Starting phenix.real_space_refine on Thu Aug 6 04:13:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oxm_70989/08_2026/9oxm_70989.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oxm_70989/08_2026/9oxm_70989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oxm_70989/08_2026/9oxm_70989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oxm_70989/08_2026/9oxm_70989.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oxm_70989/08_2026/9oxm_70989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oxm_70989/08_2026/9oxm_70989.map" } resolution = 2.79 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 4 5.49 5 S 28 5.16 5 C 8608 2.51 5 N 2084 2.21 5 O 2236 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: 12960 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3110 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 24, 'TRANS': 366} Chain breaks: 1 Chain: "B" Number of atoms: 3110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3110 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 24, 'TRANS': 366} Chain breaks: 1 Chain: "C" Number of atoms: 3110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3110 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 24, 'TRANS': 366} Chain breaks: 1 Chain: "D" Number of atoms: 3110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3110 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 24, 'TRANS': 366} Chain breaks: 1 Chain: "A" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 130 Unusual residues: {'PEE': 7} Classifications: {'RNAv2': 1, 'undetermined': 7} Modifications used: {'rna3p': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 290 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PEE:plan-1': 7, 'PEE:plan-2': 7} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 130 Unusual residues: {'PEE': 7} Classifications: {'RNAv2': 1, 'undetermined': 7} Modifications used: {'rna3p': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 290 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PEE:plan-1': 7, 'PEE:plan-2': 7} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 130 Unusual residues: {'PEE': 7} Classifications: {'RNAv2': 1, 'undetermined': 7} Modifications used: {'rna3p': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 290 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PEE:plan-1': 7, 'PEE:plan-2': 7} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 130 Unusual residues: {'PEE': 7} Classifications: {'RNAv2': 1, 'undetermined': 7} Modifications used: {'rna3p': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 290 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PEE:plan-1': 7, 'PEE:plan-2': 7} Unresolved non-hydrogen planarities: 38 Time building chain proxies: 2.90, per 1000 atoms: 0.22 Number of scatterers: 12960 At special positions: 0 Unit cell: (99.9, 99.9, 117.9, 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 4 15.00 O 2236 8.00 N 2084 7.00 C 8608 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: 1.25 Conformation dependent library (CDL) restraints added in 615.0 milliseconds 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2968 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 8 sheets defined 72.9% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 10 through 36 Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 37 through 40 Processing helix chain 'A' and resid 43 through 63 removed outlier: 3.900A pdb=" N ILE A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Proline residue: A 59 - end of helix removed outlier: 3.638A pdb=" N ALA A 63 " --> pdb=" O PRO A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.570A pdb=" N LEU A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.576A pdb=" N LEU A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 107 through 112 removed outlier: 3.730A pdb=" N ARG A 111 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 126 removed outlier: 4.135A pdb=" N SER A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 129 No H-bonds generated for 'chain 'A' and resid 127 through 129' Processing helix chain 'A' and resid 131 through 159 Processing helix chain 'A' and resid 165 through 182 Processing helix chain 'A' and resid 193 through 224 Processing helix chain 'A' and resid 226 through 246 Processing helix chain 'A' and resid 249 through 268 Processing helix chain 'A' and resid 271 through 279 removed outlier: 3.888A pdb=" N LEU A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 292 Processing helix chain 'A' and resid 294 through 299 removed outlier: 3.806A pdb=" N VAL A 299 " --> pdb=" O VAL A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 315 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.903A pdb=" N ILE A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 373 " --> pdb=" O MET A 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 368 through 373' Processing helix chain 'A' and resid 394 through 403 removed outlier: 4.240A pdb=" N ARG A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 414 Processing helix chain 'B' and resid 10 through 36 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 37 through 40 Processing helix chain 'B' and resid 43 through 63 removed outlier: 3.900A pdb=" N ILE B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Proline residue: B 59 - end of helix removed outlier: 3.639A pdb=" N ALA B 63 " --> pdb=" O PRO B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.570A pdb=" N LEU B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 removed outlier: 3.576A pdb=" N LEU B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 107 through 112 removed outlier: 3.730A pdb=" N ARG B 111 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 126 removed outlier: 4.136A pdb=" N SER B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 129 No H-bonds generated for 'chain 'B' and resid 127 through 129' Processing helix chain 'B' and resid 131 through 159 Processing helix chain 'B' and resid 165 through 182 Processing helix chain 'B' and resid 193 through 224 Processing helix chain 'B' and resid 226 through 246 Processing helix chain 'B' and resid 249 through 268 Processing helix chain 'B' and resid 271 through 279 removed outlier: 3.889A pdb=" N LEU B 279 " --> pdb=" O VAL B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 292 Processing helix chain 'B' and resid 294 through 299 removed outlier: 3.806A pdb=" N VAL B 299 " --> pdb=" O VAL B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 315 Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.903A pdb=" N ILE B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 373 " --> pdb=" O MET B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 368 through 373' Processing helix chain 'B' and resid 394 through 403 removed outlier: 4.240A pdb=" N ARG B 403 " --> pdb=" O ARG B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 414 Processing helix chain 'C' and resid 10 through 36 Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 37 through 40 Processing helix chain 'C' and resid 43 through 63 removed outlier: 3.900A pdb=" N ILE C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Proline residue: C 59 - end of helix removed outlier: 3.638A pdb=" N ALA C 63 " --> pdb=" O PRO C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.570A pdb=" N LEU C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 99 removed outlier: 3.577A pdb=" N LEU C 94 " --> pdb=" O PRO C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 107 through 112 removed outlier: 3.730A pdb=" N ARG C 111 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 126 removed outlier: 4.135A pdb=" N SER C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 129 No H-bonds generated for 'chain 'C' and resid 127 through 129' Processing helix chain 'C' and resid 131 through 159 Processing helix chain 'C' and resid 165 through 182 Processing helix chain 'C' and resid 193 through 224 Processing helix chain 'C' and resid 226 through 246 Processing helix chain 'C' and resid 249 through 268 Processing helix chain 'C' and resid 271 through 279 removed outlier: 3.889A pdb=" N LEU C 279 " --> pdb=" O VAL C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 292 Processing helix chain 'C' and resid 294 through 299 removed outlier: 3.805A pdb=" N VAL C 299 " --> pdb=" O VAL C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 315 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.903A pdb=" N ILE C 372 " --> pdb=" O GLU C 368 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 373 " --> pdb=" O MET C 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 368 through 373' Processing helix chain 'C' and resid 394 through 403 removed outlier: 4.240A pdb=" N ARG C 403 " --> pdb=" O ARG C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 414 Processing helix chain 'D' and resid 10 through 36 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 37 through 40 Processing helix chain 'D' and resid 43 through 63 removed outlier: 3.900A pdb=" N ILE D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Proline residue: D 59 - end of helix removed outlier: 3.638A pdb=" N ALA D 63 " --> pdb=" O PRO D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.570A pdb=" N LEU D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 99 removed outlier: 3.577A pdb=" N LEU D 94 " --> pdb=" O PRO D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 107 through 112 removed outlier: 3.730A pdb=" N ARG D 111 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 126 removed outlier: 4.135A pdb=" N SER D 117 " --> pdb=" O LEU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 129 No H-bonds generated for 'chain 'D' and resid 127 through 129' Processing helix chain 'D' and resid 131 through 159 Processing helix chain 'D' and resid 165 through 182 Processing helix chain 'D' and resid 193 through 224 Processing helix chain 'D' and resid 226 through 246 Processing helix chain 'D' and resid 249 through 268 Processing helix chain 'D' and resid 271 through 279 removed outlier: 3.888A pdb=" N LEU D 279 " --> pdb=" O VAL D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 292 Processing helix chain 'D' and resid 294 through 299 removed outlier: 3.806A pdb=" N VAL D 299 " --> pdb=" O VAL D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 315 Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.904A pdb=" N ILE D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU D 373 " --> pdb=" O MET D 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 368 through 373' Processing helix chain 'D' and resid 394 through 403 removed outlier: 4.240A pdb=" N ARG D 403 " --> pdb=" O ARG D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 414 Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 320 Processing sheet with id=AA2, first strand: chain 'A' and resid 327 through 329 removed outlier: 7.018A pdb=" N TYR A 327 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 7.354A 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 320 Processing sheet with id=AA4, first strand: chain 'B' and resid 327 through 329 removed outlier: 7.018A pdb=" N TYR B 327 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 7.354A 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 320 Processing sheet with id=AA6, first strand: chain 'C' and resid 327 through 329 removed outlier: 7.019A pdb=" N TYR C 327 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ALA C 383 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 3.587A 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 320 Processing sheet with id=AA8, first strand: chain 'D' and resid 327 through 329 removed outlier: 7.018A pdb=" N TYR D 327 " --> pdb=" O ALA D 383 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ALA D 383 " --> pdb=" O TYR D 327 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA D 358 " --> pdb=" O VAL D 348 " (cutoff:3.500A) 824 hydrogen bonds defined for protein. 2388 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.82 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1944 1.31 - 1.43: 3402 1.43 - 1.56: 7830 1.56 - 1.69: 8 1.69 - 1.82: 48 Bond restraints: 13232 Sorted by residual: bond pdb=" C38 PEE A 504 " pdb=" C39 PEE A 504 " ideal model delta sigma weight residual 1.523 1.300 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C38 PEE B 504 " pdb=" C39 PEE B 504 " ideal model delta sigma weight residual 1.523 1.300 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C38 PEE D 505 " pdb=" C39 PEE D 505 " 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 C 504 " pdb=" C39 PEE C 504 " 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 C 503 " pdb=" C39 PEE C 503 " ideal model delta sigma weight residual 1.523 1.305 0.218 2.00e-02 2.50e+03 1.19e+02 ... (remaining 13227 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 17277 2.74 - 5.48: 523 5.48 - 8.22: 28 8.22 - 10.96: 36 10.96 - 13.70: 16 Bond angle restraints: 17880 Sorted by residual: angle pdb=" CA TYR C 245 " pdb=" C TYR C 245 " pdb=" O TYR C 245 " ideal model delta sigma weight residual 120.90 115.91 4.99 1.03e+00 9.43e-01 2.35e+01 angle pdb=" CA TYR B 245 " pdb=" C TYR B 245 " pdb=" O TYR B 245 " ideal model delta sigma weight residual 120.90 115.91 4.99 1.03e+00 9.43e-01 2.34e+01 angle pdb=" CA TYR A 245 " pdb=" C TYR A 245 " pdb=" O TYR A 245 " ideal model delta sigma weight residual 120.90 115.93 4.97 1.03e+00 9.43e-01 2.33e+01 angle pdb=" CA TYR D 245 " pdb=" C TYR D 245 " pdb=" O TYR D 245 " ideal model delta sigma weight residual 120.90 115.94 4.96 1.03e+00 9.43e-01 2.32e+01 angle pdb=" N TYR C 245 " pdb=" CA TYR C 245 " pdb=" C TYR C 245 " ideal model delta sigma weight residual 111.03 105.95 5.08 1.11e+00 8.12e-01 2.10e+01 ... (remaining 17875 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.60: 7564 26.60 - 53.21: 384 53.21 - 79.81: 92 79.81 - 106.41: 4 106.41 - 133.02: 12 Dihedral angle restraints: 8056 sinusoidal: 3456 harmonic: 4600 Sorted by residual: dihedral pdb=" O2 PEE D 508 " pdb=" C1 PEE D 508 " pdb=" C2 PEE D 508 " pdb=" O3P PEE D 508 " ideal model delta sinusoidal sigma weight residual -59.96 73.06 -133.02 1 3.00e+01 1.11e-03 1.79e+01 dihedral pdb=" O2 PEE B 507 " pdb=" C1 PEE B 507 " pdb=" C2 PEE B 507 " pdb=" O3P PEE B 507 " ideal model delta sinusoidal sigma weight residual -59.96 73.03 -132.99 1 3.00e+01 1.11e-03 1.79e+01 dihedral pdb=" O2 PEE A 507 " pdb=" C1 PEE A 507 " pdb=" C2 PEE A 507 " pdb=" O3P PEE A 507 " ideal model delta sinusoidal sigma weight residual -59.96 73.01 -132.97 1 3.00e+01 1.11e-03 1.79e+01 ... (remaining 8053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1356 0.036 - 0.072: 485 0.072 - 0.107: 187 0.107 - 0.143: 41 0.143 - 0.179: 19 Chirality restraints: 2088 Sorted by residual: chirality pdb=" CA ILE C 184 " pdb=" N ILE C 184 " pdb=" C ILE C 184 " pdb=" CB ILE C 184 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.99e-01 chirality pdb=" CA ILE B 184 " pdb=" N ILE B 184 " pdb=" C ILE B 184 " pdb=" CB ILE B 184 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" CA ILE A 184 " pdb=" N ILE A 184 " pdb=" C ILE A 184 " pdb=" CB ILE A 184 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.79e-01 ... (remaining 2085 not shown) Planarity restraints: 2148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 245 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.67e+00 pdb=" C TYR B 245 " -0.041 2.00e-02 2.50e+03 pdb=" O TYR B 245 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS B 246 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR D 245 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.65e+00 pdb=" C TYR D 245 " 0.041 2.00e-02 2.50e+03 pdb=" O TYR D 245 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS D 246 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 245 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.62e+00 pdb=" C TYR A 245 " -0.041 2.00e-02 2.50e+03 pdb=" O TYR A 245 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS A 246 " 0.014 2.00e-02 2.50e+03 ... (remaining 2145 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 4175 2.84 - 3.36: 12946 3.36 - 3.87: 22464 3.87 - 4.39: 25232 4.39 - 4.90: 42276 Nonbonded interactions: 107093 Sorted by model distance: nonbonded pdb=" OG SER D 350 " pdb=" OD1 ASP D 352 " model vdw 2.331 3.040 nonbonded pdb=" OG SER A 350 " pdb=" OD1 ASP A 352 " model vdw 2.332 3.040 nonbonded pdb=" OG SER C 350 " pdb=" OD1 ASP C 352 " model vdw 2.332 3.040 nonbonded pdb=" OG SER B 350 " pdb=" OD1 ASP B 352 " model vdw 2.332 3.040 nonbonded pdb=" OG SER A 102 " pdb=" O3 PEE A 506 " model vdw 2.350 3.040 ... (remaining 107088 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: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 414 or (resid 504 and (name C31 or name C32 or n \ ame C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 \ or name C40)) or resid 505 or (resid 506 and (name C32 or name C33 or name C34 o \ r name C35 or name C36 or name C37 or name C38 or name C39 or name C40)) or (res \ id 507 and (name C10 or name C11 or name C12 or name C2 or name C3 or name C30 o \ r name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C \ 37 or name O2 or name O3 )))) selection = (chain 'B' and (resid 9 through 414 or (resid 504 and (name C31 or name C32 or n \ ame C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 \ or name C40)) or resid 505 or (resid 506 and (name C32 or name C33 or name C34 o \ r name C35 or name C36 or name C37 or name C38 or name C39 or name C40)) or (res \ id 507 and (name C10 or name C11 or name C12 or name C2 or name C3 or name C30 o \ r name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C \ 37 or name O2 or name O3 )))) selection = (chain 'C' and (resid 9 through 414 or (resid 504 and (name C31 or name C32 or n \ ame C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 \ or name C40)) or resid 505 or (resid 506 and (name C32 or name C33 or name C34 o \ r name C35 or name C36 or name C37 or name C38 or name C39 or name C40)) or (res \ id 507 and (name C10 or name C11 or name C12 or name C2 or name C3 or name C30 o \ r name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C \ 37 or name O2 or name O3 )))) selection = (chain 'D' and (resid 9 through 414 or (resid 504 and (name C31 or name C32 or n \ ame C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 \ or name C40)) or resid 505 or (resid 506 and (name C32 or name C33 or name C34 o \ r name C35 or name C36 or name C37 or name C38 or name C39 or name C40)) or (res \ id 507 and (name C10 or name C11 or name C12 or name C2 or name C3 or name C30 o \ r name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C \ 37 or name O2 or name O3 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.800 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 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 : 0.009 0.223 13232 Z= 0.470 Angle : 1.046 13.703 17880 Z= 0.496 Chirality : 0.045 0.179 2088 Planarity : 0.004 0.033 2148 Dihedral : 17.411 133.019 5088 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % 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: 2.82 (0.23), residues: 1548 helix: 2.61 (0.17), residues: 992 sheet: 0.16 (0.61), residues: 88 loop : 0.65 (0.32), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 29 TYR 0.023 0.002 TYR D 128 PHE 0.010 0.001 PHE D 309 TRP 0.007 0.001 TRP B 264 HIS 0.003 0.000 HIS B 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00896 / 0.47 (13232) covalent geometry : angle 1.04648 / 0.50 (17880) hydrogen bonds : bond 0.13323 / 8.94 ( 824) hydrogen bonds : angle 5.70961 / 4.04 ( 2388) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.6457 time to fit residues: 56.7857 Evaluate side-chains 60 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.0030 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.0670 chunk 149 optimal weight: 0.9980 overall best weight: 0.4328 ------------------------------------------------------------------------------- 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 = 0.3637 r_free = 0.3637 target = 0.088134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.062692 restraints weight = 31847.004| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.68 r_work: 0.2912 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13232 Z= 0.118 Angle : 0.601 8.800 17880 Z= 0.271 Chirality : 0.039 0.154 2088 Planarity : 0.004 0.032 2148 Dihedral : 13.066 98.418 2124 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.49 % Allowed : 12.65 % Favored : 85.86 % 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: 3.07 (0.22), residues: 1548 helix: 2.66 (0.16), residues: 1020 sheet: -0.15 (0.59), residues: 88 loop : 1.11 (0.34), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 29 TYR 0.021 0.001 TYR A 128 PHE 0.007 0.001 PHE D 40 TRP 0.005 0.001 TRP A 155 HIS 0.001 0.000 HIS B 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (13232) covalent geometry : angle 0.60088 / 0.27 (17880) hydrogen bonds : bond 0.03593 / 2.40 ( 824) hydrogen bonds : angle 4.30265 / 3.08 ( 2388) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7567 (m-30) REVERT: B 47 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7528 (m-30) REVERT: C 47 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7520 (m-30) REVERT: C 296 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7990 (pp) REVERT: D 47 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7470 (m-30) outliers start: 20 outliers final: 4 residues processed: 86 average time/residue: 0.6959 time to fit residues: 64.6347 Evaluate side-chains 70 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 104 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 72 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.086588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.060694 restraints weight = 32336.491| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.71 r_work: 0.2845 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13232 Z= 0.137 Angle : 0.589 8.364 17880 Z= 0.262 Chirality : 0.040 0.153 2088 Planarity : 0.004 0.034 2148 Dihedral : 10.335 59.942 2124 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.35 % Allowed : 11.46 % Favored : 85.19 % 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: 3.10 (0.22), residues: 1548 helix: 2.61 (0.16), residues: 1024 sheet: -0.02 (0.60), residues: 88 loop : 1.28 (0.34), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 29 TYR 0.025 0.001 TYR A 128 PHE 0.010 0.001 PHE A 309 TRP 0.004 0.001 TRP C 176 HIS 0.003 0.001 HIS C 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (13232) covalent geometry : angle 0.58941 / 0.26 (17880) hydrogen bonds : bond 0.03466 / 2.34 ( 824) hydrogen bonds : angle 3.95475 / 2.84 ( 2388) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 76 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7615 (m-30) REVERT: A 224 LYS cc_start: 0.8765 (mttp) cc_final: 0.8405 (ptpt) REVERT: A 410 GLN cc_start: 0.8021 (tp40) cc_final: 0.7791 (tp40) REVERT: B 47 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7634 (m-30) REVERT: B 224 LYS cc_start: 0.8808 (mttp) cc_final: 0.8479 (ptpt) REVERT: B 289 MET cc_start: 0.8784 (mmm) cc_final: 0.8499 (mmm) REVERT: B 394 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8568 (tppp) REVERT: B 410 GLN cc_start: 0.7959 (tp40) cc_final: 0.7728 (tp40) REVERT: C 47 ASP cc_start: 0.8135 (OUTLIER) cc_final: 0.7557 (m-30) REVERT: C 224 LYS cc_start: 0.8772 (mttp) cc_final: 0.8492 (ptpt) REVERT: C 394 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8594 (tppp) REVERT: C 410 GLN cc_start: 0.8019 (tp40) cc_final: 0.7814 (tp40) REVERT: D 47 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7568 (m-30) REVERT: D 224 LYS cc_start: 0.8766 (mttp) cc_final: 0.8394 (ptpt) REVERT: D 394 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8581 (tppp) outliers start: 45 outliers final: 12 residues processed: 116 average time/residue: 0.5347 time to fit residues: 68.1173 Evaluate side-chains 84 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 394 LYS Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 394 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 73 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 141 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.086276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.060192 restraints weight = 32474.099| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.76 r_work: 0.2833 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13232 Z= 0.138 Angle : 0.603 9.348 17880 Z= 0.264 Chirality : 0.040 0.152 2088 Planarity : 0.004 0.036 2148 Dihedral : 9.744 59.951 2124 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.12 % Allowed : 12.35 % Favored : 84.52 % 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: 3.17 (0.22), residues: 1548 helix: 2.64 (0.16), residues: 1028 sheet: -0.04 (0.60), residues: 88 loop : 1.40 (0.34), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 29 TYR 0.023 0.001 TYR C 128 PHE 0.008 0.001 PHE C 309 TRP 0.004 0.001 TRP A 155 HIS 0.002 0.001 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (13232) covalent geometry : angle 0.60301 / 0.26 (17880) hydrogen bonds : bond 0.03302 / 2.21 ( 824) hydrogen bonds : angle 3.84395 / 2.76 ( 2388) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 70 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7609 (m-30) REVERT: A 410 GLN cc_start: 0.7998 (tp40) cc_final: 0.7715 (tp40) REVERT: B 47 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7593 (m-30) REVERT: B 289 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8492 (mmm) REVERT: B 394 LYS cc_start: 0.8838 (tppp) cc_final: 0.8599 (tppp) REVERT: B 410 GLN cc_start: 0.7968 (tp40) cc_final: 0.7707 (tp40) REVERT: C 47 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7574 (m-30) REVERT: C 119 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7116 (tp40) REVERT: C 394 LYS cc_start: 0.8854 (tppp) cc_final: 0.8633 (tppp) REVERT: C 410 GLN cc_start: 0.7977 (tp40) cc_final: 0.7740 (tp40) REVERT: D 47 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7598 (m-30) REVERT: D 394 LYS cc_start: 0.8853 (tppp) cc_final: 0.8630 (tppp) outliers start: 42 outliers final: 10 residues processed: 108 average time/residue: 0.5572 time to fit residues: 66.2707 Evaluate side-chains 83 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 91 optimal weight: 0.0050 chunk 7 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 136 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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 = 0.3623 r_free = 0.3623 target = 0.086917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.060888 restraints weight = 32813.140| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.78 r_work: 0.2877 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9022 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13232 Z= 0.109 Angle : 0.587 8.454 17880 Z= 0.256 Chirality : 0.039 0.155 2088 Planarity : 0.004 0.037 2148 Dihedral : 9.213 59.940 2124 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.90 % Allowed : 14.21 % Favored : 82.89 % 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: 3.29 (0.22), residues: 1548 helix: 2.74 (0.16), residues: 1028 sheet: -0.03 (0.60), residues: 88 loop : 1.40 (0.34), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 29 TYR 0.022 0.001 TYR C 128 PHE 0.006 0.001 PHE A 309 TRP 0.004 0.001 TRP C 155 HIS 0.002 0.000 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (13232) covalent geometry : angle 0.58737 / 0.26 (17880) hydrogen bonds : bond 0.03100 / 2.08 ( 824) hydrogen bonds : angle 3.80761 / 2.73 ( 2388) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 73 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7552 (m-30) REVERT: A 394 LYS cc_start: 0.9064 (tptm) cc_final: 0.8778 (tppp) REVERT: A 410 GLN cc_start: 0.8029 (tp40) cc_final: 0.7756 (tp40) REVERT: B 47 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7571 (m-30) REVERT: B 289 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8463 (mmm) REVERT: B 394 LYS cc_start: 0.8921 (tppp) cc_final: 0.8672 (tppp) REVERT: B 410 GLN cc_start: 0.7968 (tp40) cc_final: 0.7668 (tp40) REVERT: C 47 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7571 (m-30) REVERT: C 394 LYS cc_start: 0.8933 (tppp) cc_final: 0.8715 (tppp) REVERT: C 410 GLN cc_start: 0.8024 (tp40) cc_final: 0.7750 (tp40) REVERT: D 47 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7607 (m-30) REVERT: D 289 MET cc_start: 0.8790 (mmm) cc_final: 0.8573 (mmm) REVERT: D 394 LYS cc_start: 0.8912 (tppp) cc_final: 0.8696 (tppp) outliers start: 39 outliers final: 10 residues processed: 111 average time/residue: 0.5359 time to fit residues: 65.5504 Evaluate side-chains 82 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 44 optimal weight: 0.2980 chunk 92 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 66 optimal weight: 0.0870 chunk 68 optimal weight: 0.1980 chunk 39 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.087160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.061261 restraints weight = 32727.877| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.77 r_work: 0.2900 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13232 Z= 0.103 Angle : 0.587 8.490 17880 Z= 0.255 Chirality : 0.039 0.154 2088 Planarity : 0.004 0.037 2148 Dihedral : 8.892 59.995 2124 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.27 % Allowed : 14.73 % Favored : 81.99 % 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: 3.36 (0.22), residues: 1548 helix: 2.82 (0.16), residues: 1028 sheet: 0.01 (0.60), residues: 88 loop : 1.38 (0.34), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 111 TYR 0.022 0.001 TYR C 128 PHE 0.006 0.001 PHE D 309 TRP 0.004 0.001 TRP C 155 HIS 0.001 0.000 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (13232) covalent geometry : angle 0.58695 / 0.25 (17880) hydrogen bonds : bond 0.02983 / 1.98 ( 824) hydrogen bonds : angle 3.71776 / 2.66 ( 2388) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 69 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7540 (m-30) REVERT: A 289 MET cc_start: 0.8784 (mmm) cc_final: 0.8493 (mmm) REVERT: A 410 GLN cc_start: 0.8091 (tp40) cc_final: 0.7788 (tp40) REVERT: B 47 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7608 (m-30) REVERT: B 289 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8491 (mmm) REVERT: B 354 LYS cc_start: 0.8906 (mmmm) cc_final: 0.8698 (mmmm) REVERT: B 394 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8663 (tppp) REVERT: B 410 GLN cc_start: 0.8051 (tp40) cc_final: 0.7716 (tp40) REVERT: C 47 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7596 (m-30) REVERT: C 410 GLN cc_start: 0.8038 (tp40) cc_final: 0.7756 (tp40) REVERT: D 47 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7615 (m-30) REVERT: D 289 MET cc_start: 0.8752 (mmm) cc_final: 0.8517 (mmm) outliers start: 44 outliers final: 13 residues processed: 110 average time/residue: 0.5129 time to fit residues: 62.5812 Evaluate side-chains 83 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 6 optimal weight: 0.0770 chunk 98 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 148 optimal weight: 0.9980 chunk 127 optimal weight: 0.0970 chunk 110 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 overall best weight: 0.6136 ------------------------------------------------------------------------------- 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 = 0.3632 r_free = 0.3632 target = 0.087787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.062573 restraints weight = 31961.900| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.80 r_work: 0.2904 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13232 Z= 0.109 Angle : 0.593 9.283 17880 Z= 0.258 Chirality : 0.039 0.156 2088 Planarity : 0.004 0.037 2148 Dihedral : 8.727 59.614 2124 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.20 % Allowed : 15.18 % Favored : 81.62 % 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: 3.41 (0.22), residues: 1548 helix: 2.86 (0.16), residues: 1028 sheet: 0.01 (0.60), residues: 88 loop : 1.37 (0.34), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 111 TYR 0.023 0.001 TYR D 128 PHE 0.006 0.001 PHE D 309 TRP 0.003 0.001 TRP C 155 HIS 0.002 0.000 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (13232) covalent geometry : angle 0.59281 / 0.26 (17880) hydrogen bonds : bond 0.02982 / 2.00 ( 824) hydrogen bonds : angle 3.68419 / 2.64 ( 2388) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 67 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7557 (m-30) REVERT: A 289 MET cc_start: 0.8806 (mmm) cc_final: 0.8586 (mmm) REVERT: A 394 LYS cc_start: 0.9133 (tptm) cc_final: 0.8853 (tptp) REVERT: A 410 GLN cc_start: 0.8128 (tp40) cc_final: 0.7812 (tp40) REVERT: B 47 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7630 (m-30) REVERT: B 289 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8500 (mmm) REVERT: B 354 LYS cc_start: 0.8947 (mmmm) cc_final: 0.8729 (mmmm) REVERT: B 394 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8695 (tppp) REVERT: B 410 GLN cc_start: 0.8063 (tp40) cc_final: 0.7741 (tp40) REVERT: C 47 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7599 (m-30) REVERT: C 410 GLN cc_start: 0.8067 (tp40) cc_final: 0.7768 (tp40) REVERT: D 47 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7652 (m-30) REVERT: D 289 MET cc_start: 0.8795 (mmm) cc_final: 0.8545 (mmm) outliers start: 43 outliers final: 17 residues processed: 108 average time/residue: 0.4730 time to fit residues: 56.9141 Evaluate side-chains 88 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 chunk 52 optimal weight: 0.4980 chunk 154 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 152 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.086506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.060429 restraints weight = 32494.393| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.73 r_work: 0.2840 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9002 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13232 Z= 0.119 Angle : 0.602 10.193 17880 Z= 0.262 Chirality : 0.039 0.161 2088 Planarity : 0.004 0.038 2148 Dihedral : 8.731 59.492 2124 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.38 % Allowed : 16.00 % Favored : 81.62 % 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: 3.44 (0.22), residues: 1548 helix: 2.87 (0.16), residues: 1024 sheet: 0.02 (0.60), residues: 88 loop : 1.44 (0.34), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 111 TYR 0.022 0.001 TYR C 128 PHE 0.007 0.001 PHE C 309 TRP 0.003 0.001 TRP C 176 HIS 0.002 0.000 HIS B 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (13232) covalent geometry : angle 0.60198 / 0.26 (17880) hydrogen bonds : bond 0.03049 / 2.04 ( 824) hydrogen bonds : angle 3.67363 / 2.64 ( 2388) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 67 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7589 (m-30) REVERT: A 354 LYS cc_start: 0.8838 (mmmm) cc_final: 0.8635 (mmmm) REVERT: A 394 LYS cc_start: 0.9165 (tptm) cc_final: 0.8877 (tptp) REVERT: A 410 GLN cc_start: 0.8166 (tp40) cc_final: 0.7851 (tp40) REVERT: B 47 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7643 (m-30) REVERT: B 354 LYS cc_start: 0.8936 (mmmm) cc_final: 0.8712 (mmmm) REVERT: B 394 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8707 (tppp) REVERT: B 410 GLN cc_start: 0.8088 (tp40) cc_final: 0.7762 (tp40) REVERT: C 47 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7625 (m-30) REVERT: C 410 GLN cc_start: 0.8088 (tp40) cc_final: 0.7784 (tp40) REVERT: D 47 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7652 (m-30) REVERT: D 289 MET cc_start: 0.8798 (mmm) cc_final: 0.8535 (mmm) REVERT: D 354 LYS cc_start: 0.8910 (mmmm) cc_final: 0.8699 (mmmm) outliers start: 32 outliers final: 18 residues processed: 97 average time/residue: 0.4983 time to fit residues: 53.6788 Evaluate side-chains 89 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 130 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 69 optimal weight: 0.0470 chunk 104 optimal weight: 2.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- 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 = 0.3598 r_free = 0.3598 target = 0.085897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.059739 restraints weight = 32736.515| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.75 r_work: 0.2821 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13232 Z= 0.137 Angle : 0.611 10.739 17880 Z= 0.267 Chirality : 0.040 0.160 2088 Planarity : 0.004 0.038 2148 Dihedral : 8.889 59.417 2124 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.90 % Allowed : 15.55 % Favored : 81.55 % 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: 3.39 (0.22), residues: 1548 helix: 2.85 (0.16), residues: 1024 sheet: -0.02 (0.59), residues: 88 loop : 1.40 (0.33), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 29 TYR 0.022 0.001 TYR C 128 PHE 0.006 0.001 PHE B 309 TRP 0.004 0.001 TRP A 176 HIS 0.002 0.000 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (13232) covalent geometry : angle 0.61079 / 0.27 (17880) hydrogen bonds : bond 0.03159 / 2.12 ( 824) hydrogen bonds : angle 3.69464 / 2.65 ( 2388) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 66 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7571 (m-30) REVERT: A 289 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8560 (mmm) REVERT: A 354 LYS cc_start: 0.8879 (mmmm) cc_final: 0.8671 (mmmm) REVERT: A 394 LYS cc_start: 0.9191 (tptm) cc_final: 0.8927 (tptp) REVERT: A 410 GLN cc_start: 0.8178 (tp40) cc_final: 0.7867 (tp40) REVERT: B 47 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7633 (m-30) REVERT: B 289 MET cc_start: 0.8848 (mmm) cc_final: 0.8567 (mmm) REVERT: B 354 LYS cc_start: 0.8950 (mmmm) cc_final: 0.8723 (mmmm) REVERT: B 394 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8714 (tppp) REVERT: B 410 GLN cc_start: 0.8142 (tp40) cc_final: 0.7860 (tp40) REVERT: C 47 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7632 (m-30) REVERT: C 289 MET cc_start: 0.8858 (mmm) cc_final: 0.8573 (mmm) REVERT: C 410 GLN cc_start: 0.8095 (tp40) cc_final: 0.7798 (tp40) REVERT: D 47 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7669 (m-30) REVERT: D 289 MET cc_start: 0.8844 (mmm) cc_final: 0.8575 (mmm) outliers start: 39 outliers final: 21 residues processed: 103 average time/residue: 0.4327 time to fit residues: 49.6801 Evaluate side-chains 92 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 65 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 67 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 122 optimal weight: 0.0010 chunk 53 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.086579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.060586 restraints weight = 32756.674| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.77 r_work: 0.2874 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9002 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13232 Z= 0.110 Angle : 0.612 10.317 17880 Z= 0.267 Chirality : 0.039 0.156 2088 Planarity : 0.004 0.038 2148 Dihedral : 8.716 58.407 2124 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.93 % Allowed : 16.44 % Favored : 81.62 % 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: 3.42 (0.22), residues: 1548 helix: 2.87 (0.16), residues: 1024 sheet: 0.04 (0.59), residues: 88 loop : 1.39 (0.34), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 356 TYR 0.021 0.001 TYR D 128 PHE 0.006 0.001 PHE A 309 TRP 0.004 0.001 TRP A 155 HIS 0.002 0.000 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (13232) covalent geometry : angle 0.61173 / 0.27 (17880) hydrogen bonds : bond 0.02991 / 2.00 ( 824) hydrogen bonds : angle 3.65852 / 2.63 ( 2388) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 68 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7541 (m-30) REVERT: A 394 LYS cc_start: 0.9211 (tptm) cc_final: 0.8942 (tptp) REVERT: A 410 GLN cc_start: 0.8208 (tp40) cc_final: 0.7901 (tp40) REVERT: B 47 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7631 (m-30) REVERT: B 289 MET cc_start: 0.8797 (mmm) cc_final: 0.8500 (mmm) REVERT: B 354 LYS cc_start: 0.8978 (mmmm) cc_final: 0.8747 (mmmm) REVERT: B 394 LYS cc_start: 0.8910 (tppp) cc_final: 0.8708 (tppp) REVERT: B 410 GLN cc_start: 0.8197 (tp40) cc_final: 0.7920 (tp40) REVERT: C 47 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7651 (m-30) REVERT: C 289 MET cc_start: 0.8847 (mmm) cc_final: 0.8551 (mmm) REVERT: C 410 GLN cc_start: 0.8154 (tp40) cc_final: 0.7865 (tp40) REVERT: D 47 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7653 (m-30) REVERT: D 289 MET cc_start: 0.8791 (mmm) cc_final: 0.8479 (mmm) outliers start: 26 outliers final: 19 residues processed: 93 average time/residue: 0.5309 time to fit residues: 54.6392 Evaluate side-chains 90 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 412 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 137 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 15 optimal weight: 0.6980 chunk 130 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 80 optimal weight: 0.3980 chunk 28 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.086432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.060297 restraints weight = 32858.941| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.78 r_work: 0.2877 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9004 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13232 Z= 0.115 Angle : 0.610 10.244 17880 Z= 0.266 Chirality : 0.039 0.157 2088 Planarity : 0.004 0.038 2148 Dihedral : 8.669 58.897 2124 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.16 % Allowed : 16.29 % Favored : 81.55 % 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: 3.41 (0.22), residues: 1548 helix: 2.87 (0.16), residues: 1024 sheet: 0.02 (0.59), residues: 88 loop : 1.36 (0.33), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 111 TYR 0.022 0.001 TYR C 128 PHE 0.006 0.001 PHE A 309 TRP 0.003 0.001 TRP A 155 HIS 0.002 0.000 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (13232) covalent geometry : angle 0.60967 / 0.27 (17880) hydrogen bonds : bond 0.03014 / 2.02 ( 824) hydrogen bonds : angle 3.64152 / 2.62 ( 2388) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3405.68 seconds wall clock time: 58 minutes 59.62 seconds (3539.62 seconds total)