Starting phenix.real_space_refine on Fri Jun 13 15:15:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7to3_26028/06_2025/7to3_26028.cif Found real_map, /net/cci-nas-00/data/ceres_data/7to3_26028/06_2025/7to3_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_26028/06_2025/7to3_26028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7to3_26028/06_2025/7to3_26028.map" model { file = "/net/cci-nas-00/data/ceres_data/7to3_26028/06_2025/7to3_26028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7to3_26028/06_2025/7to3_26028.cif" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 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: D, B Time building chain proxies: 13.78, per 1000 atoms: 0.93 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: 3.94 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.52 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: 4.68 Time building geometry restraints manager: 4.65 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: 0.07 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'B' } 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: 5.370 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: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 40.070 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 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:12.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.030 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.099 0.001 TRP D 24 HIS 0.005 0.001 HIS D 206 PHE 0.011 0.001 PHE A 510 TYR 0.009 0.001 TYR D 225 ARG 0.001 0.000 ARG D 61 Details of bonding type rmsd hydrogen bonds : bond 0.14325 ( 622) hydrogen bonds : angle 5.15609 ( 1788) covalent geometry : bond 0.00209 (15150) covalent geometry : angle 0.56717 (20654) 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 : 1.650 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: 1.6533 time to fit residues: 464.9639 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 : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 86 optimal weight: 0.0870 chunk 106 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 ASN C 8 ASN C 210 GLN D 8 ASN D 210 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.094931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.068180 restraints weight = 29379.826| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.04 r_work: 0.2934 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15152 Z= 0.151 Angle : 0.606 7.194 20654 Z= 0.292 Chirality : 0.041 0.173 2250 Planarity : 0.005 0.058 2648 Dihedral : 9.990 173.076 2088 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.49 % Allowed : 7.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.19), residues: 1830 helix: 2.41 (0.20), residues: 674 sheet: 0.46 (0.27), residues: 336 loop : -1.16 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 24 HIS 0.010 0.001 HIS C 206 PHE 0.015 0.002 PHE C 10 TYR 0.017 0.002 TYR D 286 ARG 0.008 0.001 ARG A 136 Details of bonding type rmsd hydrogen bonds : bond 0.05211 ( 622) hydrogen bonds : angle 4.40245 ( 1788) covalent geometry : bond 0.00363 (15150) covalent geometry : angle 0.60604 (20654) Misc. bond : bond 0.00077 ( 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: 23 poor density : 113 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ASN cc_start: 0.7417 (OUTLIER) cc_final: 0.7152 (m-40) REVERT: A 411 ASP cc_start: 0.7964 (m-30) cc_final: 0.7525 (m-30) REVERT: A 414 GLN cc_start: 0.8288 (mt0) cc_final: 0.7278 (mm-40) REVERT: B 37 LYS cc_start: 0.9257 (mttt) cc_final: 0.8834 (tmmm) REVERT: B 39 TRP cc_start: 0.7299 (m100) cc_final: 0.6719 (m100) REVERT: B 215 ASN cc_start: 0.7378 (OUTLIER) cc_final: 0.7124 (m-40) REVERT: B 351 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7996 (mp0) REVERT: B 411 ASP cc_start: 0.7971 (m-30) cc_final: 0.7564 (m-30) REVERT: B 414 GLN cc_start: 0.8218 (mt0) cc_final: 0.7191 (mm-40) REVERT: C 90 ASP cc_start: 0.8199 (m-30) cc_final: 0.7954 (m-30) REVERT: C 105 GLU cc_start: 0.7828 (tt0) cc_final: 0.7300 (tm-30) REVERT: C 162 LYS cc_start: 0.9017 (pttt) cc_final: 0.8126 (tppt) REVERT: C 242 ASP cc_start: 0.8954 (m-30) cc_final: 0.8106 (t0) REVERT: C 245 LYS cc_start: 0.8793 (mmmm) cc_final: 0.8477 (tptp) REVERT: D 90 ASP cc_start: 0.8290 (m-30) cc_final: 0.7964 (m-30) REVERT: D 162 LYS cc_start: 0.8920 (pttt) cc_final: 0.8093 (tppt) REVERT: D 242 ASP cc_start: 0.8947 (m-30) cc_final: 0.8100 (t0) REVERT: D 245 LYS cc_start: 0.8741 (mmmm) cc_final: 0.8391 (tptp) outliers start: 23 outliers final: 6 residues processed: 132 average time/residue: 1.4410 time to fit residues: 208.5523 Evaluate side-chains 93 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 1.609 ------------------------------------------------------------------------------- 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 29 ASN 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 33 optimal weight: 0.3980 chunk 144 optimal weight: 9.9990 chunk 132 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN B 417 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.093166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.066354 restraints weight = 29845.459| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.10 r_work: 0.2917 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2557 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= 0.146 Angle : 0.577 7.217 20654 Z= 0.274 Chirality : 0.041 0.173 2250 Planarity : 0.004 0.047 2648 Dihedral : 8.395 145.196 2088 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.55 % Allowed : 8.98 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.20), residues: 1830 helix: 2.45 (0.20), residues: 674 sheet: 0.66 (0.27), residues: 354 loop : -1.13 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 24 HIS 0.008 0.001 HIS C 206 PHE 0.014 0.002 PHE C 10 TYR 0.019 0.002 TYR C 286 ARG 0.008 0.001 ARG A 136 Details of bonding type rmsd hydrogen bonds : bond 0.04976 ( 622) hydrogen bonds : angle 4.27736 ( 1788) covalent geometry : bond 0.00347 (15150) covalent geometry : angle 0.57693 (20654) Misc. bond : bond 0.00027 ( 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 119 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASP cc_start: 0.8083 (m-30) cc_final: 0.7764 (m-30) REVERT: A 414 GLN cc_start: 0.8259 (mt0) cc_final: 0.7246 (mm-40) REVERT: B 351 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7964 (mp0) REVERT: B 411 ASP cc_start: 0.8086 (m-30) cc_final: 0.7770 (m-30) REVERT: B 414 GLN cc_start: 0.8212 (mt0) cc_final: 0.7167 (mm-40) REVERT: C 90 ASP cc_start: 0.8186 (m-30) cc_final: 0.7913 (m-30) REVERT: C 105 GLU cc_start: 0.7851 (tt0) cc_final: 0.7300 (tm-30) REVERT: C 162 LYS cc_start: 0.8942 (pttt) cc_final: 0.8063 (tppt) REVERT: C 242 ASP cc_start: 0.8961 (m-30) cc_final: 0.8077 (t0) REVERT: D 90 ASP cc_start: 0.8324 (m-30) cc_final: 0.7950 (m-30) REVERT: D 162 LYS cc_start: 0.8867 (pttt) cc_final: 0.8057 (tppt) REVERT: D 242 ASP cc_start: 0.8935 (m-30) cc_final: 0.8046 (t0) outliers start: 24 outliers final: 4 residues processed: 111 average time/residue: 1.4344 time to fit residues: 174.8065 Evaluate side-chains 85 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 9 optimal weight: 0.9990 chunk 144 optimal weight: 7.9990 chunk 127 optimal weight: 0.0870 chunk 105 optimal weight: 0.7980 chunk 163 optimal weight: 6.9990 chunk 60 optimal weight: 0.0770 chunk 136 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 overall best weight: 0.5316 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.094891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.067687 restraints weight = 28774.419| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.96 r_work: 0.2936 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15152 Z= 0.106 Angle : 0.552 7.018 20654 Z= 0.259 Chirality : 0.039 0.171 2250 Planarity : 0.004 0.039 2648 Dihedral : 7.140 89.849 2088 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.90 % Allowed : 10.53 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.20), residues: 1830 helix: 2.53 (0.20), residues: 686 sheet: 0.75 (0.27), residues: 358 loop : -1.06 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 24 HIS 0.005 0.001 HIS C 206 PHE 0.013 0.001 PHE A 510 TYR 0.019 0.001 TYR D 286 ARG 0.008 0.000 ARG C 82 Details of bonding type rmsd hydrogen bonds : bond 0.04064 ( 622) hydrogen bonds : angle 4.08550 ( 1788) covalent geometry : bond 0.00240 (15150) covalent geometry : angle 0.55176 (20654) Misc. bond : bond 0.00013 ( 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 104 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASP cc_start: 0.8209 (m-30) cc_final: 0.7923 (m-30) REVERT: A 414 GLN cc_start: 0.8446 (mt0) cc_final: 0.7544 (mm-40) REVERT: B 351 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8174 (mp0) REVERT: B 411 ASP cc_start: 0.8233 (m-30) cc_final: 0.7951 (m-30) REVERT: B 414 GLN cc_start: 0.8391 (mt0) cc_final: 0.7462 (mm-40) REVERT: C 90 ASP cc_start: 0.8269 (m-30) cc_final: 0.7960 (m-30) REVERT: C 105 GLU cc_start: 0.7975 (tt0) cc_final: 0.7558 (tm-30) REVERT: C 162 LYS cc_start: 0.8989 (pttt) cc_final: 0.8182 (tppt) REVERT: C 242 ASP cc_start: 0.8836 (m-30) cc_final: 0.8014 (t0) REVERT: C 245 LYS cc_start: 0.8702 (mmmm) cc_final: 0.8353 (tptp) REVERT: C 305 MET cc_start: 0.8895 (mpp) cc_final: 0.8567 (mpt) REVERT: D 90 ASP cc_start: 0.8403 (m-30) cc_final: 0.7965 (m-30) REVERT: D 162 LYS cc_start: 0.8935 (pttt) cc_final: 0.8176 (tppt) REVERT: D 242 ASP cc_start: 0.8815 (m-30) cc_final: 0.8023 (t0) outliers start: 14 outliers final: 1 residues processed: 100 average time/residue: 1.6071 time to fit residues: 176.3052 Evaluate side-chains 82 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 164 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 148 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.3470 r_free = 0.3470 target = 0.091204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.064310 restraints weight = 30223.032| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 3.06 r_work: 0.2856 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15152 Z= 0.174 Angle : 0.597 7.320 20654 Z= 0.286 Chirality : 0.041 0.169 2250 Planarity : 0.004 0.038 2648 Dihedral : 7.052 76.944 2088 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.23 % Allowed : 10.92 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.20), residues: 1830 helix: 2.36 (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 TRP 0.020 0.001 TRP C 24 HIS 0.006 0.001 HIS D 206 PHE 0.018 0.002 PHE C 10 TYR 0.020 0.002 TYR C 286 ARG 0.005 0.001 ARG A 132 Details of bonding type rmsd hydrogen bonds : bond 0.05337 ( 622) hydrogen bonds : angle 4.28515 ( 1788) covalent geometry : bond 0.00424 (15150) covalent geometry : angle 0.59743 (20654) Misc. bond : bond 0.00043 ( 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 101 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 1.607 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: 0.8170 (m-30) cc_final: 0.7872 (m-30) REVERT: A 414 GLN cc_start: 0.8162 (mt0) cc_final: 0.7102 (mm-40) REVERT: B 351 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8027 (mp0) REVERT: B 411 ASP cc_start: 0.8189 (m-30) cc_final: 0.7907 (m-30) REVERT: B 414 GLN cc_start: 0.8178 (mt0) cc_final: 0.7098 (mm-40) REVERT: C 90 ASP cc_start: 0.8179 (m-30) cc_final: 0.7902 (m-30) REVERT: C 105 GLU cc_start: 0.7882 (tt0) cc_final: 0.7322 (tm-30) REVERT: C 162 LYS cc_start: 0.8919 (pttt) cc_final: 0.8101 (tppt) REVERT: C 242 ASP cc_start: 0.8965 (m-30) cc_final: 0.8074 (t0) REVERT: C 245 LYS cc_start: 0.8755 (mmmm) cc_final: 0.8338 (tptp) REVERT: D 90 ASP cc_start: 0.8331 (m-30) cc_final: 0.7908 (m-30) REVERT: D 162 LYS cc_start: 0.8883 (pttt) cc_final: 0.8144 (tppt) REVERT: D 242 ASP cc_start: 0.8950 (m-30) cc_final: 0.8046 (t0) outliers start: 19 outliers final: 9 residues processed: 96 average time/residue: 1.4877 time to fit residues: 156.7757 Evaluate side-chains 90 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU 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 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 83 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 151 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 137 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 41 optimal weight: 0.0980 chunk 138 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 165 optimal weight: 0.0870 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 = 0.3512 r_free = 0.3512 target = 0.093841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.067215 restraints weight = 29746.730| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 3.06 r_work: 0.2913 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15152 Z= 0.103 Angle : 0.531 6.391 20654 Z= 0.250 Chirality : 0.039 0.165 2250 Planarity : 0.004 0.036 2648 Dihedral : 6.731 70.456 2088 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.78 % Allowed : 11.95 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.20), residues: 1830 helix: 2.58 (0.20), residues: 686 sheet: 0.88 (0.27), residues: 354 loop : -1.05 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 24 HIS 0.004 0.001 HIS D 206 PHE 0.012 0.001 PHE B 510 TYR 0.021 0.001 TYR C 286 ARG 0.008 0.000 ARG D 82 Details of bonding type rmsd hydrogen bonds : bond 0.03970 ( 622) hydrogen bonds : angle 4.05989 ( 1788) covalent geometry : bond 0.00233 (15150) covalent geometry : angle 0.53077 (20654) Misc. bond : bond 0.00015 ( 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: 12 poor density : 84 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASP cc_start: 0.8105 (m-30) cc_final: 0.7739 (m-30) REVERT: A 414 GLN cc_start: 0.8179 (mt0) cc_final: 0.7167 (mm-40) REVERT: B 351 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8010 (mp0) REVERT: B 411 ASP cc_start: 0.8100 (m-30) cc_final: 0.7736 (m-30) REVERT: B 414 GLN cc_start: 0.8127 (mt0) cc_final: 0.7101 (mm-40) REVERT: C 90 ASP cc_start: 0.8150 (m-30) cc_final: 0.7835 (m-30) REVERT: C 105 GLU cc_start: 0.7845 (tt0) cc_final: 0.7304 (tm-30) REVERT: C 162 LYS cc_start: 0.8856 (pttt) cc_final: 0.8060 (tppt) REVERT: C 242 ASP cc_start: 0.8924 (m-30) cc_final: 0.8068 (t0) REVERT: C 245 LYS cc_start: 0.8708 (mmmm) cc_final: 0.8329 (tptp) REVERT: D 162 LYS cc_start: 0.8836 (pttt) cc_final: 0.8114 (tppt) REVERT: D 242 ASP cc_start: 0.8926 (m-30) cc_final: 0.8067 (t0) REVERT: D 305 MET cc_start: 0.8840 (mpp) cc_final: 0.8345 (mpt) outliers start: 12 outliers final: 5 residues processed: 94 average time/residue: 1.4143 time to fit residues: 146.4889 Evaluate side-chains 82 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 144 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 179 optimal weight: 4.9990 chunk 174 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3475 r_free = 0.3475 target = 0.091682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.064781 restraints weight = 30094.773| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.06 r_work: 0.2862 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3124 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= 0.149 Angle : 0.575 8.416 20654 Z= 0.273 Chirality : 0.040 0.163 2250 Planarity : 0.004 0.035 2648 Dihedral : 6.829 73.659 2088 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.03 % Allowed : 12.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.20), residues: 1830 helix: 2.49 (0.21), residues: 686 sheet: 0.77 (0.27), residues: 358 loop : -1.11 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 24 HIS 0.006 0.001 HIS C 206 PHE 0.015 0.002 PHE D 10 TYR 0.014 0.002 TYR D 250 ARG 0.008 0.001 ARG D 82 Details of bonding type rmsd hydrogen bonds : bond 0.04869 ( 622) hydrogen bonds : angle 4.18493 ( 1788) covalent geometry : bond 0.00356 (15150) covalent geometry : angle 0.57460 (20654) Misc. bond : bond 0.00012 ( 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: 16 poor density : 77 time to evaluate : 1.792 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: 0.8129 (m-30) cc_final: 0.7817 (m-30) REVERT: A 414 GLN cc_start: 0.8153 (mt0) cc_final: 0.7080 (mm-40) REVERT: B 351 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8035 (mp0) REVERT: B 411 ASP cc_start: 0.8146 (m-30) cc_final: 0.7831 (m-30) REVERT: B 414 GLN cc_start: 0.8179 (mt0) cc_final: 0.7088 (mm-40) REVERT: C 90 ASP cc_start: 0.8201 (m-30) cc_final: 0.7882 (m-30) REVERT: C 162 LYS cc_start: 0.8861 (pttt) cc_final: 0.8104 (tppt) REVERT: C 242 ASP cc_start: 0.8950 (m-30) cc_final: 0.8108 (t0) REVERT: C 305 MET cc_start: 0.8836 (mpp) cc_final: 0.8322 (mpt) REVERT: D 90 ASP cc_start: 0.8402 (t0) cc_final: 0.8056 (m-30) REVERT: D 162 LYS cc_start: 0.8833 (pttt) cc_final: 0.8104 (tppt) REVERT: D 242 ASP cc_start: 0.8927 (m-30) cc_final: 0.8069 (t0) REVERT: D 305 MET cc_start: 0.8809 (mpp) cc_final: 0.8393 (mpt) outliers start: 16 outliers final: 9 residues processed: 90 average time/residue: 1.3681 time to fit residues: 135.8439 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 : 1.806 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 60 optimal weight: 0.2980 chunk 68 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 133 optimal weight: 0.2980 chunk 80 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 171 optimal weight: 0.0060 chunk 51 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.3505 r_free = 0.3505 target = 0.093535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.066789 restraints weight = 29797.078| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.07 r_work: 0.2904 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15152 Z= 0.099 Angle : 0.533 8.245 20654 Z= 0.252 Chirality : 0.039 0.163 2250 Planarity : 0.004 0.034 2648 Dihedral : 6.627 72.409 2088 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.78 % Allowed : 12.73 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.20), residues: 1830 helix: 2.65 (0.20), residues: 686 sheet: 0.93 (0.28), residues: 348 loop : -1.04 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 24 HIS 0.004 0.000 HIS C 206 PHE 0.013 0.001 PHE A 510 TYR 0.011 0.001 TYR C 317 ARG 0.009 0.000 ARG C 82 Details of bonding type rmsd hydrogen bonds : bond 0.03846 ( 622) hydrogen bonds : angle 3.99574 ( 1788) covalent geometry : bond 0.00220 (15150) covalent geometry : angle 0.53293 (20654) Misc. bond : bond 0.00003 ( 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 92 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASP cc_start: 0.8085 (m-30) cc_final: 0.7725 (m-30) REVERT: A 414 GLN cc_start: 0.8130 (mt0) cc_final: 0.7106 (mm-40) REVERT: B 351 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8056 (mp0) REVERT: B 411 ASP cc_start: 0.8094 (m-30) cc_final: 0.7730 (m-30) REVERT: B 414 GLN cc_start: 0.8149 (mt0) cc_final: 0.7093 (mm-40) REVERT: C 90 ASP cc_start: 0.8168 (m-30) cc_final: 0.7834 (m-30) REVERT: C 162 LYS cc_start: 0.8854 (pttt) cc_final: 0.8105 (tppt) REVERT: C 242 ASP cc_start: 0.8919 (m-30) cc_final: 0.8109 (t0) REVERT: C 245 LYS cc_start: 0.8711 (mmmm) cc_final: 0.8382 (tptp) REVERT: C 305 MET cc_start: 0.8802 (mpp) cc_final: 0.8318 (mpt) REVERT: D 90 ASP cc_start: 0.8389 (t0) cc_final: 0.8070 (m-30) REVERT: D 162 LYS cc_start: 0.8824 (pttt) cc_final: 0.8094 (tppt) REVERT: D 242 ASP cc_start: 0.8899 (m-30) cc_final: 0.8073 (t0) REVERT: D 305 MET cc_start: 0.8792 (mpp) cc_final: 0.8306 (mpt) outliers start: 12 outliers final: 5 residues processed: 91 average time/residue: 1.5463 time to fit residues: 154.2812 Evaluate side-chains 80 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL 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 D residue 24 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 17 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 172 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.092117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.065344 restraints weight = 29761.539| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.05 r_work: 0.2868 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3227 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= 0.135 Angle : 0.561 8.399 20654 Z= 0.266 Chirality : 0.040 0.163 2250 Planarity : 0.004 0.034 2648 Dihedral : 6.721 71.045 2088 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.65 % Allowed : 12.79 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.20), residues: 1830 helix: 2.56 (0.20), residues: 686 sheet: 0.85 (0.28), residues: 348 loop : -1.07 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 24 HIS 0.006 0.001 HIS C 206 PHE 0.014 0.001 PHE D 10 TYR 0.013 0.001 TYR C 250 ARG 0.009 0.000 ARG D 82 Details of bonding type rmsd hydrogen bonds : bond 0.04528 ( 622) hydrogen bonds : angle 4.09331 ( 1788) covalent geometry : bond 0.00323 (15150) covalent geometry : angle 0.56097 (20654) Misc. bond : bond 0.00012 ( 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 83 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASP cc_start: 0.8116 (m-30) cc_final: 0.7757 (m-30) REVERT: A 414 GLN cc_start: 0.8142 (mt0) cc_final: 0.7084 (mm-40) REVERT: B 351 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8035 (mp0) REVERT: B 411 ASP cc_start: 0.8104 (m-30) cc_final: 0.7768 (m-30) REVERT: B 414 GLN cc_start: 0.8161 (mt0) cc_final: 0.7081 (mm-40) REVERT: C 90 ASP cc_start: 0.8187 (m-30) cc_final: 0.7844 (m-30) REVERT: C 162 LYS cc_start: 0.8847 (pttt) cc_final: 0.8090 (tppt) REVERT: C 242 ASP cc_start: 0.8909 (m-30) cc_final: 0.8073 (t0) REVERT: C 305 MET cc_start: 0.8790 (mpp) cc_final: 0.8284 (mpt) REVERT: D 90 ASP cc_start: 0.8382 (t0) cc_final: 0.8063 (m-30) REVERT: D 162 LYS cc_start: 0.8812 (pttt) cc_final: 0.8083 (tppt) REVERT: D 242 ASP cc_start: 0.8880 (m-30) cc_final: 0.8028 (t0) REVERT: D 305 MET cc_start: 0.8787 (mpp) cc_final: 0.8284 (mpt) outliers start: 10 outliers final: 7 residues processed: 82 average time/residue: 1.4927 time to fit residues: 134.9126 Evaluate side-chains 79 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 1.720 ------------------------------------------------------------------------------- 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 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 144 optimal weight: 6.9990 chunk 135 optimal weight: 0.4980 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- 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 = 0.3444 r_free = 0.3444 target = 0.089809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.062951 restraints weight = 30175.461| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.04 r_work: 0.2820 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 15152 Z= 0.232 Angle : 0.635 8.533 20654 Z= 0.306 Chirality : 0.043 0.185 2250 Planarity : 0.005 0.036 2648 Dihedral : 7.143 80.690 2088 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.20), residues: 1830 helix: 2.30 (0.20), residues: 684 sheet: 0.66 (0.27), residues: 358 loop : -1.16 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 24 HIS 0.008 0.001 HIS C 206 PHE 0.024 0.002 PHE D 10 TYR 0.017 0.002 TYR D 250 ARG 0.010 0.001 ARG D 82 Details of bonding type rmsd hydrogen bonds : bond 0.05849 ( 622) hydrogen bonds : angle 4.40286 ( 1788) covalent geometry : bond 0.00575 (15150) covalent geometry : angle 0.63527 (20654) Misc. bond : bond 0.00010 ( 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: 10 poor density : 72 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASP cc_start: 0.8210 (m-30) cc_final: 0.7987 (m-30) REVERT: A 414 GLN cc_start: 0.8230 (mt0) cc_final: 0.7127 (mm-40) REVERT: B 351 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8069 (mp0) REVERT: B 411 ASP cc_start: 0.8196 (m-30) cc_final: 0.7977 (m-30) REVERT: B 414 GLN cc_start: 0.8229 (mt0) cc_final: 0.7126 (mm-40) REVERT: C 90 ASP cc_start: 0.8226 (m-30) cc_final: 0.7894 (m-30) REVERT: C 136 HIS cc_start: 0.8238 (m90) cc_final: 0.7781 (t-90) REVERT: C 162 LYS cc_start: 0.8816 (pttt) cc_final: 0.8086 (tppt) REVERT: C 242 ASP cc_start: 0.8967 (m-30) cc_final: 0.8103 (t0) REVERT: C 305 MET cc_start: 0.8819 (mpp) cc_final: 0.8384 (mpt) REVERT: D 90 ASP cc_start: 0.8355 (t0) cc_final: 0.7989 (m-30) REVERT: D 136 HIS cc_start: 0.8118 (m-70) cc_final: 0.7733 (t-170) REVERT: D 162 LYS cc_start: 0.8798 (pttt) cc_final: 0.8083 (tppt) REVERT: D 242 ASP cc_start: 0.8958 (m-30) cc_final: 0.8112 (t0) outliers start: 10 outliers final: 5 residues processed: 81 average time/residue: 1.3799 time to fit residues: 123.3967 Evaluate side-chains 76 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 1.551 ------------------------------------------------------------------------------- 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 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 71 optimal weight: 0.4980 chunk 2 optimal weight: 9.9990 chunk 165 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 162 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3480 r_free = 0.3480 target = 0.091978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.065152 restraints weight = 29926.820| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.06 r_work: 0.2861 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3333 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= 0.122 Angle : 0.558 8.166 20654 Z= 0.265 Chirality : 0.040 0.163 2250 Planarity : 0.004 0.035 2648 Dihedral : 6.902 73.194 2088 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.32 % Allowed : 13.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.20), residues: 1830 helix: 2.45 (0.20), residues: 686 sheet: 0.81 (0.28), residues: 348 loop : -1.11 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 24 HIS 0.005 0.001 HIS D 206 PHE 0.013 0.001 PHE B 510 TYR 0.011 0.001 TYR C 250 ARG 0.009 0.000 ARG D 82 Details of bonding type rmsd hydrogen bonds : bond 0.04442 ( 622) hydrogen bonds : angle 4.17847 ( 1788) covalent geometry : bond 0.00285 (15150) covalent geometry : angle 0.55768 (20654) Misc. bond : bond 0.00010 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9097.12 seconds wall clock time: 156 minutes 13.79 seconds (9373.79 seconds total)