Starting phenix.real_space_refine on Tue Nov 18 05:08:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ssx_25416/11_2025/7ssx_25416.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ssx_25416/11_2025/7ssx_25416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ssx_25416/11_2025/7ssx_25416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ssx_25416/11_2025/7ssx_25416.map" model { file = "/net/cci-nas-00/data/ceres_data/7ssx_25416/11_2025/7ssx_25416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ssx_25416/11_2025/7ssx_25416.cif" } resolution = 2.89 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= 0.005 sd= 0.092 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 3 8.98 5 S 44 5.16 5 C 7428 2.51 5 N 1868 2.21 5 O 1940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11283 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2820 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 19, 'TRANS': 326} Chain breaks: 2 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B, C, D Time building chain proxies: 2.11, per 1000 atoms: 0.19 Number of scatterers: 11283 At special positions: 0 Unit cell: (109.056, 109.908, 115.872, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 3 19.00 S 44 16.00 O 1940 8.00 N 1868 7.00 C 7428 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 409.2 milliseconds 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2600 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 4 sheets defined 71.7% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 152 through 165 removed outlier: 3.553A pdb=" N PHE A 156 " --> pdb=" O ASN A 152 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 188 Processing helix chain 'A' and resid 190 through 202 Processing helix chain 'A' and resid 214 through 226 removed outlier: 3.531A pdb=" N ARG A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN A 219 " --> pdb=" O ASP A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 256 removed outlier: 3.905A pdb=" N ARG A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 316 Processing helix chain 'A' and resid 319 through 323 removed outlier: 3.520A pdb=" N THR A 322 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 348 removed outlier: 3.629A pdb=" N LEU A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) Proline residue: A 338 - end of helix Processing helix chain 'A' and resid 361 through 370 Processing helix chain 'A' and resid 371 through 372 No H-bonds generated for 'chain 'A' and resid 371 through 372' Processing helix chain 'A' and resid 373 through 379 removed outlier: 3.629A pdb=" N LYS A 376 " --> pdb=" O ARG A 373 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG A 379 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 394 removed outlier: 3.845A pdb=" N GLN A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 421 removed outlier: 3.632A pdb=" N PHE A 418 " --> pdb=" O SER A 414 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 419 " --> pdb=" O ALA A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 433 No H-bonds generated for 'chain 'A' and resid 431 through 433' Processing helix chain 'A' and resid 434 through 444 Processing helix chain 'A' and resid 454 through 474 removed outlier: 3.976A pdb=" N VAL A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 489 removed outlier: 3.925A pdb=" N ILE A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 152 through 165 removed outlier: 3.554A pdb=" N PHE B 156 " --> pdb=" O ASN B 152 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP B 157 " --> pdb=" O ARG B 153 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 188 Processing helix chain 'B' and resid 190 through 202 Processing helix chain 'B' and resid 214 through 226 removed outlier: 3.530A pdb=" N ARG B 218 " --> pdb=" O ARG B 214 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN B 219 " --> pdb=" O ASP B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 256 removed outlier: 3.905A pdb=" N ARG B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 316 Processing helix chain 'B' and resid 319 through 323 removed outlier: 3.519A pdb=" N THR B 322 " --> pdb=" O SER B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 348 removed outlier: 3.629A pdb=" N LEU B 330 " --> pdb=" O ASN B 326 " (cutoff:3.500A) Proline residue: B 338 - end of helix Processing helix chain 'B' and resid 361 through 370 Processing helix chain 'B' and resid 371 through 372 No H-bonds generated for 'chain 'B' and resid 371 through 372' Processing helix chain 'B' and resid 373 through 379 removed outlier: 3.630A pdb=" N LYS B 376 " --> pdb=" O ARG B 373 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG B 379 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 394 removed outlier: 3.845A pdb=" N GLN B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 421 removed outlier: 3.632A pdb=" N PHE B 418 " --> pdb=" O SER B 414 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA B 419 " --> pdb=" O ALA B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 433 No H-bonds generated for 'chain 'B' and resid 431 through 433' Processing helix chain 'B' and resid 434 through 444 Processing helix chain 'B' and resid 454 through 474 removed outlier: 3.976A pdb=" N VAL B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.925A pdb=" N ILE B 479 " --> pdb=" O PRO B 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 152 through 165 removed outlier: 3.553A pdb=" N PHE C 156 " --> pdb=" O ASN C 152 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP C 157 " --> pdb=" O ARG C 153 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA C 158 " --> pdb=" O PRO C 154 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR C 163 " --> pdb=" O ILE C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 188 Processing helix chain 'C' and resid 190 through 202 Processing helix chain 'C' and resid 214 through 226 removed outlier: 3.531A pdb=" N ARG C 218 " --> pdb=" O ARG C 214 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN C 219 " --> pdb=" O ASP C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 256 removed outlier: 3.904A pdb=" N ARG C 234 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 316 Processing helix chain 'C' and resid 319 through 323 removed outlier: 3.519A pdb=" N THR C 322 " --> pdb=" O SER C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 348 removed outlier: 3.629A pdb=" N LEU C 330 " --> pdb=" O ASN C 326 " (cutoff:3.500A) Proline residue: C 338 - end of helix Processing helix chain 'C' and resid 361 through 370 Processing helix chain 'C' and resid 371 through 372 No H-bonds generated for 'chain 'C' and resid 371 through 372' Processing helix chain 'C' and resid 373 through 379 removed outlier: 3.629A pdb=" N LYS C 376 " --> pdb=" O ARG C 373 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG C 379 " --> pdb=" O LYS C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 394 removed outlier: 3.844A pdb=" N GLN C 385 " --> pdb=" O SER C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 421 removed outlier: 3.631A pdb=" N PHE C 418 " --> pdb=" O SER C 414 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA C 419 " --> pdb=" O ALA C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 433 No H-bonds generated for 'chain 'C' and resid 431 through 433' Processing helix chain 'C' and resid 434 through 444 Processing helix chain 'C' and resid 454 through 474 removed outlier: 3.976A pdb=" N VAL C 469 " --> pdb=" O ALA C 465 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C 474 " --> pdb=" O LEU C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 489 removed outlier: 3.924A pdb=" N ILE C 479 " --> pdb=" O PRO C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 124 Processing helix chain 'D' and resid 152 through 165 removed outlier: 3.553A pdb=" N PHE D 156 " --> pdb=" O ASN D 152 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP D 157 " --> pdb=" O ARG D 153 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA D 158 " --> pdb=" O PRO D 154 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR D 163 " --> pdb=" O ILE D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 188 Processing helix chain 'D' and resid 190 through 202 Processing helix chain 'D' and resid 214 through 226 removed outlier: 3.531A pdb=" N ARG D 218 " --> pdb=" O ARG D 214 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 256 removed outlier: 3.905A pdb=" N ARG D 234 " --> pdb=" O SER D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 316 Processing helix chain 'D' and resid 319 through 323 removed outlier: 3.520A pdb=" N THR D 322 " --> pdb=" O SER D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 348 removed outlier: 3.629A pdb=" N LEU D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Proline residue: D 338 - end of helix Processing helix chain 'D' and resid 361 through 370 Processing helix chain 'D' and resid 371 through 372 No H-bonds generated for 'chain 'D' and resid 371 through 372' Processing helix chain 'D' and resid 373 through 379 removed outlier: 3.629A pdb=" N LYS D 376 " --> pdb=" O ARG D 373 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG D 379 " --> pdb=" O LYS D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 394 removed outlier: 3.844A pdb=" N GLN D 385 " --> pdb=" O SER D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 421 removed outlier: 3.632A pdb=" N PHE D 418 " --> pdb=" O SER D 414 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA D 419 " --> pdb=" O ALA D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 433 No H-bonds generated for 'chain 'D' and resid 431 through 433' Processing helix chain 'D' and resid 434 through 444 Processing helix chain 'D' and resid 454 through 474 removed outlier: 3.976A pdb=" N VAL D 469 " --> pdb=" O ALA D 465 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU D 474 " --> pdb=" O LEU D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 489 removed outlier: 3.925A pdb=" N ILE D 479 " --> pdb=" O PRO D 475 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 118 Processing sheet with id=AA2, first strand: chain 'B' and resid 113 through 118 Processing sheet with id=AA3, first strand: chain 'C' and resid 113 through 118 Processing sheet with id=AA4, first strand: chain 'D' and resid 113 through 118 688 hydrogen bonds defined for protein. 2004 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: 1.56 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1766 1.32 - 1.44: 3266 1.44 - 1.56: 6468 1.56 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 11568 Sorted by residual: bond pdb=" CA GLY B 446 " pdb=" C GLY B 446 " ideal model delta sigma weight residual 1.513 1.468 0.045 1.06e-02 8.90e+03 1.77e+01 bond pdb=" CA GLY D 446 " pdb=" C GLY D 446 " ideal model delta sigma weight residual 1.513 1.468 0.044 1.06e-02 8.90e+03 1.74e+01 bond pdb=" CA GLY A 446 " pdb=" C GLY A 446 " ideal model delta sigma weight residual 1.513 1.469 0.044 1.06e-02 8.90e+03 1.70e+01 bond pdb=" CA GLY C 446 " pdb=" C GLY C 446 " ideal model delta sigma weight residual 1.513 1.469 0.043 1.06e-02 8.90e+03 1.67e+01 bond pdb=" N LEU C 211 " pdb=" CA LEU C 211 " ideal model delta sigma weight residual 1.453 1.488 -0.035 9.20e-03 1.18e+04 1.41e+01 ... (remaining 11563 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 13436 1.95 - 3.90: 2025 3.90 - 5.86: 159 5.86 - 7.81: 32 7.81 - 9.76: 24 Bond angle restraints: 15676 Sorted by residual: angle pdb=" N VAL B 445 " pdb=" CA VAL B 445 " pdb=" C VAL B 445 " ideal model delta sigma weight residual 110.62 101.10 9.52 1.02e+00 9.61e-01 8.72e+01 angle pdb=" N VAL C 445 " pdb=" CA VAL C 445 " pdb=" C VAL C 445 " ideal model delta sigma weight residual 110.62 101.13 9.49 1.02e+00 9.61e-01 8.65e+01 angle pdb=" N VAL A 445 " pdb=" CA VAL A 445 " pdb=" C VAL A 445 " ideal model delta sigma weight residual 110.62 101.14 9.48 1.02e+00 9.61e-01 8.64e+01 angle pdb=" N VAL D 445 " pdb=" CA VAL D 445 " pdb=" C VAL D 445 " ideal model delta sigma weight residual 110.62 101.14 9.48 1.02e+00 9.61e-01 8.64e+01 angle pdb=" C TYR B 447 " pdb=" CA TYR B 447 " pdb=" CB TYR B 447 " ideal model delta sigma weight residual 110.96 101.20 9.76 1.54e+00 4.22e-01 4.02e+01 ... (remaining 15671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.91: 5739 11.91 - 23.82: 789 23.82 - 35.73: 232 35.73 - 47.64: 60 47.64 - 59.55: 20 Dihedral angle restraints: 6840 sinusoidal: 2820 harmonic: 4020 Sorted by residual: dihedral pdb=" C THR C 444 " pdb=" N THR C 444 " pdb=" CA THR C 444 " pdb=" CB THR C 444 " ideal model delta harmonic sigma weight residual -122.00 -138.31 16.31 0 2.50e+00 1.60e-01 4.26e+01 dihedral pdb=" C THR B 444 " pdb=" N THR B 444 " pdb=" CA THR B 444 " pdb=" CB THR B 444 " ideal model delta harmonic sigma weight residual -122.00 -138.30 16.30 0 2.50e+00 1.60e-01 4.25e+01 dihedral pdb=" C THR A 444 " pdb=" N THR A 444 " pdb=" CA THR A 444 " pdb=" CB THR A 444 " ideal model delta harmonic sigma weight residual -122.00 -138.29 16.29 0 2.50e+00 1.60e-01 4.25e+01 ... (remaining 6837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 1420 0.116 - 0.232: 302 0.232 - 0.348: 26 0.348 - 0.463: 4 0.463 - 0.579: 4 Chirality restraints: 1756 Sorted by residual: chirality pdb=" CA THR C 444 " pdb=" N THR C 444 " pdb=" C THR C 444 " pdb=" CB THR C 444 " both_signs ideal model delta sigma weight residual False 2.53 1.95 0.58 2.00e-01 2.50e+01 8.39e+00 chirality pdb=" CA THR A 444 " pdb=" N THR A 444 " pdb=" C THR A 444 " pdb=" CB THR A 444 " both_signs ideal model delta sigma weight residual False 2.53 1.95 0.58 2.00e-01 2.50e+01 8.38e+00 chirality pdb=" CA THR B 444 " pdb=" N THR B 444 " pdb=" C THR B 444 " pdb=" CB THR B 444 " both_signs ideal model delta sigma weight residual False 2.53 1.95 0.58 2.00e-01 2.50e+01 8.38e+00 ... (remaining 1753 not shown) Planarity restraints: 1984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 134 " -0.016 2.00e-02 2.50e+03 3.14e-02 9.85e+00 pdb=" C LYS B 134 " 0.054 2.00e-02 2.50e+03 pdb=" O LYS B 134 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG B 135 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 134 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.83e+00 pdb=" C LYS D 134 " -0.054 2.00e-02 2.50e+03 pdb=" O LYS D 134 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG D 135 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 134 " 0.016 2.00e-02 2.50e+03 3.12e-02 9.77e+00 pdb=" C LYS A 134 " -0.054 2.00e-02 2.50e+03 pdb=" O LYS A 134 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG A 135 " 0.018 2.00e-02 2.50e+03 ... (remaining 1981 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.83: 3399 2.83 - 3.41: 11705 3.41 - 3.98: 20721 3.98 - 4.56: 29283 4.56 - 5.14: 41863 Nonbonded interactions: 106971 Sorted by model distance: nonbonded pdb=" NH1 ARG A 105 " pdb=" OE2 GLU B 146 " model vdw 2.251 3.120 nonbonded pdb=" O VAL C 409 " pdb=" OG SER C 413 " model vdw 2.286 3.040 nonbonded pdb=" O VAL D 409 " pdb=" OG SER D 413 " model vdw 2.286 3.040 nonbonded pdb=" O VAL A 409 " pdb=" OG SER A 413 " model vdw 2.287 3.040 nonbonded pdb=" O VAL B 409 " pdb=" OG SER B 413 " model vdw 2.287 3.040 ... (remaining 106966 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 103 through 491) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.140 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 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 : 0.012 0.079 11568 Z= 0.737 Angle : 1.375 9.762 15676 Z= 0.963 Chirality : 0.096 0.579 1756 Planarity : 0.008 0.075 1984 Dihedral : 12.346 59.552 4240 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.61 % Allowed : 3.58 % Favored : 93.81 % Cbeta Deviations : 0.92 % 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: -1.17 (0.21), residues: 1360 helix: -0.48 (0.16), residues: 916 sheet: 0.57 (0.74), residues: 48 loop : -1.35 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 170 TYR 0.014 0.002 TYR B 487 PHE 0.022 0.002 PHE C 251 TRP 0.006 0.002 TRP D 305 HIS 0.003 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.01221 (11568) covalent geometry : angle 1.37516 (15676) hydrogen bonds : bond 0.19739 ( 688) hydrogen bonds : angle 6.27555 ( 2004) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 261 time to evaluate : 0.431 Fit side-chains REVERT: A 374 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7652 (mt) outliers start: 32 outliers final: 5 residues processed: 288 average time/residue: 0.6342 time to fit residues: 195.8474 Evaluate side-chains 163 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 157 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain D residue 374 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 145 ASN B 124 GLN B 145 ASN C 124 GLN C 145 ASN D 124 GLN D 145 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.216071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.156331 restraints weight = 11497.023| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.89 r_work: 0.3154 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11568 Z= 0.152 Angle : 0.630 8.095 15676 Z= 0.337 Chirality : 0.042 0.138 1756 Planarity : 0.007 0.064 1984 Dihedral : 4.509 34.810 1548 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.04 % Allowed : 12.79 % Favored : 85.18 % 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: 1.21 (0.23), residues: 1360 helix: 1.42 (0.17), residues: 896 sheet: 1.79 (0.69), residues: 40 loop : -0.56 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 170 TYR 0.011 0.002 TYR B 139 PHE 0.022 0.002 PHE D 140 TRP 0.007 0.001 TRP A 221 HIS 0.001 0.000 HIS C 451 Details of bonding type rmsd covalent geometry : bond 0.00312 (11568) covalent geometry : angle 0.62958 (15676) hydrogen bonds : bond 0.06496 ( 688) hydrogen bonds : angle 4.31729 ( 2004) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 0.444 Fit side-chains REVERT: B 140 PHE cc_start: 0.7684 (t80) cc_final: 0.7321 (t80) REVERT: C 140 PHE cc_start: 0.7699 (t80) cc_final: 0.7330 (t80) REVERT: D 140 PHE cc_start: 0.7671 (t80) cc_final: 0.7312 (t80) outliers start: 25 outliers final: 11 residues processed: 183 average time/residue: 0.4226 time to fit residues: 86.0934 Evaluate side-chains 155 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 374 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 89 optimal weight: 20.0000 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 83 optimal weight: 0.4980 chunk 131 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.213215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.155380 restraints weight = 11680.235| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.93 r_work: 0.3120 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11568 Z= 0.129 Angle : 0.555 7.065 15676 Z= 0.293 Chirality : 0.041 0.166 1756 Planarity : 0.006 0.067 1984 Dihedral : 4.199 32.977 1544 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.93 % Allowed : 12.95 % Favored : 84.12 % 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: 2.07 (0.24), residues: 1360 helix: 2.14 (0.17), residues: 896 sheet: 1.82 (0.75), residues: 40 loop : -0.34 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 170 TYR 0.012 0.001 TYR D 139 PHE 0.026 0.001 PHE A 140 TRP 0.007 0.001 TRP A 221 HIS 0.001 0.000 HIS A 380 Details of bonding type rmsd covalent geometry : bond 0.00269 (11568) covalent geometry : angle 0.55481 (15676) hydrogen bonds : bond 0.05363 ( 688) hydrogen bonds : angle 4.08703 ( 2004) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 0.380 Fit side-chains REVERT: B 140 PHE cc_start: 0.6957 (t80) cc_final: 0.6739 (t80) REVERT: C 140 PHE cc_start: 0.6991 (t80) cc_final: 0.6772 (t80) outliers start: 36 outliers final: 14 residues processed: 180 average time/residue: 0.3436 time to fit residues: 70.6629 Evaluate side-chains 158 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 71 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 22 optimal weight: 0.5980 chunk 41 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.209655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.155429 restraints weight = 11718.700| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.91 r_work: 0.3082 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11568 Z= 0.148 Angle : 0.570 6.007 15676 Z= 0.303 Chirality : 0.042 0.165 1756 Planarity : 0.006 0.065 1984 Dihedral : 4.252 33.526 1544 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.91 % Allowed : 12.87 % Favored : 83.22 % 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: 2.26 (0.24), residues: 1360 helix: 2.30 (0.18), residues: 900 sheet: 1.96 (0.78), residues: 40 loop : -0.35 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 170 TYR 0.011 0.002 TYR B 139 PHE 0.026 0.002 PHE D 186 TRP 0.005 0.001 TRP A 221 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00325 (11568) covalent geometry : angle 0.57025 (15676) hydrogen bonds : bond 0.06188 ( 688) hydrogen bonds : angle 4.12906 ( 2004) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 156 time to evaluate : 0.463 Fit side-chains REVERT: B 225 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.6542 (tm-30) REVERT: C 225 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6570 (tm-30) REVERT: D 225 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6567 (tm-30) outliers start: 48 outliers final: 20 residues processed: 182 average time/residue: 0.3642 time to fit residues: 75.1224 Evaluate side-chains 173 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 66 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.202991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.148311 restraints weight = 11559.479| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.90 r_work: 0.2966 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 11568 Z= 0.265 Angle : 0.703 6.604 15676 Z= 0.378 Chirality : 0.048 0.158 1756 Planarity : 0.006 0.066 1984 Dihedral : 4.815 43.932 1544 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.58 % Allowed : 14.82 % Favored : 81.60 % 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: 1.65 (0.23), residues: 1360 helix: 1.83 (0.17), residues: 900 sheet: 1.83 (0.84), residues: 40 loop : -0.58 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 205 TYR 0.014 0.002 TYR D 187 PHE 0.026 0.002 PHE B 140 TRP 0.010 0.002 TRP D 437 HIS 0.006 0.001 HIS C 451 Details of bonding type rmsd covalent geometry : bond 0.00657 (11568) covalent geometry : angle 0.70287 (15676) hydrogen bonds : bond 0.08886 ( 688) hydrogen bonds : angle 4.45822 ( 2004) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 161 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.6630 (tm-30) REVERT: A 450 MET cc_start: 0.5975 (OUTLIER) cc_final: 0.5651 (tmt) REVERT: B 225 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.6604 (tm-30) REVERT: C 225 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.6651 (tm-30) REVERT: D 225 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.6619 (tm-30) outliers start: 44 outliers final: 22 residues processed: 190 average time/residue: 0.3831 time to fit residues: 81.5930 Evaluate side-chains 173 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 45 optimal weight: 0.0170 chunk 98 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 10 optimal weight: 30.0000 chunk 34 optimal weight: 0.9990 chunk 79 optimal weight: 0.2980 chunk 6 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.209966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.156970 restraints weight = 11847.550| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 1.89 r_work: 0.3147 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11568 Z= 0.126 Angle : 0.560 6.565 15676 Z= 0.297 Chirality : 0.041 0.177 1756 Planarity : 0.006 0.064 1984 Dihedral : 4.407 40.085 1544 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.69 % Allowed : 16.29 % Favored : 81.03 % 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: 2.32 (0.24), residues: 1360 helix: 2.36 (0.18), residues: 900 sheet: 1.90 (0.87), residues: 40 loop : -0.35 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 170 TYR 0.008 0.001 TYR D 139 PHE 0.025 0.001 PHE D 186 TRP 0.007 0.001 TRP A 221 HIS 0.001 0.000 HIS C 380 Details of bonding type rmsd covalent geometry : bond 0.00262 (11568) covalent geometry : angle 0.55975 (15676) hydrogen bonds : bond 0.05255 ( 688) hydrogen bonds : angle 4.06172 ( 2004) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: A 144 ARG cc_start: 0.7791 (mtm-85) cc_final: 0.7577 (mpp80) REVERT: A 225 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.6663 (tm-30) REVERT: A 328 MET cc_start: 0.6461 (OUTLIER) cc_final: 0.5858 (mtt) REVERT: A 450 MET cc_start: 0.5704 (tmt) cc_final: 0.4362 (mpt) REVERT: B 225 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.6531 (tm-30) REVERT: B 246 ILE cc_start: 0.7914 (pt) cc_final: 0.7681 (mt) REVERT: C 225 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.6650 (tm-30) REVERT: C 246 ILE cc_start: 0.7920 (pt) cc_final: 0.7688 (mt) REVERT: D 225 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.6560 (tm-30) REVERT: D 246 ILE cc_start: 0.7874 (pt) cc_final: 0.7648 (mt) outliers start: 33 outliers final: 16 residues processed: 181 average time/residue: 0.3531 time to fit residues: 72.5101 Evaluate side-chains 178 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 115 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 11 optimal weight: 0.0570 chunk 127 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 109 optimal weight: 0.0010 chunk 95 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.5706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.210983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.158019 restraints weight = 11724.391| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.87 r_work: 0.3159 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11568 Z= 0.122 Angle : 0.544 7.547 15676 Z= 0.283 Chirality : 0.040 0.167 1756 Planarity : 0.005 0.063 1984 Dihedral : 4.150 35.527 1544 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.93 % Allowed : 16.53 % Favored : 80.54 % 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: 2.46 (0.24), residues: 1360 helix: 2.55 (0.18), residues: 904 sheet: 1.90 (0.86), residues: 40 loop : -0.53 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 170 TYR 0.008 0.001 TYR C 487 PHE 0.026 0.001 PHE B 186 TRP 0.005 0.001 TRP D 221 HIS 0.001 0.000 HIS C 451 Details of bonding type rmsd covalent geometry : bond 0.00259 (11568) covalent geometry : angle 0.54446 (15676) hydrogen bonds : bond 0.04952 ( 688) hydrogen bonds : angle 3.93687 ( 2004) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 0.446 Fit side-chains REVERT: A 225 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.6714 (tm-30) REVERT: A 328 MET cc_start: 0.6374 (OUTLIER) cc_final: 0.5663 (mtt) REVERT: A 450 MET cc_start: 0.5545 (OUTLIER) cc_final: 0.4189 (mpt) REVERT: B 225 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.6575 (tm-30) REVERT: C 138 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7496 (ppp80) REVERT: C 170 ARG cc_start: 0.7762 (mmt90) cc_final: 0.7507 (tpp80) REVERT: C 225 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.6640 (tm-30) REVERT: D 225 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.6597 (tm-30) outliers start: 36 outliers final: 12 residues processed: 179 average time/residue: 0.3294 time to fit residues: 67.3464 Evaluate side-chains 171 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 20 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.203793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.146300 restraints weight = 11635.088| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.83 r_work: 0.3018 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 11568 Z= 0.236 Angle : 0.679 8.487 15676 Z= 0.358 Chirality : 0.046 0.157 1756 Planarity : 0.006 0.062 1984 Dihedral : 4.318 41.200 1540 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.28 % Allowed : 18.49 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.23), residues: 1360 helix: 2.08 (0.18), residues: 900 sheet: 1.82 (0.91), residues: 40 loop : -0.69 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 370 TYR 0.013 0.002 TYR B 187 PHE 0.026 0.002 PHE D 186 TRP 0.009 0.002 TRP C 437 HIS 0.005 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00580 (11568) covalent geometry : angle 0.67861 (15676) hydrogen bonds : bond 0.08153 ( 688) hydrogen bonds : angle 4.26445 ( 2004) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.526 Fit side-chains REVERT: A 225 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.6582 (tm-30) REVERT: B 138 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7353 (ppp80) outliers start: 28 outliers final: 13 residues processed: 160 average time/residue: 0.3456 time to fit residues: 63.3465 Evaluate side-chains 152 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 71 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.208039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.152004 restraints weight = 11574.852| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.74 r_work: 0.3119 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11568 Z= 0.141 Angle : 0.593 9.386 15676 Z= 0.307 Chirality : 0.041 0.184 1756 Planarity : 0.006 0.063 1984 Dihedral : 4.084 38.439 1540 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.79 % Allowed : 19.14 % Favored : 79.07 % 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: 2.26 (0.24), residues: 1360 helix: 2.40 (0.18), residues: 900 sheet: None (None), residues: 0 loop : -0.35 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 105 TYR 0.009 0.001 TYR B 487 PHE 0.026 0.001 PHE C 186 TRP 0.006 0.001 TRP A 221 HIS 0.001 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00318 (11568) covalent geometry : angle 0.59309 (15676) hydrogen bonds : bond 0.05717 ( 688) hydrogen bonds : angle 3.98853 ( 2004) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.487 Fit side-chains REVERT: A 225 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.6629 (tm-30) REVERT: A 328 MET cc_start: 0.6482 (OUTLIER) cc_final: 0.5855 (mtt) REVERT: B 138 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7357 (ppp80) REVERT: B 225 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.6542 (tm-30) REVERT: C 170 ARG cc_start: 0.7839 (mmt90) cc_final: 0.7606 (mmt-90) REVERT: C 225 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.6590 (tm-30) REVERT: D 138 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7426 (ppp80) REVERT: D 225 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.6565 (tm-30) outliers start: 22 outliers final: 11 residues processed: 154 average time/residue: 0.3755 time to fit residues: 65.0806 Evaluate side-chains 154 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 134 optimal weight: 0.3980 chunk 6 optimal weight: 0.7980 chunk 21 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 112 optimal weight: 0.0770 chunk 59 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.209958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.156618 restraints weight = 11660.080| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 1.87 r_work: 0.3139 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11568 Z= 0.127 Angle : 0.585 10.526 15676 Z= 0.298 Chirality : 0.040 0.192 1756 Planarity : 0.005 0.063 1984 Dihedral : 3.900 33.153 1540 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.55 % Allowed : 20.03 % Favored : 78.42 % 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: 2.36 (0.24), residues: 1360 helix: 2.54 (0.18), residues: 904 sheet: None (None), residues: 0 loop : -0.48 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 170 TYR 0.008 0.001 TYR D 487 PHE 0.030 0.001 PHE A 140 TRP 0.006 0.001 TRP A 221 HIS 0.001 0.000 HIS C 380 Details of bonding type rmsd covalent geometry : bond 0.00277 (11568) covalent geometry : angle 0.58512 (15676) hydrogen bonds : bond 0.04970 ( 688) hydrogen bonds : angle 3.85830 ( 2004) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.431 Fit side-chains REVERT: A 225 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.6637 (tm-30) REVERT: A 328 MET cc_start: 0.6393 (OUTLIER) cc_final: 0.5665 (mtt) REVERT: A 450 MET cc_start: 0.5583 (tmt) cc_final: 0.4263 (mpt) REVERT: B 138 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7334 (ppp80) REVERT: C 138 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7380 (ppp80) REVERT: C 170 ARG cc_start: 0.7848 (mmt90) cc_final: 0.7626 (mmt-90) REVERT: D 138 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7378 (ppp80) REVERT: D 170 ARG cc_start: 0.7816 (mmt90) cc_final: 0.7590 (mmt-90) REVERT: D 225 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.6529 (tm-30) outliers start: 19 outliers final: 9 residues processed: 160 average time/residue: 0.4113 time to fit residues: 73.6933 Evaluate side-chains 161 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 126 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 114 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN B 164 GLN C 164 GLN D 164 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.207458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.150345 restraints weight = 11648.679| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.83 r_work: 0.3070 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11568 Z= 0.148 Angle : 0.602 10.940 15676 Z= 0.311 Chirality : 0.042 0.175 1756 Planarity : 0.005 0.063 1984 Dihedral : 3.741 15.044 1536 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.38 % Allowed : 20.03 % Favored : 78.58 % 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: 2.27 (0.24), residues: 1360 helix: 2.47 (0.18), residues: 904 sheet: None (None), residues: 0 loop : -0.52 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 170 TYR 0.009 0.001 TYR D 487 PHE 0.026 0.001 PHE B 186 TRP 0.005 0.001 TRP A 437 HIS 0.002 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00339 (11568) covalent geometry : angle 0.60232 (15676) hydrogen bonds : bond 0.05946 ( 688) hydrogen bonds : angle 3.91948 ( 2004) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5056.09 seconds wall clock time: 86 minutes 35.11 seconds (5195.11 seconds total)