Starting phenix.real_space_refine on Wed Feb 4 14:13:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ssx_25416/02_2026/7ssx_25416.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ssx_25416/02_2026/7ssx_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ssx_25416/02_2026/7ssx_25416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ssx_25416/02_2026/7ssx_25416.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ssx_25416/02_2026/7ssx_25416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ssx_25416/02_2026/7ssx_25416.map" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.092 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 3 8.98 5 S 44 5.16 5 C 7428 2.51 5 N 1868 2.21 5 O 1940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11283 Number of models: 1 Model: "" Number of chains: 5 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: "B" 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: "C" 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: "D" 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} Time building chain proxies: 2.13, per 1000 atoms: 0.19 Number of scatterers: 11283 At special positions: 0 Unit cell: (109.056, 109.908, 115.872, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 3 19.00 S 44 16.00 O 1940 8.00 N 1868 7.00 C 7428 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 518.0 milliseconds 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2600 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 4 sheets defined 71.7% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 152 through 165 removed outlier: 3.553A pdb=" N PHE A 156 " --> pdb=" O ASN A 152 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 188 Processing helix chain 'A' and resid 190 through 202 Processing helix chain 'A' and resid 214 through 226 removed outlier: 3.531A pdb=" N ARG A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN A 219 " --> pdb=" O ASP A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 256 removed outlier: 3.905A pdb=" N ARG A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 316 Processing helix chain 'A' and resid 319 through 323 removed outlier: 3.520A pdb=" N THR A 322 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 348 removed outlier: 3.629A pdb=" N LEU A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) Proline residue: A 338 - end of helix Processing helix chain 'A' and resid 361 through 370 Processing helix chain 'A' and resid 371 through 372 No H-bonds generated for 'chain 'A' and resid 371 through 372' Processing helix chain 'A' and resid 373 through 379 removed outlier: 3.629A pdb=" N LYS A 376 " --> pdb=" O ARG A 373 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG A 379 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 394 removed outlier: 3.845A pdb=" N GLN A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 421 removed outlier: 3.632A pdb=" N PHE A 418 " --> pdb=" O SER A 414 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 419 " --> pdb=" O ALA A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 433 No H-bonds generated for 'chain 'A' and resid 431 through 433' Processing helix chain 'A' and resid 434 through 444 Processing helix chain 'A' and resid 454 through 474 removed outlier: 3.976A pdb=" N VAL A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 489 removed outlier: 3.925A pdb=" N ILE A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 152 through 165 removed outlier: 3.554A pdb=" N PHE B 156 " --> pdb=" O ASN B 152 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP B 157 " --> pdb=" O ARG B 153 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 188 Processing helix chain 'B' and resid 190 through 202 Processing helix chain 'B' and resid 214 through 226 removed outlier: 3.530A pdb=" N ARG B 218 " --> pdb=" O ARG B 214 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN B 219 " --> pdb=" O ASP B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 256 removed outlier: 3.905A pdb=" N ARG B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 316 Processing helix chain 'B' and resid 319 through 323 removed outlier: 3.519A pdb=" N THR B 322 " --> pdb=" O SER B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 348 removed outlier: 3.629A pdb=" N LEU B 330 " --> pdb=" O ASN B 326 " (cutoff:3.500A) Proline residue: B 338 - end of helix Processing helix chain 'B' and resid 361 through 370 Processing helix chain 'B' and resid 371 through 372 No H-bonds generated for 'chain 'B' and resid 371 through 372' Processing helix chain 'B' and resid 373 through 379 removed outlier: 3.630A pdb=" N LYS B 376 " --> pdb=" O ARG B 373 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG B 379 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 394 removed outlier: 3.845A pdb=" N GLN B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 421 removed outlier: 3.632A pdb=" N PHE B 418 " --> pdb=" O SER B 414 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA B 419 " --> pdb=" O ALA B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 433 No H-bonds generated for 'chain 'B' and resid 431 through 433' Processing helix chain 'B' and resid 434 through 444 Processing helix chain 'B' and resid 454 through 474 removed outlier: 3.976A pdb=" N VAL B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.925A pdb=" N ILE B 479 " --> pdb=" O PRO B 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 152 through 165 removed outlier: 3.553A pdb=" N PHE C 156 " --> pdb=" O ASN C 152 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP C 157 " --> pdb=" O ARG C 153 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA C 158 " --> pdb=" O PRO C 154 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR C 163 " --> pdb=" O ILE C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 188 Processing helix chain 'C' and resid 190 through 202 Processing helix chain 'C' and resid 214 through 226 removed outlier: 3.531A pdb=" N ARG C 218 " --> pdb=" O ARG C 214 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN C 219 " --> pdb=" O ASP C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 256 removed outlier: 3.904A pdb=" N ARG C 234 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 316 Processing helix chain 'C' and resid 319 through 323 removed outlier: 3.519A pdb=" N THR C 322 " --> pdb=" O SER C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 348 removed outlier: 3.629A pdb=" N LEU C 330 " --> pdb=" O ASN C 326 " (cutoff:3.500A) Proline residue: C 338 - end of helix Processing helix chain 'C' and resid 361 through 370 Processing helix chain 'C' and resid 371 through 372 No H-bonds generated for 'chain 'C' and resid 371 through 372' Processing helix chain 'C' and resid 373 through 379 removed outlier: 3.629A pdb=" N LYS C 376 " --> pdb=" O ARG C 373 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG C 379 " --> pdb=" O LYS C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 394 removed outlier: 3.844A pdb=" N GLN C 385 " --> pdb=" O SER C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 421 removed outlier: 3.631A pdb=" N PHE C 418 " --> pdb=" O SER C 414 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA C 419 " --> pdb=" O ALA C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 433 No H-bonds generated for 'chain 'C' and resid 431 through 433' Processing helix chain 'C' and resid 434 through 444 Processing helix chain 'C' and resid 454 through 474 removed outlier: 3.976A pdb=" N VAL C 469 " --> pdb=" O ALA C 465 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C 474 " --> pdb=" O LEU C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 489 removed outlier: 3.924A pdb=" N ILE C 479 " --> pdb=" O PRO C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 124 Processing helix chain 'D' and resid 152 through 165 removed outlier: 3.553A pdb=" N PHE D 156 " --> pdb=" O ASN D 152 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP D 157 " --> pdb=" O ARG D 153 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA D 158 " --> pdb=" O PRO D 154 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR D 163 " --> pdb=" O ILE D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 188 Processing helix chain 'D' and resid 190 through 202 Processing helix chain 'D' and resid 214 through 226 removed outlier: 3.531A pdb=" N ARG D 218 " --> pdb=" O ARG D 214 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 256 removed outlier: 3.905A pdb=" N ARG D 234 " --> pdb=" O SER D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 316 Processing helix chain 'D' and resid 319 through 323 removed outlier: 3.520A pdb=" N THR D 322 " --> pdb=" O SER D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 348 removed outlier: 3.629A pdb=" N LEU D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Proline residue: D 338 - end of helix Processing helix chain 'D' and resid 361 through 370 Processing helix chain 'D' and resid 371 through 372 No H-bonds generated for 'chain 'D' and resid 371 through 372' Processing helix chain 'D' and resid 373 through 379 removed outlier: 3.629A pdb=" N LYS D 376 " --> pdb=" O ARG D 373 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG D 379 " --> pdb=" O LYS D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 394 removed outlier: 3.844A pdb=" N GLN D 385 " --> pdb=" O SER D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 421 removed outlier: 3.632A pdb=" N PHE D 418 " --> pdb=" O SER D 414 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA D 419 " --> pdb=" O ALA D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 433 No H-bonds generated for 'chain 'D' and resid 431 through 433' Processing helix chain 'D' and resid 434 through 444 Processing helix chain 'D' and resid 454 through 474 removed outlier: 3.976A pdb=" N VAL D 469 " --> pdb=" O ALA D 465 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU D 474 " --> pdb=" O LEU D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 489 removed outlier: 3.925A pdb=" N ILE D 479 " --> pdb=" O PRO D 475 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 118 Processing sheet with id=AA2, first strand: chain 'B' and resid 113 through 118 Processing sheet with id=AA3, first strand: chain 'C' and resid 113 through 118 Processing sheet with id=AA4, first strand: chain 'D' and resid 113 through 118 688 hydrogen bonds defined for protein. 2004 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.59 Time building geometry restraints manager: 1.20 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: 2.020 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.170 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.079 11568 Z= 0.737 Angle : 1.375 9.762 15676 Z= 0.963 Chirality : 0.096 0.579 1756 Planarity : 0.008 0.075 1984 Dihedral : 12.346 59.552 4240 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.61 % Allowed : 3.58 % Favored : 93.81 % Cbeta Deviations : 0.92 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.21), residues: 1360 helix: -0.48 (0.16), residues: 916 sheet: 0.57 (0.74), residues: 48 loop : -1.35 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 170 TYR 0.014 0.002 TYR B 487 PHE 0.022 0.002 PHE C 251 TRP 0.006 0.002 TRP D 305 HIS 0.003 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.01221 (11568) covalent geometry : angle 1.37516 (15676) hydrogen bonds : bond 0.19739 ( 688) hydrogen bonds : angle 6.27555 ( 2004) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 261 time to evaluate : 0.429 Fit side-chains REVERT: A 374 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7653 (mt) outliers start: 32 outliers final: 5 residues processed: 288 average time/residue: 0.5545 time to fit residues: 171.5965 Evaluate side-chains 163 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 157 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain D residue 374 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 145 ASN B 124 GLN B 145 ASN C 124 GLN C 145 ASN D 124 GLN D 145 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.216071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.156331 restraints weight = 11497.023| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.89 r_work: 0.3154 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11568 Z= 0.152 Angle : 0.630 8.095 15676 Z= 0.337 Chirality : 0.042 0.138 1756 Planarity : 0.007 0.064 1984 Dihedral : 4.509 34.810 1548 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.04 % Allowed : 12.79 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.23), residues: 1360 helix: 1.42 (0.17), residues: 896 sheet: 1.79 (0.69), residues: 40 loop : -0.56 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 170 TYR 0.011 0.002 TYR B 139 PHE 0.022 0.002 PHE D 140 TRP 0.007 0.001 TRP A 221 HIS 0.001 0.000 HIS C 451 Details of bonding type rmsd covalent geometry : bond 0.00312 (11568) covalent geometry : angle 0.62958 (15676) hydrogen bonds : bond 0.06496 ( 688) hydrogen bonds : angle 4.31729 ( 2004) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 0.452 Fit side-chains REVERT: B 140 PHE cc_start: 0.7684 (t80) cc_final: 0.7321 (t80) REVERT: C 140 PHE cc_start: 0.7699 (t80) cc_final: 0.7330 (t80) REVERT: D 140 PHE cc_start: 0.7671 (t80) cc_final: 0.7312 (t80) outliers start: 25 outliers final: 11 residues processed: 183 average time/residue: 0.3719 time to fit residues: 75.8843 Evaluate side-chains 155 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 374 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 89 optimal weight: 20.0000 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 83 optimal weight: 0.4980 chunk 131 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.213215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.155380 restraints weight = 11680.234| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.93 r_work: 0.3121 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11568 Z= 0.129 Angle : 0.555 7.065 15676 Z= 0.293 Chirality : 0.041 0.166 1756 Planarity : 0.006 0.067 1984 Dihedral : 4.199 32.977 1544 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.93 % Allowed : 12.95 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.24), residues: 1360 helix: 2.14 (0.17), residues: 896 sheet: 1.82 (0.75), residues: 40 loop : -0.34 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 170 TYR 0.012 0.001 TYR D 139 PHE 0.026 0.001 PHE A 140 TRP 0.007 0.001 TRP A 221 HIS 0.001 0.000 HIS A 380 Details of bonding type rmsd covalent geometry : bond 0.00269 (11568) covalent geometry : angle 0.55481 (15676) hydrogen bonds : bond 0.05363 ( 688) hydrogen bonds : angle 4.08703 ( 2004) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 0.453 Fit side-chains REVERT: B 140 PHE cc_start: 0.6972 (t80) cc_final: 0.6754 (t80) REVERT: C 140 PHE cc_start: 0.7005 (t80) cc_final: 0.6787 (t80) outliers start: 36 outliers final: 14 residues processed: 180 average time/residue: 0.2907 time to fit residues: 59.8680 Evaluate side-chains 158 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 71 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.4218 r_free = 0.4218 target = 0.208241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.151449 restraints weight = 11712.240| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.84 r_work: 0.3084 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11568 Z= 0.164 Angle : 0.596 6.543 15676 Z= 0.316 Chirality : 0.043 0.158 1756 Planarity : 0.006 0.066 1984 Dihedral : 4.365 34.723 1544 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.99 % Allowed : 12.70 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.24), residues: 1360 helix: 2.21 (0.18), residues: 900 sheet: 1.89 (0.78), residues: 40 loop : -0.40 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 170 TYR 0.011 0.002 TYR A 187 PHE 0.026 0.002 PHE D 186 TRP 0.006 0.001 TRP B 437 HIS 0.003 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00371 (11568) covalent geometry : angle 0.59582 (15676) hydrogen bonds : bond 0.06778 ( 688) hydrogen bonds : angle 4.21930 ( 2004) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 154 time to evaluate : 0.450 Fit side-chains REVERT: B 225 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.6541 (tm-30) REVERT: C 225 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.6584 (tm-30) REVERT: D 138 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7321 (ptp90) REVERT: D 225 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.6548 (tm-30) outliers start: 49 outliers final: 21 residues processed: 181 average time/residue: 0.3414 time to fit residues: 69.8011 Evaluate side-chains 176 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain D residue 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 374 ILE Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 66 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.4194 r_free = 0.4194 target = 0.205816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.150385 restraints weight = 11602.489| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.88 r_work: 0.3056 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11568 Z= 0.189 Angle : 0.624 5.831 15676 Z= 0.334 Chirality : 0.044 0.149 1756 Planarity : 0.006 0.065 1984 Dihedral : 4.459 37.354 1544 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.58 % Allowed : 14.17 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.24), residues: 1360 helix: 2.11 (0.18), residues: 900 sheet: 1.80 (0.84), residues: 40 loop : -0.52 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 205 TYR 0.011 0.002 TYR D 187 PHE 0.024 0.002 PHE B 186 TRP 0.007 0.002 TRP B 437 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00448 (11568) covalent geometry : angle 0.62421 (15676) hydrogen bonds : bond 0.07281 ( 688) hydrogen bonds : angle 4.26379 ( 2004) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 159 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 135 ARG cc_start: 0.5898 (OUTLIER) cc_final: 0.5428 (ttp80) REVERT: A 328 MET cc_start: 0.6530 (OUTLIER) cc_final: 0.5927 (mtt) REVERT: B 137 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7519 (mmm) REVERT: B 225 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.6601 (tm-30) REVERT: C 225 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.6650 (tm-30) REVERT: D 138 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7358 (ptp90) REVERT: D 225 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.6619 (tm-30) outliers start: 44 outliers final: 20 residues processed: 189 average time/residue: 0.3583 time to fit residues: 75.8984 Evaluate side-chains 176 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 328 MET 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 137 MET 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 225 GLU Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 45 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 chunk 34 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4232 r_free = 0.4232 target = 0.210246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.157575 restraints weight = 11833.085| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.90 r_work: 0.3113 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3970 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= 0.130 Angle : 0.558 6.563 15676 Z= 0.294 Chirality : 0.040 0.167 1756 Planarity : 0.005 0.064 1984 Dihedral : 4.184 33.426 1544 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.26 % Allowed : 14.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.24), residues: 1360 helix: 2.44 (0.18), residues: 900 sheet: 1.87 (0.85), residues: 40 loop : -0.36 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 170 TYR 0.008 0.001 TYR A 487 PHE 0.025 0.001 PHE D 186 TRP 0.007 0.001 TRP A 221 HIS 0.001 0.000 HIS D 451 Details of bonding type rmsd covalent geometry : bond 0.00285 (11568) covalent geometry : angle 0.55794 (15676) hydrogen bonds : bond 0.05273 ( 688) hydrogen bonds : angle 4.00236 ( 2004) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 159 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 ARG cc_start: 0.5939 (OUTLIER) cc_final: 0.5438 (ttp80) REVERT: A 225 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.6706 (tm-30) REVERT: A 328 MET cc_start: 0.6415 (OUTLIER) cc_final: 0.5794 (mtt) REVERT: B 225 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.6544 (tm-30) REVERT: B 246 ILE cc_start: 0.7921 (pt) cc_final: 0.7669 (mt) REVERT: B 328 MET cc_start: 0.6434 (OUTLIER) cc_final: 0.5823 (mtt) REVERT: C 225 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.6606 (tm-30) REVERT: C 246 ILE cc_start: 0.7923 (pt) cc_final: 0.7674 (mt) REVERT: D 138 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7341 (ptp90) REVERT: D 225 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.6569 (tm-30) REVERT: D 246 ILE cc_start: 0.7908 (pt) cc_final: 0.7660 (mt) outliers start: 40 outliers final: 18 residues processed: 182 average time/residue: 0.3737 time to fit residues: 76.8981 Evaluate side-chains 182 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 328 MET 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 119 LEU 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 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 374 ILE Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 115 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 11 optimal weight: 0.0570 chunk 127 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 overall best weight: 1.3900 ------------------------------------------------------------------------------- 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 = 0.4202 r_free = 0.4202 target = 0.207031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.150301 restraints weight = 11689.773| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.76 r_work: 0.3099 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3935 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= 0.165 Angle : 0.601 7.705 15676 Z= 0.316 Chirality : 0.042 0.140 1756 Planarity : 0.006 0.063 1984 Dihedral : 4.286 34.778 1544 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.85 % Allowed : 16.21 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.24), residues: 1360 helix: 2.32 (0.18), residues: 900 sheet: 1.93 (0.88), residues: 40 loop : -0.50 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 144 TYR 0.010 0.001 TYR A 487 PHE 0.026 0.002 PHE B 186 TRP 0.006 0.001 TRP D 437 HIS 0.003 0.001 HIS C 451 Details of bonding type rmsd covalent geometry : bond 0.00382 (11568) covalent geometry : angle 0.60127 (15676) hydrogen bonds : bond 0.06577 ( 688) hydrogen bonds : angle 4.12077 ( 2004) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 0.461 Fit side-chains REVERT: A 135 ARG cc_start: 0.5976 (OUTLIER) cc_final: 0.5429 (ttp80) REVERT: A 225 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.6727 (tm-30) REVERT: A 328 MET cc_start: 0.6447 (OUTLIER) cc_final: 0.5816 (mtt) REVERT: C 170 ARG cc_start: 0.7779 (mmt90) cc_final: 0.7523 (tpp80) outliers start: 35 outliers final: 22 residues processed: 172 average time/residue: 0.3723 time to fit residues: 72.4602 Evaluate side-chains 173 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 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 255 THR Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 20 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 104 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 55 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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 = 0.4162 r_free = 0.4162 target = 0.202825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.144638 restraints weight = 11643.818| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.88 r_work: 0.3005 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 11568 Z= 0.264 Angle : 0.704 8.354 15676 Z= 0.375 Chirality : 0.048 0.158 1756 Planarity : 0.006 0.062 1984 Dihedral : 4.806 44.476 1544 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.69 % Allowed : 16.94 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.23), residues: 1360 helix: 1.87 (0.18), residues: 900 sheet: None (None), residues: 0 loop : -0.58 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 144 TYR 0.014 0.002 TYR B 187 PHE 0.026 0.002 PHE D 186 TRP 0.010 0.002 TRP A 437 HIS 0.005 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00653 (11568) covalent geometry : angle 0.70375 (15676) hydrogen bonds : bond 0.08756 ( 688) hydrogen bonds : angle 4.35452 ( 2004) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 133 time to evaluate : 0.288 Fit side-chains REVERT: A 225 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.6594 (tm-30) REVERT: B 225 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.6573 (tm-30) REVERT: C 225 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.6622 (tm-30) REVERT: D 225 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.6606 (tm-30) outliers start: 33 outliers final: 17 residues processed: 156 average time/residue: 0.2972 time to fit residues: 52.9032 Evaluate side-chains 152 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 471 THR 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 225 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 71 optimal weight: 7.9990 chunk 80 optimal weight: 0.0050 chunk 13 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 43 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- 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 = 0.4217 r_free = 0.4217 target = 0.208796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.156505 restraints weight = 11605.694| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 1.89 r_work: 0.3135 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11568 Z= 0.133 Angle : 0.574 10.669 15676 Z= 0.298 Chirality : 0.041 0.162 1756 Planarity : 0.005 0.063 1984 Dihedral : 4.350 39.645 1544 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.95 % Allowed : 18.32 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.24), residues: 1360 helix: 2.38 (0.18), residues: 900 sheet: None (None), residues: 0 loop : -0.38 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 144 TYR 0.009 0.001 TYR A 487 PHE 0.025 0.001 PHE C 186 TRP 0.007 0.001 TRP B 305 HIS 0.001 0.001 HIS D 380 Details of bonding type rmsd covalent geometry : bond 0.00291 (11568) covalent geometry : angle 0.57447 (15676) hydrogen bonds : bond 0.05356 ( 688) hydrogen bonds : angle 3.96534 ( 2004) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.306 Fit side-chains REVERT: A 450 MET cc_start: 0.5744 (tmt) cc_final: 0.4655 (mpt) REVERT: B 225 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.6467 (tm-30) REVERT: B 246 ILE cc_start: 0.7907 (pt) cc_final: 0.7665 (mt) REVERT: C 170 ARG cc_start: 0.7856 (mmt90) cc_final: 0.7620 (mmt-90) REVERT: C 225 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.6557 (tm-30) REVERT: C 246 ILE cc_start: 0.7920 (pt) cc_final: 0.7682 (mt) REVERT: D 138 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7314 (ppp80) REVERT: D 225 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.6454 (tm-30) REVERT: D 246 ILE cc_start: 0.7880 (pt) cc_final: 0.7651 (mt) outliers start: 24 outliers final: 12 residues processed: 156 average time/residue: 0.3470 time to fit residues: 60.7223 Evaluate side-chains 152 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 134 optimal weight: 0.5980 chunk 6 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.204607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.147619 restraints weight = 11650.646| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.88 r_work: 0.3024 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11568 Z= 0.211 Angle : 0.659 10.483 15676 Z= 0.346 Chirality : 0.045 0.146 1756 Planarity : 0.006 0.062 1984 Dihedral : 4.555 41.802 1544 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.55 % Allowed : 19.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.23), residues: 1360 helix: 2.15 (0.18), residues: 900 sheet: None (None), residues: 0 loop : -0.59 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 144 TYR 0.011 0.002 TYR B 226 PHE 0.026 0.002 PHE D 186 TRP 0.007 0.001 TRP A 437 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00510 (11568) covalent geometry : angle 0.65855 (15676) hydrogen bonds : bond 0.07521 ( 688) hydrogen bonds : angle 4.14585 ( 2004) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.372 Fit side-chains REVERT: D 138 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7314 (ppp80) outliers start: 19 outliers final: 15 residues processed: 140 average time/residue: 0.3258 time to fit residues: 51.7818 Evaluate side-chains 139 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 126 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 114 optimal weight: 0.0170 chunk 95 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.208900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.152731 restraints weight = 11685.274| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.90 r_work: 0.3103 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4283 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= 0.128 Angle : 0.571 10.278 15676 Z= 0.296 Chirality : 0.040 0.164 1756 Planarity : 0.006 0.063 1984 Dihedral : 4.222 36.764 1544 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.04 % Allowed : 19.22 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.24), residues: 1360 helix: 2.48 (0.18), residues: 900 sheet: None (None), residues: 0 loop : -0.43 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 170 TYR 0.008 0.001 TYR A 487 PHE 0.027 0.001 PHE B 186 TRP 0.006 0.001 TRP B 305 HIS 0.001 0.000 HIS C 451 Details of bonding type rmsd covalent geometry : bond 0.00282 (11568) covalent geometry : angle 0.57063 (15676) hydrogen bonds : bond 0.05209 ( 688) hydrogen bonds : angle 3.88243 ( 2004) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4574.85 seconds wall clock time: 78 minutes 20.66 seconds (4700.66 seconds total)