Starting phenix.real_space_refine on Wed Mar 4 17:21:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7to3_26028/03_2026/7to3_26028.cif Found real_map, /net/cci-nas-00/data/ceres_data/7to3_26028/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7to3_26028/03_2026/7to3_26028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7to3_26028/03_2026/7to3_26028.map" model { file = "/net/cci-nas-00/data/ceres_data/7to3_26028/03_2026/7to3_26028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7to3_26028/03_2026/7to3_26028.cif" } 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-dev-5986/lib/python3.9/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, 'AMP%rna2p': 1, 'ATP': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Restraints were copied for chains: B, D Time building chain proxies: 4.57, per 1000 atoms: 0.31 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: 1.36 Conformation dependent library (CDL) restraints added in 490.9 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: 0.59 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: 2.07 Time building geometry restraints manager: 1.78 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: 67 5.68 - 7.57: 5 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: 8900 34.13 - 68.26: 124 68.26 - 102.39: 2 102.39 - 136.51: 2 136.51 - 170.64: 4 Dihedral angle restraints: 9032 sinusoidal: 3670 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 9029 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: 0.02 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: 6.170 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 14.700 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 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 : 12.149 170.644 5540 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 covalent geometry : bond 0.00209 (15150) covalent geometry : angle 0.56717 (20654) hydrogen bonds : bond 0.14325 ( 622) hydrogen bonds : angle 5.15609 ( 1788) Misc. bond : bond 0.23276 ( 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 : 0.546 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: 0.7340 time to fit residues: 205.7760 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 : 0.528 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 67 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.096580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.070044 restraints weight = 29429.526| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.04 r_work: 0.2981 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15152 Z= 0.135 Angle : 0.582 6.918 20654 Z= 0.279 Chirality : 0.040 0.176 2250 Planarity : 0.005 0.059 2648 Dihedral : 10.053 168.621 2088 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.23 % Allowed : 8.07 % Favored : 90.70 % 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: 0.92 (0.20), residues: 1830 helix: 2.55 (0.20), residues: 674 sheet: 0.57 (0.27), residues: 332 loop : -1.09 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 136 TYR 0.016 0.002 TYR D 286 PHE 0.014 0.002 PHE B 510 TRP 0.035 0.001 TRP C 24 HIS 0.008 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00311 (15150) covalent geometry : angle 0.58184 (20654) hydrogen bonds : bond 0.04952 ( 622) hydrogen bonds : angle 4.36715 ( 1788) Misc. bond : bond 0.00055 ( 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 136 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.634 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: 0.7385 (m100) cc_final: 0.6675 (m100) REVERT: A 215 ASN cc_start: 0.7413 (OUTLIER) cc_final: 0.7149 (m-40) REVERT: A 411 ASP cc_start: 0.7840 (m-30) cc_final: 0.7347 (m-30) REVERT: A 414 GLN cc_start: 0.8280 (mt0) cc_final: 0.7287 (mm-40) REVERT: B 37 LYS cc_start: 0.9263 (mttt) cc_final: 0.8853 (tmmm) REVERT: B 39 TRP cc_start: 0.7263 (m100) cc_final: 0.6710 (m100) REVERT: B 215 ASN cc_start: 0.7442 (OUTLIER) cc_final: 0.7210 (m-40) REVERT: B 351 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7996 (mp0) REVERT: B 411 ASP cc_start: 0.7865 (m-30) cc_final: 0.7391 (m-30) REVERT: B 414 GLN cc_start: 0.8186 (mt0) cc_final: 0.7178 (mm-40) REVERT: C 90 ASP cc_start: 0.8192 (m-30) cc_final: 0.7952 (m-30) REVERT: C 105 GLU cc_start: 0.7830 (tt0) cc_final: 0.7342 (tm-30) REVERT: C 162 LYS cc_start: 0.8993 (pttt) cc_final: 0.7995 (tppt) REVERT: C 242 ASP cc_start: 0.8940 (m-30) cc_final: 0.8157 (t0) REVERT: C 245 LYS cc_start: 0.8771 (mmmm) cc_final: 0.8425 (tptp) REVERT: D 90 ASP cc_start: 0.8283 (m-30) cc_final: 0.7978 (m-30) REVERT: D 162 LYS cc_start: 0.8937 (pttt) cc_final: 0.8101 (tppt) REVERT: D 242 ASP cc_start: 0.8930 (m-30) cc_final: 0.8141 (t0) REVERT: D 245 LYS cc_start: 0.8732 (mmmm) cc_final: 0.8379 (tptp) outliers start: 19 outliers final: 5 residues processed: 133 average time/residue: 0.7051 time to fit residues: 101.8257 Evaluate side-chains 96 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 215 ASN 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: 4.9990 chunk 93 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 56 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3511 r_free = 0.3511 target = 0.092421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.065664 restraints weight = 30429.429| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.06 r_work: 0.2911 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15152 Z= 0.176 Angle : 0.612 7.854 20654 Z= 0.293 Chirality : 0.042 0.175 2250 Planarity : 0.005 0.047 2648 Dihedral : 8.764 152.386 2088 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.74 % Allowed : 8.91 % Favored : 89.34 % 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: 0.79 (0.20), residues: 1830 helix: 2.35 (0.20), residues: 674 sheet: 0.55 (0.27), residues: 354 loop : -1.15 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 101 TYR 0.020 0.002 TYR D 286 PHE 0.019 0.002 PHE C 10 TRP 0.027 0.001 TRP D 24 HIS 0.010 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00425 (15150) covalent geometry : angle 0.61207 (20654) hydrogen bonds : bond 0.05631 ( 622) hydrogen bonds : angle 4.42127 ( 1788) Misc. bond : bond 0.00059 ( 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 125 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLN cc_start: 0.8150 (tt0) cc_final: 0.7882 (tp-100) REVERT: A 215 ASN cc_start: 0.7532 (OUTLIER) cc_final: 0.7221 (m-40) REVERT: A 411 ASP cc_start: 0.8176 (m-30) cc_final: 0.7869 (m-30) REVERT: A 414 GLN cc_start: 0.8299 (mt0) cc_final: 0.7281 (mm-40) REVERT: B 215 ASN cc_start: 0.7521 (OUTLIER) cc_final: 0.7265 (m-40) REVERT: B 351 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7995 (mp0) REVERT: B 411 ASP cc_start: 0.8171 (m-30) cc_final: 0.7890 (m-30) REVERT: B 414 GLN cc_start: 0.8279 (mt0) cc_final: 0.7220 (mm-40) REVERT: C 90 ASP cc_start: 0.8246 (m-30) cc_final: 0.7986 (m-30) REVERT: C 105 GLU cc_start: 0.7887 (tt0) cc_final: 0.7353 (tm-30) REVERT: C 162 LYS cc_start: 0.8959 (pttt) cc_final: 0.8074 (tppt) REVERT: C 242 ASP cc_start: 0.8959 (m-30) cc_final: 0.8074 (t0) REVERT: D 90 ASP cc_start: 0.8364 (m-30) cc_final: 0.8048 (m-30) REVERT: D 162 LYS cc_start: 0.8883 (pttt) cc_final: 0.8085 (tppt) REVERT: D 242 ASP cc_start: 0.8940 (m-30) cc_final: 0.8046 (t0) outliers start: 27 outliers final: 3 residues processed: 117 average time/residue: 0.6549 time to fit residues: 83.7517 Evaluate side-chains 88 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 518 SER 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: 4.9990 chunk 48 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 150 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.094483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.067746 restraints weight = 29977.855| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 3.05 r_work: 0.2949 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15152 Z= 0.115 Angle : 0.555 7.115 20654 Z= 0.262 Chirality : 0.039 0.173 2250 Planarity : 0.004 0.041 2648 Dihedral : 7.298 95.166 2088 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.10 % Allowed : 10.01 % Favored : 88.89 % 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: 0.96 (0.20), residues: 1830 helix: 2.45 (0.20), residues: 686 sheet: 0.74 (0.27), residues: 354 loop : -1.12 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 101 TYR 0.016 0.001 TYR C 286 PHE 0.013 0.001 PHE B 510 TRP 0.021 0.001 TRP C 24 HIS 0.006 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00266 (15150) covalent geometry : angle 0.55546 (20654) hydrogen bonds : bond 0.04301 ( 622) hydrogen bonds : angle 4.18048 ( 1788) Misc. bond : bond 0.00008 ( 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: 17 poor density : 90 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASP cc_start: 0.8061 (m-30) cc_final: 0.7719 (m-30) REVERT: A 414 GLN cc_start: 0.8270 (mt0) cc_final: 0.7278 (mm-40) REVERT: B 351 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8012 (mp0) REVERT: B 411 ASP cc_start: 0.8036 (m-30) cc_final: 0.7712 (m-30) REVERT: B 414 GLN cc_start: 0.8204 (mt0) cc_final: 0.7195 (mm-40) REVERT: C 90 ASP cc_start: 0.8160 (m-30) cc_final: 0.7875 (m-30) REVERT: C 105 GLU cc_start: 0.7848 (tt0) cc_final: 0.7299 (tm-30) REVERT: C 162 LYS cc_start: 0.8936 (pttt) cc_final: 0.8096 (tppt) REVERT: C 242 ASP cc_start: 0.8940 (m-30) cc_final: 0.8073 (t0) REVERT: C 305 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8487 (mpt) REVERT: D 90 ASP cc_start: 0.8343 (m-30) cc_final: 0.7939 (m-30) REVERT: D 162 LYS cc_start: 0.8876 (pttt) cc_final: 0.8089 (tppt) REVERT: D 242 ASP cc_start: 0.8926 (m-30) cc_final: 0.8060 (t0) outliers start: 17 outliers final: 1 residues processed: 103 average time/residue: 0.6909 time to fit residues: 77.6236 Evaluate side-chains 80 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 305 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 16 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 180 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 173 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN B 550 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.092432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.065486 restraints weight = 30095.997| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.08 r_work: 0.2869 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2911 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= 0.133 Angle : 0.564 7.427 20654 Z= 0.268 Chirality : 0.040 0.168 2250 Planarity : 0.004 0.038 2648 Dihedral : 6.915 72.962 2088 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.23 % Allowed : 10.85 % Favored : 87.92 % 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: 1.00 (0.20), residues: 1830 helix: 2.46 (0.21), residues: 686 sheet: 0.82 (0.27), residues: 354 loop : -1.10 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 101 TYR 0.013 0.001 TYR D 250 PHE 0.014 0.001 PHE A 510 TRP 0.021 0.001 TRP D 24 HIS 0.006 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00316 (15150) covalent geometry : angle 0.56445 (20654) hydrogen bonds : bond 0.04671 ( 622) hydrogen bonds : angle 4.17249 ( 1788) Misc. bond : bond 0.00065 ( 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 : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASP cc_start: 0.8127 (m-30) cc_final: 0.7801 (m-30) REVERT: A 414 GLN cc_start: 0.8156 (mt0) cc_final: 0.7104 (mm-40) REVERT: B 351 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8008 (mp0) REVERT: B 411 ASP cc_start: 0.8100 (m-30) cc_final: 0.7780 (m-30) REVERT: B 414 GLN cc_start: 0.8159 (mt0) cc_final: 0.7114 (mm-40) REVERT: C 90 ASP cc_start: 0.8169 (m-30) cc_final: 0.7876 (m-30) REVERT: C 105 GLU cc_start: 0.7868 (tt0) cc_final: 0.7300 (tm-30) REVERT: C 162 LYS cc_start: 0.8928 (pttt) cc_final: 0.8094 (tppt) REVERT: C 242 ASP cc_start: 0.8947 (m-30) cc_final: 0.8067 (t0) REVERT: C 305 MET cc_start: 0.8784 (mpp) cc_final: 0.8204 (mpt) REVERT: D 90 ASP cc_start: 0.8297 (m-30) cc_final: 0.7850 (m-30) REVERT: D 162 LYS cc_start: 0.8890 (pttt) cc_final: 0.8141 (tppt) REVERT: D 242 ASP cc_start: 0.8954 (m-30) cc_final: 0.8050 (t0) REVERT: D 305 MET cc_start: 0.8781 (mpp) cc_final: 0.8383 (mpt) outliers start: 19 outliers final: 7 residues processed: 95 average time/residue: 0.6775 time to fit residues: 70.2672 Evaluate side-chains 83 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 129 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.090898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.063957 restraints weight = 29927.277| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 3.06 r_work: 0.2859 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 15152 Z= 0.194 Angle : 0.605 8.015 20654 Z= 0.290 Chirality : 0.042 0.168 2250 Planarity : 0.004 0.037 2648 Dihedral : 7.070 78.714 2088 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.16 % Allowed : 11.63 % Favored : 87.21 % 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: 0.84 (0.20), residues: 1830 helix: 2.31 (0.20), residues: 686 sheet: 0.71 (0.27), residues: 354 loop : -1.16 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 82 TYR 0.015 0.002 TYR C 250 PHE 0.019 0.002 PHE D 10 TRP 0.019 0.001 TRP D 24 HIS 0.007 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00478 (15150) covalent geometry : angle 0.60540 (20654) hydrogen bonds : bond 0.05511 ( 622) hydrogen bonds : angle 4.35467 ( 1788) Misc. bond : bond 0.00030 ( 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 96 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASP cc_start: 0.8202 (m-30) cc_final: 0.7924 (m-30) REVERT: A 414 GLN cc_start: 0.8198 (mt0) cc_final: 0.7134 (mm-40) REVERT: B 351 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8061 (mp0) REVERT: B 411 ASP cc_start: 0.8187 (m-30) cc_final: 0.7919 (m-30) REVERT: B 414 GLN cc_start: 0.8209 (mt0) cc_final: 0.7148 (mm-40) REVERT: C 90 ASP cc_start: 0.8214 (m-30) cc_final: 0.7924 (m-30) REVERT: C 162 LYS cc_start: 0.8880 (pttt) cc_final: 0.8094 (tppt) REVERT: C 242 ASP cc_start: 0.8955 (m-30) cc_final: 0.8098 (t0) REVERT: C 267 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7353 (tpp) REVERT: D 90 ASP cc_start: 0.8325 (m-30) cc_final: 0.7872 (m-30) REVERT: D 162 LYS cc_start: 0.8847 (pttt) cc_final: 0.8150 (tppt) REVERT: D 242 ASP cc_start: 0.8952 (m-30) cc_final: 0.8079 (t0) outliers start: 18 outliers final: 7 residues processed: 89 average time/residue: 0.6587 time to fit residues: 64.1536 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 : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 267 MET 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: 2.9990 chunk 33 optimal weight: 4.9990 chunk 68 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.092034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.065245 restraints weight = 29830.037| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.05 r_work: 0.2869 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3141 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= 0.124 Angle : 0.552 7.029 20654 Z= 0.262 Chirality : 0.040 0.164 2250 Planarity : 0.004 0.035 2648 Dihedral : 6.861 72.800 2088 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.90 % Allowed : 12.21 % Favored : 86.89 % 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: 0.96 (0.20), residues: 1830 helix: 2.45 (0.20), residues: 686 sheet: 0.74 (0.27), residues: 358 loop : -1.12 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 82 TYR 0.012 0.001 TYR D 250 PHE 0.014 0.001 PHE A 510 TRP 0.019 0.001 TRP D 24 HIS 0.005 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00292 (15150) covalent geometry : angle 0.55248 (20654) hydrogen bonds : bond 0.04502 ( 622) hydrogen bonds : angle 4.18621 ( 1788) Misc. bond : bond 0.00014 ( 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 93 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASP cc_start: 0.8108 (m-30) cc_final: 0.7773 (m-30) REVERT: A 414 GLN cc_start: 0.8119 (mt0) cc_final: 0.7075 (mm-40) REVERT: B 351 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8044 (mp0) REVERT: B 411 ASP cc_start: 0.8130 (m-30) cc_final: 0.7793 (m-30) REVERT: B 414 GLN cc_start: 0.8152 (mt0) cc_final: 0.7078 (mm-40) REVERT: C 90 ASP cc_start: 0.8165 (m-30) cc_final: 0.7837 (m-30) REVERT: C 162 LYS cc_start: 0.8865 (pttt) cc_final: 0.8114 (tppt) REVERT: C 242 ASP cc_start: 0.8937 (m-30) cc_final: 0.8110 (t0) REVERT: C 305 MET cc_start: 0.8743 (mpp) cc_final: 0.8250 (mpt) REVERT: D 136 HIS cc_start: 0.8259 (m90) cc_final: 0.7732 (t70) REVERT: D 162 LYS cc_start: 0.8827 (pttt) cc_final: 0.8104 (tppt) REVERT: D 242 ASP cc_start: 0.8934 (m-30) cc_final: 0.8077 (t0) outliers start: 14 outliers final: 8 residues processed: 91 average time/residue: 0.6366 time to fit residues: 63.5282 Evaluate side-chains 83 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 47 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain C residue 24 TRP Chi-restraints excluded: chain D residue 24 TRP 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: 1.9990 chunk 65 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 151 optimal weight: 0.0770 chunk 166 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 171 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.090999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.064132 restraints weight = 30185.045| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.05 r_work: 0.2856 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15152 Z= 0.161 Angle : 0.594 8.328 20654 Z= 0.282 Chirality : 0.041 0.164 2250 Planarity : 0.004 0.035 2648 Dihedral : 6.942 75.976 2088 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.71 % Allowed : 12.86 % Favored : 86.43 % 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: 0.88 (0.20), residues: 1830 helix: 2.38 (0.20), residues: 686 sheet: 0.67 (0.27), residues: 358 loop : -1.15 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 82 TYR 0.014 0.002 TYR C 250 PHE 0.017 0.002 PHE D 10 TRP 0.020 0.001 TRP D 24 HIS 0.006 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00392 (15150) covalent geometry : angle 0.59404 (20654) hydrogen bonds : bond 0.05096 ( 622) hydrogen bonds : angle 4.26331 ( 1788) Misc. bond : bond 0.00017 ( 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 86 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASP cc_start: 0.8149 (m-30) cc_final: 0.7824 (m-30) REVERT: A 414 GLN cc_start: 0.8161 (mt0) cc_final: 0.7093 (mm-40) REVERT: B 351 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8057 (mp0) REVERT: B 411 ASP cc_start: 0.8149 (m-30) cc_final: 0.7826 (m-30) REVERT: B 414 GLN cc_start: 0.8175 (mt0) cc_final: 0.7086 (mm-40) REVERT: C 90 ASP cc_start: 0.8204 (m-30) cc_final: 0.7874 (m-30) REVERT: C 136 HIS cc_start: 0.8270 (m90) cc_final: 0.7731 (t70) REVERT: C 162 LYS cc_start: 0.8845 (pttt) cc_final: 0.8080 (tppt) REVERT: C 242 ASP cc_start: 0.8952 (m-30) cc_final: 0.8115 (t0) REVERT: C 305 MET cc_start: 0.8733 (mpp) cc_final: 0.8243 (mpt) REVERT: D 90 ASP cc_start: 0.8401 (t0) cc_final: 0.8065 (m-30) REVERT: D 136 HIS cc_start: 0.8259 (m90) cc_final: 0.7720 (t70) REVERT: D 162 LYS cc_start: 0.8808 (pttt) cc_final: 0.8084 (tppt) REVERT: D 242 ASP cc_start: 0.8939 (m-30) cc_final: 0.8090 (t0) REVERT: D 305 MET cc_start: 0.8782 (mpp) cc_final: 0.8272 (mpt) outliers start: 11 outliers final: 8 residues processed: 85 average time/residue: 0.6997 time to fit residues: 65.1940 Evaluate side-chains 82 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 47 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 188 LYS 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: 0.1980 chunk 95 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 chunk 127 optimal weight: 0.4980 chunk 147 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.093076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.066517 restraints weight = 29963.396| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.05 r_work: 0.2912 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15152 Z= 0.107 Angle : 0.547 8.304 20654 Z= 0.257 Chirality : 0.039 0.163 2250 Planarity : 0.004 0.034 2648 Dihedral : 6.715 70.792 2088 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 2.85 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: 1.09 (0.20), residues: 1830 helix: 2.58 (0.20), residues: 686 sheet: 0.83 (0.28), residues: 348 loop : -1.07 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 82 TYR 0.010 0.001 TYR C 250 PHE 0.013 0.001 PHE A 510 TRP 0.020 0.001 TRP D 24 HIS 0.004 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00243 (15150) covalent geometry : angle 0.54714 (20654) hydrogen bonds : bond 0.04036 ( 622) hydrogen bonds : angle 4.07849 ( 1788) Misc. bond : bond 0.00006 ( 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 82 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASP cc_start: 0.8117 (m-30) cc_final: 0.7765 (m-30) REVERT: A 414 GLN cc_start: 0.8143 (mt0) cc_final: 0.7102 (mm-40) REVERT: B 351 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8071 (mp0) REVERT: B 411 ASP cc_start: 0.8098 (m-30) cc_final: 0.7733 (m-30) REVERT: B 414 GLN cc_start: 0.8141 (mt0) cc_final: 0.7097 (mm-40) REVERT: C 90 ASP cc_start: 0.8176 (m-30) cc_final: 0.7855 (m-30) REVERT: C 136 HIS cc_start: 0.8272 (m90) cc_final: 0.7687 (t70) REVERT: C 162 LYS cc_start: 0.8827 (pttt) cc_final: 0.8078 (tppt) REVERT: C 242 ASP cc_start: 0.8906 (m-30) cc_final: 0.8086 (t0) REVERT: C 305 MET cc_start: 0.8732 (mpp) cc_final: 0.8272 (mpt) REVERT: D 90 ASP cc_start: 0.8394 (t0) cc_final: 0.8062 (m-30) REVERT: D 162 LYS cc_start: 0.8788 (pttt) cc_final: 0.8073 (tppt) REVERT: D 242 ASP cc_start: 0.8911 (m-30) cc_final: 0.8088 (t0) REVERT: D 305 MET cc_start: 0.8783 (mpp) cc_final: 0.8317 (mpt) outliers start: 9 outliers final: 4 residues processed: 82 average time/residue: 0.6930 time to fit residues: 62.4596 Evaluate side-chains 73 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain B residue 49 VAL 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: 0.9980 chunk 156 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.092120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.065314 restraints weight = 29884.860| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.06 r_work: 0.2874 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3301 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= 0.130 Angle : 0.568 8.623 20654 Z= 0.268 Chirality : 0.040 0.162 2250 Planarity : 0.004 0.034 2648 Dihedral : 6.742 71.307 2088 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.52 % Allowed : 13.37 % Favored : 86.11 % 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: 2.56 (0.20), residues: 686 sheet: 0.81 (0.28), residues: 348 loop : -1.07 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 82 TYR 0.012 0.001 TYR C 250 PHE 0.014 0.001 PHE A 510 TRP 0.021 0.001 TRP D 24 HIS 0.006 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00308 (15150) covalent geometry : angle 0.56773 (20654) hydrogen bonds : bond 0.04415 ( 622) hydrogen bonds : angle 4.10358 ( 1788) Misc. bond : bond 0.00009 ( 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 78 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASP cc_start: 0.8106 (m-30) cc_final: 0.7769 (m-30) REVERT: A 414 GLN cc_start: 0.8142 (mt0) cc_final: 0.7077 (mm-40) REVERT: B 351 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8062 (mp0) REVERT: B 411 ASP cc_start: 0.8116 (m-30) cc_final: 0.7769 (m-30) REVERT: B 414 GLN cc_start: 0.8143 (mt0) cc_final: 0.7064 (mm-40) REVERT: C 90 ASP cc_start: 0.8184 (m-30) cc_final: 0.7840 (m-30) REVERT: C 136 HIS cc_start: 0.8274 (m90) cc_final: 0.7683 (t70) REVERT: C 162 LYS cc_start: 0.8813 (pttt) cc_final: 0.8077 (tppt) REVERT: C 242 ASP cc_start: 0.8929 (m-30) cc_final: 0.8106 (t0) REVERT: C 305 MET cc_start: 0.8717 (mpp) cc_final: 0.8238 (mpt) REVERT: D 90 ASP cc_start: 0.8339 (t0) cc_final: 0.7992 (m-30) REVERT: D 139 GLN cc_start: 0.8921 (tt0) cc_final: 0.8429 (mp10) REVERT: D 162 LYS cc_start: 0.8795 (pttt) cc_final: 0.8066 (tppt) REVERT: D 242 ASP cc_start: 0.8924 (m-30) cc_final: 0.8097 (t0) REVERT: D 305 MET cc_start: 0.8774 (mpp) cc_final: 0.8285 (mpt) outliers start: 8 outliers final: 7 residues processed: 76 average time/residue: 0.7095 time to fit residues: 59.0817 Evaluate side-chains 77 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain C residue 24 TRP Chi-restraints excluded: chain C residue 83 MET 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: 0.8980 chunk 96 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 121 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.092278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.065560 restraints weight = 29822.297| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.04 r_work: 0.2896 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15152 Z= 0.128 Angle : 0.568 8.580 20654 Z= 0.268 Chirality : 0.040 0.162 2250 Planarity : 0.004 0.058 2648 Dihedral : 6.774 71.707 2088 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.52 % Allowed : 13.37 % Favored : 86.11 % 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: 1.08 (0.20), residues: 1830 helix: 2.56 (0.20), residues: 686 sheet: 0.83 (0.28), residues: 348 loop : -1.05 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 82 TYR 0.012 0.001 TYR C 250 PHE 0.014 0.001 PHE B 510 TRP 0.021 0.001 TRP D 24 HIS 0.005 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00302 (15150) covalent geometry : angle 0.56800 (20654) hydrogen bonds : bond 0.04430 ( 622) hydrogen bonds : angle 4.10868 ( 1788) Misc. bond : bond 0.00009 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4139.99 seconds wall clock time: 71 minutes 18.71 seconds (4278.71 seconds total)