Starting phenix.real_space_refine on Sun Dec 29 19:51:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ssx_25416/12_2024/7ssx_25416.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ssx_25416/12_2024/7ssx_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_25416/12_2024/7ssx_25416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ssx_25416/12_2024/7ssx_25416.map" model { file = "/net/cci-nas-00/data/ceres_data/7ssx_25416/12_2024/7ssx_25416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ssx_25416/12_2024/7ssx_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 6.12, per 1000 atoms: 0.54 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: 2.75 Conformation dependent library (CDL) restraints added in 1.5 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: 1.11 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: 3.39 Time building geometry restraints manager: 3.15 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: 2.220 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: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 26.170 Find NCS groups from input model: 0.700 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:12.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.680 ------------------------------------------------------------------------------- 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= 0.776 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 *********************** 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 : 1.351 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: 1.3176 time to fit residues: 408.7303 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 : 1.336 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 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= 0.200 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 *********************** 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 : 1.339 Fit side-chains outliers start: 26 outliers final: 11 residues processed: 185 average time/residue: 0.9206 time to fit residues: 190.3895 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 : 1.187 ------------------------------------------------------------------------------- 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 68 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 11568 Z= 0.365 Angle : 0.697 7.176 15676 Z= 0.373 Chirality : 0.047 0.160 1756 Planarity : 0.007 0.068 1984 Dihedral : 4.880 44.325 1544 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.07 % Allowed : 12.54 % Favored : 83.39 % 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: 1.41 (0.23), residues: 1360 helix: 1.58 (0.17), residues: 900 sheet: 1.48 (0.71), residues: 40 loop : -0.47 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 437 HIS 0.005 0.001 HIS C 451 PHE 0.022 0.002 PHE D 251 TYR 0.014 0.002 TYR D 139 ARG 0.004 0.000 ARG A 170 *********************** 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 226 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 176 time to evaluate : 1.254 Fit side-chains REVERT: B 132 ASP cc_start: 0.7158 (p0) cc_final: 0.6868 (p0) REVERT: B 138 ARG cc_start: 0.7070 (OUTLIER) cc_final: 0.6783 (ppp80) REVERT: C 138 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.6746 (ppp80) REVERT: D 132 ASP cc_start: 0.7161 (p0) cc_final: 0.6903 (p0) REVERT: D 138 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.6755 (ppp80) outliers start: 50 outliers final: 30 residues processed: 211 average time/residue: 0.7371 time to fit residues: 177.4639 Evaluate side-chains 173 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 337 ILE 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 119 LEU Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 312 VAL 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 246 ILE Chi-restraints excluded: chain C residue 312 VAL 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 138 ARG Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 312 VAL 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 122 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 64 optimal weight: 0.0980 chunk 13 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 124 optimal weight: 0.8980 chunk 131 optimal weight: 0.5980 chunk 117 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 109 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11568 Z= 0.156 Angle : 0.539 7.332 15676 Z= 0.284 Chirality : 0.041 0.168 1756 Planarity : 0.006 0.065 1984 Dihedral : 4.360 39.422 1544 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.01 % Allowed : 14.33 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.24), residues: 1360 helix: 2.30 (0.18), residues: 896 sheet: 1.76 (0.77), residues: 40 loop : -0.24 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 221 HIS 0.001 0.000 HIS A 451 PHE 0.025 0.001 PHE D 186 TYR 0.010 0.001 TYR D 139 ARG 0.005 0.000 ARG A 170 *********************** 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 195 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 1.207 Fit side-chains REVERT: A 225 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.6759 (tm-30) REVERT: B 157 ASP cc_start: 0.6815 (p0) cc_final: 0.6589 (p0) REVERT: B 225 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.6814 (tm-30) REVERT: D 225 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.6807 (tm-30) outliers start: 37 outliers final: 11 residues processed: 185 average time/residue: 0.7285 time to fit residues: 153.3980 Evaluate side-chains 164 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 1.267 ------------------------------------------------------------------------------- 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 471 THR 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 471 THR Chi-restraints excluded: chain C residue 255 THR 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 471 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 90 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 11568 Z= 0.390 Angle : 0.679 6.220 15676 Z= 0.362 Chirality : 0.047 0.157 1756 Planarity : 0.006 0.066 1984 Dihedral : 4.067 15.857 1536 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.83 % Allowed : 14.09 % Favored : 82.08 % 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: 1.73 (0.23), residues: 1360 helix: 1.91 (0.17), residues: 900 sheet: 1.77 (0.84), residues: 40 loop : -0.57 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 437 HIS 0.004 0.001 HIS A 451 PHE 0.024 0.002 PHE B 186 TYR 0.013 0.002 TYR D 187 ARG 0.003 0.000 ARG C 205 *********************** 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 198 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 151 time to evaluate : 1.158 Fit side-chains revert: symmetry clash REVERT: B 225 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.6793 (tm-30) REVERT: D 225 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.6784 (tm-30) outliers start: 47 outliers final: 21 residues processed: 183 average time/residue: 0.8408 time to fit residues: 172.7185 Evaluate side-chains 168 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 1.181 ------------------------------------------------------------------------------- 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 471 THR Chi-restraints excluded: chain B residue 119 LEU 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 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 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 118 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 131 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3918 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= 0.211 Angle : 0.577 6.541 15676 Z= 0.305 Chirality : 0.041 0.135 1756 Planarity : 0.006 0.064 1984 Dihedral : 3.888 15.698 1536 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.69 % Allowed : 15.64 % Favored : 81.68 % 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: 2.19 (0.24), residues: 1360 helix: 2.30 (0.18), residues: 900 sheet: 1.85 (0.86), residues: 40 loop : -0.47 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 221 HIS 0.002 0.001 HIS C 451 PHE 0.025 0.001 PHE D 186 TYR 0.009 0.001 TYR C 139 ARG 0.003 0.000 ARG A 170 *********************** 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 182 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 1.256 Fit side-chains REVERT: A 225 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6878 (tm-30) REVERT: B 225 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6703 (tm-30) REVERT: D 225 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6694 (tm-30) outliers start: 33 outliers final: 15 residues processed: 172 average time/residue: 0.7721 time to fit residues: 150.4351 Evaluate side-chains 163 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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 471 THR 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 369 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain C residue 146 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 110 optimal weight: 0.2980 chunk 73 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11568 Z= 0.248 Angle : 0.607 7.410 15676 Z= 0.317 Chirality : 0.042 0.140 1756 Planarity : 0.006 0.064 1984 Dihedral : 3.899 15.391 1536 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.52 % Allowed : 16.37 % Favored : 81.11 % 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: 2.12 (0.24), residues: 1360 helix: 2.26 (0.18), residues: 900 sheet: 1.96 (0.87), residues: 40 loop : -0.56 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 221 HIS 0.002 0.001 HIS D 451 PHE 0.026 0.002 PHE B 186 TYR 0.010 0.001 TYR B 487 ARG 0.003 0.000 ARG A 170 *********************** 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 179 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 1.276 Fit side-chains REVERT: A 225 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.6866 (tm-30) REVERT: B 225 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6705 (tm-30) REVERT: C 225 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.6770 (tm-30) outliers start: 31 outliers final: 21 residues processed: 169 average time/residue: 0.8107 time to fit residues: 154.4478 Evaluate side-chains 166 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 1.226 ------------------------------------------------------------------------------- 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 430 SER Chi-restraints excluded: chain A residue 471 THR 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 369 VAL 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 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 430 SER Chi-restraints excluded: chain C residue 471 THR 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 430 SER 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 78 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 89 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 0.0270 chunk 103 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 overall best weight: 1.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11568 Z= 0.237 Angle : 0.610 8.399 15676 Z= 0.318 Chirality : 0.042 0.138 1756 Planarity : 0.006 0.063 1984 Dihedral : 3.861 15.301 1536 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.44 % Allowed : 17.59 % Favored : 79.97 % 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: 2.19 (0.24), residues: 1360 helix: 2.32 (0.18), residues: 900 sheet: 2.00 (0.90), residues: 40 loop : -0.56 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 437 HIS 0.002 0.001 HIS A 451 PHE 0.026 0.001 PHE D 186 TYR 0.010 0.001 TYR B 487 ARG 0.003 0.000 ARG A 170 *********************** 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 170 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 1.307 Fit side-chains REVERT: A 225 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.6866 (tm-30) REVERT: B 225 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6671 (tm-30) outliers start: 30 outliers final: 20 residues processed: 163 average time/residue: 0.7393 time to fit residues: 137.2998 Evaluate side-chains 162 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 1.285 ------------------------------------------------------------------------------- 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 430 SER Chi-restraints excluded: chain A residue 471 THR 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 369 VAL Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 471 THR 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 430 SER 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 122 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.4005 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= 0.364 Angle : 0.686 9.482 15676 Z= 0.359 Chirality : 0.046 0.152 1756 Planarity : 0.006 0.063 1984 Dihedral : 4.059 15.761 1536 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.28 % Allowed : 17.92 % Favored : 79.80 % 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: 1.78 (0.24), residues: 1360 helix: 2.03 (0.18), residues: 896 sheet: 1.92 (0.92), residues: 40 loop : -0.77 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 437 HIS 0.004 0.001 HIS A 451 PHE 0.026 0.002 PHE B 186 TYR 0.013 0.002 TYR A 187 ARG 0.003 0.000 ARG C 370 *********************** 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 162 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 1.218 Fit side-chains REVERT: A 225 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.6833 (tm-30) REVERT: B 225 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.6759 (tm-30) REVERT: D 225 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.6749 (tm-30) outliers start: 28 outliers final: 19 residues processed: 157 average time/residue: 0.8359 time to fit residues: 148.4212 Evaluate side-chains 153 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 1.350 ------------------------------------------------------------------------------- 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 374 ILE Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 146 GLU 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 430 SER Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain C residue 146 GLU 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 146 GLU Chi-restraints excluded: chain D residue 225 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 89 optimal weight: 9.9990 chunk 135 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4204 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= 0.197 Angle : 0.609 11.946 15676 Z= 0.312 Chirality : 0.040 0.133 1756 Planarity : 0.006 0.063 1984 Dihedral : 3.838 15.730 1536 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.47 % Allowed : 19.22 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.24), residues: 1360 helix: 2.35 (0.18), residues: 900 sheet: 2.04 (0.94), residues: 40 loop : -0.62 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 305 HIS 0.001 0.001 HIS D 451 PHE 0.025 0.001 PHE D 186 TYR 0.009 0.001 TYR B 487 ARG 0.003 0.000 ARG A 170 ********************** 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 151 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 1.230 Fit side-chains REVERT: A 225 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.6881 (tm-30) REVERT: B 225 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6762 (tm-30) REVERT: D 225 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.6769 (tm-30) outliers start: 18 outliers final: 11 residues processed: 147 average time/residue: 0.8259 time to fit residues: 137.0577 Evaluate side-chains 143 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 1.326 ------------------------------------------------------------------------------- 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 225 GLU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain D residue 146 GLU 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 33 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 45 optimal weight: 0.1980 chunk 110 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.207814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.149677 restraints weight = 11545.637| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.75 r_work: 0.3149 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4242 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= 0.200 Angle : 0.589 9.939 15676 Z= 0.304 Chirality : 0.040 0.132 1756 Planarity : 0.006 0.063 1984 Dihedral : 3.758 15.876 1536 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.30 % Allowed : 19.38 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.24), residues: 1360 helix: 2.44 (0.18), residues: 904 sheet: 1.88 (0.91), residues: 40 loop : -0.79 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 305 HIS 0.003 0.001 HIS A 451 PHE 0.028 0.001 PHE A 140 TYR 0.009 0.001 TYR C 487 ARG 0.003 0.000 ARG A 170 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3538.04 seconds wall clock time: 65 minutes 2.73 seconds (3902.73 seconds total)