Starting phenix.real_space_refine on Thu Jul 2 22:10:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nec_49305/07_2026/9nec_49305.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nec_49305/07_2026/9nec_49305.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nec_49305/07_2026/9nec_49305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nec_49305/07_2026/9nec_49305.map" model { file = "/net/cci-nas-00/data/ceres_data/9nec_49305/07_2026/9nec_49305.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nec_49305/07_2026/9nec_49305.cif" } resolution = 3.2 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= -0.002 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 2 8.98 5 S 32 5.16 5 C 6916 2.51 5 N 1573 2.21 5 O 1716 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10239 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2426 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 16, 'TRANS': 299} Chain breaks: 5 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 9, 'ASP:plan': 4, 'ASN:plan1': 4} Unresolved non-hydrogen planarities: 119 Chain: "B" Number of atoms: 2432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2432 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 16, 'TRANS': 299} Chain breaks: 5 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 9, 'ASP:plan': 4, 'ASN:plan1': 4} Unresolved non-hydrogen planarities: 117 Chain: "C" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2437 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 16, 'TRANS': 300} Chain breaks: 5 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 192 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 9, 'ASP:plan': 4, 'ASN:plan1': 4} Unresolved non-hydrogen planarities: 117 Chain: "D" Number of atoms: 2428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2428 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 16, 'TRANS': 300} Chain breaks: 5 Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 10, 'ASP:plan': 4, 'ASN:plan1': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 125 Chain: "G" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 83 Unusual residues: {'ACE': 1} Classifications: {'peptide': 12, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 11} Chain: "H" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 88 Ad-hoc single atom residues: {' K': 2} Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 6} Chain breaks: 2 Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-1': 7, 'POV:plan-2': 6, 'POV:plan-3': 6} Unresolved non-hydrogen planarities: 67 Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 63 Unusual residues: {'POV': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 299 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-1': 6, 'POV:plan-2': 5, 'POV:plan-3': 4} Unresolved non-hydrogen planarities: 53 Chain: "C" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 101 Unusual residues: {'POV': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 367 Unresolved non-hydrogen angles: 442 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'POV:plan-3': 7, 'POV:plan-1': 7, 'POV:plan-2': 6} Unresolved non-hydrogen planarities: 71 Chain: "D" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 100 Unusual residues: {'POV': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 368 Unresolved non-hydrogen angles: 444 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'POV:plan-1': 8, 'POV:plan-2': 7, 'POV:plan-3': 7} Unresolved non-hydrogen planarities: 77 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.50, per 1000 atoms: 0.24 Number of scatterers: 10239 At special positions: 0 Unit cell: (107.07, 106.24, 111.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 2 19.00 S 32 16.00 O 1716 8.00 N 1573 7.00 C 6916 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 387.8 milliseconds 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2440 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 4 sheets defined 69.1% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 112 through 117 Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.637A pdb=" N ARG A 129 " --> pdb=" O ASP A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 159 removed outlier: 3.595A pdb=" N ILE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 181 removed outlier: 3.591A pdb=" N PHE A 173 " --> pdb=" O PRO A 169 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 193 removed outlier: 3.910A pdb=" N PHE A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 248 removed outlier: 3.831A pdb=" N ILE A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 298 removed outlier: 3.540A pdb=" N ILE A 282 " --> pdb=" O PRO A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 326 removed outlier: 3.617A pdb=" N ILE A 320 " --> pdb=" O ASP A 316 " (cutoff:3.500A) Proline residue: A 322 - end of helix Processing helix chain 'A' and resid 358 through 368 Processing helix chain 'A' and resid 369 through 378 removed outlier: 3.654A pdb=" N LEU A 375 " --> pdb=" O ILE A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 392 removed outlier: 3.624A pdb=" N GLN A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 417 Processing helix chain 'A' and resid 428 through 441 removed outlier: 4.371A pdb=" N TRP A 434 " --> pdb=" O PRO A 430 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N TRP A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 472 Processing helix chain 'A' and resid 473 through 489 removed outlier: 3.743A pdb=" N ILE A 477 " --> pdb=" O PRO A 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 125 through 130 removed outlier: 3.632A pdb=" N ARG B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 159 removed outlier: 3.801A pdb=" N ILE B 152 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR B 156 " --> pdb=" O ILE B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 181 removed outlier: 3.613A pdb=" N PHE B 173 " --> pdb=" O PRO B 169 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR B 180 " --> pdb=" O GLU B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 192 removed outlier: 3.722A pdb=" N GLU B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 248 Processing helix chain 'B' and resid 278 through 298 removed outlier: 3.622A pdb=" N ILE B 282 " --> pdb=" O PRO B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 319 Processing helix chain 'B' and resid 320 through 326 removed outlier: 3.610A pdb=" N PHE B 324 " --> pdb=" O ILE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 368 Processing helix chain 'B' and resid 369 through 378 removed outlier: 3.623A pdb=" N ARG B 377 " --> pdb=" O LYS B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 392 removed outlier: 3.584A pdb=" N GLN B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 418 Processing helix chain 'B' and resid 428 through 441 removed outlier: 4.358A pdb=" N TRP B 434 " --> pdb=" O PRO B 430 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N TRP B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 472 Processing helix chain 'B' and resid 473 through 488 removed outlier: 3.916A pdb=" N ILE B 477 " --> pdb=" O PRO B 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 117 Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.539A pdb=" N ARG C 129 " --> pdb=" O ASP C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 159 removed outlier: 3.667A pdb=" N ILE C 152 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR C 156 " --> pdb=" O ILE C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 181 removed outlier: 3.677A pdb=" N PHE C 173 " --> pdb=" O PRO C 169 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TYR C 180 " --> pdb=" O GLU C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 192 removed outlier: 3.680A pdb=" N GLU C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 248 removed outlier: 4.131A pdb=" N VAL C 228 " --> pdb=" O GLN C 224 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 298 removed outlier: 3.623A pdb=" N ILE C 282 " --> pdb=" O PRO C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 327 removed outlier: 3.508A pdb=" N ILE C 320 " --> pdb=" O ASP C 316 " (cutoff:3.500A) Proline residue: C 322 - end of helix removed outlier: 3.647A pdb=" N LEU C 327 " --> pdb=" O TYR C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 368 Processing helix chain 'C' and resid 369 through 378 Processing helix chain 'C' and resid 379 through 392 removed outlier: 3.671A pdb=" N GLN C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 418 removed outlier: 3.607A pdb=" N GLU C 418 " --> pdb=" O VAL C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 441 removed outlier: 4.429A pdb=" N TRP C 434 " --> pdb=" O PRO C 430 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N TRP C 435 " --> pdb=" O ASP C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 472 Processing helix chain 'C' and resid 473 through 489 removed outlier: 3.820A pdb=" N ILE C 477 " --> pdb=" O PRO C 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 118 removed outlier: 4.473A pdb=" N PHE D 118 " --> pdb=" O THR D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 130 removed outlier: 3.552A pdb=" N ARG D 129 " --> pdb=" O ASP D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 159 removed outlier: 3.720A pdb=" N ILE D 152 " --> pdb=" O SER D 148 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR D 156 " --> pdb=" O ILE D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 181 removed outlier: 3.532A pdb=" N PHE D 173 " --> pdb=" O PRO D 169 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS D 178 " --> pdb=" O SER D 174 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR D 180 " --> pdb=" O GLU D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 192 removed outlier: 3.673A pdb=" N GLU D 192 " --> pdb=" O ASN D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 248 removed outlier: 3.950A pdb=" N VAL D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 298 removed outlier: 3.729A pdb=" N ILE D 282 " --> pdb=" O PRO D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 319 Processing helix chain 'D' and resid 320 through 326 removed outlier: 3.632A pdb=" N PHE D 324 " --> pdb=" O ILE D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 368 Processing helix chain 'D' and resid 369 through 378 Processing helix chain 'D' and resid 379 through 392 removed outlier: 3.637A pdb=" N GLN D 383 " --> pdb=" O SER D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 418 removed outlier: 3.576A pdb=" N GLU D 418 " --> pdb=" O VAL D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 441 removed outlier: 4.301A pdb=" N TRP D 434 " --> pdb=" O PRO D 430 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TRP D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 472 Processing helix chain 'D' and resid 473 through 489 removed outlier: 3.933A pdb=" N ILE D 477 " --> pdb=" O PRO D 473 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 106 through 111 removed outlier: 3.665A pdb=" N GLU A 139 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 106 through 111 removed outlier: 3.553A pdb=" N GLU B 139 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 106 through 111 removed outlier: 3.620A pdb=" N GLU C 139 " --> pdb=" O ASP C 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 106 through 111 removed outlier: 3.676A pdb=" N GLU D 139 " --> pdb=" O ASP D 134 " (cutoff:3.500A) 615 hydrogen bonds defined for protein. 1755 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: 1.62 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1515 1.31 - 1.44: 2927 1.44 - 1.56: 5901 1.56 - 1.68: 67 1.68 - 1.81: 48 Bond restraints: 10458 Sorted by residual: bond pdb=" C31 POV B 701 " pdb=" O31 POV B 701 " ideal model delta sigma weight residual 1.327 1.442 -0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" C31 POV A 701 " pdb=" O31 POV A 701 " ideal model delta sigma weight residual 1.327 1.442 -0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" C31 POV C 707 " pdb=" O31 POV C 707 " ideal model delta sigma weight residual 1.327 1.441 -0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" C31 POV A 705 " pdb=" O31 POV A 705 " ideal model delta sigma weight residual 1.327 1.441 -0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" C31 POV C 702 " pdb=" O31 POV C 702 " ideal model delta sigma weight residual 1.327 1.441 -0.114 2.00e-02 2.50e+03 3.25e+01 ... (remaining 10453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 13622 1.98 - 3.97: 304 3.97 - 5.95: 160 5.95 - 7.94: 20 7.94 - 9.92: 17 Bond angle restraints: 14123 Sorted by residual: angle pdb=" N ARG A 227 " pdb=" CA ARG A 227 " pdb=" C ARG A 227 " ideal model delta sigma weight residual 112.54 107.68 4.86 1.22e+00 6.72e-01 1.59e+01 angle pdb=" N PHE A 190 " pdb=" CA PHE A 190 " pdb=" C PHE A 190 " ideal model delta sigma weight residual 112.89 108.26 4.63 1.24e+00 6.50e-01 1.39e+01 angle pdb=" N ALA A 226 " pdb=" CA ALA A 226 " pdb=" C ALA A 226 " ideal model delta sigma weight residual 113.18 108.82 4.36 1.21e+00 6.83e-01 1.30e+01 angle pdb=" N ARG A 191 " pdb=" CA ARG A 191 " pdb=" C ARG A 191 " ideal model delta sigma weight residual 111.07 107.25 3.82 1.07e+00 8.73e-01 1.28e+01 angle pdb=" N GLU A 192 " pdb=" CA GLU A 192 " pdb=" C GLU A 192 " ideal model delta sigma weight residual 111.82 107.74 4.08 1.16e+00 7.43e-01 1.24e+01 ... (remaining 14118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.93: 5705 24.93 - 49.86: 320 49.86 - 74.80: 55 74.80 - 99.73: 4 99.73 - 124.66: 4 Dihedral angle restraints: 6088 sinusoidal: 2339 harmonic: 3749 Sorted by residual: dihedral pdb=" C3 POV D 707 " pdb=" C31 POV D 707 " pdb=" O31 POV D 707 " pdb=" C32 POV D 707 " ideal model delta sinusoidal sigma weight residual 172.61 47.95 124.66 1 3.00e+01 1.11e-03 1.67e+01 dihedral pdb=" C3 POV D 702 " pdb=" C31 POV D 702 " pdb=" O31 POV D 702 " pdb=" C32 POV D 702 " ideal model delta sinusoidal sigma weight residual 172.61 62.23 110.38 1 3.00e+01 1.11e-03 1.44e+01 dihedral pdb=" C3 POV A 701 " pdb=" C31 POV A 701 " pdb=" O31 POV A 701 " pdb=" C32 POV A 701 " ideal model delta sinusoidal sigma weight residual 172.61 64.98 107.63 1 3.00e+01 1.11e-03 1.39e+01 ... (remaining 6085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1132 0.040 - 0.080: 403 0.080 - 0.119: 86 0.119 - 0.159: 17 0.159 - 0.199: 1 Chirality restraints: 1639 Sorted by residual: chirality pdb=" CA ILE A 187 " pdb=" N ILE A 187 " pdb=" C ILE A 187 " pdb=" CB ILE A 187 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.88e-01 chirality pdb=" CB VAL A 228 " pdb=" CA VAL A 228 " pdb=" CG1 VAL A 228 " pdb=" CG2 VAL A 228 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CA LEU D 472 " pdb=" N LEU D 472 " pdb=" C LEU D 472 " pdb=" CB LEU D 472 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.84e-01 ... (remaining 1636 not shown) Planarity restraints: 1728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 125 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO D 126 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO D 126 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO D 126 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 474 " -0.030 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO A 475 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 475 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 475 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 89 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO C 90 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 90 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 90 " -0.024 5.00e-02 4.00e+02 ... (remaining 1725 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.79: 2599 2.79 - 3.38: 11649 3.38 - 3.97: 18684 3.97 - 4.55: 26632 4.55 - 5.14: 38159 Nonbonded interactions: 97723 Sorted by model distance: nonbonded pdb=" NH1 ARG A 144 " pdb=" OE1 GLU A 176 " model vdw 2.208 3.120 nonbonded pdb=" NH2 ARG C 144 " pdb=" OE1 GLU C 176 " model vdw 2.287 3.120 nonbonded pdb=" O LYS H 13 " pdb=" ND1 HIS H 16 " model vdw 2.305 3.120 nonbonded pdb=" OG1 THR A 284 " pdb=" OH TYR A 323 " model vdw 2.310 3.040 nonbonded pdb=" OD1 ASN B 482 " pdb=" OH TYR G 8 " model vdw 2.313 3.040 ... (remaining 97718 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 84 through 218 or (resid 219 and (name N or name CA or nam \ e C or name O or name CB )) or resid 220 or (resid 221 and (name N or name CA or \ name C or name O or name CB )) or resid 222 through 223 or (resid 224 through 2 \ 27 and (name N or name CA or name C or name O or name CB )) or resid 228 through \ 488 or (resid 705 and (name C31 or name C32 or name C33 or name C34 or name C35 \ )) or (resid 707 and (name C32 or name C33 or name C34 or name C35 or name C36 o \ r name C37)))) selection = (chain 'B' and (resid 84 through 189 or (resid 190 through 193 and (name N or na \ me CA or name C or name O or name CB )) or resid 216 through 218 or (resid 219 a \ nd (name N or name CA or name C or name O or name CB )) or resid 220 or (resid 2 \ 21 and (name N or name CA or name C or name O or name CB )) or resid 222 through \ 361 or (resid 362 and (name N or name CA or name C or name O or name CB )) or r \ esid 363 through 488 or (resid 701 and (name C31 or name C32 or name C33 or name \ C34 or name C35)) or (resid 703 and (name C32 or name C33 or name C34 or name C \ 35 or name C36 or name C37)))) selection = (chain 'C' and (resid 84 through 189 or (resid 190 through 193 and (name N or na \ me CA or name C or name O or name CB )) or resid 216 through 218 or (resid 219 a \ nd (name N or name CA or name C or name O or name CB )) or resid 220 through 223 \ or (resid 224 through 227 and (name N or name CA or name C or name O or name CB \ )) or resid 228 through 488 or (resid 705 and (name C31 or name C32 or name C33 \ or name C34 or name C35)) or (resid 707 and (name C32 or name C33 or name C34 o \ r name C35 or name C36 or name C37)))) selection = (chain 'D' and (resid 84 through 189 or (resid 190 through 193 and (name N or na \ me CA or name C or name O or name CB )) or resid 216 through 220 or (resid 221 a \ nd (name N or name CA or name C or name O or name CB )) or resid 222 through 223 \ or (resid 224 through 227 and (name N or name CA or name C or name O or name CB \ )) or resid 228 through 488 or (resid 705 and (name C31 or name C32 or name C33 \ or name C34 or name C35)) or (resid 707 and (name C32 or name C33 or name C34 o \ r name C35 or name C36 or name C37)))) } 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: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.060 Find NCS groups from input model: 0.220 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 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 : 0.008 0.115 10458 Z= 0.379 Angle : 0.889 9.921 14123 Z= 0.395 Chirality : 0.041 0.199 1639 Planarity : 0.005 0.104 1728 Dihedral : 15.945 124.662 3648 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.57 (0.25), residues: 1235 helix: 2.15 (0.20), residues: 753 sheet: -0.80 (0.56), residues: 66 loop : -0.72 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 144 TYR 0.007 0.001 TYR D 155 PHE 0.016 0.001 PHE B 217 TRP 0.005 0.001 TRP D 289 HIS 0.003 0.001 HIS H 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00753 / 0.38 (10458) covalent geometry : angle 0.88915 / 0.40 (14123) hydrogen bonds : bond 0.16349 / 10.46 ( 615) hydrogen bonds : angle 5.11542 / 3.72 ( 1755) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 431 ASP cc_start: 0.8816 (t70) cc_final: 0.8532 (t0) REVERT: B 100 VAL cc_start: 0.7356 (m) cc_final: 0.7148 (p) REVERT: B 134 ASP cc_start: 0.7323 (m-30) cc_final: 0.6626 (t0) REVERT: D 134 ASP cc_start: 0.7173 (m-30) cc_final: 0.6246 (t0) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.0970 time to fit residues: 21.4104 Evaluate side-chains 116 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 123 optimal weight: 0.3980 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.124549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.096506 restraints weight = 23848.352| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 3.06 r_work: 0.3330 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10458 Z= 0.176 Angle : 0.585 6.423 14123 Z= 0.300 Chirality : 0.043 0.155 1639 Planarity : 0.005 0.072 1728 Dihedral : 11.853 80.251 1604 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.00 % Allowed : 7.41 % Favored : 91.59 % 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: 1.63 (0.25), residues: 1235 helix: 2.10 (0.19), residues: 781 sheet: 0.96 (0.78), residues: 40 loop : -0.93 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 144 TYR 0.016 0.002 TYR G 8 PHE 0.027 0.002 PHE D 190 TRP 0.007 0.001 TRP A 454 HIS 0.004 0.001 HIS H 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (10458) covalent geometry : angle 0.58469 / 0.30 (14123) hydrogen bonds : bond 0.04480 / 2.95 ( 615) hydrogen bonds : angle 3.82730 / 2.78 ( 1755) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 283 GLU cc_start: 0.9022 (tp30) cc_final: 0.8794 (tp30) REVERT: A 431 ASP cc_start: 0.9242 (t70) cc_final: 0.8844 (t0) REVERT: B 143 ASP cc_start: 0.8772 (t0) cc_final: 0.8504 (t0) REVERT: B 312 MET cc_start: 0.9082 (mmt) cc_final: 0.8771 (tpp) REVERT: D 133 PHE cc_start: 0.8408 (t80) cc_final: 0.8203 (t80) REVERT: D 134 ASP cc_start: 0.7515 (m-30) cc_final: 0.6555 (t0) outliers start: 10 outliers final: 8 residues processed: 122 average time/residue: 0.0963 time to fit residues: 16.9353 Evaluate side-chains 114 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 467 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 61 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 93 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 73 optimal weight: 0.4980 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.123014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.094797 restraints weight = 23861.017| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 3.08 r_work: 0.3300 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10458 Z= 0.194 Angle : 0.584 6.773 14123 Z= 0.301 Chirality : 0.043 0.147 1639 Planarity : 0.005 0.061 1728 Dihedral : 10.041 63.664 1604 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.90 % Allowed : 10.31 % Favored : 88.79 % 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: 1.54 (0.25), residues: 1235 helix: 2.06 (0.19), residues: 785 sheet: -0.41 (0.72), residues: 52 loop : -0.93 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 144 TYR 0.015 0.001 TYR G 8 PHE 0.019 0.002 PHE C 118 TRP 0.006 0.001 TRP A 454 HIS 0.007 0.001 HIS H 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.19 (10458) covalent geometry : angle 0.58367 / 0.30 (14123) hydrogen bonds : bond 0.04522 / 3.00 ( 615) hydrogen bonds : angle 3.74291 / 2.72 ( 1755) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.9047 (tp30) cc_final: 0.8800 (tp30) REVERT: A 427 LYS cc_start: 0.9215 (mmtt) cc_final: 0.8999 (mmtm) REVERT: A 431 ASP cc_start: 0.9275 (t70) cc_final: 0.8877 (t0) REVERT: B 134 ASP cc_start: 0.7296 (m-30) cc_final: 0.6418 (t0) REVERT: D 134 ASP cc_start: 0.7459 (m-30) cc_final: 0.6484 (t0) REVERT: D 431 ASP cc_start: 0.9030 (t0) cc_final: 0.8813 (m-30) outliers start: 9 outliers final: 8 residues processed: 118 average time/residue: 0.0875 time to fit residues: 15.0245 Evaluate side-chains 115 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 467 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 82 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 87 optimal weight: 0.0980 chunk 6 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 = 0.3880 r_free = 0.3880 target = 0.123780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.095789 restraints weight = 23980.756| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 3.09 r_work: 0.3318 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10458 Z= 0.147 Angle : 0.553 7.845 14123 Z= 0.281 Chirality : 0.041 0.139 1639 Planarity : 0.004 0.055 1728 Dihedral : 9.263 59.076 1604 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.50 % Allowed : 11.51 % Favored : 86.99 % 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: 1.63 (0.25), residues: 1235 helix: 2.12 (0.19), residues: 789 sheet: 0.23 (0.77), residues: 45 loop : -0.98 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 144 TYR 0.017 0.001 TYR G 8 PHE 0.021 0.001 PHE D 190 TRP 0.006 0.001 TRP A 454 HIS 0.005 0.001 HIS H 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (10458) covalent geometry : angle 0.55257 / 0.28 (14123) hydrogen bonds : bond 0.04046 / 2.69 ( 615) hydrogen bonds : angle 3.59673 / 2.62 ( 1755) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 283 GLU cc_start: 0.9029 (tp30) cc_final: 0.8788 (tp30) REVERT: A 427 LYS cc_start: 0.9183 (mmtt) cc_final: 0.8979 (mmtm) REVERT: A 431 ASP cc_start: 0.9168 (t70) cc_final: 0.8779 (t0) REVERT: B 134 ASP cc_start: 0.7469 (m-30) cc_final: 0.6544 (t0) REVERT: D 134 ASP cc_start: 0.7493 (m-30) cc_final: 0.6630 (t0) outliers start: 15 outliers final: 13 residues processed: 121 average time/residue: 0.0861 time to fit residues: 15.3366 Evaluate side-chains 117 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 472 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 47 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 62 optimal weight: 0.5980 overall best weight: 3.7188 ------------------------------------------------------------------------------- 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 = 0.3821 r_free = 0.3821 target = 0.120406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.092077 restraints weight = 23827.403| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 3.04 r_work: 0.3236 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 10458 Z= 0.276 Angle : 0.643 8.006 14123 Z= 0.331 Chirality : 0.045 0.167 1639 Planarity : 0.005 0.060 1728 Dihedral : 9.157 59.888 1604 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.89 % Favored : 96.03 % Rotamer: Outliers : 2.60 % Allowed : 12.31 % Favored : 85.09 % 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: 1.31 (0.25), residues: 1235 helix: 1.93 (0.19), residues: 789 sheet: -1.41 (0.62), residues: 66 loop : -0.98 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 144 TYR 0.017 0.002 TYR A 156 PHE 0.023 0.002 PHE D 133 TRP 0.007 0.001 TRP A 454 HIS 0.008 0.001 HIS H 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00660 / 0.28 (10458) covalent geometry : angle 0.64323 / 0.33 (14123) hydrogen bonds : bond 0.04826 / 3.20 ( 615) hydrogen bonds : angle 3.92368 / 2.85 ( 1755) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 382 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9153 (mp) REVERT: A 427 LYS cc_start: 0.9258 (mmtt) cc_final: 0.9035 (mmtm) REVERT: A 431 ASP cc_start: 0.9294 (t70) cc_final: 0.8879 (t0) REVERT: D 134 ASP cc_start: 0.7438 (m-30) cc_final: 0.6540 (t0) REVERT: D 180 TYR cc_start: 0.6765 (m-80) cc_final: 0.6544 (m-80) REVERT: D 431 ASP cc_start: 0.8726 (m-30) cc_final: 0.8468 (m-30) outliers start: 26 outliers final: 22 residues processed: 126 average time/residue: 0.0851 time to fit residues: 15.5745 Evaluate side-chains 127 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 478 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 90 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 89 optimal weight: 0.2980 chunk 101 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- 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 = 0.3877 r_free = 0.3877 target = 0.124061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.096083 restraints weight = 23776.425| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.06 r_work: 0.3311 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10458 Z= 0.120 Angle : 0.543 8.431 14123 Z= 0.274 Chirality : 0.041 0.138 1639 Planarity : 0.004 0.051 1728 Dihedral : 8.219 59.017 1604 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.48 % Favored : 96.44 % Rotamer: Outliers : 1.10 % Allowed : 15.22 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.71 (0.25), residues: 1235 helix: 2.25 (0.19), residues: 783 sheet: 0.60 (0.91), residues: 30 loop : -1.04 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 144 TYR 0.013 0.001 TYR G 8 PHE 0.010 0.001 PHE A 108 TRP 0.006 0.001 TRP C 289 HIS 0.003 0.000 HIS H 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (10458) covalent geometry : angle 0.54303 / 0.27 (14123) hydrogen bonds : bond 0.03757 / 2.51 ( 615) hydrogen bonds : angle 3.47060 / 2.53 ( 1755) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 283 GLU cc_start: 0.9042 (tp30) cc_final: 0.8802 (tp30) REVERT: A 427 LYS cc_start: 0.9253 (mmtt) cc_final: 0.9047 (mmtm) REVERT: A 431 ASP cc_start: 0.9189 (t70) cc_final: 0.8755 (t0) REVERT: D 134 ASP cc_start: 0.7496 (m-30) cc_final: 0.6650 (t0) REVERT: D 180 TYR cc_start: 0.6902 (m-80) cc_final: 0.6608 (m-80) outliers start: 11 outliers final: 10 residues processed: 124 average time/residue: 0.0880 time to fit residues: 15.7863 Evaluate side-chains 121 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 478 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 29 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 chunk 7 optimal weight: 8.9990 chunk 68 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 86 optimal weight: 0.3980 chunk 117 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 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 = 0.3891 r_free = 0.3891 target = 0.124914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.097031 restraints weight = 23478.772| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.07 r_work: 0.3324 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10458 Z= 0.114 Angle : 0.547 9.901 14123 Z= 0.272 Chirality : 0.041 0.136 1639 Planarity : 0.004 0.050 1728 Dihedral : 7.571 58.674 1604 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.40 % Favored : 96.52 % Rotamer: Outliers : 1.30 % Allowed : 16.52 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.25), residues: 1235 helix: 2.25 (0.19), residues: 791 sheet: 0.70 (0.92), residues: 30 loop : -0.99 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 371 TYR 0.012 0.001 TYR G 8 PHE 0.022 0.001 PHE D 133 TRP 0.005 0.001 TRP C 289 HIS 0.003 0.000 HIS H 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (10458) covalent geometry : angle 0.54710 / 0.27 (14123) hydrogen bonds : bond 0.03567 / 2.37 ( 615) hydrogen bonds : angle 3.34684 / 2.44 ( 1755) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 283 GLU cc_start: 0.9049 (tp30) cc_final: 0.8816 (tp30) REVERT: A 427 LYS cc_start: 0.9250 (mmtt) cc_final: 0.9046 (mmtm) REVERT: A 431 ASP cc_start: 0.9169 (t70) cc_final: 0.8740 (t0) REVERT: D 134 ASP cc_start: 0.7537 (m-30) cc_final: 0.6723 (t0) outliers start: 13 outliers final: 11 residues processed: 126 average time/residue: 0.0823 time to fit residues: 15.1334 Evaluate side-chains 121 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 478 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 7 optimal weight: 0.0050 chunk 36 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 97 optimal weight: 0.4980 chunk 62 optimal weight: 6.9990 chunk 48 optimal weight: 0.0670 chunk 55 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.124052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.096060 restraints weight = 23495.199| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 3.06 r_work: 0.3308 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10458 Z= 0.133 Angle : 0.569 10.867 14123 Z= 0.281 Chirality : 0.041 0.164 1639 Planarity : 0.004 0.048 1728 Dihedral : 7.413 57.666 1604 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.48 % Favored : 96.44 % Rotamer: Outliers : 1.50 % Allowed : 16.62 % Favored : 81.88 % 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: 1.70 (0.25), residues: 1235 helix: 2.21 (0.19), residues: 792 sheet: 0.72 (0.94), residues: 30 loop : -1.05 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 144 TYR 0.019 0.001 TYR B 219 PHE 0.010 0.001 PHE A 108 TRP 0.005 0.001 TRP C 289 HIS 0.004 0.001 HIS H 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (10458) covalent geometry : angle 0.56934 / 0.28 (14123) hydrogen bonds : bond 0.03723 / 2.47 ( 615) hydrogen bonds : angle 3.38474 / 2.47 ( 1755) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.264 Fit side-chains REVERT: A 283 GLU cc_start: 0.9056 (tp30) cc_final: 0.8820 (tp30) REVERT: A 427 LYS cc_start: 0.9247 (mmtt) cc_final: 0.9045 (mmtm) REVERT: A 431 ASP cc_start: 0.9190 (t70) cc_final: 0.8781 (t0) REVERT: D 133 PHE cc_start: 0.8456 (t80) cc_final: 0.8159 (t80) REVERT: D 134 ASP cc_start: 0.7591 (m-30) cc_final: 0.6601 (t70) outliers start: 15 outliers final: 13 residues processed: 125 average time/residue: 0.0826 time to fit residues: 15.3328 Evaluate side-chains 123 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 478 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 99 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.124311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.096417 restraints weight = 23565.999| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 3.07 r_work: 0.3312 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10458 Z= 0.127 Angle : 0.572 11.842 14123 Z= 0.281 Chirality : 0.041 0.139 1639 Planarity : 0.004 0.047 1728 Dihedral : 7.203 59.969 1604 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.56 % Favored : 96.36 % Rotamer: Outliers : 1.30 % Allowed : 16.82 % Favored : 81.88 % 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: 1.69 (0.24), residues: 1235 helix: 2.20 (0.19), residues: 792 sheet: 0.69 (0.93), residues: 30 loop : -1.06 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 146 TYR 0.020 0.001 TYR B 219 PHE 0.009 0.001 PHE B 108 TRP 0.005 0.001 TRP A 454 HIS 0.004 0.001 HIS H 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (10458) covalent geometry : angle 0.57198 / 0.28 (14123) hydrogen bonds : bond 0.03678 / 2.44 ( 615) hydrogen bonds : angle 3.37314 / 2.45 ( 1755) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.423 Fit side-chains REVERT: A 283 GLU cc_start: 0.9054 (tp30) cc_final: 0.8820 (tp30) REVERT: A 427 LYS cc_start: 0.9244 (mmtt) cc_final: 0.9042 (mmtm) REVERT: A 431 ASP cc_start: 0.9184 (t70) cc_final: 0.8774 (t0) REVERT: B 148 SER cc_start: 0.7499 (t) cc_final: 0.7126 (p) REVERT: D 133 PHE cc_start: 0.8446 (t80) cc_final: 0.8166 (t80) REVERT: D 134 ASP cc_start: 0.7520 (m-30) cc_final: 0.6497 (t70) outliers start: 13 outliers final: 11 residues processed: 119 average time/residue: 0.0885 time to fit residues: 15.5588 Evaluate side-chains 120 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 478 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 117 optimal weight: 6.9990 chunk 87 optimal weight: 0.0770 chunk 118 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 chunk 84 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 6 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.4940 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.125947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.098334 restraints weight = 23233.902| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 3.03 r_work: 0.3348 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10458 Z= 0.111 Angle : 0.562 12.075 14123 Z= 0.275 Chirality : 0.040 0.137 1639 Planarity : 0.004 0.046 1728 Dihedral : 6.507 58.457 1604 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.40 % Favored : 96.52 % Rotamer: Outliers : 1.20 % Allowed : 17.22 % Favored : 81.58 % 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: 1.74 (0.24), residues: 1235 helix: 2.25 (0.19), residues: 790 sheet: 0.79 (0.91), residues: 30 loop : -1.06 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 146 TYR 0.014 0.001 TYR B 219 PHE 0.008 0.001 PHE B 410 TRP 0.006 0.001 TRP B 434 HIS 0.003 0.000 HIS H 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (10458) covalent geometry : angle 0.56209 / 0.27 (14123) hydrogen bonds : bond 0.03274 / 2.18 ( 615) hydrogen bonds : angle 3.20291 / 2.33 ( 1755) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.306 Fit side-chains REVERT: A 143 ASP cc_start: 0.8430 (t0) cc_final: 0.8157 (t0) REVERT: A 427 LYS cc_start: 0.9228 (mmtt) cc_final: 0.9016 (mmtm) REVERT: A 431 ASP cc_start: 0.9105 (t70) cc_final: 0.8687 (t0) REVERT: B 148 SER cc_start: 0.7423 (t) cc_final: 0.7148 (p) REVERT: D 133 PHE cc_start: 0.8414 (t80) cc_final: 0.8117 (t80) REVERT: D 134 ASP cc_start: 0.7559 (m-30) cc_final: 0.6503 (t70) REVERT: H 14 ARG cc_start: 0.5035 (mmp-170) cc_final: 0.4739 (mmp-170) outliers start: 12 outliers final: 12 residues processed: 127 average time/residue: 0.0849 time to fit residues: 15.9632 Evaluate side-chains 124 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 478 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 7 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 91 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.122023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.093820 restraints weight = 23612.905| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 3.07 r_work: 0.3266 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 10458 Z= 0.209 Angle : 0.636 12.522 14123 Z= 0.315 Chirality : 0.043 0.152 1639 Planarity : 0.004 0.050 1728 Dihedral : 7.128 56.498 1604 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.05 % Favored : 95.87 % Rotamer: Outliers : 1.50 % Allowed : 17.42 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.25), residues: 1235 helix: 2.11 (0.19), residues: 794 sheet: 0.75 (0.95), residues: 30 loop : -1.09 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 144 TYR 0.021 0.001 TYR B 219 PHE 0.014 0.001 PHE C 118 TRP 0.006 0.001 TRP A 454 HIS 0.006 0.001 HIS H 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.21 (10458) covalent geometry : angle 0.63556 / 0.31 (14123) hydrogen bonds : bond 0.04352 / 2.87 ( 615) hydrogen bonds : angle 3.57766 / 2.60 ( 1755) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2062.94 seconds wall clock time: 36 minutes 12.57 seconds (2172.57 seconds total)