Starting phenix.real_space_refine on Sat Sep 12 09:59:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7to3_26028/09_2026/7to3_26028.cif Found real_map, /net/cci-nas-00/data/ceres_data/7to3_26028/09_2026/7to3_26028.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7to3_26028/09_2026/7to3_26028.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7to3_26028/09_2026/7to3_26028.cif" model { file = "/net/cci-nas-00/data/ceres_data/7to3_26028/09_2026/7to3_26028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7to3_26028/09_2026/7to3_26028.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7to3_26028/09_2026/7to3_26028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7to3_26028/09_2026/7to3_26028.map" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 44 5.16 5 C 9346 2.51 5 N 2572 2.21 5 O 2786 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: 14764 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4421 Classifications: {'peptide': 568} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 533} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2878 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 335} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 83 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'RNAv2': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Restraints were copied for chains: B, D Time building chain proxies: 5.10, per 1000 atoms: 0.35 Number of scatterers: 14764 At special positions: 0 Unit cell: (147, 126.84, 110.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 44 16.00 P 12 15.00 Mg 4 11.99 O 2786 8.00 N 2572 7.00 C 9346 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 620.7 milliseconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3492 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 12 sheets defined 40.5% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 9 through 22 Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 128 through 150 Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 181 through 187 removed outlier: 3.624A pdb=" N TRP A 185 " --> pdb=" O ASP A 181 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER A 187 " --> pdb=" O PRO A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 removed outlier: 3.552A pdb=" N LYS A 231 " --> pdb=" O PRO A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 269 Processing helix chain 'A' and resid 271 through 286 Processing helix chain 'A' and resid 362 through 366 Processing helix chain 'A' and resid 373 through 378 Processing helix chain 'A' and resid 387 through 401 removed outlier: 3.694A pdb=" N SER A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET A 392 " --> pdb=" O SER A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 421 removed outlier: 4.150A pdb=" N HIS A 421 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 428 Processing helix chain 'A' and resid 431 through 442 Processing helix chain 'A' and resid 460 through 468 Processing helix chain 'A' and resid 479 through 488 removed outlier: 3.538A pdb=" N LEU A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 506 No H-bonds generated for 'chain 'A' and resid 504 through 506' Processing helix chain 'A' and resid 520 through 531 removed outlier: 3.915A pdb=" N ALA A 524 " --> pdb=" O PRO A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 577 Processing helix chain 'B' and resid 9 through 22 Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 128 through 150 Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 181 through 187 removed outlier: 3.624A pdb=" N TRP B 185 " --> pdb=" O ASP B 181 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER B 187 " --> pdb=" O PRO B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 231 removed outlier: 3.552A pdb=" N LYS B 231 " --> pdb=" O PRO B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 269 Processing helix chain 'B' and resid 271 through 286 Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 373 through 378 Processing helix chain 'B' and resid 387 through 401 removed outlier: 3.693A pdb=" N SER B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET B 392 " --> pdb=" O SER B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 421 removed outlier: 4.149A pdb=" N HIS B 421 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 428 Processing helix chain 'B' and resid 431 through 442 Processing helix chain 'B' and resid 460 through 468 Processing helix chain 'B' and resid 479 through 488 removed outlier: 3.538A pdb=" N LEU B 483 " --> pdb=" O ASP B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 506 No H-bonds generated for 'chain 'B' and resid 504 through 506' Processing helix chain 'B' and resid 520 through 531 removed outlier: 3.916A pdb=" N ALA B 524 " --> pdb=" O PRO B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 577 Processing helix chain 'C' and resid 3 through 14 Processing helix chain 'C' and resid 17 through 38 Processing helix chain 'C' and resid 52 through 57 Processing helix chain 'C' and resid 84 through 91 Processing helix chain 'C' and resid 92 through 100 Processing helix chain 'C' and resid 131 through 142 Processing helix chain 'C' and resid 206 through 221 removed outlier: 4.029A pdb=" N GLN C 210 " --> pdb=" O HIS C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 239 Processing helix chain 'C' and resid 249 through 260 Processing helix chain 'C' and resid 266 through 282 Processing helix chain 'C' and resid 282 through 288 Processing helix chain 'C' and resid 303 through 307 removed outlier: 3.605A pdb=" N ALA C 306 " --> pdb=" O ASP C 303 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ARG C 307 " --> pdb=" O VAL C 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 303 through 307' Processing helix chain 'C' and resid 309 through 333 removed outlier: 3.556A pdb=" N ALA C 332 " --> pdb=" O ARG C 328 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER C 333 " --> pdb=" O ASN C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 348 removed outlier: 3.960A pdb=" N LEU C 346 " --> pdb=" O LEU C 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 14 Processing helix chain 'D' and resid 17 through 38 Processing helix chain 'D' and resid 52 through 57 Processing helix chain 'D' and resid 84 through 91 Processing helix chain 'D' and resid 92 through 100 Processing helix chain 'D' and resid 131 through 142 Processing helix chain 'D' and resid 206 through 221 removed outlier: 4.030A pdb=" N GLN D 210 " --> pdb=" O HIS D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 239 Processing helix chain 'D' and resid 249 through 260 Processing helix chain 'D' and resid 266 through 282 Processing helix chain 'D' and resid 282 through 288 Processing helix chain 'D' and resid 303 through 307 removed outlier: 3.606A pdb=" N ALA D 306 " --> pdb=" O ASP D 303 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ARG D 307 " --> pdb=" O VAL D 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 303 through 307' Processing helix chain 'D' and resid 309 through 333 removed outlier: 3.556A pdb=" N ALA D 332 " --> pdb=" O ARG D 328 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER D 333 " --> pdb=" O ASN D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 348 removed outlier: 3.961A pdb=" N LEU D 346 " --> pdb=" O LEU D 342 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 221 through 222 removed outlier: 3.746A pdb=" N ARG A 221 " --> pdb=" O PHE A 212 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N SER A 196 " --> pdb=" O ARG A 210 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N PHE A 212 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N PHE A 194 " --> pdb=" O PHE A 212 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N SER A 197 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N THR A 236 " --> pdb=" O SER A 197 " (cutoff:3.500A) removed outlier: 9.291A pdb=" N LEU A 294 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ASN A 237 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N LEU A 296 " --> pdb=" O ASN A 237 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL A 239 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N GLY A 298 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N SER A 241 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG A 311 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 11.321A pdb=" N ILE A 312 " --> pdb=" O ASN A 360 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ASN A 360 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N TRP A 314 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N THR A 358 " --> pdb=" O TRP A 314 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA A 316 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N TRP A 355 " --> pdb=" O GLN A 167 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N ARG A 357 " --> pdb=" O PRO A 169 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N THR A 171 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N GLN A 359 " --> pdb=" O THR A 171 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE A 173 " --> pdb=" O GLN A 359 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEU A 207 " --> pdb=" O PHE A 170 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL A 172 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N LEU A 209 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N GLY A 174 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N GLU A 211 " --> pdb=" O GLY A 174 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 448 through 452 removed outlier: 6.519A pdb=" N GLN A 405 " --> pdb=" O ARG A 450 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N PHE A 452 " --> pdb=" O GLN A 405 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE A 407 " --> pdb=" O PHE A 452 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AA6, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AA7, first strand: chain 'B' and resid 221 through 222 removed outlier: 3.746A pdb=" N ARG B 221 " --> pdb=" O PHE B 212 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N SER B 196 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N PHE B 212 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N PHE B 194 " --> pdb=" O PHE B 212 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N SER B 197 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N THR B 236 " --> pdb=" O SER B 197 " (cutoff:3.500A) removed outlier: 9.291A pdb=" N LEU B 294 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ASN B 237 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N LEU B 296 " --> pdb=" O ASN B 237 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL B 239 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N GLY B 298 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N SER B 241 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG B 311 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 11.322A pdb=" N ILE B 312 " --> pdb=" O ASN B 360 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ASN B 360 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N TRP B 314 " --> pdb=" O THR B 358 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N THR B 358 " --> pdb=" O TRP B 314 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA B 316 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N TRP B 355 " --> pdb=" O GLN B 167 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N ARG B 357 " --> pdb=" O PRO B 169 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N THR B 171 " --> pdb=" O ARG B 357 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N GLN B 359 " --> pdb=" O THR B 171 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE B 173 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LEU B 207 " --> pdb=" O PHE B 170 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL B 172 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N LEU B 209 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N GLY B 174 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N GLU B 211 " --> pdb=" O GLY B 174 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 448 through 452 removed outlier: 6.518A pdb=" N GLN B 405 " --> pdb=" O ARG B 450 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N PHE B 452 " --> pdb=" O GLN B 405 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE B 407 " --> pdb=" O PHE B 452 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 51 removed outlier: 6.584A pdb=" N VAL C 75 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR C 48 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL C 73 " --> pdb=" O THR C 48 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LEU C 50 " --> pdb=" O ASP C 71 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP C 71 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL C 70 " --> pdb=" O ASP C 121 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL C 123 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE C 72 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N THR C 125 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL C 74 " --> pdb=" O THR C 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 192 through 195 Processing sheet with id=AB2, first strand: chain 'D' and resid 45 through 51 removed outlier: 6.583A pdb=" N VAL D 75 " --> pdb=" O VAL D 46 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR D 48 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL D 73 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LEU D 50 " --> pdb=" O ASP D 71 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP D 71 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL D 70 " --> pdb=" O ASP D 121 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL D 123 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE D 72 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N THR D 125 " --> pdb=" O ILE D 72 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL D 74 " --> pdb=" O THR D 125 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 192 through 195 626 hydrogen bonds defined for protein. 1788 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: 1.80 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4847 1.35 - 1.46: 3467 1.46 - 1.58: 6746 1.58 - 1.69: 18 1.69 - 1.81: 72 Bond restraints: 15150 Sorted by residual: bond pdb=" C4' AMP C 401 " pdb=" O4' AMP C 401 " ideal model delta sigma weight residual 1.426 1.454 -0.028 2.00e-02 2.50e+03 2.00e+00 bond pdb=" C4' AMP D 401 " pdb=" O4' AMP D 401 " ideal model delta sigma weight residual 1.426 1.453 -0.027 2.00e-02 2.50e+03 1.82e+00 bond pdb=" CA TRP D 24 " pdb=" CB TRP D 24 " ideal model delta sigma weight residual 1.528 1.549 -0.021 1.59e-02 3.96e+03 1.75e+00 bond pdb=" CA TRP C 24 " pdb=" CB TRP C 24 " ideal model delta sigma weight residual 1.528 1.549 -0.021 1.59e-02 3.96e+03 1.68e+00 bond pdb=" C2' AMP D 401 " pdb=" O2' AMP D 401 " ideal model delta sigma weight residual 1.432 1.412 0.020 2.00e-02 2.50e+03 1.00e+00 ... (remaining 15145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 20327 1.89 - 3.78: 251 3.78 - 5.68: 65 5.68 - 7.57: 7 7.57 - 9.46: 4 Bond angle restraints: 20654 Sorted by residual: angle pdb=" N ILE B 220 " pdb=" CA ILE B 220 " pdb=" C ILE B 220 " ideal model delta sigma weight residual 113.71 110.28 3.43 9.50e-01 1.11e+00 1.31e+01 angle pdb=" N ILE A 220 " pdb=" CA ILE A 220 " pdb=" C ILE A 220 " ideal model delta sigma weight residual 113.71 110.29 3.42 9.50e-01 1.11e+00 1.30e+01 angle pdb=" N TRP C 24 " pdb=" CA TRP C 24 " pdb=" CB TRP C 24 " ideal model delta sigma weight residual 110.16 115.00 -4.84 1.48e+00 4.57e-01 1.07e+01 angle pdb=" N TRP D 24 " pdb=" CA TRP D 24 " pdb=" CB TRP D 24 " ideal model delta sigma weight residual 110.16 114.93 -4.77 1.48e+00 4.57e-01 1.04e+01 angle pdb=" C1' AMP D 401 " pdb=" C2' AMP D 401 " pdb=" C3' AMP D 401 " ideal model delta sigma weight residual 111.00 101.54 9.46 3.00e+00 1.11e-01 9.94e+00 ... (remaining 20649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.13: 8864 34.13 - 68.26: 100 68.26 - 102.39: 0 102.39 - 136.51: 2 136.51 - 170.64: 4 Dihedral angle restraints: 8970 sinusoidal: 3608 harmonic: 5362 Sorted by residual: dihedral pdb=" O2A ADP D 405 " pdb=" O3A ADP D 405 " pdb=" PA ADP D 405 " pdb=" PB ADP D 405 " ideal model delta sinusoidal sigma weight residual 300.00 129.36 170.64 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O2A ADP C 405 " pdb=" O3A ADP C 405 " pdb=" PA ADP C 405 " pdb=" PB ADP C 405 " ideal model delta sinusoidal sigma weight residual 300.00 129.37 170.63 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C5' AMP C 401 " pdb=" O5' AMP C 401 " pdb=" P AMP C 401 " pdb=" O3P AMP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 148.68 151.32 1 2.00e+01 2.50e-03 4.51e+01 ... (remaining 8967 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1869 0.047 - 0.094: 290 0.094 - 0.141: 85 0.141 - 0.188: 4 0.188 - 0.235: 2 Chirality restraints: 2250 Sorted by residual: chirality pdb=" C3' AMP D 401 " pdb=" C2' AMP D 401 " pdb=" C4' AMP D 401 " pdb=" O3' AMP D 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.75 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" C3' AMP C 401 " pdb=" C2' AMP C 401 " pdb=" C4' AMP C 401 " pdb=" O3' AMP C 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.74 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA ILE A 74 " pdb=" N ILE A 74 " pdb=" C ILE A 74 " pdb=" CB ILE A 74 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.95e-01 ... (remaining 2247 not shown) Planarity restraints: 2648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 24 " -0.034 2.00e-02 2.50e+03 3.68e-02 3.38e+01 pdb=" CG TRP D 24 " 0.099 2.00e-02 2.50e+03 pdb=" CD1 TRP D 24 " -0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP D 24 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 24 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP D 24 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 24 " -0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 24 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 24 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 24 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 24 " 0.034 2.00e-02 2.50e+03 3.67e-02 3.36e+01 pdb=" CG TRP C 24 " -0.098 2.00e-02 2.50e+03 pdb=" CD1 TRP C 24 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP C 24 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 24 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP C 24 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP C 24 " 0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 24 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 24 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 24 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 49 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO B 50 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 50 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 50 " 0.027 5.00e-02 4.00e+02 ... (remaining 2645 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 34 2.63 - 3.20: 12066 3.20 - 3.76: 22019 3.76 - 4.33: 31687 4.33 - 4.90: 51683 Nonbonded interactions: 117489 Sorted by model distance: nonbonded pdb="MG MG C 403 " pdb=" O2B ATP C 404 " model vdw 2.062 2.170 nonbonded pdb="MG MG D 403 " pdb=" O2B ATP D 404 " model vdw 2.062 2.170 nonbonded pdb=" OD2 ASP C 69 " pdb="MG MG C 402 " model vdw 2.079 2.170 nonbonded pdb=" OD2 ASP D 69 " pdb="MG MG D 402 " model vdw 2.080 2.170 nonbonded pdb=" O ALA C 132 " pdb=" ND1 HIS C 136 " model vdw 2.317 3.120 ... (remaining 117484 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.900 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.750 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 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 0.233 15152 Z= 0.292 Angle : 0.567 9.460 20654 Z= 0.286 Chirality : 0.038 0.235 2250 Planarity : 0.004 0.049 2648 Dihedral : 11.699 170.644 5478 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.85 (0.19), residues: 1830 helix: 2.69 (0.20), residues: 664 sheet: 0.57 (0.27), residues: 348 loop : -1.32 (0.19), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 61 TYR 0.009 0.001 TYR D 225 PHE 0.011 0.001 PHE A 510 TRP 0.099 0.001 TRP D 24 HIS 0.005 0.001 HIS D 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.12 (15150) covalent geometry : angle 0.56746 / 0.29 (20654) hydrogen bonds : bond 0.14325 / 9.59 ( 622) hydrogen bonds : angle 5.15609 / 3.63 ( 1788) Misc. bond : bond 0.23276 / 11.68 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASP cc_start: 0.7289 (m-30) cc_final: 0.7036 (m-30) REVERT: A 414 GLN cc_start: 0.8130 (mt0) cc_final: 0.7498 (mm-40) REVERT: B 37 LYS cc_start: 0.9103 (mttt) cc_final: 0.8877 (tmmm) REVERT: B 39 TRP cc_start: 0.7299 (m100) cc_final: 0.6744 (m100) REVERT: B 411 ASP cc_start: 0.7264 (m-30) cc_final: 0.7008 (m-30) REVERT: B 414 GLN cc_start: 0.8084 (mt0) cc_final: 0.7458 (mm-40) REVERT: C 90 ASP cc_start: 0.8213 (m-30) cc_final: 0.8006 (m-30) REVERT: C 242 ASP cc_start: 0.8406 (m-30) cc_final: 0.7928 (t0) REVERT: D 242 ASP cc_start: 0.8403 (m-30) cc_final: 0.7938 (t0) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.7900 time to fit residues: 222.1789 Evaluate side-chains 112 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.0770 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 94 ASN C 8 ASN C 210 GLN C 254 HIS D 8 ASN D 210 GLN D 254 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.096391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.069824 restraints weight = 29438.740| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.04 r_work: 0.2957 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15152 Z= 0.135 Angle : 0.585 6.749 20654 Z= 0.281 Chirality : 0.040 0.173 2250 Planarity : 0.005 0.058 2648 Dihedral : 8.824 171.115 2026 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.23 % Allowed : 8.01 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.89 (0.19), residues: 1830 helix: 2.49 (0.20), residues: 674 sheet: 0.57 (0.27), residues: 332 loop : -1.08 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 136 TYR 0.017 0.002 TYR D 286 PHE 0.014 0.002 PHE B 510 TRP 0.033 0.001 TRP C 24 HIS 0.009 0.001 HIS C 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (15150) covalent geometry : angle 0.58530 / 0.28 (20654) hydrogen bonds : bond 0.04777 / 3.18 ( 622) hydrogen bonds : angle 4.33017 / 3.03 ( 1788) Misc. bond : bond 0.00058 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TRP cc_start: 0.7389 (m100) cc_final: 0.6696 (m100) REVERT: A 215 ASN cc_start: 0.7447 (OUTLIER) cc_final: 0.7170 (m-40) REVERT: A 411 ASP cc_start: 0.7880 (m-30) cc_final: 0.7396 (m-30) REVERT: A 414 GLN cc_start: 0.8267 (mt0) cc_final: 0.7270 (mm-40) REVERT: B 37 LYS cc_start: 0.9257 (mttt) cc_final: 0.8830 (tmmm) REVERT: B 39 TRP cc_start: 0.7279 (m100) cc_final: 0.6708 (m100) REVERT: B 351 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7992 (mp0) REVERT: B 411 ASP cc_start: 0.7893 (m-30) cc_final: 0.7436 (m-30) REVERT: B 414 GLN cc_start: 0.8186 (mt0) cc_final: 0.7175 (mm-40) REVERT: C 90 ASP cc_start: 0.8191 (m-30) cc_final: 0.7942 (m-30) REVERT: C 105 GLU cc_start: 0.7823 (tt0) cc_final: 0.7329 (tm-30) REVERT: C 162 LYS cc_start: 0.9012 (pttt) cc_final: 0.8059 (tppt) REVERT: C 242 ASP cc_start: 0.8930 (m-30) cc_final: 0.8133 (t0) REVERT: C 245 LYS cc_start: 0.8748 (mmmm) cc_final: 0.8438 (tptp) REVERT: D 90 ASP cc_start: 0.8303 (m-30) cc_final: 0.7978 (m-30) REVERT: D 162 LYS cc_start: 0.8922 (pttt) cc_final: 0.8090 (tppt) REVERT: D 242 ASP cc_start: 0.8937 (m-30) cc_final: 0.8129 (t0) outliers start: 19 outliers final: 5 residues processed: 130 average time/residue: 0.6790 time to fit residues: 96.1842 Evaluate side-chains 95 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain D residue 194 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 56 optimal weight: 10.0000 chunk 4 optimal weight: 0.3980 chunk 64 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 ASN B 67 GLN B 417 ASN C 254 HIS D 254 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.091675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.064840 restraints weight = 30369.491| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.10 r_work: 0.2880 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15152 Z= 0.187 Angle : 0.620 7.745 20654 Z= 0.297 Chirality : 0.042 0.176 2250 Planarity : 0.005 0.047 2648 Dihedral : 7.159 147.157 2026 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.87 % Allowed : 8.98 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.74 (0.20), residues: 1830 helix: 2.32 (0.20), residues: 674 sheet: 0.57 (0.27), residues: 354 loop : -1.20 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 136 TYR 0.022 0.002 TYR D 286 PHE 0.019 0.002 PHE C 10 TRP 0.028 0.001 TRP D 24 HIS 0.011 0.001 HIS D 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 (15150) covalent geometry : angle 0.62038 / 0.30 (20654) hydrogen bonds : bond 0.05834 / 3.88 ( 622) hydrogen bonds : angle 4.44828 / 3.11 ( 1788) Misc. bond : bond 0.00003 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLN cc_start: 0.8146 (tt0) cc_final: 0.7873 (tp-100) REVERT: A 215 ASN cc_start: 0.7508 (OUTLIER) cc_final: 0.7256 (m-40) REVERT: A 411 ASP cc_start: 0.8147 (m-30) cc_final: 0.7879 (m-30) REVERT: A 414 GLN cc_start: 0.8305 (mt0) cc_final: 0.7277 (mm-40) REVERT: B 215 ASN cc_start: 0.7484 (OUTLIER) cc_final: 0.7233 (m-40) REVERT: B 351 GLU cc_start: 0.8395 (mt-10) cc_final: 0.7975 (mp0) REVERT: B 411 ASP cc_start: 0.8142 (m-30) cc_final: 0.7907 (m-30) REVERT: B 414 GLN cc_start: 0.8220 (mt0) cc_final: 0.7152 (mm-40) REVERT: C 90 ASP cc_start: 0.8227 (m-30) cc_final: 0.7986 (m-30) REVERT: C 105 GLU cc_start: 0.7881 (tt0) cc_final: 0.7329 (tm-30) REVERT: C 162 LYS cc_start: 0.8952 (pttt) cc_final: 0.8102 (tppt) REVERT: C 242 ASP cc_start: 0.8975 (m-30) cc_final: 0.8070 (t0) REVERT: D 90 ASP cc_start: 0.8364 (m-30) cc_final: 0.8032 (m-30) REVERT: D 162 LYS cc_start: 0.8875 (pttt) cc_final: 0.8079 (tppt) REVERT: D 242 ASP cc_start: 0.8959 (m-30) cc_final: 0.8045 (t0) outliers start: 29 outliers final: 5 residues processed: 117 average time/residue: 0.6463 time to fit residues: 82.9997 Evaluate side-chains 89 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain D residue 194 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 155 optimal weight: 3.9990 chunk 48 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 170 optimal weight: 0.6980 chunk 150 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.095098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.068395 restraints weight = 29684.106| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 3.00 r_work: 0.2960 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15152 Z= 0.114 Angle : 0.558 7.087 20654 Z= 0.263 Chirality : 0.039 0.174 2250 Planarity : 0.004 0.040 2648 Dihedral : 5.663 89.835 2026 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.97 % Allowed : 10.27 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.94 (0.20), residues: 1830 helix: 2.45 (0.20), residues: 686 sheet: 0.76 (0.27), residues: 354 loop : -1.15 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 82 TYR 0.016 0.001 TYR C 286 PHE 0.013 0.001 PHE B 510 TRP 0.021 0.001 TRP D 24 HIS 0.005 0.001 HIS C 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (15150) covalent geometry : angle 0.55842 / 0.26 (20654) hydrogen bonds : bond 0.04326 / 2.87 ( 622) hydrogen bonds : angle 4.19780 / 2.94 ( 1788) Misc. bond : bond 0.00006 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASP cc_start: 0.8226 (m-30) cc_final: 0.7955 (m-30) REVERT: A 414 GLN cc_start: 0.8429 (mt0) cc_final: 0.7498 (mm-40) REVERT: B 351 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8110 (mp0) REVERT: B 411 ASP cc_start: 0.8242 (m-30) cc_final: 0.8005 (m-30) REVERT: B 414 GLN cc_start: 0.8382 (mt0) cc_final: 0.7429 (mm-40) REVERT: C 90 ASP cc_start: 0.8252 (m-30) cc_final: 0.7956 (m-30) REVERT: C 105 GLU cc_start: 0.7950 (tt0) cc_final: 0.7491 (tm-30) REVERT: C 162 LYS cc_start: 0.8969 (pttt) cc_final: 0.8166 (tppt) REVERT: C 242 ASP cc_start: 0.8887 (m-30) cc_final: 0.8050 (t0) REVERT: C 305 MET cc_start: 0.8852 (mpp) cc_final: 0.8561 (mpt) REVERT: D 90 ASP cc_start: 0.8393 (m-30) cc_final: 0.7979 (m-30) REVERT: D 162 LYS cc_start: 0.8917 (pttt) cc_final: 0.8168 (tppt) REVERT: D 242 ASP cc_start: 0.8879 (m-30) cc_final: 0.8041 (t0) outliers start: 15 outliers final: 1 residues processed: 103 average time/residue: 0.6802 time to fit residues: 76.7294 Evaluate side-chains 81 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 194 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 16 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 180 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 173 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 GLN B 67 GLN B 550 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.093019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.066238 restraints weight = 30044.690| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.07 r_work: 0.2900 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15152 Z= 0.116 Angle : 0.553 7.728 20654 Z= 0.260 Chirality : 0.039 0.168 2250 Planarity : 0.004 0.037 2648 Dihedral : 5.203 62.272 2026 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.23 % Allowed : 11.11 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1.05 (0.20), residues: 1830 helix: 2.51 (0.21), residues: 686 sheet: 0.88 (0.27), residues: 354 loop : -1.09 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 281 TYR 0.021 0.001 TYR C 286 PHE 0.013 0.001 PHE A 510 TRP 0.021 0.001 TRP D 24 HIS 0.005 0.001 HIS C 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (15150) covalent geometry : angle 0.55305 / 0.26 (20654) hydrogen bonds : bond 0.04310 / 2.86 ( 622) hydrogen bonds : angle 4.11181 / 2.86 ( 1788) Misc. bond : bond 0.00042 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASP cc_start: 0.8058 (m-30) cc_final: 0.7695 (m-30) REVERT: A 414 GLN cc_start: 0.8191 (mt0) cc_final: 0.7144 (mm-40) REVERT: B 351 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7994 (mp0) REVERT: B 411 ASP cc_start: 0.8071 (m-30) cc_final: 0.7745 (m-30) REVERT: B 414 GLN cc_start: 0.8144 (mt0) cc_final: 0.7112 (mm-40) REVERT: C 90 ASP cc_start: 0.8149 (m-30) cc_final: 0.7863 (m-30) REVERT: C 105 GLU cc_start: 0.7860 (tt0) cc_final: 0.7304 (tm-30) REVERT: C 162 LYS cc_start: 0.8912 (pttt) cc_final: 0.8088 (tppt) REVERT: C 242 ASP cc_start: 0.8960 (m-30) cc_final: 0.8089 (t0) REVERT: D 90 ASP cc_start: 0.8299 (m-30) cc_final: 0.7852 (m-30) REVERT: D 162 LYS cc_start: 0.8868 (pttt) cc_final: 0.8119 (tppt) REVERT: D 242 ASP cc_start: 0.8957 (m-30) cc_final: 0.8071 (t0) REVERT: D 305 MET cc_start: 0.8801 (mpp) cc_final: 0.8405 (mpt) outliers start: 19 outliers final: 8 residues processed: 94 average time/residue: 0.6980 time to fit residues: 71.7066 Evaluate side-chains 84 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain C residue 24 TRP Chi-restraints excluded: chain D residue 24 TRP Chi-restraints excluded: chain D residue 83 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 174 optimal weight: 0.8980 chunk 129 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.092764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.066036 restraints weight = 29753.213| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 3.06 r_work: 0.2900 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15152 Z= 0.128 Angle : 0.557 7.640 20654 Z= 0.262 Chirality : 0.040 0.166 2250 Planarity : 0.004 0.037 2648 Dihedral : 5.166 70.537 2026 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.03 % Allowed : 12.14 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1.07 (0.20), residues: 1830 helix: 2.51 (0.20), residues: 686 sheet: 0.90 (0.27), residues: 354 loop : -1.08 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 82 TYR 0.014 0.001 TYR C 317 PHE 0.013 0.001 PHE A 510 TRP 0.020 0.001 TRP D 24 HIS 0.005 0.001 HIS D 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (15150) covalent geometry : angle 0.55717 / 0.26 (20654) hydrogen bonds : bond 0.04474 / 2.97 ( 622) hydrogen bonds : angle 4.12631 / 2.86 ( 1788) Misc. bond : bond 0.00006 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASP cc_start: 0.8160 (m-30) cc_final: 0.7813 (m-30) REVERT: A 414 GLN cc_start: 0.8160 (mt0) cc_final: 0.7121 (mm-40) REVERT: B 351 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8037 (mp0) REVERT: B 411 ASP cc_start: 0.8149 (m-30) cc_final: 0.7807 (m-30) REVERT: B 414 GLN cc_start: 0.8168 (mt0) cc_final: 0.7118 (mm-40) REVERT: C 90 ASP cc_start: 0.8174 (m-30) cc_final: 0.7845 (m-30) REVERT: C 105 GLU cc_start: 0.7870 (tt0) cc_final: 0.7329 (tm-30) REVERT: C 162 LYS cc_start: 0.8884 (pttt) cc_final: 0.8067 (tppt) REVERT: C 242 ASP cc_start: 0.8924 (m-30) cc_final: 0.8074 (t0) REVERT: C 305 MET cc_start: 0.8865 (mpp) cc_final: 0.8471 (mpt) REVERT: D 162 LYS cc_start: 0.8862 (pttt) cc_final: 0.8142 (tppt) REVERT: D 242 ASP cc_start: 0.8929 (m-30) cc_final: 0.8054 (t0) REVERT: D 305 MET cc_start: 0.8826 (mpp) cc_final: 0.8323 (mpt) outliers start: 16 outliers final: 7 residues processed: 91 average time/residue: 0.6633 time to fit residues: 66.4504 Evaluate side-chains 85 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain C residue 24 TRP Chi-restraints excluded: chain D residue 24 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 35 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.092166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.065278 restraints weight = 29831.535| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.06 r_work: 0.2864 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15152 Z= 0.131 Angle : 0.558 7.178 20654 Z= 0.263 Chirality : 0.040 0.164 2250 Planarity : 0.004 0.036 2648 Dihedral : 5.235 80.152 2026 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.10 % Allowed : 12.21 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1.06 (0.20), residues: 1830 helix: 2.52 (0.20), residues: 686 sheet: 0.89 (0.28), residues: 354 loop : -1.09 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 82 TYR 0.013 0.001 TYR C 250 PHE 0.014 0.001 PHE A 510 TRP 0.020 0.001 TRP C 24 HIS 0.005 0.001 HIS D 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (15150) covalent geometry : angle 0.55849 / 0.26 (20654) hydrogen bonds : bond 0.04546 / 3.01 ( 622) hydrogen bonds : angle 4.13329 / 2.87 ( 1788) Misc. bond : bond 0.00007 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASP cc_start: 0.8173 (m-30) cc_final: 0.7820 (m-30) REVERT: A 414 GLN cc_start: 0.8144 (mt0) cc_final: 0.7084 (mm-40) REVERT: B 351 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8018 (mp0) REVERT: B 411 ASP cc_start: 0.8152 (m-30) cc_final: 0.7816 (m-30) REVERT: B 414 GLN cc_start: 0.8134 (mt0) cc_final: 0.7078 (mm-40) REVERT: C 90 ASP cc_start: 0.8192 (m-30) cc_final: 0.7871 (m-30) REVERT: C 162 LYS cc_start: 0.8861 (pttt) cc_final: 0.8090 (tppt) REVERT: C 242 ASP cc_start: 0.8932 (m-30) cc_final: 0.8114 (t0) REVERT: C 305 MET cc_start: 0.8813 (mpp) cc_final: 0.8295 (mpt) REVERT: D 90 ASP cc_start: 0.8393 (t0) cc_final: 0.8076 (m-30) REVERT: D 162 LYS cc_start: 0.8837 (pttt) cc_final: 0.8101 (tppt) REVERT: D 242 ASP cc_start: 0.8932 (m-30) cc_final: 0.8074 (t0) REVERT: D 305 MET cc_start: 0.8780 (mpp) cc_final: 0.8297 (mpt) outliers start: 17 outliers final: 9 residues processed: 91 average time/residue: 0.6334 time to fit residues: 63.5729 Evaluate side-chains 84 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain C residue 24 TRP Chi-restraints excluded: chain D residue 24 TRP Chi-restraints excluded: chain D residue 91 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 120 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 166 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 171 optimal weight: 0.9980 chunk 177 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.092049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.065231 restraints weight = 30069.758| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.07 r_work: 0.2863 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15152 Z= 0.132 Angle : 0.558 6.866 20654 Z= 0.264 Chirality : 0.040 0.163 2250 Planarity : 0.004 0.035 2648 Dihedral : 5.298 85.774 2026 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.78 % Allowed : 12.92 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1.06 (0.20), residues: 1830 helix: 2.53 (0.20), residues: 686 sheet: 0.83 (0.27), residues: 358 loop : -1.09 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 82 TYR 0.013 0.001 TYR D 250 PHE 0.014 0.001 PHE A 510 TRP 0.020 0.001 TRP D 24 HIS 0.006 0.001 HIS D 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (15150) covalent geometry : angle 0.55766 / 0.26 (20654) hydrogen bonds : bond 0.04547 / 3.01 ( 622) hydrogen bonds : angle 4.15162 / 2.88 ( 1788) Misc. bond : bond 0.00013 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASP cc_start: 0.8125 (m-30) cc_final: 0.7801 (m-30) REVERT: A 414 GLN cc_start: 0.8140 (mt0) cc_final: 0.7081 (mm-40) REVERT: B 351 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8050 (mp0) REVERT: B 411 ASP cc_start: 0.8119 (m-30) cc_final: 0.7787 (m-30) REVERT: B 414 GLN cc_start: 0.8155 (mt0) cc_final: 0.7077 (mm-40) REVERT: C 90 ASP cc_start: 0.8193 (m-30) cc_final: 0.7874 (m-30) REVERT: C 162 LYS cc_start: 0.8851 (pttt) cc_final: 0.8088 (tppt) REVERT: C 242 ASP cc_start: 0.8917 (m-30) cc_final: 0.8097 (t0) REVERT: C 305 MET cc_start: 0.8807 (mpp) cc_final: 0.8326 (mpt) REVERT: D 90 ASP cc_start: 0.8353 (t0) cc_final: 0.8066 (m-30) REVERT: D 162 LYS cc_start: 0.8824 (pttt) cc_final: 0.8091 (tppt) REVERT: D 242 ASP cc_start: 0.8919 (m-30) cc_final: 0.8057 (t0) REVERT: D 305 MET cc_start: 0.8772 (mpp) cc_final: 0.8346 (mpt) outliers start: 12 outliers final: 9 residues processed: 86 average time/residue: 0.6863 time to fit residues: 64.5744 Evaluate side-chains 84 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain C residue 24 TRP Chi-restraints excluded: chain D residue 24 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 19 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 176 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 147 optimal weight: 0.1980 chunk 25 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.092453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.065633 restraints weight = 29966.157| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 3.07 r_work: 0.2880 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15152 Z= 0.120 Angle : 0.550 6.590 20654 Z= 0.259 Chirality : 0.039 0.163 2250 Planarity : 0.004 0.034 2648 Dihedral : 5.303 89.248 2026 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.84 % Allowed : 12.86 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1.11 (0.20), residues: 1830 helix: 2.59 (0.20), residues: 686 sheet: 0.85 (0.27), residues: 358 loop : -1.06 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 82 TYR 0.012 0.001 TYR C 250 PHE 0.013 0.001 PHE A 510 TRP 0.020 0.001 TRP C 24 HIS 0.006 0.001 HIS C 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (15150) covalent geometry : angle 0.55016 / 0.26 (20654) hydrogen bonds : bond 0.04309 / 2.86 ( 622) hydrogen bonds : angle 4.10213 / 2.84 ( 1788) Misc. bond : bond 0.00010 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASP cc_start: 0.8110 (m-30) cc_final: 0.7760 (m-30) REVERT: A 414 GLN cc_start: 0.8129 (mt0) cc_final: 0.7078 (mm-40) REVERT: B 351 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8044 (mp0) REVERT: B 411 ASP cc_start: 0.8106 (m-30) cc_final: 0.7773 (m-30) REVERT: B 414 GLN cc_start: 0.8144 (mt0) cc_final: 0.7081 (mm-40) REVERT: C 90 ASP cc_start: 0.8175 (m-30) cc_final: 0.7842 (m-30) REVERT: C 162 LYS cc_start: 0.8839 (pttt) cc_final: 0.8075 (tppt) REVERT: C 242 ASP cc_start: 0.8897 (m-30) cc_final: 0.8079 (t0) REVERT: C 305 MET cc_start: 0.8797 (mpp) cc_final: 0.8307 (mpt) REVERT: D 90 ASP cc_start: 0.8375 (t0) cc_final: 0.8082 (m-30) REVERT: D 162 LYS cc_start: 0.8806 (pttt) cc_final: 0.8074 (tppt) REVERT: D 242 ASP cc_start: 0.8905 (m-30) cc_final: 0.8044 (t0) REVERT: D 305 MET cc_start: 0.8763 (mpp) cc_final: 0.8269 (mpt) outliers start: 13 outliers final: 8 residues processed: 87 average time/residue: 0.6824 time to fit residues: 65.2034 Evaluate side-chains 79 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain C residue 24 TRP Chi-restraints excluded: chain D residue 24 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 140 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.092489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.065719 restraints weight = 29811.065| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.06 r_work: 0.2883 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15152 Z= 0.118 Angle : 0.548 6.753 20654 Z= 0.258 Chirality : 0.039 0.163 2250 Planarity : 0.004 0.035 2648 Dihedral : 5.148 82.486 2026 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.58 % Allowed : 13.05 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1.15 (0.20), residues: 1830 helix: 2.61 (0.20), residues: 686 sheet: 0.86 (0.28), residues: 358 loop : -1.03 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 82 TYR 0.012 0.001 TYR C 250 PHE 0.013 0.001 PHE A 510 TRP 0.021 0.001 TRP D 24 HIS 0.005 0.001 HIS D 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (15150) covalent geometry : angle 0.54808 / 0.26 (20654) hydrogen bonds : bond 0.04255 / 2.82 ( 622) hydrogen bonds : angle 4.08006 / 2.83 ( 1788) Misc. bond : bond 0.00007 / 0.00 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASP cc_start: 0.8102 (m-30) cc_final: 0.7740 (m-30) REVERT: A 414 GLN cc_start: 0.8147 (mt0) cc_final: 0.7081 (mm-40) REVERT: B 351 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8046 (mp0) REVERT: B 411 ASP cc_start: 0.8090 (m-30) cc_final: 0.7732 (m-30) REVERT: B 414 GLN cc_start: 0.8204 (mt0) cc_final: 0.7150 (mm-40) REVERT: C 90 ASP cc_start: 0.8178 (m-30) cc_final: 0.7840 (m-30) REVERT: C 162 LYS cc_start: 0.8827 (pttt) cc_final: 0.8068 (tppt) REVERT: C 242 ASP cc_start: 0.8911 (m-30) cc_final: 0.8097 (t0) REVERT: C 305 MET cc_start: 0.8759 (mpp) cc_final: 0.8277 (mpt) REVERT: D 90 ASP cc_start: 0.8369 (t0) cc_final: 0.8080 (m-30) REVERT: D 162 LYS cc_start: 0.8797 (pttt) cc_final: 0.8074 (tppt) REVERT: D 242 ASP cc_start: 0.8917 (m-30) cc_final: 0.8084 (t0) REVERT: D 305 MET cc_start: 0.8755 (mpp) cc_final: 0.8227 (mpt) outliers start: 9 outliers final: 8 residues processed: 81 average time/residue: 0.6444 time to fit residues: 57.3953 Evaluate side-chains 79 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain C residue 24 TRP Chi-restraints excluded: chain D residue 24 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 67 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.092219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.065595 restraints weight = 29929.841| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.03 r_work: 0.2885 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15152 Z= 0.132 Angle : 0.561 6.539 20654 Z= 0.265 Chirality : 0.040 0.162 2250 Planarity : 0.004 0.059 2648 Dihedral : 5.115 78.585 2026 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.65 % Allowed : 13.11 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1.12 (0.20), residues: 1830 helix: 2.56 (0.20), residues: 686 sheet: 0.85 (0.28), residues: 358 loop : -1.03 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 82 TYR 0.013 0.001 TYR C 250 PHE 0.014 0.001 PHE A 510 TRP 0.020 0.001 TRP D 24 HIS 0.005 0.001 HIS D 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (15150) covalent geometry : angle 0.56072 / 0.26 (20654) hydrogen bonds : bond 0.04505 / 2.99 ( 622) hydrogen bonds : angle 4.13015 / 2.87 ( 1788) Misc. bond : bond 0.00013 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4366.67 seconds wall clock time: 75 minutes 18.75 seconds (4518.75 seconds total)