Starting phenix.real_space_refine on Tue Jul 29 10:38:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ssx_25416/07_2025/7ssx_25416.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ssx_25416/07_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_25416/07_2025/7ssx_25416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ssx_25416/07_2025/7ssx_25416.map" model { file = "/net/cci-nas-00/data/ceres_data/7ssx_25416/07_2025/7ssx_25416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ssx_25416/07_2025/7ssx_25416.cif" } resolution = 2.89 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= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.93, per 1000 atoms: 0.53 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: 2.55 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.09 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: 2.91 Time building geometry restraints manager: 3.03 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.140 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: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 25.670 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.810 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.21), 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 TRP 0.006 0.002 TRP D 305 HIS 0.003 0.001 HIS B 451 PHE 0.022 0.002 PHE C 251 TYR 0.014 0.002 TYR B 487 ARG 0.004 0.001 ARG B 170 Details of bonding type rmsd hydrogen bonds : bond 0.19739 ( 688) hydrogen bonds : angle 6.27555 ( 2004) covalent geometry : bond 0.01221 (11568) covalent geometry : angle 1.37516 (15676) *********************** 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 : 1.316 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: 1.2632 time to fit residues: 391.4115 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 : 1.221 ------------------------------------------------------------------------------- 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 114 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 55 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.215995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.156723 restraints weight = 11408.001| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.01 r_work: 0.3145 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11568 Z= 0.150 Angle : 0.627 7.899 15676 Z= 0.335 Chirality : 0.042 0.138 1756 Planarity : 0.007 0.065 1984 Dihedral : 4.526 35.111 1548 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.12 % Allowed : 13.27 % Favored : 84.61 % 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: 1.20 (0.23), residues: 1360 helix: 1.41 (0.17), residues: 896 sheet: 1.75 (0.68), residues: 40 loop : -0.54 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 221 HIS 0.001 0.000 HIS C 451 PHE 0.021 0.002 PHE D 140 TYR 0.011 0.002 TYR B 139 ARG 0.008 0.000 ARG A 170 Details of bonding type rmsd hydrogen bonds : bond 0.06413 ( 688) hydrogen bonds : angle 4.29701 ( 2004) covalent geometry : bond 0.00313 (11568) covalent geometry : angle 0.62671 (15676) *********************** 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 197 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 1.215 Fit side-chains REVERT: B 140 PHE cc_start: 0.7997 (t80) cc_final: 0.7640 (t80) REVERT: C 140 PHE cc_start: 0.7995 (t80) cc_final: 0.7647 (t80) REVERT: D 140 PHE cc_start: 0.7969 (t80) cc_final: 0.7635 (t80) outliers start: 26 outliers final: 11 residues processed: 185 average time/residue: 0.8960 time to fit residues: 184.9187 Evaluate side-chains 157 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 1.354 ------------------------------------------------------------------------------- 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 13 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 62 optimal weight: 0.0670 chunk 112 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- 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 = 0.4200 r_free = 0.4200 target = 0.206226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.147454 restraints weight = 11627.362| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.91 r_work: 0.3039 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11568 Z= 0.198 Angle : 0.654 7.229 15676 Z= 0.349 Chirality : 0.045 0.155 1756 Planarity : 0.007 0.069 1984 Dihedral : 4.666 40.192 1544 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.42 % Allowed : 13.03 % Favored : 83.55 % 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: 1.58 (0.23), residues: 1360 helix: 1.71 (0.17), residues: 900 sheet: 1.62 (0.71), residues: 40 loop : -0.43 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 437 HIS 0.004 0.001 HIS A 451 PHE 0.022 0.002 PHE A 251 TYR 0.014 0.002 TYR D 139 ARG 0.005 0.000 ARG A 170 Details of bonding type rmsd hydrogen bonds : bond 0.07815 ( 688) hydrogen bonds : angle 4.38620 ( 2004) covalent geometry : bond 0.00464 (11568) covalent geometry : angle 0.65434 (15676) *********************** 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 200 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 158 time to evaluate : 1.196 Fit side-chains REVERT: A 450 MET cc_start: 0.6006 (OUTLIER) cc_final: 0.5544 (tmt) outliers start: 42 outliers final: 21 residues processed: 186 average time/residue: 0.7406 time to fit residues: 155.6401 Evaluate side-chains 169 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 119 LEU 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 39 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 41 optimal weight: 0.0270 chunk 89 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 10 optimal weight: 40.0000 overall best weight: 0.7242 ------------------------------------------------------------------------------- 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 = 0.4241 r_free = 0.4241 target = 0.210873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.157173 restraints weight = 11660.907| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.89 r_work: 0.3134 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11568 Z= 0.127 Angle : 0.546 6.191 15676 Z= 0.289 Chirality : 0.041 0.166 1756 Planarity : 0.006 0.066 1984 Dihedral : 4.311 36.393 1544 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.50 % Allowed : 13.27 % 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 (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: 2.20 (0.24), residues: 1360 helix: 2.25 (0.18), residues: 896 sheet: 1.74 (0.77), residues: 40 loop : -0.29 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 221 HIS 0.001 0.000 HIS A 451 PHE 0.025 0.001 PHE D 140 TYR 0.008 0.001 TYR A 487 ARG 0.004 0.000 ARG A 170 Details of bonding type rmsd hydrogen bonds : bond 0.05352 ( 688) hydrogen bonds : angle 4.07817 ( 2004) covalent geometry : bond 0.00267 (11568) covalent geometry : angle 0.54587 (15676) *********************** 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 205 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.6610 (tm-30) REVERT: B 138 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7663 (ppp80) REVERT: B 225 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.6628 (tm-30) REVERT: B 246 ILE cc_start: 0.7939 (pt) cc_final: 0.7694 (mt) REVERT: C 138 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7662 (ppp80) REVERT: C 225 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.6657 (tm-30) REVERT: C 246 ILE cc_start: 0.7939 (pt) cc_final: 0.7697 (mt) REVERT: D 225 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.6642 (tm-30) REVERT: D 246 ILE cc_start: 0.7926 (pt) cc_final: 0.7682 (mt) outliers start: 43 outliers final: 19 residues processed: 191 average time/residue: 0.7925 time to fit residues: 171.0346 Evaluate side-chains 178 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 1.300 ------------------------------------------------------------------------------- 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 366 ILE 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 138 ARG Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 255 THR 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 471 THR Chi-restraints excluded: chain C residue 138 ARG 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 366 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 43 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 112 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.4197 r_free = 0.4197 target = 0.206306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.150643 restraints weight = 11507.183| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.92 r_work: 0.3026 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11568 Z= 0.190 Angle : 0.614 5.962 15676 Z= 0.327 Chirality : 0.044 0.148 1756 Planarity : 0.006 0.065 1984 Dihedral : 4.441 38.173 1544 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.34 % Allowed : 14.82 % Favored : 81.84 % 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: 2.01 (0.24), residues: 1360 helix: 2.12 (0.18), residues: 900 sheet: 1.79 (0.81), residues: 40 loop : -0.43 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 437 HIS 0.003 0.001 HIS A 451 PHE 0.023 0.002 PHE B 186 TYR 0.012 0.002 TYR D 187 ARG 0.002 0.000 ARG C 370 Details of bonding type rmsd hydrogen bonds : bond 0.07156 ( 688) hydrogen bonds : angle 4.22957 ( 2004) covalent geometry : bond 0.00455 (11568) covalent geometry : angle 0.61443 (15676) *********************** 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 192 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 1.153 Fit side-chains revert: symmetry clash REVERT: B 138 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7698 (ppp80) REVERT: B 225 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.6615 (tm-30) REVERT: C 138 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7492 (ppp80) REVERT: C 225 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.6665 (tm-30) REVERT: D 138 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7450 (ppp80) REVERT: D 225 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.6638 (tm-30) outliers start: 41 outliers final: 25 residues processed: 181 average time/residue: 0.7839 time to fit residues: 159.5709 Evaluate side-chains 178 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 255 THR 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 471 THR Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 255 THR 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 138 ARG Chi-restraints excluded: chain C residue 146 GLU 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 138 ARG Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 255 THR 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 7 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 112 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4223 r_free = 0.4223 target = 0.209416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.156858 restraints weight = 11771.143| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 1.94 r_work: 0.3125 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11568 Z= 0.135 Angle : 0.564 6.557 15676 Z= 0.297 Chirality : 0.041 0.150 1756 Planarity : 0.005 0.064 1984 Dihedral : 4.226 34.971 1544 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.01 % Allowed : 15.55 % Favored : 81.43 % 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: 2.36 (0.24), residues: 1360 helix: 2.39 (0.18), residues: 900 sheet: 1.91 (0.83), residues: 40 loop : -0.33 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 221 HIS 0.001 0.001 HIS A 451 PHE 0.025 0.001 PHE A 140 TYR 0.008 0.001 TYR C 487 ARG 0.003 0.000 ARG A 170 Details of bonding type rmsd hydrogen bonds : bond 0.05613 ( 688) hydrogen bonds : angle 4.03413 ( 2004) covalent geometry : bond 0.00297 (11568) covalent geometry : angle 0.56423 (15676) *********************** 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 189 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 1.228 Fit side-chains revert: symmetry clash REVERT: A 225 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.6682 (tm-30) REVERT: B 138 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7624 (ppp80) REVERT: B 225 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.6581 (tm-30) REVERT: C 138 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7612 (ppp80) REVERT: C 225 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.6659 (tm-30) REVERT: D 138 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7605 (ppp80) REVERT: D 225 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.6604 (tm-30) outliers start: 37 outliers final: 21 residues processed: 176 average time/residue: 0.7637 time to fit residues: 153.6177 Evaluate side-chains 174 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 225 GLU 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 430 SER 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 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 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 119 LEU Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 146 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 105 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 94 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 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 = 0.4226 r_free = 0.4226 target = 0.209990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.154960 restraints weight = 11814.989| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.88 r_work: 0.3123 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11568 Z= 0.126 Angle : 0.555 7.589 15676 Z= 0.289 Chirality : 0.040 0.184 1756 Planarity : 0.005 0.063 1984 Dihedral : 4.068 31.771 1544 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.93 % Allowed : 16.29 % Favored : 80.78 % 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: 2.43 (0.24), residues: 1360 helix: 2.49 (0.18), residues: 904 sheet: 1.93 (0.84), residues: 40 loop : -0.44 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 221 HIS 0.001 0.001 HIS B 451 PHE 0.026 0.001 PHE B 186 TYR 0.008 0.001 TYR C 487 ARG 0.003 0.000 ARG A 170 Details of bonding type rmsd hydrogen bonds : bond 0.05077 ( 688) hydrogen bonds : angle 3.95330 ( 2004) covalent geometry : bond 0.00273 (11568) covalent geometry : angle 0.55509 (15676) *********************** 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 184 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 1.336 Fit side-chains REVERT: A 225 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.6759 (tm-30) REVERT: B 138 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7607 (ppp80) REVERT: B 225 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.6570 (tm-30) REVERT: C 138 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7584 (ppp80) REVERT: C 225 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.6640 (tm-30) REVERT: D 138 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7581 (ppp80) REVERT: D 225 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.6590 (tm-30) outliers start: 36 outliers final: 13 residues processed: 173 average time/residue: 0.7246 time to fit residues: 142.8274 Evaluate side-chains 167 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 1.259 ------------------------------------------------------------------------------- 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 369 VAL Chi-restraints excluded: chain A residue 374 ILE 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 255 THR 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 225 GLU Chi-restraints excluded: chain C residue 255 THR 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 255 THR 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 24 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.4210 r_free = 0.4210 target = 0.208152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.152990 restraints weight = 11718.157| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.77 r_work: 0.3088 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4019 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 : 0.582 8.684 15676 Z= 0.303 Chirality : 0.041 0.164 1756 Planarity : 0.005 0.063 1984 Dihedral : 3.863 33.106 1538 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.44 % Allowed : 17.43 % Favored : 80.13 % 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: 2.29 (0.24), residues: 1360 helix: 2.39 (0.18), residues: 904 sheet: 1.96 (0.86), residues: 40 loop : -0.54 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 221 HIS 0.002 0.001 HIS C 451 PHE 0.026 0.001 PHE D 186 TYR 0.009 0.001 TYR B 487 ARG 0.004 0.000 ARG C 144 Details of bonding type rmsd hydrogen bonds : bond 0.06069 ( 688) hydrogen bonds : angle 4.02471 ( 2004) covalent geometry : bond 0.00338 (11568) covalent geometry : angle 0.58182 (15676) *********************** 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 179 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 1.325 Fit side-chains REVERT: A 225 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6639 (tm-30) REVERT: B 138 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7614 (ppp80) REVERT: C 138 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7575 (ppp80) REVERT: C 170 ARG cc_start: 0.7778 (mmt90) cc_final: 0.7515 (tpp80) REVERT: C 225 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.6565 (tm-30) REVERT: D 138 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7569 (ppp80) REVERT: D 328 MET cc_start: 0.6436 (OUTLIER) cc_final: 0.5787 (mtt) outliers start: 30 outliers final: 18 residues processed: 170 average time/residue: 0.7379 time to fit residues: 142.1596 Evaluate side-chains 170 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 225 GLU 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 138 ARG 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 430 SER 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 255 THR 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 146 GLU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 328 MET 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 65 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 = 0.4190 r_free = 0.4190 target = 0.205813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.149255 restraints weight = 11707.887| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.81 r_work: 0.3076 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11568 Z= 0.180 Angle : 0.630 9.568 15676 Z= 0.329 Chirality : 0.043 0.147 1756 Planarity : 0.006 0.062 1984 Dihedral : 3.988 35.448 1538 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.28 % Allowed : 18.08 % Favored : 79.64 % 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: 2.16 (0.24), residues: 1360 helix: 2.28 (0.18), residues: 900 sheet: 1.96 (0.89), residues: 40 loop : -0.52 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 437 HIS 0.003 0.001 HIS B 451 PHE 0.026 0.002 PHE B 186 TYR 0.011 0.001 TYR D 187 ARG 0.004 0.000 ARG C 144 Details of bonding type rmsd hydrogen bonds : bond 0.06923 ( 688) hydrogen bonds : angle 4.14749 ( 2004) covalent geometry : bond 0.00426 (11568) covalent geometry : angle 0.63050 (15676) *********************** 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: 28 poor density : 135 time to evaluate : 1.162 Fit side-chains REVERT: A 225 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.6551 (tm-30) REVERT: A 450 MET cc_start: 0.5694 (tmt) cc_final: 0.4345 (mpt) REVERT: B 138 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7535 (ppp80) REVERT: B 225 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.6439 (tm-30) REVERT: B 328 MET cc_start: 0.6487 (OUTLIER) cc_final: 0.5900 (mtt) REVERT: C 138 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7509 (ppp80) REVERT: C 225 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.6480 (tm-30) REVERT: C 328 MET cc_start: 0.6481 (OUTLIER) cc_final: 0.5902 (mtt) REVERT: D 138 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7524 (ppp80) REVERT: D 225 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.6449 (tm-30) outliers start: 28 outliers final: 17 residues processed: 156 average time/residue: 0.7958 time to fit residues: 140.1458 Evaluate side-chains 158 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 225 GLU 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 138 ARG Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 430 SER 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 255 THR Chi-restraints excluded: chain C residue 328 MET 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 146 GLU 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 471 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 57 optimal weight: 0.4980 chunk 117 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 97 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4219 r_free = 0.4219 target = 0.208887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.152768 restraints weight = 11603.944| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.86 r_work: 0.3126 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4197 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= 0.133 Angle : 0.579 10.399 15676 Z= 0.298 Chirality : 0.040 0.171 1756 Planarity : 0.005 0.062 1984 Dihedral : 3.815 31.917 1538 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.36 % Allowed : 18.24 % Favored : 79.40 % 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: 2.34 (0.24), residues: 1360 helix: 2.46 (0.18), residues: 904 sheet: 1.94 (0.90), residues: 40 loop : -0.59 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 221 HIS 0.001 0.001 HIS A 451 PHE 0.027 0.001 PHE A 140 TYR 0.009 0.001 TYR D 487 ARG 0.004 0.000 ARG C 144 Details of bonding type rmsd hydrogen bonds : bond 0.05389 ( 688) hydrogen bonds : angle 3.94943 ( 2004) covalent geometry : bond 0.00296 (11568) covalent geometry : angle 0.57896 (15676) ********************** 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 170 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 1.574 Fit side-chains REVERT: A 225 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.6575 (tm-30) REVERT: A 450 MET cc_start: 0.5506 (tmt) cc_final: 0.4127 (mpt) REVERT: B 138 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7552 (ppp80) REVERT: B 328 MET cc_start: 0.6378 (OUTLIER) cc_final: 0.5742 (mtt) REVERT: C 138 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7528 (ppp80) REVERT: C 170 ARG cc_start: 0.7846 (mmt90) cc_final: 0.7613 (mmt-90) REVERT: C 225 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.6623 (tm-30) REVERT: C 328 MET cc_start: 0.6365 (OUTLIER) cc_final: 0.5743 (mtt) REVERT: D 138 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7510 (ppp80) REVERT: D 225 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.6513 (tm-30) outliers start: 29 outliers final: 15 residues processed: 159 average time/residue: 1.0178 time to fit residues: 182.9252 Evaluate side-chains 164 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 1.631 ------------------------------------------------------------------------------- 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 369 VAL Chi-restraints excluded: chain A residue 374 ILE 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 255 THR Chi-restraints excluded: chain B residue 328 MET 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 225 GLU Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 328 MET 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 146 GLU 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 471 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 85 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN D 164 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.204022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.145639 restraints weight = 11606.097| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.79 r_work: 0.3057 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11568 Z= 0.220 Angle : 0.673 11.718 15676 Z= 0.351 Chirality : 0.045 0.146 1756 Planarity : 0.006 0.062 1984 Dihedral : 4.082 37.593 1538 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.04 % Allowed : 18.49 % Favored : 79.48 % 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: 1.96 (0.24), residues: 1360 helix: 2.15 (0.18), residues: 900 sheet: 1.94 (0.93), residues: 40 loop : -0.69 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 437 HIS 0.004 0.001 HIS A 451 PHE 0.027 0.002 PHE C 186 TYR 0.011 0.002 TYR D 226 ARG 0.004 0.000 ARG C 144 Details of bonding type rmsd hydrogen bonds : bond 0.07742 ( 688) hydrogen bonds : angle 4.18482 ( 2004) covalent geometry : bond 0.00537 (11568) covalent geometry : angle 0.67341 (15676) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10950.26 seconds wall clock time: 193 minutes 5.90 seconds (11585.90 seconds total)