Starting phenix.real_space_refine on Sun May 3 13:56:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oxl_70988/05_2026/9oxl_70988.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oxl_70988/05_2026/9oxl_70988.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oxl_70988/05_2026/9oxl_70988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oxl_70988/05_2026/9oxl_70988.map" model { file = "/net/cci-nas-00/data/ceres_data/9oxl_70988/05_2026/9oxl_70988.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oxl_70988/05_2026/9oxl_70988.cif" } resolution = 2.62 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= -0.000 sd= 0.001 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 P 12 5.49 5 S 28 5.16 5 C 8812 2.51 5 N 2104 2.21 5 O 2312 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13268 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3142 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 24, 'TRANS': 370} Chain breaks: 1 Chain: "B" Number of atoms: 3142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3142 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 24, 'TRANS': 370} Chain breaks: 1 Chain: "C" Number of atoms: 3142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3142 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 24, 'TRANS': 370} Chain breaks: 1 Chain: "D" Number of atoms: 3142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3142 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 24, 'TRANS': 370} Chain breaks: 1 Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 175 Unusual residues: {'PEE': 7} Classifications: {'RNA': 1, 'undetermined': 7} Modifications used: {'rna3p': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 232 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PEE:plan-1': 4, 'PEE:plan-2': 4} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 175 Unusual residues: {'PEE': 7} Classifications: {'RNA': 1, 'undetermined': 7} Modifications used: {'rna3p': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 232 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PEE:plan-1': 4, 'PEE:plan-2': 4} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 137 Unusual residues: {'PEE': 6} Classifications: {'RNA': 1, 'undetermined': 6} Modifications used: {'rna3p': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PEE:plan-1': 4, 'PEE:plan-2': 4} Unresolved non-hydrogen planarities: 29 Chain: "D" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 213 Unusual residues: {'PEE': 8} Classifications: {'RNA': 1, 'undetermined': 8} Modifications used: {'rna3p': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 245 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PEE:plan-1': 4, 'PEE:plan-2': 4} Unresolved non-hydrogen planarities: 29 Time building chain proxies: 3.24, per 1000 atoms: 0.24 Number of scatterers: 13268 At special positions: 0 Unit cell: (101.7, 101.7, 117, 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) S 28 16.00 P 12 15.00 O 2312 8.00 N 2104 7.00 C 8812 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: 1.10 Conformation dependent library (CDL) restraints added in 489.9 milliseconds 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3000 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 8 sheets defined 71.2% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 9 through 36 removed outlier: 3.964A pdb=" N LEU A 13 " --> pdb=" O PRO A 9 " (cutoff:3.500A) Proline residue: A 31 - end of helix removed outlier: 3.518A pdb=" N VAL A 35 " --> pdb=" O PRO A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 40 removed outlier: 3.873A pdb=" N PHE A 40 " --> pdb=" O PRO A 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 37 through 40' Processing helix chain 'A' and resid 43 through 63 removed outlier: 4.273A pdb=" N ILE A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Proline residue: A 59 - end of helix removed outlier: 3.802A pdb=" N ALA A 63 " --> pdb=" O PRO A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 87 Processing helix chain 'A' and resid 90 through 98 Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 107 through 112 removed outlier: 3.881A pdb=" N ARG A 111 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 126 removed outlier: 4.133A pdb=" N SER A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 158 Processing helix chain 'A' and resid 165 through 182 Processing helix chain 'A' and resid 193 through 224 removed outlier: 3.766A pdb=" N LYS A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 246 removed outlier: 3.654A pdb=" N LEU A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 268 Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 280 through 293 Processing helix chain 'A' and resid 294 through 299 Processing helix chain 'A' and resid 300 through 303 removed outlier: 3.666A pdb=" N LYS A 303 " --> pdb=" O PRO A 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 300 through 303' Processing helix chain 'A' and resid 306 through 315 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.724A pdb=" N ILE A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 403 removed outlier: 4.272A pdb=" N ARG A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 414 removed outlier: 3.772A pdb=" N GLN A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 36 Proline residue: B 31 - end of helix removed outlier: 3.517A pdb=" N VAL B 35 " --> pdb=" O PRO B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 40 removed outlier: 3.873A pdb=" N PHE B 40 " --> pdb=" O PRO B 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 37 through 40' Processing helix chain 'B' and resid 43 through 63 removed outlier: 4.273A pdb=" N ILE B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Proline residue: B 59 - end of helix removed outlier: 3.802A pdb=" N ALA B 63 " --> pdb=" O PRO B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 87 Processing helix chain 'B' and resid 90 through 98 Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 107 through 112 removed outlier: 3.882A pdb=" N ARG B 111 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 126 removed outlier: 4.132A pdb=" N SER B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 158 Processing helix chain 'B' and resid 165 through 182 Processing helix chain 'B' and resid 193 through 224 removed outlier: 3.766A pdb=" N LYS B 224 " --> pdb=" O SER B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 246 removed outlier: 3.653A pdb=" N LEU B 230 " --> pdb=" O ASP B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 268 Processing helix chain 'B' and resid 271 through 277 Processing helix chain 'B' and resid 280 through 293 Processing helix chain 'B' and resid 294 through 299 Processing helix chain 'B' and resid 300 through 303 removed outlier: 3.667A pdb=" N LYS B 303 " --> pdb=" O PRO B 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 300 through 303' Processing helix chain 'B' and resid 306 through 315 Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.725A pdb=" N ILE B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 403 removed outlier: 4.272A pdb=" N ARG B 403 " --> pdb=" O ARG B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 414 removed outlier: 3.772A pdb=" N GLN B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 36 Proline residue: C 31 - end of helix removed outlier: 3.517A pdb=" N VAL C 35 " --> pdb=" O PRO C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 40 removed outlier: 3.873A pdb=" N PHE C 40 " --> pdb=" O PRO C 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 37 through 40' Processing helix chain 'C' and resid 43 through 63 removed outlier: 4.273A pdb=" N ILE C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Proline residue: C 59 - end of helix removed outlier: 3.802A pdb=" N ALA C 63 " --> pdb=" O PRO C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 87 Processing helix chain 'C' and resid 90 through 98 Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 107 through 112 removed outlier: 3.881A pdb=" N ARG C 111 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 126 removed outlier: 4.133A pdb=" N SER C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 158 Processing helix chain 'C' and resid 165 through 182 Processing helix chain 'C' and resid 193 through 224 removed outlier: 3.766A pdb=" N LYS C 224 " --> pdb=" O SER C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 246 removed outlier: 3.654A pdb=" N LEU C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 268 Processing helix chain 'C' and resid 271 through 277 Processing helix chain 'C' and resid 280 through 293 Processing helix chain 'C' and resid 294 through 299 Processing helix chain 'C' and resid 300 through 303 removed outlier: 3.667A pdb=" N LYS C 303 " --> pdb=" O PRO C 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 300 through 303' Processing helix chain 'C' and resid 306 through 315 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.724A pdb=" N ILE C 372 " --> pdb=" O GLU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 403 removed outlier: 4.273A pdb=" N ARG C 403 " --> pdb=" O ARG C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 414 removed outlier: 3.772A pdb=" N GLN C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU C 413 " --> pdb=" O ALA C 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 36 Proline residue: D 31 - end of helix removed outlier: 3.517A pdb=" N VAL D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 40 removed outlier: 3.873A pdb=" N PHE D 40 " --> pdb=" O PRO D 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 37 through 40' Processing helix chain 'D' and resid 43 through 63 removed outlier: 4.273A pdb=" N ILE D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Proline residue: D 59 - end of helix removed outlier: 3.801A pdb=" N ALA D 63 " --> pdb=" O PRO D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 87 Processing helix chain 'D' and resid 90 through 98 Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 107 through 112 removed outlier: 3.881A pdb=" N ARG D 111 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 126 removed outlier: 4.132A pdb=" N SER D 117 " --> pdb=" O LEU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 158 Processing helix chain 'D' and resid 165 through 182 Processing helix chain 'D' and resid 193 through 224 removed outlier: 3.766A pdb=" N LYS D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 246 removed outlier: 3.654A pdb=" N LEU D 230 " --> pdb=" O ASP D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 268 Processing helix chain 'D' and resid 271 through 277 Processing helix chain 'D' and resid 280 through 293 Processing helix chain 'D' and resid 294 through 299 Processing helix chain 'D' and resid 300 through 303 removed outlier: 3.666A pdb=" N LYS D 303 " --> pdb=" O PRO D 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 300 through 303' Processing helix chain 'D' and resid 306 through 315 Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.725A pdb=" N ILE D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 403 removed outlier: 4.272A pdb=" N ARG D 403 " --> pdb=" O ARG D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 414 removed outlier: 3.773A pdb=" N GLN D 410 " --> pdb=" O GLU D 406 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU D 413 " --> pdb=" O ALA D 409 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 322 Processing sheet with id=AA2, first strand: chain 'A' and resid 327 through 329 removed outlier: 6.795A pdb=" N TYR A 327 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ALA A 383 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 358 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 318 through 322 Processing sheet with id=AA4, first strand: chain 'B' and resid 327 through 329 removed outlier: 6.795A pdb=" N TYR B 327 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ALA B 383 " --> pdb=" O TYR B 327 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA B 358 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 318 through 322 Processing sheet with id=AA6, first strand: chain 'C' and resid 327 through 329 removed outlier: 6.796A pdb=" N TYR C 327 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ALA C 383 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA C 358 " --> pdb=" O VAL C 348 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 318 through 322 Processing sheet with id=AA8, first strand: chain 'D' and resid 327 through 329 removed outlier: 6.795A pdb=" N TYR D 327 " --> pdb=" O ALA D 383 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ALA D 383 " --> pdb=" O TYR D 327 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA D 358 " --> pdb=" O VAL D 348 " (cutoff:3.500A) 808 hydrogen bonds defined for protein. 2352 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.23 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1984 1.30 - 1.43: 3376 1.43 - 1.55: 8095 1.55 - 1.68: 41 1.68 - 1.80: 48 Bond restraints: 13544 Sorted by residual: bond pdb=" C18 PEE D 509 " pdb=" C19 PEE D 509 " ideal model delta sigma weight residual 1.523 1.300 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C18 PEE B 507 " pdb=" C19 PEE B 507 " ideal model delta sigma weight residual 1.523 1.301 0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C18 PEE A 507 " pdb=" C19 PEE A 507 " ideal model delta sigma weight residual 1.523 1.301 0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C38 PEE B 502 " pdb=" C39 PEE B 502 " ideal model delta sigma weight residual 1.523 1.301 0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C38 PEE D 503 " pdb=" C39 PEE D 503 " ideal model delta sigma weight residual 1.523 1.301 0.222 2.00e-02 2.50e+03 1.23e+02 ... (remaining 13539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 17831 3.30 - 6.59: 377 6.59 - 9.89: 40 9.89 - 13.19: 40 13.19 - 16.48: 8 Bond angle restraints: 18296 Sorted by residual: angle pdb=" O3P PEE C 506 " pdb=" P PEE C 506 " pdb=" O4P PEE C 506 " ideal model delta sigma weight residual 92.91 109.39 -16.48 3.00e+00 1.11e-01 3.02e+01 angle pdb=" O3P PEE D 507 " pdb=" P PEE D 507 " pdb=" O4P PEE D 507 " ideal model delta sigma weight residual 92.91 109.39 -16.48 3.00e+00 1.11e-01 3.02e+01 angle pdb=" O3P PEE A 506 " pdb=" P PEE A 506 " pdb=" O4P PEE A 506 " ideal model delta sigma weight residual 92.91 109.38 -16.47 3.00e+00 1.11e-01 3.01e+01 angle pdb=" O3P PEE B 506 " pdb=" P PEE B 506 " pdb=" O4P PEE B 506 " ideal model delta sigma weight residual 92.91 109.37 -16.46 3.00e+00 1.11e-01 3.01e+01 angle pdb=" O3P PEE D 508 " pdb=" P PEE D 508 " pdb=" O4P PEE D 508 " ideal model delta sigma weight residual 92.91 109.06 -16.15 3.00e+00 1.11e-01 2.90e+01 ... (remaining 18291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.47: 7888 28.47 - 56.94: 336 56.94 - 85.40: 44 85.40 - 113.87: 4 113.87 - 142.34: 16 Dihedral angle restraints: 8288 sinusoidal: 3640 harmonic: 4648 Sorted by residual: dihedral pdb=" C2 PEE B 502 " pdb=" C10 PEE B 502 " pdb=" O2 PEE B 502 " pdb=" O4 PEE B 502 " ideal model delta sinusoidal sigma weight residual 2.73 -139.61 142.34 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" C2 PEE C 502 " pdb=" C10 PEE C 502 " pdb=" O2 PEE C 502 " pdb=" O4 PEE C 502 " ideal model delta sinusoidal sigma weight residual 2.73 -139.60 142.33 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" C2 PEE A 502 " pdb=" C10 PEE A 502 " pdb=" O2 PEE A 502 " pdb=" O4 PEE A 502 " ideal model delta sinusoidal sigma weight residual 2.73 -139.59 142.32 1 3.00e+01 1.11e-03 1.91e+01 ... (remaining 8285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1438 0.040 - 0.079: 453 0.079 - 0.119: 173 0.119 - 0.159: 24 0.159 - 0.199: 28 Chirality restraints: 2116 Sorted by residual: chirality pdb=" C2 PEE D 507 " pdb=" C1 PEE D 507 " pdb=" C3 PEE D 507 " pdb=" O2 PEE D 507 " both_signs ideal model delta sigma weight residual False -2.33 -2.53 0.20 2.00e-01 2.50e+01 9.86e-01 chirality pdb=" C2 PEE B 506 " pdb=" C1 PEE B 506 " pdb=" C3 PEE B 506 " pdb=" O2 PEE B 506 " both_signs ideal model delta sigma weight residual False -2.33 -2.52 0.20 2.00e-01 2.50e+01 9.59e-01 chirality pdb=" C2 PEE A 506 " pdb=" C1 PEE A 506 " pdb=" C3 PEE A 506 " pdb=" O2 PEE A 506 " both_signs ideal model delta sigma weight residual False -2.33 -2.52 0.20 2.00e-01 2.50e+01 9.57e-01 ... (remaining 2113 not shown) Planarity restraints: 2196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 280 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.09e+00 pdb=" C PRO A 280 " -0.030 2.00e-02 2.50e+03 pdb=" O PRO A 280 " 0.011 2.00e-02 2.50e+03 pdb=" N HIS A 281 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 280 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.08e+00 pdb=" C PRO C 280 " 0.030 2.00e-02 2.50e+03 pdb=" O PRO C 280 " -0.011 2.00e-02 2.50e+03 pdb=" N HIS C 281 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 280 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.06e+00 pdb=" C PRO B 280 " 0.030 2.00e-02 2.50e+03 pdb=" O PRO B 280 " -0.011 2.00e-02 2.50e+03 pdb=" N HIS B 281 " -0.010 2.00e-02 2.50e+03 ... (remaining 2193 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 4050 2.84 - 3.35: 12877 3.35 - 3.87: 22682 3.87 - 4.38: 25871 4.38 - 4.90: 43920 Nonbonded interactions: 109400 Sorted by model distance: nonbonded pdb=" OG SER B 361 " pdb=" OE1 GLU B 362 " model vdw 2.322 3.040 nonbonded pdb=" OG SER A 361 " pdb=" OE1 GLU A 362 " model vdw 2.323 3.040 nonbonded pdb=" OG SER C 361 " pdb=" OE1 GLU C 362 " model vdw 2.323 3.040 nonbonded pdb=" OG SER D 361 " pdb=" OE1 GLU D 362 " model vdw 2.323 3.040 nonbonded pdb=" OD2 ASP C 312 " pdb=" OH TYR C 404 " model vdw 2.412 3.040 ... (remaining 109395 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 9 through 414 or (resid 503 and (name C10 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name O4 )) or (resid 504 through 505 and (name C15 or name C16 or \ name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C2 \ 3 or name C24 or name C25)) or (resid 506 and (name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name \ C23)) or resid 507)) selection = (chain 'B' and (resid 9 through 414 or (resid 503 and (name C10 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name O4 )) or (resid 504 through 505 and (name C15 or name C16 or \ name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C2 \ 3 or name C24 or name C25)) or (resid 506 and (name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name \ C23)) or resid 507)) selection = (chain 'C' and (resid 9 through 414 or (resid 503 and (name C10 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name O4 )) or (resid 504 through 505 and (name C15 or name C16 or \ name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C2 \ 3 or name C24 or name C25)) or (resid 506 and (name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name \ C23)) or resid 507)) selection = (chain 'D' and (resid 9 through 414 or (resid 503 and (name C10 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name O4 )) or (resid 504 through 505 and (name C15 or name C16 or \ name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C2 \ 3 or name C24 or name C25)) or (resid 506 and (name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name \ C23)) or (resid 507 and (name C13 or name C14 or name C15 or name C16 or name C1 \ 7 or name C18 or name C19 or name C20 or name C21 or name C22)))) } 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: 2.870 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.970 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 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 : 0.011 0.223 13544 Z= 0.580 Angle : 1.155 16.481 18296 Z= 0.543 Chirality : 0.048 0.199 2116 Planarity : 0.005 0.030 2196 Dihedral : 17.066 142.340 5288 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.29 % Allowed : 7.37 % Favored : 92.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.21), residues: 1564 helix: 1.46 (0.16), residues: 988 sheet: -0.57 (0.57), residues: 88 loop : -0.14 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 29 TYR 0.010 0.001 TYR C 186 PHE 0.011 0.001 PHE D 242 TRP 0.009 0.001 TRP D 264 HIS 0.003 0.001 HIS D 316 Details of bonding type rmsd covalent geometry : bond 0.01101 (13544) covalent geometry : angle 1.15483 (18296) hydrogen bonds : bond 0.13129 ( 808) hydrogen bonds : angle 6.26018 ( 2352) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 136 time to evaluate : 0.495 Fit side-chains REVERT: A 47 ASP cc_start: 0.7654 (m-30) cc_final: 0.7307 (m-30) REVERT: B 47 ASP cc_start: 0.7888 (m-30) cc_final: 0.7520 (m-30) REVERT: B 128 TYR cc_start: 0.7952 (p90) cc_final: 0.7715 (p90) REVERT: B 334 MET cc_start: 0.7475 (mmm) cc_final: 0.7271 (tpt) REVERT: C 47 ASP cc_start: 0.7992 (m-30) cc_final: 0.7551 (m-30) REVERT: C 273 ARG cc_start: 0.7979 (mtm-85) cc_final: 0.7754 (mtt90) REVERT: C 318 GLU cc_start: 0.8467 (tt0) cc_final: 0.8226 (tt0) REVERT: D 47 ASP cc_start: 0.7964 (m-30) cc_final: 0.7573 (m-30) REVERT: D 334 MET cc_start: 0.7347 (mmm) cc_final: 0.7050 (tpt) outliers start: 4 outliers final: 2 residues processed: 140 average time/residue: 0.8899 time to fit residues: 132.3282 Evaluate side-chains 71 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 128 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3615 r_free = 0.3615 target = 0.095466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.066186 restraints weight = 27067.851| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.59 r_work: 0.2824 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13544 Z= 0.144 Angle : 0.576 7.806 18296 Z= 0.279 Chirality : 0.040 0.134 2116 Planarity : 0.004 0.033 2196 Dihedral : 15.730 131.950 2304 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.62 % Allowed : 11.87 % Favored : 86.50 % 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: 1.77 (0.21), residues: 1564 helix: 1.95 (0.16), residues: 1016 sheet: -1.08 (0.56), residues: 88 loop : -0.04 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 399 TYR 0.025 0.001 TYR A 128 PHE 0.008 0.001 PHE A 365 TRP 0.009 0.001 TRP C 264 HIS 0.002 0.001 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00318 (13544) covalent geometry : angle 0.57583 (18296) hydrogen bonds : bond 0.04186 ( 808) hydrogen bonds : angle 4.57381 ( 2352) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.544 Fit side-chains REVERT: A 47 ASP cc_start: 0.7614 (m-30) cc_final: 0.7058 (m-30) REVERT: B 47 ASP cc_start: 0.7752 (m-30) cc_final: 0.7025 (m-30) REVERT: B 119 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.7285 (tp40) REVERT: B 128 TYR cc_start: 0.8044 (p90) cc_final: 0.7805 (p90) REVERT: C 47 ASP cc_start: 0.7844 (m-30) cc_final: 0.7199 (m-30) REVERT: C 77 LEU cc_start: 0.8343 (mm) cc_final: 0.8011 (mt) REVERT: C 273 ARG cc_start: 0.8398 (mtm-85) cc_final: 0.8055 (mtt90) REVERT: C 318 GLU cc_start: 0.8998 (tt0) cc_final: 0.8472 (tt0) REVERT: D 26 TYR cc_start: 0.8878 (OUTLIER) cc_final: 0.8609 (m-10) REVERT: D 47 ASP cc_start: 0.7778 (m-30) cc_final: 0.7178 (m-30) REVERT: D 334 MET cc_start: 0.7414 (mmm) cc_final: 0.7200 (tpt) outliers start: 22 outliers final: 2 residues processed: 100 average time/residue: 0.7717 time to fit residues: 83.0935 Evaluate side-chains 73 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain D residue 26 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 109 optimal weight: 9.9990 chunk 141 optimal weight: 0.0000 chunk 119 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 11 optimal weight: 0.4980 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.094912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.065489 restraints weight = 27437.825| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.63 r_work: 0.2834 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13544 Z= 0.132 Angle : 0.562 7.440 18296 Z= 0.267 Chirality : 0.040 0.135 2116 Planarity : 0.004 0.036 2196 Dihedral : 13.572 133.266 2302 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.21 % Allowed : 12.98 % Favored : 84.81 % 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: 2.12 (0.22), residues: 1564 helix: 2.23 (0.16), residues: 1024 sheet: -1.15 (0.52), residues: 88 loop : 0.09 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 273 TYR 0.030 0.001 TYR C 128 PHE 0.007 0.001 PHE A 365 TRP 0.008 0.001 TRP C 264 HIS 0.001 0.000 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00299 (13544) covalent geometry : angle 0.56230 (18296) hydrogen bonds : bond 0.03611 ( 808) hydrogen bonds : angle 4.17596 ( 2352) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7612 (m-30) cc_final: 0.6870 (m-30) REVERT: B 47 ASP cc_start: 0.7663 (m-30) cc_final: 0.6885 (m-30) REVERT: B 128 TYR cc_start: 0.8069 (p90) cc_final: 0.7815 (p90) REVERT: B 273 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7948 (mtt90) REVERT: C 47 ASP cc_start: 0.7857 (m-30) cc_final: 0.6954 (m-30) REVERT: C 77 LEU cc_start: 0.8347 (mm) cc_final: 0.8024 (mt) REVERT: C 273 ARG cc_start: 0.8398 (mtm-85) cc_final: 0.7936 (mtt90) REVERT: D 26 TYR cc_start: 0.8811 (OUTLIER) cc_final: 0.8517 (m-10) REVERT: D 47 ASP cc_start: 0.7767 (m-30) cc_final: 0.6919 (m-30) REVERT: D 273 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7845 (mtt90) REVERT: D 334 MET cc_start: 0.7531 (mmm) cc_final: 0.7330 (tpt) outliers start: 30 outliers final: 0 residues processed: 102 average time/residue: 0.7141 time to fit residues: 78.6967 Evaluate side-chains 75 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 273 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 137 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 146 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.094824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.065402 restraints weight = 26591.002| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.58 r_work: 0.2839 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13544 Z= 0.128 Angle : 0.566 9.811 18296 Z= 0.264 Chirality : 0.039 0.136 2116 Planarity : 0.004 0.036 2196 Dihedral : 12.813 133.122 2302 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.55 % Allowed : 14.31 % Favored : 84.14 % 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: 2.34 (0.22), residues: 1564 helix: 2.30 (0.16), residues: 1052 sheet: -1.09 (0.52), residues: 88 loop : 0.31 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.023 0.001 TYR A 128 PHE 0.006 0.001 PHE A 242 TRP 0.009 0.001 TRP C 264 HIS 0.001 0.000 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00292 (13544) covalent geometry : angle 0.56592 (18296) hydrogen bonds : bond 0.03440 ( 808) hydrogen bonds : angle 4.01636 ( 2352) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.550 Fit side-chains REVERT: B 47 ASP cc_start: 0.7685 (m-30) cc_final: 0.6996 (m-30) REVERT: B 289 MET cc_start: 0.8688 (ttp) cc_final: 0.8460 (mtp) REVERT: C 47 ASP cc_start: 0.7861 (m-30) cc_final: 0.6966 (m-30) REVERT: C 77 LEU cc_start: 0.8356 (mm) cc_final: 0.8033 (mt) REVERT: C 273 ARG cc_start: 0.8410 (mtm-85) cc_final: 0.7970 (mtt90) REVERT: D 26 TYR cc_start: 0.8786 (OUTLIER) cc_final: 0.8481 (m-10) REVERT: D 47 ASP cc_start: 0.7810 (m-30) cc_final: 0.7091 (m-30) REVERT: D 273 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7862 (mtt90) outliers start: 21 outliers final: 0 residues processed: 94 average time/residue: 0.7579 time to fit residues: 76.8796 Evaluate side-chains 68 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 273 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 84 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3587 r_free = 0.3587 target = 0.094025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.064536 restraints weight = 26836.974| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.59 r_work: 0.2815 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13544 Z= 0.150 Angle : 0.574 8.064 18296 Z= 0.270 Chirality : 0.040 0.135 2116 Planarity : 0.004 0.036 2196 Dihedral : 12.370 132.597 2302 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.14 % Allowed : 14.31 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.43 (0.22), residues: 1564 helix: 2.36 (0.16), residues: 1036 sheet: -1.01 (0.53), residues: 88 loop : 0.44 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.027 0.001 TYR B 128 PHE 0.007 0.001 PHE A 365 TRP 0.008 0.001 TRP C 264 HIS 0.002 0.001 HIS B 316 Details of bonding type rmsd covalent geometry : bond 0.00352 (13544) covalent geometry : angle 0.57434 (18296) hydrogen bonds : bond 0.03486 ( 808) hydrogen bonds : angle 3.94460 ( 2352) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 0.501 Fit side-chains revert: symmetry clash REVERT: B 273 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7986 (mmm-85) REVERT: B 289 MET cc_start: 0.8711 (ttp) cc_final: 0.8503 (mtp) REVERT: C 47 ASP cc_start: 0.7843 (m-30) cc_final: 0.7344 (m-30) REVERT: C 77 LEU cc_start: 0.8310 (mm) cc_final: 0.7990 (mt) REVERT: C 273 ARG cc_start: 0.8438 (mtm-85) cc_final: 0.8212 (mmm-85) REVERT: D 26 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.8523 (m-10) REVERT: D 47 ASP cc_start: 0.7739 (m-30) cc_final: 0.7284 (m-30) outliers start: 29 outliers final: 2 residues processed: 98 average time/residue: 0.7493 time to fit residues: 79.3001 Evaluate side-chains 73 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 266 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 100 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 95 optimal weight: 0.0670 chunk 3 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 150 optimal weight: 8.9990 chunk 147 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.7718 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.094372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.065038 restraints weight = 26569.527| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.58 r_work: 0.2828 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13544 Z= 0.123 Angle : 0.565 8.045 18296 Z= 0.264 Chirality : 0.039 0.137 2116 Planarity : 0.004 0.037 2196 Dihedral : 11.991 132.905 2302 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.70 % Allowed : 15.34 % Favored : 82.96 % 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: 2.55 (0.22), residues: 1564 helix: 2.36 (0.16), residues: 1060 sheet: -1.05 (0.52), residues: 88 loop : 0.65 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 29 TYR 0.023 0.001 TYR A 128 PHE 0.006 0.001 PHE A 242 TRP 0.008 0.001 TRP C 264 HIS 0.002 0.001 HIS C 316 Details of bonding type rmsd covalent geometry : bond 0.00283 (13544) covalent geometry : angle 0.56547 (18296) hydrogen bonds : bond 0.03279 ( 808) hydrogen bonds : angle 3.87600 ( 2352) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8118 (m-30) cc_final: 0.7430 (m-30) REVERT: B 47 ASP cc_start: 0.8008 (m-30) cc_final: 0.7418 (m-30) REVERT: B 128 TYR cc_start: 0.8096 (p90) cc_final: 0.7890 (p90) REVERT: B 273 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.8001 (mtt90) REVERT: B 289 MET cc_start: 0.8713 (ttp) cc_final: 0.8492 (mtp) REVERT: C 47 ASP cc_start: 0.7869 (m-30) cc_final: 0.7320 (m-30) REVERT: C 77 LEU cc_start: 0.8323 (mm) cc_final: 0.8016 (mt) REVERT: C 273 ARG cc_start: 0.8399 (mtm-85) cc_final: 0.8178 (mmm-85) REVERT: D 26 TYR cc_start: 0.8789 (OUTLIER) cc_final: 0.8483 (m-10) REVERT: D 47 ASP cc_start: 0.7773 (m-30) cc_final: 0.7273 (m-30) REVERT: D 273 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7967 (mmt90) REVERT: D 369 MET cc_start: 0.8120 (mtt) cc_final: 0.7821 (mtm) outliers start: 23 outliers final: 2 residues processed: 94 average time/residue: 0.8465 time to fit residues: 85.2302 Evaluate side-chains 73 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 273 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 85 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 25 optimal weight: 0.3980 chunk 121 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 148 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 56 optimal weight: 0.0070 overall best weight: 1.4802 ------------------------------------------------------------------------------- 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 = 0.3574 r_free = 0.3574 target = 0.092987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.063570 restraints weight = 26856.845| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.59 r_work: 0.2800 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13544 Z= 0.174 Angle : 0.597 8.249 18296 Z= 0.281 Chirality : 0.040 0.133 2116 Planarity : 0.004 0.037 2196 Dihedral : 11.887 132.205 2302 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.99 % Allowed : 14.97 % Favored : 83.04 % 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: 2.60 (0.22), residues: 1564 helix: 2.46 (0.16), residues: 1028 sheet: -1.02 (0.52), residues: 88 loop : 0.66 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 29 TYR 0.024 0.001 TYR D 128 PHE 0.007 0.001 PHE A 365 TRP 0.008 0.001 TRP C 264 HIS 0.002 0.001 HIS C 316 Details of bonding type rmsd covalent geometry : bond 0.00415 (13544) covalent geometry : angle 0.59652 (18296) hydrogen bonds : bond 0.03509 ( 808) hydrogen bonds : angle 3.90786 ( 2352) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 70 time to evaluate : 0.494 Fit side-chains REVERT: A 47 ASP cc_start: 0.8132 (m-30) cc_final: 0.7459 (m-30) REVERT: B 47 ASP cc_start: 0.7990 (m-30) cc_final: 0.7344 (m-30) REVERT: B 125 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8494 (mp) REVERT: B 128 TYR cc_start: 0.8127 (p90) cc_final: 0.7906 (p90) REVERT: B 273 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8011 (mmt90) REVERT: B 289 MET cc_start: 0.8725 (ttp) cc_final: 0.8511 (mtp) REVERT: C 47 ASP cc_start: 0.7890 (m-30) cc_final: 0.7369 (m-30) REVERT: C 77 LEU cc_start: 0.8306 (mm) cc_final: 0.7994 (mt) REVERT: C 289 MET cc_start: 0.8665 (ttp) cc_final: 0.8465 (mtp) REVERT: D 26 TYR cc_start: 0.8848 (OUTLIER) cc_final: 0.8563 (m-10) REVERT: D 47 ASP cc_start: 0.7794 (m-30) cc_final: 0.7272 (m-30) REVERT: D 273 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.8007 (mmt90) outliers start: 27 outliers final: 6 residues processed: 93 average time/residue: 0.7303 time to fit residues: 73.5746 Evaluate side-chains 76 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 277 LYS Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 273 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 23 optimal weight: 0.8980 chunk 8 optimal weight: 0.0370 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 98 optimal weight: 0.0770 chunk 135 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 overall best weight: 0.5416 ------------------------------------------------------------------------------- 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 = 0.3595 r_free = 0.3595 target = 0.094237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.064854 restraints weight = 26629.513| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.59 r_work: 0.2831 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13544 Z= 0.117 Angle : 0.588 8.207 18296 Z= 0.276 Chirality : 0.039 0.134 2116 Planarity : 0.004 0.038 2196 Dihedral : 11.569 132.978 2302 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.25 % Allowed : 16.22 % Favored : 82.52 % 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: 2.66 (0.22), residues: 1564 helix: 2.41 (0.16), residues: 1060 sheet: -1.04 (0.51), residues: 88 loop : 0.81 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 273 TYR 0.024 0.001 TYR A 128 PHE 0.006 0.001 PHE C 64 TRP 0.009 0.001 TRP C 264 HIS 0.002 0.000 HIS C 316 Details of bonding type rmsd covalent geometry : bond 0.00267 (13544) covalent geometry : angle 0.58814 (18296) hydrogen bonds : bond 0.03194 ( 808) hydrogen bonds : angle 3.86360 ( 2352) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8119 (m-30) cc_final: 0.7443 (m-30) REVERT: B 47 ASP cc_start: 0.7955 (m-30) cc_final: 0.7333 (m-30) REVERT: B 273 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7964 (mmt90) REVERT: B 289 MET cc_start: 0.8724 (ttp) cc_final: 0.8502 (mtp) REVERT: C 47 ASP cc_start: 0.7896 (m-30) cc_final: 0.7328 (m-30) REVERT: C 77 LEU cc_start: 0.8319 (mm) cc_final: 0.8019 (mt) REVERT: D 47 ASP cc_start: 0.7784 (m-30) cc_final: 0.7312 (m-30) REVERT: D 273 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7972 (mmt90) outliers start: 17 outliers final: 8 residues processed: 83 average time/residue: 0.8160 time to fit residues: 72.8478 Evaluate side-chains 77 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 277 LYS Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 273 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 102 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.093176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.063645 restraints weight = 26894.448| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.60 r_work: 0.2806 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13544 Z= 0.165 Angle : 0.615 8.274 18296 Z= 0.290 Chirality : 0.040 0.131 2116 Planarity : 0.004 0.057 2196 Dihedral : 11.699 132.345 2302 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.33 % Allowed : 16.59 % 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 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: 2.64 (0.22), residues: 1564 helix: 2.47 (0.16), residues: 1032 sheet: -1.05 (0.51), residues: 88 loop : 0.72 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 273 TYR 0.025 0.001 TYR B 128 PHE 0.007 0.001 PHE A 365 TRP 0.007 0.001 TRP C 264 HIS 0.002 0.001 HIS D 316 Details of bonding type rmsd covalent geometry : bond 0.00396 (13544) covalent geometry : angle 0.61464 (18296) hydrogen bonds : bond 0.03431 ( 808) hydrogen bonds : angle 3.88689 ( 2352) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.571 Fit side-chains REVERT: A 47 ASP cc_start: 0.8148 (m-30) cc_final: 0.7468 (m-30) REVERT: B 47 ASP cc_start: 0.7978 (m-30) cc_final: 0.7339 (m-30) REVERT: B 289 MET cc_start: 0.8727 (ttp) cc_final: 0.8510 (mtp) REVERT: C 77 LEU cc_start: 0.8340 (mm) cc_final: 0.8041 (mt) REVERT: D 273 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.8012 (mmt90) REVERT: D 303 LYS cc_start: 0.8449 (mmmm) cc_final: 0.8244 (mmmt) outliers start: 18 outliers final: 10 residues processed: 84 average time/residue: 0.7653 time to fit residues: 69.4370 Evaluate side-chains 79 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 277 LYS Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 273 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 120 optimal weight: 3.9990 chunk 80 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 129 optimal weight: 0.7980 chunk 95 optimal weight: 0.3980 chunk 149 optimal weight: 2.9990 chunk 117 optimal weight: 8.9990 chunk 7 optimal weight: 0.0980 chunk 132 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.094629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.065078 restraints weight = 26894.963| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.61 r_work: 0.2823 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13544 Z= 0.118 Angle : 0.596 8.301 18296 Z= 0.281 Chirality : 0.039 0.135 2116 Planarity : 0.004 0.059 2196 Dihedral : 11.460 132.988 2302 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.74 % Allowed : 17.18 % 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 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: 2.72 (0.22), residues: 1564 helix: 2.44 (0.16), residues: 1060 sheet: -1.03 (0.51), residues: 88 loop : 0.93 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 273 TYR 0.018 0.001 TYR A 128 PHE 0.006 0.001 PHE B 64 TRP 0.009 0.001 TRP C 264 HIS 0.002 0.000 HIS C 316 Details of bonding type rmsd covalent geometry : bond 0.00270 (13544) covalent geometry : angle 0.59628 (18296) hydrogen bonds : bond 0.03146 ( 808) hydrogen bonds : angle 3.83844 ( 2352) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8092 (m-30) cc_final: 0.7417 (m-30) REVERT: B 47 ASP cc_start: 0.7949 (m-30) cc_final: 0.7310 (m-30) REVERT: B 128 TYR cc_start: 0.8137 (p90) cc_final: 0.7900 (p90) REVERT: B 289 MET cc_start: 0.8721 (ttp) cc_final: 0.8500 (mtp) REVERT: C 47 ASP cc_start: 0.8168 (m-30) cc_final: 0.7447 (m-30) REVERT: C 77 LEU cc_start: 0.8329 (mm) cc_final: 0.8021 (mt) REVERT: D 47 ASP cc_start: 0.8105 (m-30) cc_final: 0.7455 (m-30) REVERT: D 273 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7993 (mmt90) outliers start: 10 outliers final: 7 residues processed: 81 average time/residue: 0.8057 time to fit residues: 70.4643 Evaluate side-chains 75 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 273 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 117 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.0170 chunk 30 optimal weight: 0.4980 chunk 82 optimal weight: 0.6980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 412 GLN D 412 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.094525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.064975 restraints weight = 27107.374| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.61 r_work: 0.2824 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13544 Z= 0.124 Angle : 0.603 9.347 18296 Z= 0.283 Chirality : 0.039 0.139 2116 Planarity : 0.004 0.062 2196 Dihedral : 11.377 132.960 2302 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.74 % Allowed : 17.26 % Favored : 82.01 % 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: 2.68 (0.22), residues: 1564 helix: 2.41 (0.17), residues: 1048 sheet: -1.05 (0.51), residues: 88 loop : 0.96 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 273 TYR 0.012 0.001 TYR A 245 PHE 0.006 0.001 PHE A 64 TRP 0.009 0.001 TRP C 264 HIS 0.002 0.000 HIS B 316 Details of bonding type rmsd covalent geometry : bond 0.00287 (13544) covalent geometry : angle 0.60318 (18296) hydrogen bonds : bond 0.03152 ( 808) hydrogen bonds : angle 3.82723 ( 2352) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3791.24 seconds wall clock time: 65 minutes 30.40 seconds (3930.40 seconds total)