Starting phenix.real_space_refine on Thu Aug 6 05:28:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oxl_70988/08_2026/9oxl_70988.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oxl_70988/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9oxl_70988/08_2026/9oxl_70988.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oxl_70988/08_2026/9oxl_70988.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oxl_70988/08_2026/9oxl_70988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oxl_70988/08_2026/9oxl_70988.map" } 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-2.2rc3-6140/lib/python3.11/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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: 3.19, 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: 1.14 Conformation dependent library (CDL) restraints added in 555.3 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: 0.37 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: 2.67 Time building geometry restraints manager: 1.55 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: 17827 3.30 - 6.59: 365 6.59 - 9.89: 52 9.89 - 13.19: 44 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: 7892 28.47 - 56.94: 336 56.94 - 85.40: 44 85.40 - 113.87: 0 113.87 - 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: 457 0.079 - 0.119: 173 0.119 - 0.159: 24 0.159 - 0.199: 24 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: 4.150 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.810 Find NCS groups from input model: 0.400 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: 0.010 Load rotamer database and sin/cos tables:10.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 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= 0.578 Angle : 1.180 16.481 18296 Z= 0.534 Chirality : 0.048 0.199 2116 Planarity : 0.005 0.030 2196 Dihedral : 16.767 142.340 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/Z covalent geometry : bond 0.01101 / 0.58 (13544) covalent geometry : angle 1.18035 / 0.53 (18296) hydrogen bonds : bond 0.13129 / 8.85 ( 808) hydrogen bonds : angle 6.26018 / 4.43 ( 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 : 0.414 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: 0.7555 time to fit residues: 112.8014 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 : 0.395 ------------------------------------------------------------------------------- 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... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.095383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.066060 restraints weight = 27052.447| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.60 r_work: 0.2819 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13544 Z= 0.138 Angle : 0.612 8.512 18296 Z= 0.279 Chirality : 0.041 0.155 2116 Planarity : 0.004 0.034 2196 Dihedral : 14.302 119.458 2304 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.62 % Allowed : 12.02 % Favored : 86.36 % 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: 1.96 (0.16), residues: 1016 sheet: -1.07 (0.55), residues: 88 loop : -0.05 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 273 TYR 0.027 0.001 TYR A 128 PHE 0.009 0.001 PHE A 365 TRP 0.008 0.001 TRP C 264 HIS 0.002 0.001 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (13544) covalent geometry : angle 0.61233 / 0.28 (18296) hydrogen bonds : bond 0.03964 / 2.57 ( 808) hydrogen bonds : angle 4.48305 / 3.17 ( 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 105 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.515 Fit side-chains REVERT: A 47 ASP cc_start: 0.7620 (m-30) cc_final: 0.6962 (m-30) REVERT: B 26 TYR cc_start: 0.8902 (OUTLIER) cc_final: 0.8697 (m-10) REVERT: B 47 ASP cc_start: 0.7729 (m-30) cc_final: 0.6995 (m-30) REVERT: B 119 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.7270 (tp40) REVERT: B 128 TYR cc_start: 0.8030 (p90) cc_final: 0.7783 (p90) REVERT: C 47 ASP cc_start: 0.7854 (m-30) cc_final: 0.7106 (m-30) REVERT: C 77 LEU cc_start: 0.8344 (mm) cc_final: 0.8009 (mt) REVERT: C 273 ARG cc_start: 0.8410 (mtm-85) cc_final: 0.8064 (mtt90) REVERT: C 318 GLU cc_start: 0.9008 (tt0) cc_final: 0.8471 (tt0) REVERT: D 26 TYR cc_start: 0.8865 (OUTLIER) cc_final: 0.8536 (m-10) REVERT: D 47 ASP cc_start: 0.7836 (m-30) cc_final: 0.7102 (m-30) REVERT: D 334 MET cc_start: 0.7445 (mmm) cc_final: 0.7233 (tpt) outliers start: 22 outliers final: 3 residues processed: 101 average time/residue: 0.6231 time to fit residues: 68.2452 Evaluate side-chains 76 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 289 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 3 optimal weight: 0.0570 chunk 15 optimal weight: 2.9990 chunk 109 optimal weight: 9.9990 chunk 141 optimal weight: 0.1980 chunk 119 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.095297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.065839 restraints weight = 26825.449| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.59 r_work: 0.2848 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13544 Z= 0.128 Angle : 0.600 8.511 18296 Z= 0.268 Chirality : 0.040 0.154 2116 Planarity : 0.004 0.037 2196 Dihedral : 12.383 102.998 2302 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.99 % Allowed : 13.35 % Favored : 84.66 % 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: 2.16 (0.22), residues: 1564 helix: 2.27 (0.16), residues: 1024 sheet: -1.18 (0.52), residues: 88 loop : 0.10 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 273 TYR 0.028 0.001 TYR C 128 PHE 0.006 0.001 PHE A 365 TRP 0.009 0.001 TRP C 264 HIS 0.001 0.000 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (13544) covalent geometry : angle 0.59962 / 0.27 (18296) hydrogen bonds : bond 0.03607 / 2.34 ( 808) hydrogen bonds : angle 4.19246 / 2.97 ( 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 104 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7600 (m-30) cc_final: 0.6826 (m-30) REVERT: B 47 ASP cc_start: 0.7700 (m-30) cc_final: 0.6873 (m-30) REVERT: B 128 TYR cc_start: 0.8074 (p90) cc_final: 0.7817 (p90) REVERT: B 273 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7917 (mtt90) REVERT: C 47 ASP cc_start: 0.7860 (m-30) cc_final: 0.7017 (m-30) REVERT: C 77 LEU cc_start: 0.8355 (mm) cc_final: 0.8029 (mt) REVERT: C 273 ARG cc_start: 0.8396 (mtm-85) cc_final: 0.7930 (mtt90) REVERT: D 26 TYR cc_start: 0.8787 (OUTLIER) cc_final: 0.8489 (m-10) REVERT: D 47 ASP cc_start: 0.7784 (m-30) cc_final: 0.6929 (m-30) REVERT: D 273 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7853 (mtt90) REVERT: D 334 MET cc_start: 0.7521 (mmm) cc_final: 0.7303 (tpt) outliers start: 27 outliers final: 0 residues processed: 102 average time/residue: 0.7198 time to fit residues: 79.5125 Evaluate side-chains 73 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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: 2.9990 chunk 126 optimal weight: 2.9990 chunk 111 optimal weight: 0.4980 chunk 57 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 148 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 41 optimal weight: 0.0970 chunk 146 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.095318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.065914 restraints weight = 26499.179| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.58 r_work: 0.2850 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.1947 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= 0.116 Angle : 0.597 8.430 18296 Z= 0.263 Chirality : 0.040 0.150 2116 Planarity : 0.004 0.036 2196 Dihedral : 11.464 101.431 2302 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.40 % Allowed : 14.31 % Favored : 84.29 % 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: 2.37 (0.22), residues: 1564 helix: 2.33 (0.16), residues: 1052 sheet: -1.11 (0.52), residues: 88 loop : 0.33 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 273 TYR 0.024 0.001 TYR D 128 PHE 0.006 0.001 PHE A 242 TRP 0.009 0.001 TRP C 264 HIS 0.001 0.000 HIS C 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (13544) covalent geometry : angle 0.59695 / 0.26 (18296) hydrogen bonds : bond 0.03373 / 2.18 ( 808) hydrogen bonds : angle 4.01583 / 2.84 ( 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 93 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.526 Fit side-chains REVERT: B 47 ASP cc_start: 0.7693 (m-30) cc_final: 0.7043 (m-30) REVERT: C 47 ASP cc_start: 0.7868 (m-30) cc_final: 0.6967 (m-30) REVERT: C 77 LEU cc_start: 0.8371 (mm) cc_final: 0.8053 (mt) REVERT: C 273 ARG cc_start: 0.8410 (mtm-85) cc_final: 0.7958 (mtt90) REVERT: D 26 TYR cc_start: 0.8771 (OUTLIER) cc_final: 0.8465 (m-10) REVERT: D 47 ASP cc_start: 0.7813 (m-30) cc_final: 0.6933 (m-30) REVERT: D 273 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7838 (mtt90) outliers start: 19 outliers final: 0 residues processed: 93 average time/residue: 0.7183 time to fit residues: 72.5346 Evaluate side-chains 73 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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: 0.7980 chunk 15 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 137 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 84 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.095308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.065822 restraints weight = 26694.744| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.60 r_work: 0.2849 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13544 Z= 0.116 Angle : 0.597 8.911 18296 Z= 0.263 Chirality : 0.040 0.151 2116 Planarity : 0.004 0.036 2196 Dihedral : 10.890 101.037 2302 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.29 % Allowed : 14.16 % 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: 2.50 (0.22), residues: 1564 helix: 2.37 (0.16), residues: 1056 sheet: -1.04 (0.53), residues: 88 loop : 0.52 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 29 TYR 0.029 0.001 TYR B 128 PHE 0.006 0.001 PHE A 242 TRP 0.008 0.001 TRP C 264 HIS 0.001 0.000 HIS C 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (13544) covalent geometry : angle 0.59670 / 0.26 (18296) hydrogen bonds : bond 0.03277 / 2.12 ( 808) hydrogen bonds : angle 3.92387 / 2.77 ( 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 105 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 74 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: B 47 ASP cc_start: 0.7700 (m-30) cc_final: 0.7295 (m-30) REVERT: B 273 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7977 (mtt90) REVERT: C 47 ASP cc_start: 0.7842 (m-30) cc_final: 0.7338 (m-30) REVERT: C 77 LEU cc_start: 0.8349 (mm) cc_final: 0.8034 (mt) REVERT: C 273 ARG cc_start: 0.8401 (mtm-85) cc_final: 0.8186 (mmm-85) REVERT: D 47 ASP cc_start: 0.7794 (m-30) cc_final: 0.7419 (m-30) REVERT: D 273 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7947 (mtt90) outliers start: 31 outliers final: 2 residues processed: 100 average time/residue: 0.7192 time to fit residues: 77.7072 Evaluate side-chains 74 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 100 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 95 optimal weight: 0.2980 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 150 optimal weight: 5.9990 chunk 147 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 chunk 139 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.094918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.065586 restraints weight = 26537.392| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.59 r_work: 0.2843 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13544 Z= 0.118 Angle : 0.598 8.496 18296 Z= 0.263 Chirality : 0.039 0.151 2116 Planarity : 0.004 0.036 2196 Dihedral : 10.532 101.261 2302 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.84 % Allowed : 14.90 % Favored : 83.26 % 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: 2.58 (0.22), residues: 1564 helix: 2.38 (0.16), residues: 1060 sheet: -1.03 (0.52), residues: 88 loop : 0.70 (0.32), residues: 416 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 0.005 0.001 PHE A 242 TRP 0.008 0.001 TRP C 264 HIS 0.002 0.000 HIS C 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (13544) covalent geometry : angle 0.59844 / 0.26 (18296) hydrogen bonds : bond 0.03239 / 2.10 ( 808) hydrogen bonds : angle 3.86008 / 2.72 ( 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: 25 poor density : 72 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8106 (m-30) cc_final: 0.7430 (m-30) REVERT: B 273 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7984 (mtt90) REVERT: C 47 ASP cc_start: 0.7881 (m-30) cc_final: 0.7317 (m-30) REVERT: C 77 LEU cc_start: 0.8322 (mm) cc_final: 0.8014 (mt) REVERT: C 125 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8466 (mp) REVERT: C 128 TYR cc_start: 0.8102 (p90) cc_final: 0.7891 (p90) REVERT: D 47 ASP cc_start: 0.7767 (m-30) cc_final: 0.7330 (m-30) outliers start: 25 outliers final: 4 residues processed: 94 average time/residue: 0.6943 time to fit residues: 70.4835 Evaluate side-chains 76 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 125 ILE Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 266 THR 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: 0.0370 chunk 121 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 56 optimal weight: 0.3980 overall best weight: 1.6662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.092705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.063206 restraints weight = 26867.037| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.58 r_work: 0.2794 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13544 Z= 0.188 Angle : 0.640 8.685 18296 Z= 0.287 Chirality : 0.041 0.155 2116 Planarity : 0.004 0.037 2196 Dihedral : 10.664 104.839 2302 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.92 % Allowed : 15.27 % Favored : 82.82 % 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: 2.56 (0.22), residues: 1564 helix: 2.38 (0.16), residues: 1032 sheet: -0.98 (0.52), residues: 88 loop : 0.75 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 29 TYR 0.012 0.001 TYR A 245 PHE 0.010 0.001 PHE A 365 TRP 0.006 0.001 TRP C 264 HIS 0.002 0.001 HIS C 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 (13544) covalent geometry : angle 0.64033 / 0.29 (18296) hydrogen bonds : bond 0.03660 / 2.37 ( 808) hydrogen bonds : angle 3.92366 / 2.77 ( 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 100 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 0.503 Fit side-chains REVERT: A 47 ASP cc_start: 0.8124 (m-30) cc_final: 0.7454 (m-30) REVERT: B 47 ASP cc_start: 0.8055 (m-30) cc_final: 0.7450 (m-30) REVERT: B 273 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.8012 (mmt90) REVERT: C 47 ASP cc_start: 0.7871 (m-30) cc_final: 0.7321 (m-30) REVERT: C 77 LEU cc_start: 0.8311 (mm) cc_final: 0.7993 (mt) REVERT: C 125 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8481 (mp) REVERT: C 128 TYR cc_start: 0.8120 (p90) cc_final: 0.7883 (p90) REVERT: C 289 MET cc_start: 0.8718 (ttp) cc_final: 0.8484 (mtp) REVERT: D 26 TYR cc_start: 0.8861 (OUTLIER) cc_final: 0.8540 (m-10) REVERT: D 273 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.8010 (mmt90) outliers start: 26 outliers final: 3 residues processed: 96 average time/residue: 0.6443 time to fit residues: 67.0981 Evaluate side-chains 77 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 266 THR 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: 0.9980 chunk 8 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 135 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.094205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.064718 restraints weight = 26584.681| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.59 r_work: 0.2825 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.2494 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= 0.119 Angle : 0.625 8.605 18296 Z= 0.278 Chirality : 0.040 0.149 2116 Planarity : 0.004 0.037 2196 Dihedral : 10.133 100.256 2302 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.40 % Allowed : 16.15 % Favored : 82.45 % 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: 2.63 (0.22), residues: 1564 helix: 2.34 (0.16), residues: 1064 sheet: -1.02 (0.52), residues: 88 loop : 0.92 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 29 TYR 0.022 0.001 TYR D 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/Z covalent geometry : bond 0.00279 / 0.12 (13544) covalent geometry : angle 0.62476 / 0.28 (18296) hydrogen bonds : bond 0.03235 / 2.10 ( 808) hydrogen bonds : angle 3.87043 / 2.72 ( 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 91 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.368 Fit side-chains REVERT: A 47 ASP cc_start: 0.8104 (m-30) cc_final: 0.7420 (m-30) REVERT: B 47 ASP cc_start: 0.8042 (m-30) cc_final: 0.7434 (m-30) REVERT: B 77 LEU cc_start: 0.8381 (mm) cc_final: 0.8114 (mt) REVERT: B 273 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7997 (mmt90) REVERT: C 47 ASP cc_start: 0.7893 (m-30) cc_final: 0.7289 (m-30) REVERT: C 77 LEU cc_start: 0.8322 (mm) cc_final: 0.8020 (mt) REVERT: C 125 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8470 (mp) REVERT: C 128 TYR cc_start: 0.8115 (p90) cc_final: 0.7892 (p90) REVERT: D 47 ASP cc_start: 0.8104 (m-30) cc_final: 0.7472 (m-30) REVERT: D 273 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7971 (mmt90) outliers start: 19 outliers final: 5 residues processed: 88 average time/residue: 0.6275 time to fit residues: 59.8258 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 : 0.419 ------------------------------------------------------------------------------- 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 125 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 102 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 7 optimal weight: 0.0050 chunk 5 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.094304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.064830 restraints weight = 26837.293| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.60 r_work: 0.2824 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13544 Z= 0.122 Angle : 0.631 8.568 18296 Z= 0.282 Chirality : 0.040 0.151 2116 Planarity : 0.004 0.038 2196 Dihedral : 9.948 101.637 2302 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.18 % Allowed : 16.59 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.66 (0.22), residues: 1564 helix: 2.36 (0.16), residues: 1064 sheet: -0.99 (0.52), residues: 88 loop : 0.98 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 29 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 C 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (13544) covalent geometry : angle 0.63084 / 0.28 (18296) hydrogen bonds : bond 0.03215 / 2.09 ( 808) hydrogen bonds : angle 3.86410 / 2.71 ( 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 86 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8111 (m-30) cc_final: 0.7439 (m-30) REVERT: B 47 ASP cc_start: 0.8060 (m-30) cc_final: 0.7456 (m-30) REVERT: B 77 LEU cc_start: 0.8394 (mm) cc_final: 0.8125 (mt) REVERT: B 273 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.8001 (mmt90) REVERT: C 77 LEU cc_start: 0.8329 (mm) cc_final: 0.8017 (mt) REVERT: C 125 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8462 (mp) REVERT: C 128 TYR cc_start: 0.8123 (p90) cc_final: 0.7891 (p90) REVERT: D 47 ASP cc_start: 0.8115 (m-30) cc_final: 0.7482 (m-30) outliers start: 16 outliers final: 7 residues processed: 84 average time/residue: 0.5441 time to fit residues: 49.7992 Evaluate side-chains 78 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 125 ILE Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 266 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 120 optimal weight: 1.9990 chunk 80 optimal weight: 0.1980 chunk 24 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.094460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.064828 restraints weight = 26829.832| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.60 r_work: 0.2817 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13544 Z= 0.125 Angle : 0.633 8.560 18296 Z= 0.283 Chirality : 0.040 0.151 2116 Planarity : 0.004 0.038 2196 Dihedral : 9.889 101.760 2302 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.88 % Allowed : 16.96 % Favored : 82.15 % 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: 2.70 (0.22), residues: 1564 helix: 2.44 (0.17), residues: 1036 sheet: -1.02 (0.51), residues: 88 loop : 0.95 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 29 TYR 0.023 0.001 TYR D 128 PHE 0.006 0.001 PHE D 64 TRP 0.008 0.001 TRP C 264 HIS 0.002 0.001 HIS C 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (13544) covalent geometry : angle 0.63275 / 0.28 (18296) hydrogen bonds : bond 0.03188 / 2.07 ( 808) hydrogen bonds : angle 3.82579 / 2.69 ( 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 82 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.528 Fit side-chains REVERT: A 47 ASP cc_start: 0.8116 (m-30) cc_final: 0.7411 (m-30) REVERT: B 47 ASP cc_start: 0.8086 (m-30) cc_final: 0.7473 (m-30) REVERT: B 77 LEU cc_start: 0.8381 (mm) cc_final: 0.8128 (mt) REVERT: B 273 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.8022 (mmt90) REVERT: C 47 ASP cc_start: 0.8170 (m-30) cc_final: 0.7455 (m-30) REVERT: C 77 LEU cc_start: 0.8327 (mm) cc_final: 0.8018 (mt) REVERT: C 125 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8513 (mp) REVERT: C 128 TYR cc_start: 0.8122 (p90) cc_final: 0.7901 (p90) REVERT: D 47 ASP cc_start: 0.8104 (m-30) cc_final: 0.7494 (m-30) REVERT: D 77 LEU cc_start: 0.8306 (mm) cc_final: 0.8065 (mt) outliers start: 12 outliers final: 8 residues processed: 82 average time/residue: 0.5577 time to fit residues: 49.7749 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 : 0.320 ------------------------------------------------------------------------------- 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 125 ILE 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 266 THR 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: 0.9980 chunk 63 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 GLN B 412 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.094318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.064714 restraints weight = 27056.653| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.60 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: 0.8979 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13544 Z= 0.129 Angle : 0.638 9.556 18296 Z= 0.284 Chirality : 0.040 0.151 2116 Planarity : 0.004 0.038 2196 Dihedral : 9.891 102.299 2302 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.18 % Allowed : 16.67 % Favored : 82.15 % 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: 2.67 (0.22), residues: 1564 helix: 2.38 (0.16), residues: 1048 sheet: -1.02 (0.51), residues: 88 loop : 0.99 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 29 TYR 0.012 0.001 TYR A 245 PHE 0.006 0.001 PHE B 64 TRP 0.008 0.001 TRP C 264 HIS 0.002 0.001 HIS B 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (13544) covalent geometry : angle 0.63849 / 0.28 (18296) hydrogen bonds : bond 0.03225 / 2.10 ( 808) hydrogen bonds : angle 3.82978 / 2.69 ( 2352) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3461.02 seconds wall clock time: 59 minutes 53.59 seconds (3593.59 seconds total)