Starting phenix.real_space_refine on Thu Sep 26 01:18:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pim_13442/09_2024/7pim_13442.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pim_13442/09_2024/7pim_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pim_13442/09_2024/7pim_13442.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pim_13442/09_2024/7pim_13442.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pim_13442/09_2024/7pim_13442.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pim_13442/09_2024/7pim_13442.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 6.90, per 1000 atoms: 0.58 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: 3.01 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.16 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: 3.27 Time building geometry restraints manager: 3.47 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'H' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'G' 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: 0.270 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: 0.360 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 28.570 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 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= 0.123 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 : 45.64 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.004 0.000 TRP F 371 HIS 0.001 0.000 HIS F 316 PHE 0.003 0.000 PHE A 285 TYR 0.004 0.001 TYR A 313 ARG 0.001 0.000 ARG A 453 *********************** 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 110 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 0.313 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: A 197 GLN cc_start: 0.9491 (tp40) cc_final: 0.9273 (tp-100) REVERT: A 198 VAL cc_start: 0.9435 (m) cc_final: 0.9202 (p) REVERT: A 201 GLN cc_start: 0.9499 (mm110) cc_final: 0.9295 (pt0) REVERT: A 233 LYS cc_start: 0.9503 (ttpp) cc_final: 0.9215 (ttpp) REVERT: A 251 HIS cc_start: 0.9097 (t-90) cc_final: 0.8889 (t70) REVERT: A 264 TYR cc_start: 0.7727 (m-10) cc_final: 0.7280 (m-10) REVERT: A 266 GLU cc_start: 0.9248 (pm20) cc_final: 0.8977 (pm20) REVERT: A 268 ASN cc_start: 0.8882 (t0) cc_final: 0.8575 (p0) REVERT: A 308 PHE cc_start: 0.8445 (t80) cc_final: 0.7858 (t80) REVERT: A 339 LEU cc_start: 0.9166 (mm) cc_final: 0.8897 (mm) REVERT: A 344 PHE cc_start: 0.9385 (t80) cc_final: 0.8766 (t80) REVERT: A 356 LEU cc_start: 0.9635 (tt) cc_final: 0.9379 (tt) REVERT: A 362 GLU cc_start: 0.9405 (mp0) cc_final: 0.9168 (mp0) REVERT: A 441 LYS cc_start: 0.9228 (ttmm) cc_final: 0.8781 (mtpt) REVERT: A 491 HIS cc_start: 0.9169 (m170) cc_final: 0.8508 (t-170) outliers start: 1 outliers final: 0 residues processed: 110 average time/residue: 0.1839 time to fit residues: 23.3153 Evaluate side-chains 80 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.313 Evaluate side-chains 7 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 6 time to evaluate : 0.021 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 6 average time/residue: 0.7264 time to fit residues: 4.4098 Evaluate side-chains 3 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 0.0370 chunk 103 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 64 optimal weight: 0.0040 chunk 79 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 overall best weight: 0.7272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 286 GLN ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3394 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= 0.166 Angle : 0.527 6.204 15712 Z= 0.274 Chirality : 0.038 0.172 1684 Planarity : 0.004 0.020 2068 Dihedral : 4.044 42.072 1568 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 51.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.33 % Allowed : 1.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.22), residues: 1396 helix: 1.04 (0.18), residues: 808 sheet: -0.55 (0.46), residues: 136 loop : 0.75 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 232 HIS 0.003 0.001 HIS F 491 PHE 0.024 0.001 PHE B 255 TYR 0.019 0.001 TYR F 422 ARG 0.006 0.001 ARG G 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 0.310 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: F 197 GLN cc_start: 0.9517 (tp40) cc_final: 0.9248 (tp-100) REVERT: F 198 VAL cc_start: 0.9504 (m) cc_final: 0.9222 (p) REVERT: F 201 GLN cc_start: 0.9486 (mm110) cc_final: 0.9207 (pt0) REVERT: F 223 GLU cc_start: 0.9089 (pm20) cc_final: 0.8684 (pp20) REVERT: F 233 LYS cc_start: 0.9566 (ttpp) cc_final: 0.9225 (ttpp) REVERT: F 251 HIS cc_start: 0.9094 (t-90) cc_final: 0.8865 (t70) REVERT: F 264 TYR cc_start: 0.7625 (m-10) cc_final: 0.7365 (m-10) REVERT: F 266 GLU cc_start: 0.9203 (pm20) cc_final: 0.8964 (pm20) REVERT: F 268 ASN cc_start: 0.8739 (t0) cc_final: 0.8456 (p0) REVERT: F 286 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8323 (pm20) REVERT: F 305 PHE cc_start: 0.9014 (m-80) cc_final: 0.8805 (m-80) REVERT: F 308 PHE cc_start: 0.8549 (t80) cc_final: 0.7811 (t80) REVERT: F 321 MET cc_start: 0.8104 (tpt) cc_final: 0.7823 (tpt) REVERT: F 338 MET cc_start: 0.8843 (mmp) cc_final: 0.8602 (mmp) REVERT: F 339 LEU cc_start: 0.9235 (mm) cc_final: 0.8946 (mm) REVERT: F 341 ASP cc_start: 0.9159 (t0) cc_final: 0.8915 (t0) REVERT: F 344 PHE cc_start: 0.9525 (t80) cc_final: 0.8872 (t80) REVERT: F 346 GLN cc_start: 0.8343 (tm-30) cc_final: 0.7913 (tm-30) REVERT: F 350 ASP cc_start: 0.7933 (m-30) cc_final: 0.7373 (m-30) REVERT: F 362 GLU cc_start: 0.9369 (mp0) cc_final: 0.9162 (mp0) REVERT: F 369 LEU cc_start: 0.9714 (tp) cc_final: 0.9435 (mt) REVERT: F 396 TYR cc_start: 0.9273 (t80) cc_final: 0.9043 (t80) REVERT: F 441 LYS cc_start: 0.9091 (ttmm) cc_final: 0.8520 (mtpt) REVERT: F 466 ILE cc_start: 0.8750 (mm) cc_final: 0.8531 (mm) REVERT: F 473 GLN cc_start: 0.9425 (mp10) cc_final: 0.9163 (mp10) REVERT: F 491 HIS cc_start: 0.9231 (m170) cc_final: 0.8524 (t-170) outliers start: 1 outliers final: 0 residues processed: 88 average time/residue: 0.1811 time to fit residues: 18.3574 Evaluate side-chains 76 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 0.301 Evaluate side-chains 3 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.044 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.9866 time to fit residues: 3.0036 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 123 optimal weight: 0.2980 chunk 133 optimal weight: 0.0470 chunk 110 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 99 optimal weight: 0.0000 overall best weight: 1.2686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11592 Z= 0.187 Angle : 0.555 8.806 15712 Z= 0.280 Chirality : 0.038 0.132 1684 Planarity : 0.005 0.075 2068 Dihedral : 4.190 34.810 1568 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 52.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.22), residues: 1396 helix: 0.52 (0.18), residues: 812 sheet: -0.77 (0.46), residues: 136 loop : 0.51 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 165 HIS 0.002 0.001 HIS A 251 PHE 0.015 0.001 PHE A 255 TYR 0.014 0.001 TYR D 422 ARG 0.009 0.000 ARG B 476 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.323 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: F 197 GLN cc_start: 0.9505 (tp40) cc_final: 0.9247 (tp-100) REVERT: F 198 VAL cc_start: 0.9499 (m) cc_final: 0.9224 (p) REVERT: F 201 GLN cc_start: 0.9485 (mm110) cc_final: 0.9201 (pt0) REVERT: F 233 LYS cc_start: 0.9581 (ttpp) cc_final: 0.9234 (ttpp) REVERT: F 266 GLU cc_start: 0.9300 (pm20) cc_final: 0.9007 (pm20) REVERT: F 268 ASN cc_start: 0.8895 (t0) cc_final: 0.8463 (p0) REVERT: F 299 PHE cc_start: 0.8845 (t80) cc_final: 0.8629 (t80) REVERT: F 308 PHE cc_start: 0.8572 (t80) cc_final: 0.7865 (t80) REVERT: F 321 MET cc_start: 0.8203 (tpt) cc_final: 0.7954 (tpt) REVERT: F 338 MET cc_start: 0.8924 (mmp) cc_final: 0.8632 (mmp) REVERT: F 339 LEU cc_start: 0.9216 (mm) cc_final: 0.8957 (mm) REVERT: F 341 ASP cc_start: 0.9172 (t0) cc_final: 0.8932 (t0) REVERT: F 344 PHE cc_start: 0.9513 (t80) cc_final: 0.8822 (t80) REVERT: F 346 GLN cc_start: 0.8390 (tm-30) cc_final: 0.8179 (tm-30) REVERT: F 350 ASP cc_start: 0.8010 (m-30) cc_final: 0.7605 (m-30) REVERT: F 410 ARG cc_start: 0.8949 (ptp-170) cc_final: 0.8122 (ptp-170) REVERT: F 445 ARG cc_start: 0.7831 (ttt180) cc_final: 0.7624 (ttt180) REVERT: F 466 ILE cc_start: 0.8692 (mm) cc_final: 0.8449 (mm) REVERT: F 491 HIS cc_start: 0.9214 (m170) cc_final: 0.8239 (t-170) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1855 time to fit residues: 18.0314 Evaluate side-chains 75 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.319 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.022 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 1.3082 time to fit residues: 2.6612 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 59 optimal weight: 0.1980 chunk 83 optimal weight: 30.0000 chunk 124 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 286 GLN ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11592 Z= 0.175 Angle : 0.518 7.288 15712 Z= 0.266 Chirality : 0.036 0.145 1684 Planarity : 0.005 0.077 2068 Dihedral : 4.144 29.811 1568 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 55.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.33 % Allowed : 2.34 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.22), residues: 1396 helix: 0.54 (0.18), residues: 796 sheet: -1.01 (0.44), residues: 136 loop : 0.19 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 371 HIS 0.002 0.000 HIS A 246 PHE 0.014 0.001 PHE A 255 TYR 0.015 0.001 TYR B 264 ARG 0.005 0.000 ARG B 445 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 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 fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 0.325 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: F 197 GLN cc_start: 0.9514 (tp40) cc_final: 0.9268 (tp-100) REVERT: F 198 VAL cc_start: 0.9488 (m) cc_final: 0.9238 (p) REVERT: F 201 GLN cc_start: 0.9490 (mm110) cc_final: 0.9199 (pt0) REVERT: F 233 LYS cc_start: 0.9577 (ttpp) cc_final: 0.9215 (ttpp) REVERT: F 251 HIS cc_start: 0.9254 (t70) cc_final: 0.9012 (t70) REVERT: F 264 TYR cc_start: 0.7582 (m-10) cc_final: 0.7337 (m-80) REVERT: F 266 GLU cc_start: 0.9299 (pm20) cc_final: 0.8997 (pm20) REVERT: F 268 ASN cc_start: 0.8898 (t0) cc_final: 0.8472 (p0) REVERT: F 308 PHE cc_start: 0.8553 (t80) cc_final: 0.7863 (t80) REVERT: F 338 MET cc_start: 0.8940 (mmp) cc_final: 0.8643 (mmp) REVERT: F 339 LEU cc_start: 0.9258 (mm) cc_final: 0.8979 (mm) REVERT: F 341 ASP cc_start: 0.9174 (t0) cc_final: 0.8934 (t0) REVERT: F 344 PHE cc_start: 0.9469 (t80) cc_final: 0.8799 (t80) REVERT: F 362 GLU cc_start: 0.9305 (mp0) cc_final: 0.9080 (mp0) REVERT: F 410 ARG cc_start: 0.8895 (ptp-170) cc_final: 0.8055 (ptp-170) REVERT: F 441 LYS cc_start: 0.9370 (tmtt) cc_final: 0.9050 (mtpt) REVERT: F 466 ILE cc_start: 0.8689 (mm) cc_final: 0.8402 (mm) REVERT: F 479 LEU cc_start: 0.9540 (mt) cc_final: 0.9323 (mt) REVERT: F 491 HIS cc_start: 0.9209 (m170) cc_final: 0.8332 (t-170) outliers start: 1 outliers final: 1 residues processed: 82 average time/residue: 0.1802 time to fit residues: 17.0917 Evaluate side-chains 73 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 0.295 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.020 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 1.2318 time to fit residues: 2.5015 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 97 optimal weight: 0.0170 chunk 54 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 overall best weight: 3.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 483 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11592 Z= 0.216 Angle : 0.530 4.846 15712 Z= 0.285 Chirality : 0.037 0.254 1684 Planarity : 0.004 0.044 2068 Dihedral : 4.170 22.420 1568 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 68.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.22), residues: 1396 helix: -0.01 (0.17), residues: 832 sheet: -1.47 (0.42), residues: 136 loop : 0.43 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 165 HIS 0.006 0.001 HIS D 177 PHE 0.015 0.002 PHE B 412 TYR 0.013 0.002 TYR A 264 ARG 0.003 0.000 ARG D 476 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 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 fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 166 PHE cc_start: 0.9675 (p90) cc_final: 0.9423 (p90) REVERT: F 197 GLN cc_start: 0.9502 (tp40) cc_final: 0.9202 (tp-100) REVERT: F 198 VAL cc_start: 0.9519 (m) cc_final: 0.9298 (p) REVERT: F 201 GLN cc_start: 0.9501 (mm110) cc_final: 0.9146 (pt0) REVERT: F 251 HIS cc_start: 0.9337 (t70) cc_final: 0.8585 (t70) REVERT: F 252 LEU cc_start: 0.9146 (mm) cc_final: 0.8878 (mm) REVERT: F 255 PHE cc_start: 0.8802 (p90) cc_final: 0.8380 (p90) REVERT: F 264 TYR cc_start: 0.7740 (m-10) cc_final: 0.7417 (m-80) REVERT: F 266 GLU cc_start: 0.9382 (pm20) cc_final: 0.8952 (pm20) REVERT: F 308 PHE cc_start: 0.8658 (t80) cc_final: 0.8088 (t80) REVERT: F 338 MET cc_start: 0.9113 (mmp) cc_final: 0.8627 (mmp) REVERT: F 339 LEU cc_start: 0.9263 (mm) cc_final: 0.8973 (mm) REVERT: F 341 ASP cc_start: 0.9135 (t0) cc_final: 0.8863 (t0) REVERT: F 344 PHE cc_start: 0.9395 (t80) cc_final: 0.8751 (t80) REVERT: F 346 GLN cc_start: 0.8569 (tm-30) cc_final: 0.8174 (tm-30) REVERT: F 412 PHE cc_start: 0.8909 (t80) cc_final: 0.8690 (t80) REVERT: F 439 ASP cc_start: 0.8552 (t70) cc_final: 0.8297 (t0) REVERT: F 441 LYS cc_start: 0.9222 (tmtt) cc_final: 0.8911 (mtpt) REVERT: F 443 LYS cc_start: 0.8781 (mtpt) cc_final: 0.8077 (mtpt) REVERT: F 491 HIS cc_start: 0.9281 (m170) cc_final: 0.8453 (t-170) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1803 time to fit residues: 17.3374 Evaluate side-chains 66 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.309 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.021 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 1.2258 time to fit residues: 2.4896 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 131 optimal weight: 0.0970 chunk 109 optimal weight: 9.9990 chunk 60 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 69 optimal weight: 0.0030 chunk 126 optimal weight: 8.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11592 Z= 0.141 Angle : 0.475 5.582 15712 Z= 0.248 Chirality : 0.037 0.163 1684 Planarity : 0.003 0.018 2068 Dihedral : 3.833 22.321 1568 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 57.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.22), residues: 1396 helix: 0.46 (0.18), residues: 832 sheet: -1.33 (0.42), residues: 136 loop : 0.48 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 232 HIS 0.005 0.001 HIS F 215 PHE 0.013 0.001 PHE A 255 TYR 0.011 0.001 TYR D 264 ARG 0.007 0.001 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 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 fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.295 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: F 197 GLN cc_start: 0.9505 (tp40) cc_final: 0.9278 (tp-100) REVERT: F 198 VAL cc_start: 0.9496 (m) cc_final: 0.9262 (p) REVERT: F 251 HIS cc_start: 0.9203 (t70) cc_final: 0.8483 (t70) REVERT: F 255 PHE cc_start: 0.8792 (p90) cc_final: 0.8409 (p90) REVERT: F 264 TYR cc_start: 0.7731 (m-10) cc_final: 0.6850 (m-80) REVERT: F 308 PHE cc_start: 0.8564 (t80) cc_final: 0.7981 (t80) REVERT: F 338 MET cc_start: 0.8964 (mmp) cc_final: 0.8645 (mmp) REVERT: F 339 LEU cc_start: 0.9245 (mm) cc_final: 0.8945 (mm) REVERT: F 341 ASP cc_start: 0.9164 (t0) cc_final: 0.8892 (t0) REVERT: F 344 PHE cc_start: 0.9410 (t80) cc_final: 0.8753 (t80) REVERT: F 346 GLN cc_start: 0.8573 (tm-30) cc_final: 0.8121 (tm-30) REVERT: F 362 GLU cc_start: 0.9320 (mp0) cc_final: 0.9114 (mp0) REVERT: F 441 LYS cc_start: 0.9204 (tmtt) cc_final: 0.8992 (mtpt) REVERT: F 445 ARG cc_start: 0.7966 (ttt180) cc_final: 0.7195 (ttm110) REVERT: F 455 PHE cc_start: 0.8465 (p90) cc_final: 0.8123 (p90) REVERT: F 476 ARG cc_start: 0.8399 (mtp85) cc_final: 0.8087 (mtt-85) REVERT: F 483 GLN cc_start: 0.9122 (mt0) cc_final: 0.8475 (tm-30) REVERT: F 491 HIS cc_start: 0.9330 (m170) cc_final: 0.8425 (t-170) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1972 time to fit residues: 19.6298 Evaluate side-chains 68 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.323 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.024 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 1.2654 time to fit residues: 2.5724 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 chunk 110 optimal weight: 0.0040 chunk 73 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.5408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11592 Z= 0.149 Angle : 0.468 5.296 15712 Z= 0.255 Chirality : 0.036 0.120 1684 Planarity : 0.004 0.045 2068 Dihedral : 3.797 22.148 1568 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 61.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.22), residues: 1396 helix: 0.48 (0.18), residues: 824 sheet: -1.48 (0.40), residues: 136 loop : 0.50 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 165 HIS 0.005 0.001 HIS F 215 PHE 0.010 0.001 PHE A 255 TYR 0.010 0.001 TYR F 264 ARG 0.003 0.000 ARG F 445 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.345 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: F 223 GLU cc_start: 0.9406 (pm20) cc_final: 0.9142 (pp20) REVERT: F 251 HIS cc_start: 0.9253 (t70) cc_final: 0.8435 (t70) REVERT: F 255 PHE cc_start: 0.8818 (p90) cc_final: 0.8520 (p90) REVERT: F 264 TYR cc_start: 0.7736 (m-10) cc_final: 0.7236 (m-80) REVERT: F 265 ARG cc_start: 0.8679 (mpp-170) cc_final: 0.8379 (mmt180) REVERT: F 266 GLU cc_start: 0.9452 (pm20) cc_final: 0.9136 (pm20) REVERT: F 308 PHE cc_start: 0.8578 (t80) cc_final: 0.8005 (t80) REVERT: F 338 MET cc_start: 0.9010 (mmp) cc_final: 0.8649 (mmp) REVERT: F 339 LEU cc_start: 0.9305 (mm) cc_final: 0.8993 (mm) REVERT: F 341 ASP cc_start: 0.9136 (t0) cc_final: 0.8877 (t0) REVERT: F 344 PHE cc_start: 0.9389 (t80) cc_final: 0.8687 (t80) REVERT: F 362 GLU cc_start: 0.9324 (mp0) cc_final: 0.9119 (mp0) REVERT: F 439 ASP cc_start: 0.8450 (t70) cc_final: 0.8086 (t0) REVERT: F 441 LYS cc_start: 0.9168 (tmtt) cc_final: 0.8713 (ttmt) REVERT: F 443 LYS cc_start: 0.8794 (mtpt) cc_final: 0.8093 (mtpt) REVERT: F 445 ARG cc_start: 0.8161 (ttt180) cc_final: 0.7405 (ttm110) REVERT: F 455 PHE cc_start: 0.8464 (p90) cc_final: 0.8159 (p90) REVERT: F 483 GLN cc_start: 0.9075 (mt0) cc_final: 0.8430 (tm-30) REVERT: F 491 HIS cc_start: 0.9376 (m170) cc_final: 0.8535 (t-170) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1874 time to fit residues: 18.3070 Evaluate side-chains 67 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.290 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.023 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 1.2988 time to fit residues: 2.6383 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 83 optimal weight: 8.9990 chunk 89 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.5805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 11592 Z= 0.227 Angle : 0.533 6.718 15712 Z= 0.294 Chirality : 0.036 0.128 1684 Planarity : 0.005 0.098 2068 Dihedral : 4.184 24.325 1568 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 72.14 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.22), residues: 1396 helix: 0.03 (0.18), residues: 832 sheet: -1.83 (0.40), residues: 136 loop : 0.29 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 371 HIS 0.004 0.001 HIS F 215 PHE 0.012 0.002 PHE B 412 TYR 0.012 0.001 TYR D 264 ARG 0.022 0.001 ARG D 476 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 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 fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.336 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: F 223 GLU cc_start: 0.9406 (pm20) cc_final: 0.9153 (pp20) REVERT: F 251 HIS cc_start: 0.9229 (t70) cc_final: 0.8432 (t70) REVERT: F 255 PHE cc_start: 0.8919 (p90) cc_final: 0.8477 (p90) REVERT: F 266 GLU cc_start: 0.9479 (pm20) cc_final: 0.9228 (pm20) REVERT: F 308 PHE cc_start: 0.8623 (t80) cc_final: 0.8108 (t80) REVERT: F 338 MET cc_start: 0.9138 (mmp) cc_final: 0.8669 (mmp) REVERT: F 341 ASP cc_start: 0.9080 (t0) cc_final: 0.8791 (t0) REVERT: F 344 PHE cc_start: 0.9376 (t80) cc_final: 0.8712 (t80) REVERT: F 439 ASP cc_start: 0.8594 (t70) cc_final: 0.8357 (t0) REVERT: F 441 LYS cc_start: 0.9140 (tmtt) cc_final: 0.8707 (ttmt) REVERT: F 455 PHE cc_start: 0.8582 (p90) cc_final: 0.8260 (p90) REVERT: F 479 LEU cc_start: 0.9574 (mt) cc_final: 0.9270 (mt) REVERT: F 491 HIS cc_start: 0.9054 (m170) cc_final: 0.8028 (t-170) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1789 time to fit residues: 16.4731 Evaluate side-chains 66 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.338 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.023 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 1.2425 time to fit residues: 2.5256 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 1.9990 chunk 125 optimal weight: 0.0170 chunk 73 optimal weight: 0.0980 chunk 53 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 110 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 overall best weight: 0.5220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.5946 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= 0.173 Angle : 0.483 4.103 15712 Z= 0.264 Chirality : 0.037 0.123 1684 Planarity : 0.004 0.070 2068 Dihedral : 4.041 24.897 1568 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 63.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.22), residues: 1396 helix: 0.26 (0.18), residues: 840 sheet: -1.64 (0.42), residues: 136 loop : 0.47 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 371 HIS 0.014 0.001 HIS B 215 PHE 0.029 0.002 PHE B 376 TYR 0.015 0.001 TYR B 264 ARG 0.015 0.001 ARG D 476 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.321 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: F 166 PHE cc_start: 0.9564 (p90) cc_final: 0.9359 (p90) REVERT: F 223 GLU cc_start: 0.9380 (pm20) cc_final: 0.9163 (pp20) REVERT: F 251 HIS cc_start: 0.9086 (t70) cc_final: 0.8255 (t70) REVERT: F 255 PHE cc_start: 0.8894 (p90) cc_final: 0.8467 (p90) REVERT: F 266 GLU cc_start: 0.9437 (pm20) cc_final: 0.9187 (pm20) REVERT: F 286 GLN cc_start: 0.9115 (mt0) cc_final: 0.8874 (mp10) REVERT: F 308 PHE cc_start: 0.8516 (t80) cc_final: 0.7988 (t80) REVERT: F 338 MET cc_start: 0.8865 (mmp) cc_final: 0.8501 (mmp) REVERT: F 339 LEU cc_start: 0.9295 (mm) cc_final: 0.8969 (mm) REVERT: F 341 ASP cc_start: 0.9113 (t0) cc_final: 0.8846 (t0) REVERT: F 344 PHE cc_start: 0.9443 (t80) cc_final: 0.8784 (t80) REVERT: F 346 GLN cc_start: 0.8610 (tm-30) cc_final: 0.7988 (tm-30) REVERT: F 356 LEU cc_start: 0.9587 (tt) cc_final: 0.9367 (tt) REVERT: F 362 GLU cc_start: 0.9323 (mp0) cc_final: 0.9096 (mp0) REVERT: F 439 ASP cc_start: 0.8462 (t70) cc_final: 0.8255 (t0) REVERT: F 441 LYS cc_start: 0.9211 (tmtt) cc_final: 0.8673 (ttmt) REVERT: F 445 ARG cc_start: 0.7801 (ttt180) cc_final: 0.7179 (ttm110) REVERT: F 455 PHE cc_start: 0.8376 (p90) cc_final: 0.8061 (p90) REVERT: F 479 LEU cc_start: 0.9590 (mt) cc_final: 0.9295 (mt) REVERT: F 491 HIS cc_start: 0.8943 (m170) cc_final: 0.7927 (t-170) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1740 time to fit residues: 16.4106 Evaluate side-chains 70 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.314 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.022 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 1.2076 time to fit residues: 2.4555 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 89 optimal weight: 0.0970 chunk 135 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 83 optimal weight: 0.0000 chunk 66 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 114 optimal weight: 0.2980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.6099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11592 Z= 0.156 Angle : 0.470 4.234 15712 Z= 0.252 Chirality : 0.036 0.125 1684 Planarity : 0.004 0.057 2068 Dihedral : 3.764 23.465 1568 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 65.11 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.22), residues: 1396 helix: 0.43 (0.18), residues: 836 sheet: -1.54 (0.43), residues: 136 loop : 0.50 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 371 HIS 0.004 0.001 HIS F 215 PHE 0.019 0.001 PHE B 376 TYR 0.008 0.001 TYR F 264 ARG 0.013 0.001 ARG B 476 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.319 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: F 251 HIS cc_start: 0.9067 (t70) cc_final: 0.8251 (t70) REVERT: F 255 PHE cc_start: 0.8886 (p90) cc_final: 0.8494 (p90) REVERT: F 264 TYR cc_start: 0.7614 (m-80) cc_final: 0.7183 (m-80) REVERT: F 265 ARG cc_start: 0.8815 (mpp-170) cc_final: 0.8551 (mmt180) REVERT: F 266 GLU cc_start: 0.9442 (pm20) cc_final: 0.9163 (pm20) REVERT: F 286 GLN cc_start: 0.9109 (mt0) cc_final: 0.8884 (mp10) REVERT: F 308 PHE cc_start: 0.8508 (t80) cc_final: 0.7972 (t80) REVERT: F 338 MET cc_start: 0.8834 (mmp) cc_final: 0.8484 (mmp) REVERT: F 339 LEU cc_start: 0.9303 (mm) cc_final: 0.8951 (mm) REVERT: F 341 ASP cc_start: 0.9124 (t0) cc_final: 0.8856 (t0) REVERT: F 344 PHE cc_start: 0.9411 (t80) cc_final: 0.8784 (t80) REVERT: F 346 GLN cc_start: 0.8650 (tm-30) cc_final: 0.8047 (tm-30) REVERT: F 362 GLU cc_start: 0.9373 (mp0) cc_final: 0.8958 (mp0) REVERT: F 439 ASP cc_start: 0.8463 (t70) cc_final: 0.8182 (t0) REVERT: F 441 LYS cc_start: 0.9196 (tmtt) cc_final: 0.8684 (ttmt) REVERT: F 445 ARG cc_start: 0.8012 (ttt180) cc_final: 0.7404 (ttm110) REVERT: F 455 PHE cc_start: 0.8380 (p90) cc_final: 0.8127 (p90) REVERT: F 491 HIS cc_start: 0.8829 (m170) cc_final: 0.7843 (t-170) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1664 time to fit residues: 15.7960 Evaluate side-chains 68 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.318 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.022 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 1.2188 time to fit residues: 2.4780 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 10.0000 chunk 99 optimal weight: 0.0270 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 108 optimal weight: 0.0870 chunk 45 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 0.0770 chunk 94 optimal weight: 9.9990 chunk 6 optimal weight: 0.0870 overall best weight: 0.1752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.091765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.069359 restraints weight = 10818.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.071702 restraints weight = 7765.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.073462 restraints weight = 6049.111| |-----------------------------------------------------------------------------| r_work (final): 0.3311 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.207166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.167571 restraints weight = 667.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.173267 restraints weight = 407.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.176832 restraints weight = 296.167| |-----------------------------------------------------------------------------| r_work (final): 0.4633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.6239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11592 Z= 0.133 Angle : 0.457 4.512 15712 Z= 0.244 Chirality : 0.036 0.122 1684 Planarity : 0.004 0.049 2068 Dihedral : 3.620 24.181 1568 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 59.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.23), residues: 1396 helix: 0.71 (0.18), residues: 832 sheet: -1.43 (0.44), residues: 136 loop : 0.53 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 371 HIS 0.004 0.001 HIS D 215 PHE 0.012 0.001 PHE F 347 TYR 0.013 0.001 TYR F 264 ARG 0.011 0.001 ARG A 476 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2031.05 seconds wall clock time: 41 minutes 54.45 seconds (2514.45 seconds total)