 (p90) REVERT: B 457 VAL cc_start: 0.9201 (m) cc_final: 0.8796 (m) REVERT: B 466 ILE cc_start: 0.8716 (mm) cc_final: 0.8403 (mm) REVERT: B 491 HIS cc_start: 0.9064 (m170) cc_final: 0.7955 (t-170) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.0708 time to fit residues: 6.8264 Evaluate side-chains 68 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.107 Evaluate side-chains 2 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.019 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.5158 time to fit residues: 1.0471 Evaluate side-chains 2 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 128 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 121 optimal weight: 0.1980 chunk 91 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.086518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.065410 restraints weight = 11217.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.067600 restraints weight = 7935.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.069241 restraints weight = 6101.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.070550 restraints weight = 4995.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.071547 restraints weight = 4259.746| |-----------------------------------------------------------------------------| r_work (final): 0.3287 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.219420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.192019 restraints weight = 654.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.200455 restraints weight = 279.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.204369 restraints weight = 168.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.211606 restraints weight = 132.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.214342 restraints weight = 70.830| |-----------------------------------------------------------------------------| r_work (final): 0.4908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.5776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11592 Z= 0.154 Angle : 0.504 4.775 15712 Z= 0.272 Chirality : 0.036 0.124 1684 Planarity : 0.004 0.064 2068 Dihedral : 3.984 23.412 1568 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 70.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.22), residues: 1396 helix: 0.85 (0.18), residues: 832 sheet: -0.86 (0.44), residues: 136 loop : 0.76 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 476 TYR 0.009 0.001 TYR A 213 PHE 0.012 0.002 PHE B 412 TRP 0.009 0.001 TRP B 165 HIS 0.003 0.001 HIS B 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (11592) covalent geometry : angle 0.50434 / 0.27 (15712) hydrogen bonds : bond 0.03286 / 2.24 ( 636) hydrogen bonds : angle 5.90475 / 4.27 ( 1872) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 251 HIS cc_start: 0.9188 (t-90) cc_final: 0.8484 (t70) REVERT: B 255 PHE cc_start: 0.8752 (p90) cc_final: 0.8426 (p90) REVERT: B 264 TYR cc_start: 0.7172 (m-80) cc_final: 0.6793 (m-80) REVERT: B 265 ARG cc_start: 0.8595 (mpp-170) cc_final: 0.8284 (mmt180) REVERT: B 266 GLU cc_start: 0.9206 (pm20) cc_final: 0.8806 (pm20) REVERT: B 308 PHE cc_start: 0.8667 (t80) cc_final: 0.8145 (t80) REVERT: B 338 MET cc_start: 0.8823 (mmp) cc_final: 0.8452 (mmp) REVERT: B 341 ASP cc_start: 0.9045 (t0) cc_final: 0.8827 (t0) REVERT: B 344 PHE cc_start: 0.9277 (t80) cc_final: 0.8599 (t80) REVERT: B 362 GLU cc_start: 0.9191 (mp0) cc_final: 0.8906 (mp0) REVERT: B 455 PHE cc_start: 0.8477 (p90) cc_final: 0.8088 (p90) REVERT: B 457 VAL cc_start: 0.9318 (m) cc_final: 0.8927 (m) REVERT: B 491 HIS cc_start: 0.8866 (m170) cc_final: 0.7827 (t-170) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0649 time to fit residues: 5.9075 Evaluate side-chains 63 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.103 Evaluate side-chains 2 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.008 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.5079 time to fit residues: 1.0321 Evaluate side-chains 2 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 47 optimal weight: 1.9990 chunk 70 optimal weight: 20.0000 chunk 9 optimal weight: 0.9990 chunk 98 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 39 optimal weight: 0.0070 chunk 104 optimal weight: 10.0000 chunk 93 optimal weight: 0.0370 chunk 121 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 110 optimal weight: 0.4980 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.088169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.066540 restraints weight = 10844.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.068762 restraints weight = 7640.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.070521 restraints weight = 5879.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.071802 restraints weight = 4774.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.072760 restraints weight = 4062.110| |-----------------------------------------------------------------------------| r_work (final): 0.3302 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.219609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.180511 restraints weight = 597.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.189002 restraints weight = 296.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.195423 restraints weight = 175.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.198848 restraints weight = 122.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.201771 restraints weight = 99.838| |-----------------------------------------------------------------------------| r_work (final): 0.4913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.5960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 11592 Z= 0.117 Angle : 0.458 6.427 15712 Z= 0.244 Chirality : 0.036 0.126 1684 Planarity : 0.004 0.067 2068 Dihedral : 3.844 24.600 1568 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 65.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.23), residues: 1396 helix: 1.09 (0.18), residues: 832 sheet: -0.65 (0.45), residues: 136 loop : 0.84 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 476 TYR 0.008 0.001 TYR B 264 PHE 0.014 0.001 PHE A 285 TRP 0.003 0.001 TRP D 371 HIS 0.003 0.001 HIS B 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (11592) covalent geometry : angle 0.45850 / 0.24 (15712) hydrogen bonds : bond 0.03331 / 2.30 ( 636) hydrogen bonds : angle 5.64741 / 4.09 ( 1872) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.083 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: B 251 HIS cc_start: 0.9073 (t-90) cc_final: 0.8410 (t70) REVERT: B 255 PHE cc_start: 0.8775 (p90) cc_final: 0.8433 (p90) REVERT: B 264 TYR cc_start: 0.6985 (m-80) cc_final: 0.6541 (m-80) REVERT: B 265 ARG cc_start: 0.8498 (mpp-170) cc_final: 0.8138 (mmt180) REVERT: B 266 GLU cc_start: 0.9217 (pm20) cc_final: 0.8867 (pm20) REVERT: B 308 PHE cc_start: 0.8558 (t80) cc_final: 0.8043 (t80) REVERT: B 321 MET cc_start: 0.7528 (tpt) cc_final: 0.7323 (tpt) REVERT: B 338 MET cc_start: 0.8667 (mmp) cc_final: 0.8374 (mmp) REVERT: B 344 PHE cc_start: 0.9353 (t80) cc_final: 0.8715 (t80) REVERT: B 356 LEU cc_start: 0.9548 (tt) cc_final: 0.9290 (tt) REVERT: B 362 GLU cc_start: 0.9172 (mp0) cc_final: 0.8816 (mp0) REVERT: B 441 LYS cc_start: 0.9276 (tmtt) cc_final: 0.8755 (ttmt) REVERT: B 445 ARG cc_start: 0.7842 (ttt180) cc_final: 0.7063 (ttm110) REVERT: B 455 PHE cc_start: 0.8345 (p90) cc_final: 0.8088 (p90) REVERT: B 457 VAL cc_start: 0.9236 (m) cc_final: 0.8916 (m) REVERT: B 473 GLN cc_start: 0.9279 (mp10) cc_final: 0.9042 (mp10) REVERT: B 479 LEU cc_start: 0.9524 (mt) cc_final: 0.9208 (mt) REVERT: B 491 HIS cc_start: 0.8591 (m170) cc_final: 0.7446 (t-170) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.0739 time to fit residues: 7.3358 Evaluate side-chains 72 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.075 Evaluate side-chains 2 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.008 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.4148 time to fit residues: 0.8447 Evaluate side-chains 2 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 2 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 40 optimal weight: 0.6980 chunk 134 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 3 optimal weight: 20.0000 chunk 52 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 107 optimal weight: 0.0570 overall best weight: 1.0500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.088460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.067086 restraints weight = 10641.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.069300 restraints weight = 7529.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.070979 restraints weight = 5795.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.072308 restraints weight = 4729.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.073318 restraints weight = 4017.020| |-----------------------------------------------------------------------------| r_work (final): 0.3321 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.223635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.180147 restraints weight = 567.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.189073 restraints weight = 310.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.194931 restraints weight = 189.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.199441 restraints weight = 141.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.201561 restraints weight = 109.279| |-----------------------------------------------------------------------------| r_work (final): 0.4852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.6121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 11592 Z= 0.103 Angle : 0.442 4.295 15712 Z= 0.237 Chirality : 0.035 0.126 1684 Planarity : 0.006 0.093 2068 Dihedral : 3.739 23.479 1568 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 61.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.23), residues: 1396 helix: 1.33 (0.18), residues: 824 sheet: -0.53 (0.46), residues: 136 loop : 0.75 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 476 TYR 0.005 0.001 TYR D 213 PHE 0.012 0.001 PHE A 347 TRP 0.004 0.001 TRP B 371 HIS 0.004 0.001 HIS B 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (11592) covalent geometry : angle 0.44197 / 0.24 (15712) hydrogen bonds : bond 0.03153 / 2.17 ( 636) hydrogen bonds : angle 5.45659 / 3.94 ( 1872) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.105 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: B 251 HIS cc_start: 0.9097 (t-90) cc_final: 0.8452 (t70) REVERT: B 255 PHE cc_start: 0.8831 (p90) cc_final: 0.8616 (p90) REVERT: B 258 LEU cc_start: 0.9557 (mm) cc_final: 0.9227 (mm) REVERT: B 264 TYR cc_start: 0.7042 (m-80) cc_final: 0.6653 (m-80) REVERT: B 265 ARG cc_start: 0.8555 (mpp-170) cc_final: 0.8169 (mmt180) REVERT: B 266 GLU cc_start: 0.9234 (pm20) cc_final: 0.8895 (pm20) REVERT: B 308 PHE cc_start: 0.8557 (t80) cc_final: 0.8123 (t80) REVERT: B 331 GLU cc_start: 0.8623 (mp0) cc_final: 0.8264 (mm-30) REVERT: B 338 MET cc_start: 0.8710 (mmp) cc_final: 0.8376 (mmp) REVERT: B 339 LEU cc_start: 0.9328 (mm) cc_final: 0.8971 (mm) REVERT: B 341 ASP cc_start: 0.9056 (t0) cc_final: 0.8850 (t0) REVERT: B 344 PHE cc_start: 0.9340 (t80) cc_final: 0.8689 (t80) REVERT: B 350 ASP cc_start: 0.8248 (m-30) cc_final: 0.7667 (m-30) REVERT: B 356 LEU cc_start: 0.9548 (tt) cc_final: 0.9301 (tt) REVERT: B 362 GLU cc_start: 0.9270 (mp0) cc_final: 0.8898 (mp0) REVERT: B 441 LYS cc_start: 0.9137 (tmtt) cc_final: 0.8635 (ttmt) REVERT: B 445 ARG cc_start: 0.8066 (ttt180) cc_final: 0.7348 (ttm110) REVERT: B 455 PHE cc_start: 0.8302 (p90) cc_final: 0.8009 (p90) REVERT: B 457 VAL cc_start: 0.9361 (m) cc_final: 0.8704 (m) REVERT: B 473 GLN cc_start: 0.9244 (mp10) cc_final: 0.8976 (mp10) REVERT: B 479 LEU cc_start: 0.9430 (mt) cc_final: 0.9137 (pp) REVERT: B 491 HIS cc_start: 0.8456 (m170) cc_final: 0.7215 (t-170) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.0641 time to fit residues: 6.3089 Evaluate side-chains 69 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.111 Evaluate side-chains 2 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.008 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.4942 time to fit residues: 1.0031 Evaluate side-chains 2 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 34 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 116 optimal weight: 9.9990 chunk 126 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 90 optimal weight: 0.0970 chunk 5 optimal weight: 0.6980 chunk 103 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 overall best weight: 2.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.086499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.064820 restraints weight = 11274.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.066851 restraints weight = 8270.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.068453 restraints weight = 6524.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.069702 restraints weight = 5409.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.070650 restraints weight = 4652.122| |-----------------------------------------------------------------------------| r_work (final): 0.3275 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4831 r_free = 0.4831 target = 0.221608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.195354 restraints weight = 586.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.204581 restraints weight = 245.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.210304 restraints weight = 123.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.213020 restraints weight = 69.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.215208 restraints weight = 46.192| |-----------------------------------------------------------------------------| r_work (final): 0.4910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.6333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11592 Z= 0.124 Angle : 0.458 3.662 15712 Z= 0.248 Chirality : 0.036 0.127 1684 Planarity : 0.004 0.041 2068 Dihedral : 3.782 24.581 1568 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 67.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.23), residues: 1396 helix: 1.17 (0.18), residues: 824 sheet: -0.66 (0.45), residues: 136 loop : 0.85 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 476 TYR 0.006 0.001 TYR F 243 PHE 0.010 0.001 PHE F 255 TRP 0.005 0.001 TRP D 371 HIS 0.004 0.001 HIS F 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (11592) covalent geometry : angle 0.45848 / 0.25 (15712) hydrogen bonds : bond 0.03085 / 2.14 ( 636) hydrogen bonds : angle 5.65112 / 4.11 ( 1872) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1161.61 seconds wall clock time: 21 minutes 20.79 seconds (1280.79 seconds total)