Starting phenix.real_space_refine on Fri Sep 11 19:50:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y2f_72409/09_2026/9y2f_72409.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y2f_72409/09_2026/9y2f_72409.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y2f_72409/09_2026/9y2f_72409.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y2f_72409/09_2026/9y2f_72409.map" model { file = "/net/cci-nas-00/data/ceres_data/9y2f_72409/09_2026/9y2f_72409.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y2f_72409/09_2026/9y2f_72409.cif" } resolution = 4.6 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= 0.004 sd= 0.028 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 6892 2.51 5 N 1900 2.21 5 O 2078 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-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10924 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1783 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 215} Chain: "A" Number of atoms: 3679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3679 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 22, 'TRANS': 461} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 4, 'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 65 Chain: "D" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1783 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 215} Chain: "B" Number of atoms: 3679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3679 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 22, 'TRANS': 461} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 4, 'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 65 Time building chain proxies: 2.70, per 1000 atoms: 0.25 Number of scatterers: 10924 At special positions: 0 Unit cell: (134.25, 90.75, 120.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 2078 8.00 N 1900 7.00 C 6892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 39 " distance=2.03 Simple disulfide: pdb=" SG CYS C 189 " - pdb=" SG CYS C 215 " distance=2.03 Simple disulfide: pdb=" SG CYS C 191 " - pdb=" SG CYS C 245 " distance=2.03 Simple disulfide: pdb=" SG CYS A 67 " - pdb=" SG CYS A 109 " distance=2.04 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 374 " - pdb=" SG CYS A 390 " distance=2.02 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 437 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 39 " distance=2.03 Simple disulfide: pdb=" SG CYS D 189 " - pdb=" SG CYS D 215 " distance=2.03 Simple disulfide: pdb=" SG CYS D 191 " - pdb=" SG CYS D 245 " distance=2.03 Simple disulfide: pdb=" SG CYS B 67 " - pdb=" SG CYS B 109 " distance=2.04 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 390 " distance=2.03 Simple disulfide: pdb=" SG CYS B 430 " - pdb=" SG CYS B 437 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 409.9 milliseconds 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2636 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 8 sheets defined 33.5% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'C' and resid 71 through 76 removed outlier: 3.657A pdb=" N LEU C 75 " --> pdb=" O LEU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 124 Processing helix chain 'C' and resid 145 through 150 removed outlier: 3.610A pdb=" N SER C 148 " --> pdb=" O THR C 145 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU C 149 " --> pdb=" O ALA C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 190 through 204 removed outlier: 3.936A pdb=" N GLY C 195 " --> pdb=" O CYS C 191 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N PHE C 196 " --> pdb=" O ASP C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 213 removed outlier: 4.154A pdb=" N ARG C 212 " --> pdb=" O ASN C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 222 Processing helix chain 'C' and resid 236 through 248 removed outlier: 3.910A pdb=" N VAL C 240 " --> pdb=" O ASN C 236 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASN C 247 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY C 248 " --> pdb=" O LYS C 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 92 Processing helix chain 'A' and resid 111 through 125 removed outlier: 4.399A pdb=" N ALA A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 171 removed outlier: 3.584A pdb=" N MET A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU A 171 " --> pdb=" O ASN A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 217 removed outlier: 3.846A pdb=" N GLN A 205 " --> pdb=" O PRO A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 246 removed outlier: 4.423A pdb=" N GLY A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 276 Processing helix chain 'A' and resid 288 through 302 Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 344 through 353 removed outlier: 3.767A pdb=" N ALA A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 373 Processing helix chain 'A' and resid 407 through 430 removed outlier: 3.948A pdb=" N VAL A 411 " --> pdb=" O LYS A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 443 removed outlier: 3.941A pdb=" N GLU A 441 " --> pdb=" O CYS A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 454 removed outlier: 3.602A pdb=" N ASN A 454 " --> pdb=" O LYS A 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 76 removed outlier: 3.655A pdb=" N LEU D 75 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 145 through 150 removed outlier: 3.612A pdb=" N SER D 148 " --> pdb=" O THR D 145 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU D 149 " --> pdb=" O ALA D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 171 removed outlier: 3.506A pdb=" N PHE D 171 " --> pdb=" O GLY D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 204 removed outlier: 3.936A pdb=" N GLY D 195 " --> pdb=" O CYS D 191 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N PHE D 196 " --> pdb=" O ASP D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 213 removed outlier: 4.150A pdb=" N ARG D 212 " --> pdb=" O ASN D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 222 Processing helix chain 'D' and resid 236 through 248 removed outlier: 3.911A pdb=" N VAL D 240 " --> pdb=" O ASN D 236 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASN D 247 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY D 248 " --> pdb=" O LYS D 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 92 Processing helix chain 'B' and resid 111 through 125 removed outlier: 4.399A pdb=" N ALA B 125 " --> pdb=" O THR B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 171 removed outlier: 3.583A pdb=" N MET B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU B 171 " --> pdb=" O ASN B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 217 removed outlier: 3.853A pdb=" N GLN B 205 " --> pdb=" O PRO B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 246 removed outlier: 4.425A pdb=" N GLY B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 276 Processing helix chain 'B' and resid 288 through 302 Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 344 through 353 removed outlier: 3.768A pdb=" N ALA B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 373 Processing helix chain 'B' and resid 407 through 430 removed outlier: 3.949A pdb=" N VAL B 411 " --> pdb=" O LYS B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 443 removed outlier: 3.937A pdb=" N GLU B 441 " --> pdb=" O CYS B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 454 removed outlier: 3.603A pdb=" N ASN B 454 " --> pdb=" O LYS B 450 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 38 through 39 removed outlier: 6.554A pdb=" N LEU C 60 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU C 84 " --> pdb=" O GLN C 109 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LEU C 132 " --> pdb=" O ASP C 157 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE C 156 " --> pdb=" O VAL C 179 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 45 removed outlier: 6.056A pdb=" N LEU A 51 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU A 106 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N GLY A 53 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR A 50 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLY A 152 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 9.059A pdb=" N ILE A 177 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL A 153 " --> pdb=" O ILE A 177 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 249 through 250 removed outlier: 7.701A pdb=" N TYR A 220 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 9.226A pdb=" N VAL A 284 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N SER A 222 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL A 283 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TRP A 310 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N ILE A 336 " --> pdb=" O TRP A 310 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ALA A 333 " --> pdb=" O TYR A 482 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TYR A 482 " --> pdb=" O ALA A 333 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A 335 " --> pdb=" O PHE A 480 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE A 480 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN A 337 " --> pdb=" O ASP A 478 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N TYR A 477 " --> pdb=" O GLN A 497 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLN A 497 " --> pdb=" O TYR A 477 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE A 479 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN A 481 " --> pdb=" O ARG A 493 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 374 through 375 Processing sheet with id=AA5, first strand: chain 'D' and resid 38 through 39 removed outlier: 6.556A pdb=" N LEU D 60 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU D 84 " --> pdb=" O GLN D 109 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LEU D 132 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D 156 " --> pdb=" O VAL D 179 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 43 through 45 removed outlier: 6.069A pdb=" N LEU B 51 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU B 106 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N GLY B 53 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR B 50 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY B 152 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 9.061A pdb=" N ILE B 177 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL B 153 " --> pdb=" O ILE B 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 249 through 250 removed outlier: 7.699A pdb=" N TYR B 220 " --> pdb=" O ALA B 282 " (cutoff:3.500A) removed outlier: 9.228A pdb=" N VAL B 284 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N SER B 222 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL B 283 " --> pdb=" O VAL B 311 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TRP B 310 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N ILE B 336 " --> pdb=" O TRP B 310 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ALA B 333 " --> pdb=" O TYR B 482 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR B 482 " --> pdb=" O ALA B 333 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR B 335 " --> pdb=" O PHE B 480 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE B 480 " --> pdb=" O THR B 335 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B 337 " --> pdb=" O ASP B 478 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N TYR B 477 " --> pdb=" O GLN B 497 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLN B 497 " --> pdb=" O TYR B 477 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE B 479 " --> pdb=" O ILE B 495 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN B 481 " --> pdb=" O ARG B 493 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 374 through 375 319 hydrogen bonds defined for protein. 906 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: 1.63 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3692 1.34 - 1.46: 2452 1.46 - 1.58: 4936 1.58 - 1.70: 0 1.70 - 1.81: 76 Bond restraints: 11156 Sorted by residual: bond pdb=" N GLU D 28 " pdb=" CA GLU D 28 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.35e-02 5.49e+03 5.87e+00 bond pdb=" N LYS B 389 " pdb=" CA LYS B 389 " ideal model delta sigma weight residual 1.456 1.483 -0.026 1.27e-02 6.20e+03 4.33e+00 bond pdb=" N LYS B 375 " pdb=" CA LYS B 375 " ideal model delta sigma weight residual 1.458 1.481 -0.023 1.19e-02 7.06e+03 3.80e+00 bond pdb=" C LEU A 96 " pdb=" O LEU A 96 " ideal model delta sigma weight residual 1.235 1.230 0.004 4.70e-03 4.53e+04 8.88e-01 bond pdb=" N VAL B 65 " pdb=" CA VAL B 65 " ideal model delta sigma weight residual 1.468 1.459 0.010 1.05e-02 9.07e+03 8.63e-01 ... (remaining 11151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 14858 1.62 - 3.24: 262 3.24 - 4.87: 32 4.87 - 6.49: 4 6.49 - 8.11: 4 Bond angle restraints: 15160 Sorted by residual: angle pdb=" N GLN A 404 " pdb=" CA GLN A 404 " pdb=" C GLN A 404 " ideal model delta sigma weight residual 111.02 115.54 -4.52 1.25e+00 6.40e-01 1.30e+01 angle pdb=" N VAL A 305 " pdb=" CA VAL A 305 " pdb=" C VAL A 305 " ideal model delta sigma weight residual 113.20 109.79 3.41 9.60e-01 1.09e+00 1.26e+01 angle pdb=" N VAL B 305 " pdb=" CA VAL B 305 " pdb=" C VAL B 305 " ideal model delta sigma weight residual 113.20 109.80 3.40 9.60e-01 1.09e+00 1.25e+01 angle pdb=" CA LYS B 389 " pdb=" C LYS B 389 " pdb=" O LYS B 389 " ideal model delta sigma weight residual 121.15 118.12 3.03 1.10e+00 8.26e-01 7.58e+00 angle pdb=" N GLU D 28 " pdb=" CA GLU D 28 " pdb=" C GLU D 28 " ideal model delta sigma weight residual 113.23 110.26 2.97 1.22e+00 6.72e-01 5.92e+00 ... (remaining 15155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 6093 16.89 - 33.78: 472 33.78 - 50.67: 111 50.67 - 67.56: 13 67.56 - 84.45: 14 Dihedral angle restraints: 6703 sinusoidal: 2605 harmonic: 4098 Sorted by residual: dihedral pdb=" CB CYS A 374 " pdb=" SG CYS A 374 " pdb=" SG CYS A 390 " pdb=" CB CYS A 390 " ideal model delta sinusoidal sigma weight residual -86.00 -170.45 84.45 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CB CYS B 374 " pdb=" SG CYS B 374 " pdb=" SG CYS B 390 " pdb=" CB CYS B 390 " ideal model delta sinusoidal sigma weight residual -86.00 -170.42 84.42 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CB CYS A 67 " pdb=" SG CYS A 67 " pdb=" SG CYS A 109 " pdb=" CB CYS A 109 " ideal model delta sinusoidal sigma weight residual 93.00 32.84 60.16 1 1.00e+01 1.00e-02 4.82e+01 ... (remaining 6700 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1173 0.037 - 0.074: 363 0.074 - 0.111: 131 0.111 - 0.148: 16 0.148 - 0.185: 3 Chirality restraints: 1686 Sorted by residual: chirality pdb=" CA LYS B 389 " pdb=" N LYS B 389 " pdb=" C LYS B 389 " pdb=" CB LYS B 389 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.56e-01 chirality pdb=" CG LEU C 36 " pdb=" CB LEU C 36 " pdb=" CD1 LEU C 36 " pdb=" CD2 LEU C 36 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CG LEU D 36 " pdb=" CB LEU D 36 " pdb=" CD1 LEU D 36 " pdb=" CD2 LEU D 36 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.78e-01 ... (remaining 1683 not shown) Planarity restraints: 2000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 388 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.27e+00 pdb=" C ARG B 388 " 0.036 2.00e-02 2.50e+03 pdb=" O ARG B 388 " -0.014 2.00e-02 2.50e+03 pdb=" N LYS B 389 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 65 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO B 66 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 66 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 66 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 65 " 0.021 5.00e-02 4.00e+02 3.14e-02 1.57e+00 pdb=" N PRO A 66 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " 0.018 5.00e-02 4.00e+02 ... (remaining 1997 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 7552 3.05 - 3.51: 11888 3.51 - 3.98: 16644 3.98 - 4.44: 19582 4.44 - 4.90: 29716 Nonbonded interactions: 85382 Sorted by model distance: nonbonded pdb=" O ASP D 30 " pdb=" O VAL D 34 " model vdw 2.591 3.040 nonbonded pdb=" O ASP C 30 " pdb=" O VAL C 34 " model vdw 2.591 3.040 nonbonded pdb=" O LEU D 62 " pdb=" O ASN D 85 " model vdw 2.592 3.040 nonbonded pdb=" O LEU C 62 " pdb=" O ASN C 85 " model vdw 2.592 3.040 nonbonded pdb=" OE2 GLU D 28 " pdb=" NZ LYS B 389 " model vdw 2.604 3.120 ... (remaining 85377 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: 0.02 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'D' } pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' } Set refine NCS operators NCS operators will be refined. 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 group one per residue 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: 5.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.130 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 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 : 0.003 0.033 11169 Z= 0.172 Angle : 0.555 8.109 15186 Z= 0.297 Chirality : 0.041 0.185 1686 Planarity : 0.004 0.032 2000 Dihedral : 12.910 76.739 4028 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 0.17 % Allowed : 0.34 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.30 (0.23), residues: 1412 helix: 1.24 (0.26), residues: 412 sheet: -2.10 (0.38), residues: 172 loop : -1.77 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 72 TYR 0.011 0.001 TYR B 402 PHE 0.008 0.001 PHE D 78 TRP 0.012 0.001 TRP C 35 HIS 0.004 0.001 HIS D 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.17 (11156) covalent geometry : angle 0.55469 / 0.30 (15160) SS BOND : bond 0.00311 / 0.19 ( 13) SS BOND : angle 0.68901 / 0.47 ( 26) hydrogen bonds : bond 0.12655 / 8.56 ( 319) hydrogen bonds : angle 6.36144 / 4.25 ( 906) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 66 LYS cc_start: 0.8742 (mmmm) cc_final: 0.8033 (mmmt) REVERT: C 105 LEU cc_start: 0.9532 (tp) cc_final: 0.9322 (mt) REVERT: C 123 LEU cc_start: 0.9393 (mt) cc_final: 0.9094 (mp) REVERT: C 126 MET cc_start: 0.9269 (mtm) cc_final: 0.8863 (mmm) REVERT: C 147 PHE cc_start: 0.9399 (m-80) cc_final: 0.8924 (m-80) REVERT: C 153 LEU cc_start: 0.9357 (mt) cc_final: 0.9028 (mm) REVERT: C 167 ASP cc_start: 0.8147 (t70) cc_final: 0.7710 (t0) REVERT: C 170 THR cc_start: 0.5704 (m) cc_final: 0.4136 (p) REVERT: C 182 LEU cc_start: 0.8970 (mt) cc_final: 0.8439 (tt) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0820 time to fit residues: 5.0775 Evaluate side-chains 32 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.075 Evaluate side-chains 91 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ILE cc_start: 0.9458 (mm) cc_final: 0.9189 (mm) REVERT: A 80 GLU cc_start: 0.9443 (mm-30) cc_final: 0.8746 (mm-30) REVERT: A 86 LEU cc_start: 0.9634 (mt) cc_final: 0.9398 (tt) REVERT: A 91 SER cc_start: 0.9327 (m) cc_final: 0.9123 (p) REVERT: A 116 LEU cc_start: 0.9152 (mt) cc_final: 0.8771 (mp) REVERT: A 128 GLN cc_start: 0.8283 (tp40) cc_final: 0.7844 (tm-30) REVERT: A 148 GLU cc_start: 0.9057 (tt0) cc_final: 0.8855 (pt0) REVERT: A 149 LYS cc_start: 0.8947 (tptt) cc_final: 0.8540 (tptp) REVERT: A 150 VAL cc_start: 0.9550 (m) cc_final: 0.9183 (p) REVERT: A 164 MET cc_start: 0.9085 (mmt) cc_final: 0.8748 (mmm) REVERT: A 177 ILE cc_start: 0.9670 (mt) cc_final: 0.9072 (mm) REVERT: A 236 GLU cc_start: 0.9408 (tt0) cc_final: 0.8895 (pt0) REVERT: A 248 LEU cc_start: 0.9288 (tp) cc_final: 0.8943 (tp) REVERT: A 361 ASN cc_start: 0.9101 (t0) cc_final: 0.8617 (t0) REVERT: A 399 ASP cc_start: 0.9142 (m-30) cc_final: 0.8812 (t0) REVERT: A 413 ASP cc_start: 0.9351 (m-30) cc_final: 0.9110 (m-30) REVERT: A 440 MET cc_start: 0.9127 (ttp) cc_final: 0.8920 (ttp) REVERT: A 469 LYS cc_start: 0.9681 (mmtt) cc_final: 0.9479 (mtpp) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.0604 time to fit residues: 6.9907 Evaluate side-chains 67 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.0010 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.0060 chunk 91 optimal weight: 0.0770 chunk 55 optimal weight: 6.9990 overall best weight: 0.2760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 43 GLN A 138 ASN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 ASN A 420 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.060115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.044213 restraints weight = 12518.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.046029 restraints weight = 7698.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.047445 restraints weight = 5321.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.048327 restraints weight = 4012.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.049067 restraints weight = 3289.571| |-----------------------------------------------------------------------------| r_work (final): 0.3313 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.076504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.060382 restraints weight = 15208.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.062562 restraints weight = 9485.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.064120 restraints weight = 6669.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.065272 restraints weight = 5105.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.066156 restraints weight = 4138.997| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11169 Z= 0.115 Angle : 0.611 9.729 15186 Z= 0.310 Chirality : 0.043 0.150 1686 Planarity : 0.004 0.037 2000 Dihedral : 4.432 27.245 1530 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 0.34 % Allowed : 3.97 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.28 (0.23), residues: 1412 helix: 1.07 (0.26), residues: 434 sheet: -1.87 (0.41), residues: 162 loop : -1.79 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 359 TYR 0.010 0.001 TYR B 349 PHE 0.029 0.001 PHE A 122 TRP 0.026 0.002 TRP D 25 HIS 0.009 0.001 HIS A 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (11156) covalent geometry : angle 0.59948 / 0.31 (15160) SS BOND : bond 0.00355 / 0.24 ( 13) SS BOND : angle 2.90519 / 1.82 ( 26) hydrogen bonds : bond 0.03475 / 2.38 ( 319) hydrogen bonds : angle 5.18777 / 3.47 ( 906) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 118 LEU cc_start: 0.8944 (tp) cc_final: 0.8338 (tp) REVERT: D 147 PHE cc_start: 0.9190 (m-80) cc_final: 0.8798 (m-80) REVERT: D 166 LEU cc_start: 0.8780 (tp) cc_final: 0.8478 (tp) REVERT: D 170 THR cc_start: 0.4929 (m) cc_final: 0.3937 (m) REVERT: D 230 ARG cc_start: 0.8713 (tpp80) cc_final: 0.8226 (ttp80) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0669 time to fit residues: 3.3715 Evaluate side-chains 30 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.098 Evaluate side-chains 79 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ILE cc_start: 0.9465 (mm) cc_final: 0.9083 (mm) REVERT: A 79 LEU cc_start: 0.9495 (mm) cc_final: 0.9224 (mm) REVERT: A 80 GLU cc_start: 0.9351 (mm-30) cc_final: 0.8570 (mm-30) REVERT: A 91 SER cc_start: 0.9285 (m) cc_final: 0.9079 (p) REVERT: A 128 GLN cc_start: 0.8305 (tp40) cc_final: 0.7855 (tm-30) REVERT: A 149 LYS cc_start: 0.8874 (tptt) cc_final: 0.8459 (tptp) REVERT: A 150 VAL cc_start: 0.9464 (m) cc_final: 0.9072 (p) REVERT: A 176 GLN cc_start: 0.8176 (tm-30) cc_final: 0.7903 (tm-30) REVERT: A 193 ASP cc_start: 0.9012 (p0) cc_final: 0.8738 (p0) REVERT: A 236 GLU cc_start: 0.9367 (tt0) cc_final: 0.8774 (pt0) REVERT: A 310 TRP cc_start: 0.7400 (m-90) cc_final: 0.7011 (m-90) REVERT: A 361 ASN cc_start: 0.9089 (t0) cc_final: 0.8776 (t0) REVERT: A 399 ASP cc_start: 0.8984 (m-30) cc_final: 0.8619 (t0) REVERT: A 413 ASP cc_start: 0.9288 (m-30) cc_final: 0.8992 (m-30) REVERT: A 440 MET cc_start: 0.9105 (ttp) cc_final: 0.8809 (ttm) REVERT: A 469 LYS cc_start: 0.9712 (mmtt) cc_final: 0.9479 (mtpp) outliers start: 2 outliers final: 2 residues processed: 78 average time/residue: 0.0559 time to fit residues: 5.6274 Evaluate side-chains 64 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 24 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 82 optimal weight: 0.2980 chunk 62 optimal weight: 5.9990 chunk 90 optimal weight: 0.2980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 GLN A 420 HIS ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.060839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.044804 restraints weight = 11971.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.046644 restraints weight = 7207.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.048015 restraints weight = 5004.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.048968 restraints weight = 3790.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.049662 restraints weight = 3104.515| |-----------------------------------------------------------------------------| r_work (final): 0.3299 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.077451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.062988 restraints weight = 14448.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.065026 restraints weight = 8921.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.066481 restraints weight = 6213.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.067546 restraints weight = 4725.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.068368 restraints weight = 3813.282| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 11169 Z= 0.118 Angle : 0.612 11.730 15186 Z= 0.311 Chirality : 0.044 0.231 1686 Planarity : 0.005 0.086 2000 Dihedral : 4.377 25.997 1530 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.28 (0.23), residues: 1412 helix: 1.05 (0.25), residues: 432 sheet: -1.73 (0.42), residues: 158 loop : -1.80 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 359 TYR 0.015 0.001 TYR A 477 PHE 0.012 0.001 PHE A 122 TRP 0.020 0.002 TRP D 25 HIS 0.009 0.001 HIS A 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (11156) covalent geometry : angle 0.59545 / 0.30 (15160) SS BOND : bond 0.00292 / 0.19 ( 13) SS BOND : angle 3.49712 / 2.17 ( 26) hydrogen bonds : bond 0.03286 / 2.25 ( 319) hydrogen bonds : angle 5.02600 / 3.37 ( 906) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 147 PHE cc_start: 0.9210 (m-80) cc_final: 0.8793 (m-80) REVERT: D 166 LEU cc_start: 0.8808 (tp) cc_final: 0.8492 (tp) REVERT: D 170 THR cc_start: 0.4954 (m) cc_final: 0.4118 (m) REVERT: D 230 ARG cc_start: 0.8682 (tpp80) cc_final: 0.8212 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0664 time to fit residues: 2.8189 Evaluate side-chains 27 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.059 Evaluate side-chains 69 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 ILE cc_start: 0.9368 (mm) cc_final: 0.9049 (mm) REVERT: B 79 LEU cc_start: 0.9518 (mm) cc_final: 0.9141 (mm) REVERT: B 80 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8470 (mm-30) REVERT: B 91 SER cc_start: 0.9292 (m) cc_final: 0.9073 (p) REVERT: B 128 GLN cc_start: 0.8239 (tp40) cc_final: 0.7762 (tm-30) REVERT: B 149 LYS cc_start: 0.9001 (tptt) cc_final: 0.8587 (tptp) REVERT: B 150 VAL cc_start: 0.9510 (m) cc_final: 0.9057 (p) REVERT: B 176 GLN cc_start: 0.8409 (tm-30) cc_final: 0.7915 (tm-30) REVERT: B 193 ASP cc_start: 0.9002 (p0) cc_final: 0.8685 (p0) REVERT: B 310 TRP cc_start: 0.7396 (m-90) cc_final: 0.6918 (m-90) REVERT: B 361 ASN cc_start: 0.9090 (t0) cc_final: 0.8793 (t0) REVERT: B 399 ASP cc_start: 0.8781 (m-30) cc_final: 0.8435 (t0) REVERT: B 413 ASP cc_start: 0.9272 (m-30) cc_final: 0.8955 (m-30) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.0705 time to fit residues: 6.1444 Evaluate side-chains 55 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 14 optimal weight: 0.0470 chunk 96 optimal weight: 5.9990 chunk 134 optimal weight: 0.4980 chunk 5 optimal weight: 9.9990 overall best weight: 1.2682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 43 GLN ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 GLN B 420 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.060467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.044458 restraints weight = 12916.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.046200 restraints weight = 7809.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.047534 restraints weight = 5482.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.048315 restraints weight = 4214.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.048904 restraints weight = 3531.786| |-----------------------------------------------------------------------------| r_work (final): 0.3308 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.075731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.060773 restraints weight = 14859.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.062758 restraints weight = 9229.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.064224 restraints weight = 6499.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.065304 restraints weight = 4969.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.066109 restraints weight = 4024.274| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11169 Z= 0.121 Angle : 0.596 10.579 15186 Z= 0.301 Chirality : 0.043 0.211 1686 Planarity : 0.004 0.040 2000 Dihedral : 4.420 26.704 1530 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.23), residues: 1412 helix: 0.98 (0.25), residues: 438 sheet: -1.55 (0.42), residues: 158 loop : -1.86 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 359 TYR 0.033 0.001 TYR A 477 PHE 0.039 0.002 PHE A 122 TRP 0.009 0.001 TRP A 511 HIS 0.009 0.001 HIS B 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (11156) covalent geometry : angle 0.58413 / 0.30 (15160) SS BOND : bond 0.00280 / 0.18 ( 13) SS BOND : angle 2.87624 / 1.81 ( 26) hydrogen bonds : bond 0.03168 / 2.16 ( 319) hydrogen bonds : angle 4.73007 / 3.19 ( 906) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 147 PHE cc_start: 0.9203 (m-80) cc_final: 0.8790 (m-80) REVERT: D 156 ILE cc_start: 0.9341 (tp) cc_final: 0.9140 (tp) REVERT: D 166 LEU cc_start: 0.8814 (tp) cc_final: 0.8501 (tp) REVERT: D 170 THR cc_start: 0.4920 (m) cc_final: 0.4076 (m) REVERT: D 230 ARG cc_start: 0.8689 (tpp80) cc_final: 0.8218 (ttp80) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0744 time to fit residues: 2.7452 Evaluate side-chains 25 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.065 Evaluate side-chains 65 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 SER cc_start: 0.9325 (m) cc_final: 0.9117 (p) REVERT: A 148 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8630 (pt0) REVERT: A 149 LYS cc_start: 0.8924 (tptt) cc_final: 0.8491 (tptp) REVERT: A 150 VAL cc_start: 0.9486 (m) cc_final: 0.9082 (p) REVERT: A 176 GLN cc_start: 0.8268 (tm-30) cc_final: 0.7782 (tm-30) REVERT: A 193 ASP cc_start: 0.8988 (p0) cc_final: 0.8487 (p0) REVERT: A 232 GLU cc_start: 0.9108 (pt0) cc_final: 0.8473 (pp20) REVERT: A 233 LYS cc_start: 0.9381 (mmtp) cc_final: 0.8238 (mmmm) REVERT: A 310 TRP cc_start: 0.7391 (m-90) cc_final: 0.6908 (m-90) REVERT: A 361 ASN cc_start: 0.9167 (t0) cc_final: 0.8951 (t0) REVERT: A 399 ASP cc_start: 0.8937 (m-30) cc_final: 0.8523 (t0) REVERT: A 413 ASP cc_start: 0.9313 (m-30) cc_final: 0.8990 (m-30) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0716 time to fit residues: 5.7289 Evaluate side-chains 57 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 137 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 54 optimal weight: 0.0770 chunk 95 optimal weight: 0.0980 chunk 119 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 126 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 49 optimal weight: 0.0020 chunk 93 optimal weight: 2.9990 overall best weight: 0.8148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 GLN A 420 HIS D 102 GLN ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.060178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.044330 restraints weight = 12199.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.046153 restraints weight = 7510.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.047574 restraints weight = 5272.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.048498 restraints weight = 4015.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.049205 restraints weight = 3285.079| |-----------------------------------------------------------------------------| r_work (final): 0.3309 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.076992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.062549 restraints weight = 14868.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.064517 restraints weight = 9168.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.065880 restraints weight = 6421.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.066934 restraints weight = 4899.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.067547 restraints weight = 3961.685| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11169 Z= 0.115 Angle : 0.589 8.139 15186 Z= 0.298 Chirality : 0.043 0.241 1686 Planarity : 0.004 0.043 2000 Dihedral : 4.332 25.112 1530 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.33 (0.23), residues: 1412 helix: 0.94 (0.25), residues: 438 sheet: -1.65 (0.42), residues: 158 loop : -1.84 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 340 TYR 0.007 0.001 TYR A 367 PHE 0.036 0.001 PHE A 122 TRP 0.023 0.002 TRP C 25 HIS 0.009 0.001 HIS A 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (11156) covalent geometry : angle 0.57949 / 0.29 (15160) SS BOND : bond 0.00213 / 0.14 ( 13) SS BOND : angle 2.65154 / 1.63 ( 26) hydrogen bonds : bond 0.03073 / 2.09 ( 319) hydrogen bonds : angle 4.74085 / 3.21 ( 906) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 126 MET cc_start: 0.8659 (mpp) cc_final: 0.8229 (mpp) REVERT: D 147 PHE cc_start: 0.9174 (m-80) cc_final: 0.8802 (m-80) REVERT: D 166 LEU cc_start: 0.8829 (tp) cc_final: 0.8387 (tp) REVERT: D 170 THR cc_start: 0.4917 (m) cc_final: 0.4180 (p) REVERT: D 230 ARG cc_start: 0.8641 (tpp80) cc_final: 0.8184 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0663 time to fit residues: 2.6653 Evaluate side-chains 25 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.087 Evaluate side-chains 66 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8643 (mp0) REVERT: B 148 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8653 (pt0) REVERT: B 149 LYS cc_start: 0.8994 (tptt) cc_final: 0.8586 (tptp) REVERT: B 150 VAL cc_start: 0.9504 (m) cc_final: 0.9090 (p) REVERT: B 176 GLN cc_start: 0.8292 (tm-30) cc_final: 0.7863 (tm-30) REVERT: B 193 ASP cc_start: 0.8981 (p0) cc_final: 0.8390 (p0) REVERT: B 232 GLU cc_start: 0.8896 (pt0) cc_final: 0.8598 (mt-10) REVERT: B 334 ILE cc_start: 0.9017 (mp) cc_final: 0.8714 (mm) REVERT: B 361 ASN cc_start: 0.9110 (t0) cc_final: 0.8843 (t0) REVERT: B 413 ASP cc_start: 0.9260 (m-30) cc_final: 0.8948 (m-30) REVERT: B 425 MET cc_start: 0.9057 (ppp) cc_final: 0.8790 (tmm) REVERT: B 428 ASP cc_start: 0.8840 (t70) cc_final: 0.8605 (t70) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0650 time to fit residues: 5.4068 Evaluate side-chains 49 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 10 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 18 optimal weight: 0.0170 chunk 109 optimal weight: 0.5980 chunk 5 optimal weight: 10.0000 chunk 65 optimal weight: 0.0980 chunk 28 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 overall best weight: 2.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 GLN B 420 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.059196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.044170 restraints weight = 13325.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.045930 restraints weight = 8246.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.047229 restraints weight = 5725.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.048011 restraints weight = 4357.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.048620 restraints weight = 3615.705| |-----------------------------------------------------------------------------| r_work (final): 0.3319 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.074340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.059870 restraints weight = 15092.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.061776 restraints weight = 9468.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.063159 restraints weight = 6675.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.064121 restraints weight = 5114.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.064893 restraints weight = 4185.027| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11169 Z= 0.153 Angle : 0.602 9.028 15186 Z= 0.311 Chirality : 0.043 0.202 1686 Planarity : 0.004 0.050 2000 Dihedral : 4.527 26.951 1530 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.46 (0.23), residues: 1412 helix: 0.81 (0.26), residues: 438 sheet: -1.75 (0.42), residues: 158 loop : -1.90 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 395 TYR 0.013 0.001 TYR D 46 PHE 0.031 0.002 PHE B 122 TRP 0.014 0.002 TRP A 511 HIS 0.008 0.001 HIS B 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (11156) covalent geometry : angle 0.59685 / 0.31 (15160) SS BOND : bond 0.00250 / 0.16 ( 13) SS BOND : angle 1.94594 / 1.21 ( 26) hydrogen bonds : bond 0.03110 / 2.11 ( 319) hydrogen bonds : angle 4.94217 / 3.37 ( 906) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 84 LEU cc_start: 0.9074 (tp) cc_final: 0.8867 (tp) REVERT: D 126 MET cc_start: 0.8801 (mpp) cc_final: 0.8383 (mpp) REVERT: D 147 PHE cc_start: 0.9131 (m-80) cc_final: 0.8725 (m-80) REVERT: D 153 LEU cc_start: 0.9439 (mt) cc_final: 0.9188 (mm) REVERT: D 166 LEU cc_start: 0.8804 (tp) cc_final: 0.8349 (tp) REVERT: D 170 THR cc_start: 0.4857 (m) cc_final: 0.4091 (p) REVERT: D 230 ARG cc_start: 0.8719 (tpp80) cc_final: 0.8221 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0744 time to fit residues: 2.7326 Evaluate side-chains 25 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.071 Evaluate side-chains 59 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8630 (pt0) REVERT: A 149 LYS cc_start: 0.8967 (tptt) cc_final: 0.8594 (tptp) REVERT: A 150 VAL cc_start: 0.9499 (m) cc_final: 0.9066 (p) REVERT: A 176 GLN cc_start: 0.8196 (tm-30) cc_final: 0.7761 (tm-30) REVERT: A 193 ASP cc_start: 0.8973 (p0) cc_final: 0.8420 (p0) REVERT: A 236 GLU cc_start: 0.9420 (tt0) cc_final: 0.9041 (pt0) REVERT: A 310 TRP cc_start: 0.7506 (m-90) cc_final: 0.6876 (m-90) REVERT: A 361 ASN cc_start: 0.9156 (t0) cc_final: 0.8890 (t0) REVERT: A 413 ASP cc_start: 0.9293 (m-30) cc_final: 0.9005 (m-30) REVERT: A 428 ASP cc_start: 0.8894 (t70) cc_final: 0.8638 (t70) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.0626 time to fit residues: 4.7887 Evaluate side-chains 43 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 123 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 93 optimal weight: 0.4980 chunk 52 optimal weight: 0.0670 chunk 29 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 86 optimal weight: 0.0770 chunk 41 optimal weight: 9.9990 overall best weight: 1.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 GLN A 420 HIS ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.059180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.044239 restraints weight = 12911.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.045897 restraints weight = 7896.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.047168 restraints weight = 5614.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.048106 restraints weight = 4303.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.048630 restraints weight = 3507.099| |-----------------------------------------------------------------------------| r_work (final): 0.3324 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.074306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.059468 restraints weight = 15278.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.061475 restraints weight = 9352.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.062925 restraints weight = 6485.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.063980 restraints weight = 4934.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.064699 restraints weight = 3990.576| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11169 Z= 0.129 Angle : 0.607 7.505 15186 Z= 0.310 Chirality : 0.043 0.150 1686 Planarity : 0.004 0.054 2000 Dihedral : 4.443 25.363 1530 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.35 (0.23), residues: 1412 helix: 0.96 (0.26), residues: 422 sheet: -1.78 (0.42), residues: 158 loop : -1.79 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 340 TYR 0.008 0.001 TYR D 46 PHE 0.032 0.001 PHE B 122 TRP 0.012 0.001 TRP A 511 HIS 0.008 0.001 HIS A 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (11156) covalent geometry : angle 0.60083 / 0.31 (15160) SS BOND : bond 0.00385 / 0.26 ( 13) SS BOND : angle 2.20564 / 1.38 ( 26) hydrogen bonds : bond 0.03127 / 2.08 ( 319) hydrogen bonds : angle 4.88591 / 3.34 ( 906) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 126 MET cc_start: 0.8981 (mpp) cc_final: 0.8587 (mpp) REVERT: D 147 PHE cc_start: 0.9147 (m-80) cc_final: 0.8707 (m-80) REVERT: D 153 LEU cc_start: 0.9446 (mt) cc_final: 0.9171 (mm) REVERT: D 166 LEU cc_start: 0.8828 (tp) cc_final: 0.8386 (tp) REVERT: D 170 THR cc_start: 0.4996 (m) cc_final: 0.4228 (p) REVERT: D 230 ARG cc_start: 0.8705 (tpp80) cc_final: 0.8230 (ttt180) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0777 time to fit residues: 2.8397 Evaluate side-chains 27 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.077 Evaluate side-chains 59 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ASP cc_start: 0.9173 (m-30) cc_final: 0.8959 (m-30) REVERT: A 117 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8629 (mp0) REVERT: A 148 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8605 (pt0) REVERT: A 149 LYS cc_start: 0.8930 (tptt) cc_final: 0.8526 (tptp) REVERT: A 150 VAL cc_start: 0.9478 (m) cc_final: 0.9049 (p) REVERT: A 176 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7670 (tm-30) REVERT: A 193 ASP cc_start: 0.9091 (p0) cc_final: 0.8563 (p0) REVERT: A 310 TRP cc_start: 0.7476 (m-90) cc_final: 0.6911 (m-90) REVERT: A 361 ASN cc_start: 0.9135 (t0) cc_final: 0.8817 (t0) REVERT: A 413 ASP cc_start: 0.9317 (m-30) cc_final: 0.9024 (m-30) REVERT: A 425 MET cc_start: 0.9151 (ppp) cc_final: 0.8720 (tmm) REVERT: A 428 ASP cc_start: 0.8909 (t70) cc_final: 0.8652 (t70) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.0680 time to fit residues: 5.1198 Evaluate side-chains 45 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 99 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 42 optimal weight: 0.2980 chunk 20 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 19 optimal weight: 0.0170 chunk 124 optimal weight: 0.4980 overall best weight: 1.1420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.060712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.045690 restraints weight = 12912.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.047326 restraints weight = 7897.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.048522 restraints weight = 5549.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.049313 restraints weight = 4268.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.049908 restraints weight = 3544.151| |-----------------------------------------------------------------------------| r_work (final): 0.3352 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.075373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.060075 restraints weight = 15196.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.062037 restraints weight = 9368.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.063464 restraints weight = 6596.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.064397 restraints weight = 5068.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.065213 restraints weight = 4174.288| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11169 Z= 0.119 Angle : 0.612 8.646 15186 Z= 0.308 Chirality : 0.045 0.339 1686 Planarity : 0.004 0.054 2000 Dihedral : 4.472 25.101 1530 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.42 (0.23), residues: 1412 helix: 0.95 (0.26), residues: 422 sheet: -1.70 (0.42), residues: 148 loop : -1.90 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 476 TYR 0.038 0.001 TYR B 84 PHE 0.033 0.001 PHE B 122 TRP 0.014 0.001 TRP A 511 HIS 0.009 0.001 HIS A 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (11156) covalent geometry : angle 0.60783 / 0.31 (15160) SS BOND : bond 0.00361 / 0.24 ( 13) SS BOND : angle 1.86943 / 1.17 ( 26) hydrogen bonds : bond 0.03183 / 2.07 ( 319) hydrogen bonds : angle 4.63443 / 3.16 ( 906) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 LEU cc_start: 0.9010 (tp) cc_final: 0.8713 (tp) REVERT: C 126 MET cc_start: 0.8472 (mpp) cc_final: 0.8054 (mpp) REVERT: C 147 PHE cc_start: 0.9145 (m-80) cc_final: 0.8854 (m-80) REVERT: C 153 LEU cc_start: 0.9456 (mt) cc_final: 0.9191 (mm) REVERT: C 166 LEU cc_start: 0.8835 (tp) cc_final: 0.8397 (tp) REVERT: C 170 THR cc_start: 0.5039 (m) cc_final: 0.4280 (p) REVERT: C 230 ARG cc_start: 0.8717 (tpp80) cc_final: 0.8240 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0704 time to fit residues: 2.6551 Evaluate side-chains 28 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.059 Evaluate side-chains 61 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ILE cc_start: 0.9381 (mm) cc_final: 0.8981 (mm) REVERT: A 79 LEU cc_start: 0.9453 (mm) cc_final: 0.9093 (mm) REVERT: A 80 GLU cc_start: 0.9298 (mm-30) cc_final: 0.8555 (mm-30) REVERT: A 87 ASP cc_start: 0.9085 (m-30) cc_final: 0.8789 (m-30) REVERT: A 117 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8630 (mp0) REVERT: A 148 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8598 (pt0) REVERT: A 149 LYS cc_start: 0.8908 (tptt) cc_final: 0.8520 (tptp) REVERT: A 150 VAL cc_start: 0.9456 (m) cc_final: 0.9025 (p) REVERT: A 164 MET cc_start: 0.9350 (mmt) cc_final: 0.8984 (mmt) REVERT: A 176 GLN cc_start: 0.8107 (tm-30) cc_final: 0.7667 (tm-30) REVERT: A 193 ASP cc_start: 0.9098 (p0) cc_final: 0.8563 (p0) REVERT: A 310 TRP cc_start: 0.7446 (m-90) cc_final: 0.6931 (m-90) REVERT: A 361 ASN cc_start: 0.9164 (t0) cc_final: 0.8733 (t0) REVERT: A 413 ASP cc_start: 0.9305 (m-30) cc_final: 0.8996 (m-30) REVERT: A 425 MET cc_start: 0.9162 (ppp) cc_final: 0.8851 (tmm) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0694 time to fit residues: 5.3244 Evaluate side-chains 50 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 51 optimal weight: 6.9990 chunk 27 optimal weight: 0.0060 chunk 135 optimal weight: 1.9990 chunk 114 optimal weight: 0.2980 chunk 54 optimal weight: 0.4980 chunk 91 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 63 optimal weight: 0.1980 chunk 59 optimal weight: 3.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 GLN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.060464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.045254 restraints weight = 12268.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.046959 restraints weight = 7555.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.048200 restraints weight = 5348.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.049130 restraints weight = 4132.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.049549 restraints weight = 3392.134| |-----------------------------------------------------------------------------| r_work (final): 0.3328 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.076319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.060776 restraints weight = 14695.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.062808 restraints weight = 9148.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.064260 restraints weight = 6458.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.065375 restraints weight = 4937.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.066121 restraints weight = 3995.931| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11169 Z= 0.113 Angle : 0.634 8.646 15186 Z= 0.315 Chirality : 0.045 0.253 1686 Planarity : 0.004 0.057 2000 Dihedral : 4.397 23.939 1530 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.49 (0.22), residues: 1412 helix: 0.89 (0.26), residues: 438 sheet: -1.80 (0.40), residues: 158 loop : -1.97 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 359 TYR 0.018 0.001 TYR B 477 PHE 0.037 0.001 PHE A 122 TRP 0.039 0.002 TRP C 25 HIS 0.009 0.001 HIS A 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (11156) covalent geometry : angle 0.63136 / 0.31 (15160) SS BOND : bond 0.00171 / 0.12 ( 13) SS BOND : angle 1.51715 / 0.96 ( 26) hydrogen bonds : bond 0.03126 / 2.04 ( 319) hydrogen bonds : angle 4.58865 / 3.15 ( 906) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 84 LEU cc_start: 0.8962 (tp) cc_final: 0.8680 (tp) REVERT: D 123 LEU cc_start: 0.9315 (tp) cc_final: 0.8895 (tt) REVERT: D 126 MET cc_start: 0.8486 (mpp) cc_final: 0.8280 (mpp) REVERT: D 166 LEU cc_start: 0.8888 (tp) cc_final: 0.8467 (tp) REVERT: D 230 ARG cc_start: 0.8723 (tpp80) cc_final: 0.8202 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0731 time to fit residues: 2.6842 Evaluate side-chains 27 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.068 Evaluate side-chains 60 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ASP cc_start: 0.9110 (m-30) cc_final: 0.8815 (m-30) REVERT: A 117 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8639 (mp0) REVERT: A 148 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8596 (pt0) REVERT: A 149 LYS cc_start: 0.8899 (tptt) cc_final: 0.8506 (tptp) REVERT: A 150 VAL cc_start: 0.9463 (m) cc_final: 0.9034 (p) REVERT: A 164 MET cc_start: 0.9335 (mmt) cc_final: 0.8913 (mmt) REVERT: A 176 GLN cc_start: 0.8093 (tm-30) cc_final: 0.7656 (tm-30) REVERT: A 193 ASP cc_start: 0.9108 (p0) cc_final: 0.8585 (p0) REVERT: A 236 GLU cc_start: 0.9422 (tt0) cc_final: 0.9031 (pt0) REVERT: A 310 TRP cc_start: 0.7428 (m-90) cc_final: 0.6911 (m-90) REVERT: A 361 ASN cc_start: 0.9172 (t0) cc_final: 0.8846 (t0) REVERT: A 413 ASP cc_start: 0.9293 (m-30) cc_final: 0.8976 (m-30) REVERT: A 425 MET cc_start: 0.9157 (ppp) cc_final: 0.8745 (tmm) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0687 time to fit residues: 5.2096 Evaluate side-chains 49 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 13 optimal weight: 0.0470 chunk 15 optimal weight: 20.0000 chunk 30 optimal weight: 0.1980 chunk 97 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 139 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 135 optimal weight: 0.0060 chunk 49 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 overall best weight: 0.5896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 GLN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.060662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.045074 restraints weight = 12702.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.046753 restraints weight = 7972.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.047977 restraints weight = 5675.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.048787 restraints weight = 4418.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.049410 restraints weight = 3691.612| |-----------------------------------------------------------------------------| r_work (final): 0.3349 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.076074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.059934 restraints weight = 14716.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.061965 restraints weight = 9225.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.063458 restraints weight = 6578.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.064560 restraints weight = 5079.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.065376 restraints weight = 4153.819| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11169 Z= 0.119 Angle : 0.650 8.428 15186 Z= 0.329 Chirality : 0.045 0.235 1686 Planarity : 0.004 0.057 2000 Dihedral : 4.561 27.149 1530 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.22), residues: 1412 helix: 0.74 (0.25), residues: 432 sheet: -1.94 (0.37), residues: 186 loop : -1.87 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 340 TYR 0.023 0.001 TYR B 84 PHE 0.032 0.001 PHE A 122 TRP 0.015 0.001 TRP A 511 HIS 0.009 0.001 HIS A 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (11156) covalent geometry : angle 0.64855 / 0.33 (15160) SS BOND : bond 0.00209 / 0.14 ( 13) SS BOND : angle 1.36426 / 0.86 ( 26) hydrogen bonds : bond 0.03393 / 2.28 ( 319) hydrogen bonds : angle 4.76123 / 3.23 ( 906) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 83 ASP cc_start: 0.9114 (m-30) cc_final: 0.8383 (m-30) REVERT: D 84 LEU cc_start: 0.9004 (tp) cc_final: 0.8661 (tp) REVERT: D 166 LEU cc_start: 0.8745 (tp) cc_final: 0.8456 (tp) REVERT: D 230 ARG cc_start: 0.8702 (tpp80) cc_final: 0.8185 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0686 time to fit residues: 2.5312 Evaluate side-chains 27 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.078 Evaluate side-chains 56 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ASP cc_start: 0.9152 (m-30) cc_final: 0.8849 (m-30) REVERT: A 117 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8596 (mp0) REVERT: A 148 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8592 (pt0) REVERT: A 149 LYS cc_start: 0.8832 (tptt) cc_final: 0.8440 (tptp) REVERT: A 176 GLN cc_start: 0.8080 (tm-30) cc_final: 0.7641 (tm-30) REVERT: A 193 ASP cc_start: 0.9151 (p0) cc_final: 0.8523 (p0) REVERT: A 310 TRP cc_start: 0.7408 (m-90) cc_final: 0.6914 (m-90) REVERT: A 340 ARG cc_start: 0.8149 (tpp80) cc_final: 0.7865 (tpp80) REVERT: A 361 ASN cc_start: 0.9167 (t0) cc_final: 0.8826 (t0) REVERT: A 413 ASP cc_start: 0.9270 (m-30) cc_final: 0.8972 (m-30) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0692 time to fit residues: 4.8907 Evaluate side-chains 48 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 18 optimal weight: 8.9990 chunk 119 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 86 optimal weight: 0.0370 chunk 56 optimal weight: 0.0470 chunk 59 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 58 optimal weight: 0.3980 chunk 96 optimal weight: 5.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.061137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.045105 restraints weight = 12671.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.046832 restraints weight = 7981.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.048033 restraints weight = 5689.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.048947 restraints weight = 4430.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.049529 restraints weight = 3673.053| |-----------------------------------------------------------------------------| r_work (final): 0.3355 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.077290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.061406 restraints weight = 14297.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.063433 restraints weight = 9022.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.064883 restraints weight = 6424.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.066013 restraints weight = 4942.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.066672 restraints weight = 4028.595| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11169 Z= 0.112 Angle : 0.637 8.528 15186 Z= 0.316 Chirality : 0.044 0.196 1686 Planarity : 0.004 0.060 2000 Dihedral : 4.386 24.888 1530 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.45 (0.22), residues: 1412 helix: 0.85 (0.26), residues: 428 sheet: -1.90 (0.37), residues: 186 loop : -1.81 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 476 TYR 0.023 0.001 TYR B 477 PHE 0.036 0.001 PHE B 122 TRP 0.012 0.001 TRP A 511 HIS 0.008 0.001 HIS B 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (11156) covalent geometry : angle 0.63563 / 0.32 (15160) SS BOND : bond 0.00234 / 0.15 ( 13) SS BOND : angle 1.24539 / 0.78 ( 26) hydrogen bonds : bond 0.03001 / 2.00 ( 319) hydrogen bonds : angle 4.54481 / 3.10 ( 906) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1443.57 seconds wall clock time: 25 minutes 51.58 seconds (1551.58 seconds total)