Starting phenix.real_space_refine on Fri Sep 11 05:27:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zd0_11172/09_2026/6zd0_11172.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zd0_11172/09_2026/6zd0_11172.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6zd0_11172/09_2026/6zd0_11172.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zd0_11172/09_2026/6zd0_11172.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zd0_11172/09_2026/6zd0_11172.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zd0_11172/09_2026/6zd0_11172.map" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.014 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: 3 Type Number sf(0) Gaussians C 4752 2.51 5 N 1611 2.21 5 O 1599 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7962 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 2271 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 397} Link IDs: {'PTRANS': 19, 'TRANS': 440} Chain breaks: 2 Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 1406 Unresolved non-hydrogen angles: 1811 Unresolved non-hydrogen dihedrals: 1174 Unresolved non-hydrogen chiralities: 131 Planarities with less than four sites: {'ASN:plan1': 36, 'GLU:plan': 21, 'ASP:plan': 20, 'TYR:plan': 20, 'TRP:plan': 7, 'GLN:plan1': 17, 'HIS:plan': 9, 'ARG:plan': 18, 'PHE:plan': 15} Unresolved non-hydrogen planarities: 748 Chain: "B" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 383 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 2, 'TRANS': 74} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 251 Unresolved non-hydrogen angles: 322 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 10, 'ASP:plan': 5, 'PHE:plan': 4, 'TRP:plan': 1, 'GLU:plan': 5, 'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 153 Chain: "C" Number of atoms: 2271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 2271 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 397} Link IDs: {'PTRANS': 19, 'TRANS': 440} Chain breaks: 2 Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 1406 Unresolved non-hydrogen angles: 1811 Unresolved non-hydrogen dihedrals: 1174 Unresolved non-hydrogen chiralities: 131 Planarities with less than four sites: {'ASN:plan1': 36, 'GLU:plan': 21, 'ASP:plan': 20, 'TYR:plan': 20, 'TRP:plan': 7, 'GLN:plan1': 17, 'HIS:plan': 9, 'ARG:plan': 18, 'PHE:plan': 15} Unresolved non-hydrogen planarities: 748 Chain: "D" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 383 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 2, 'TRANS': 74} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 251 Unresolved non-hydrogen angles: 322 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 10, 'ASP:plan': 5, 'PHE:plan': 4, 'TRP:plan': 1, 'GLU:plan': 5, 'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 153 Chain: "E" Number of atoms: 2271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 2271 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 397} Link IDs: {'PTRANS': 19, 'TRANS': 440} Chain breaks: 2 Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 1406 Unresolved non-hydrogen angles: 1811 Unresolved non-hydrogen dihedrals: 1174 Unresolved non-hydrogen chiralities: 131 Planarities with less than four sites: {'ASN:plan1': 36, 'GLU:plan': 21, 'ASP:plan': 20, 'TYR:plan': 20, 'TRP:plan': 7, 'GLN:plan1': 17, 'HIS:plan': 9, 'ARG:plan': 18, 'PHE:plan': 15} Unresolved non-hydrogen planarities: 748 Chain: "F" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 383 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 2, 'TRANS': 74} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 251 Unresolved non-hydrogen angles: 322 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 10, 'ASP:plan': 5, 'PHE:plan': 4, 'TRP:plan': 1, 'GLU:plan': 5, 'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 153 Time building chain proxies: 2.21, per 1000 atoms: 0.28 Number of scatterers: 7962 At special positions: 0 Unit cell: (126, 102.2, 110.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1599 8.00 N 1611 7.00 C 4752 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 441.8 milliseconds 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3060 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 31 sheets defined 26.8% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 56 through 69 Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 121 through 125 Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 177 through 196 removed outlier: 3.819A pdb=" N TRP A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLN A 194 " --> pdb=" O GLU A 190 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR A 196 " --> pdb=" O TRP A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 200 removed outlier: 4.026A pdb=" N HIS A 200 " --> pdb=" O SER A 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 197 through 200' Processing helix chain 'A' and resid 215 through 224 Processing helix chain 'A' and resid 226 through 231 removed outlier: 3.554A pdb=" N VAL A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 235 removed outlier: 4.026A pdb=" N ASN A 235 " --> pdb=" O ALA A 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 232 through 235' Processing helix chain 'A' and resid 237 through 243 removed outlier: 3.867A pdb=" N VAL A 241 " --> pdb=" O ASP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 271 Processing helix chain 'A' and resid 277 through 284 Processing helix chain 'A' and resid 315 through 326 Processing helix chain 'A' and resid 336 through 342 Processing helix chain 'A' and resid 358 through 363 removed outlier: 3.658A pdb=" N GLY A 363 " --> pdb=" O LYS A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 372 removed outlier: 3.637A pdb=" N LEU A 368 " --> pdb=" O ASN A 364 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS A 369 " --> pdb=" O ILE A 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 24 Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'C' and resid 57 through 71 Processing helix chain 'C' and resid 74 through 79 Processing helix chain 'C' and resid 121 through 128 removed outlier: 5.559A pdb=" N ASP C 126 " --> pdb=" O ALA C 123 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG C 127 " --> pdb=" O ASN C 124 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 128 " --> pdb=" O ASP C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 142 Processing helix chain 'C' and resid 177 through 196 Processing helix chain 'C' and resid 197 through 200 removed outlier: 4.079A pdb=" N HIS C 200 " --> pdb=" O SER C 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 197 through 200' Processing helix chain 'C' and resid 215 through 224 Processing helix chain 'C' and resid 226 through 231 Processing helix chain 'C' and resid 232 through 235 removed outlier: 3.970A pdb=" N ASN C 235 " --> pdb=" O ALA C 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 232 through 235' Processing helix chain 'C' and resid 237 through 243 Processing helix chain 'C' and resid 267 through 272 Processing helix chain 'C' and resid 277 through 284 Processing helix chain 'C' and resid 315 through 326 removed outlier: 4.271A pdb=" N ALA C 319 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS C 326 " --> pdb=" O ASP C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 342 removed outlier: 3.569A pdb=" N ASN C 342 " --> pdb=" O ASN C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 363 removed outlier: 4.415A pdb=" N GLY C 363 " --> pdb=" O LYS C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 374 Processing helix chain 'D' and resid 46 through 54 Processing helix chain 'D' and resid 71 through 75 removed outlier: 3.556A pdb=" N GLN D 74 " --> pdb=" O PHE D 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 71 Processing helix chain 'E' and resid 74 through 79 Processing helix chain 'E' and resid 121 through 128 removed outlier: 5.016A pdb=" N ASP E 126 " --> pdb=" O ALA E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 142 Processing helix chain 'E' and resid 177 through 196 Processing helix chain 'E' and resid 197 through 200 removed outlier: 3.743A pdb=" N HIS E 200 " --> pdb=" O SER E 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 197 through 200' Processing helix chain 'E' and resid 216 through 222 Processing helix chain 'E' and resid 226 through 231 removed outlier: 3.572A pdb=" N VAL E 230 " --> pdb=" O ASP E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 243 removed outlier: 3.605A pdb=" N VAL E 241 " --> pdb=" O ASP E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 284 Processing helix chain 'E' and resid 316 through 324 removed outlier: 4.170A pdb=" N ASP E 322 " --> pdb=" O GLN E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 342 removed outlier: 4.024A pdb=" N ASN E 342 " --> pdb=" O ASN E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 363 removed outlier: 4.013A pdb=" N GLY E 363 " --> pdb=" O LYS E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 374 Processing helix chain 'F' and resid 41 through 45 Processing helix chain 'F' and resid 46 through 55 Processing helix chain 'F' and resid 71 through 75 Processing sheet with id=A, first strand: chain 'A' and resid 91 through 97 Processing sheet with id=B, first strand: chain 'A' and resid 106 through 115 removed outlier: 6.356A pdb=" N HIS A 81 " --> pdb=" O ASN A 405 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ASP A 407 " --> pdb=" O HIS A 81 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N GLY A 83 " --> pdb=" O ASP A 407 " (cutoff:3.500A) removed outlier: 11.913A pdb=" N ILE A 409 " --> pdb=" O GLY A 83 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'A' and resid 133 through 135 Processing sheet with id=D, first strand: chain 'A' and resid 170 through 173 removed outlier: 4.003A pdb=" N THR A 259 " --> pdb=" O ASN A 160 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TYR A 300 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR A 259 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL A 298 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 388 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N GLY A 301 " --> pdb=" O PRO A 386 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'A' and resid 208 through 212 Processing sheet with id=F, first strand: chain 'A' and resid 467 through 470 Processing sheet with id=G, first strand: chain 'A' and resid 431 through 436 Processing sheet with id=H, first strand: chain 'A' and resid 437 through 442 Processing sheet with id=I, first strand: chain 'A' and resid 479 through 483 removed outlier: 4.163A pdb=" N ILE A 479 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 503 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL A 481 " --> pdb=" O ASN A 501 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ASN A 501 " --> pdb=" O VAL A 481 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL A 483 " --> pdb=" O SER A 499 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N SER A 499 " --> pdb=" O VAL A 483 " (cutoff:3.500A) No H-bonds generated for sheet with id=I Processing sheet with id=J, first strand: chain 'B' and resid 2 through 4 Processing sheet with id=K, first strand: chain 'B' and resid 34 through 40 Processing sheet with id=L, first strand: chain 'C' and resid 80 through 82 removed outlier: 5.927A pdb=" N GLN C 403 " --> pdb=" O HIS C 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=L Processing sheet with id=M, first strand: chain 'C' and resid 90 through 97 Processing sheet with id=N, first strand: chain 'C' and resid 108 through 111 Processing sheet with id=O, first strand: chain 'C' and resid 133 through 135 removed outlier: 6.601A pdb=" N THR C 390 " --> pdb=" O SER C 296 " (cutoff:3.500A) Processing sheet with id=P, first strand: chain 'C' and resid 170 through 173 removed outlier: 7.170A pdb=" N TYR C 300 " --> pdb=" O TYR C 257 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N THR C 259 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL C 298 " --> pdb=" O THR C 259 " (cutoff:3.500A) Processing sheet with id=Q, first strand: chain 'C' and resid 208 through 212 Processing sheet with id=R, first strand: chain 'C' and resid 468 through 470 removed outlier: 3.523A pdb=" N THR C 516 " --> pdb=" O HIS C 519 " (cutoff:3.500A) Processing sheet with id=S, first strand: chain 'C' and resid 431 through 436 removed outlier: 3.864A pdb=" N TYR C 498 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLY C 485 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LEU C 496 " --> pdb=" O GLY C 485 " (cutoff:3.500A) Processing sheet with id=T, first strand: chain 'C' and resid 437 through 443 Processing sheet with id=U, first strand: chain 'D' and resid 2 through 4 Processing sheet with id=V, first strand: chain 'D' and resid 34 through 40 Processing sheet with id=W, first strand: chain 'E' and resid 80 through 82 removed outlier: 5.893A pdb=" N GLN E 403 " --> pdb=" O HIS E 81 " (cutoff:3.500A) Processing sheet with id=X, first strand: chain 'E' and resid 170 through 173 removed outlier: 3.777A pdb=" N THR E 259 " --> pdb=" O ASN E 160 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N TYR E 300 " --> pdb=" O TYR E 257 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR E 346 " --> pdb=" O LYS E 307 " (cutoff:3.500A) Processing sheet with id=Y, first strand: chain 'E' and resid 209 through 212 Processing sheet with id=Z, first strand: chain 'E' and resid 466 through 472 removed outlier: 3.696A pdb=" N THR E 513 " --> pdb=" O ASN E 424 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS E 525 " --> pdb=" O ASN E 510 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'E' and resid 449 through 454 Processing sheet with id=AB, first strand: chain 'E' and resid 293 through 299 removed outlier: 3.714A pdb=" N SER E 296 " --> pdb=" O THR E 390 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N THR E 390 " --> pdb=" O SER E 296 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL E 298 " --> pdb=" O SER E 388 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N SER E 388 " --> pdb=" O VAL E 298 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain 'E' and resid 479 through 483 removed outlier: 4.017A pdb=" N ILE E 479 " --> pdb=" O LEU E 503 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL E 481 " --> pdb=" O ASN E 501 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ASN E 501 " --> pdb=" O VAL E 481 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL E 483 " --> pdb=" O SER E 499 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N SER E 499 " --> pdb=" O VAL E 483 " (cutoff:3.500A) Processing sheet with id=AD, first strand: chain 'F' and resid 2 through 4 Processing sheet with id=AE, first strand: chain 'F' and resid 34 through 40 483 hydrogen bonds defined for protein. 1272 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.49 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 1599 1.29 - 1.35: 1596 1.35 - 1.42: 3 1.42 - 1.49: 1611 1.49 - 1.55: 3141 Bond restraints: 7950 Sorted by residual: bond pdb=" C ASN E 160 " pdb=" N LEU E 161 " ideal model delta sigma weight residual 1.329 1.387 -0.058 1.21e-02 6.83e+03 2.28e+01 bond pdb=" C VAL A 385 " pdb=" N PRO A 386 " ideal model delta sigma weight residual 1.331 1.356 -0.025 1.27e-02 6.20e+03 3.96e+00 bond pdb=" C TYR C 408 " pdb=" N ILE C 409 " ideal model delta sigma weight residual 1.335 1.313 0.021 1.14e-02 7.69e+03 3.54e+00 bond pdb=" C LEU A 76 " pdb=" N ASN A 77 " ideal model delta sigma weight residual 1.332 1.313 0.019 1.29e-02 6.01e+03 2.22e+00 bond pdb=" C GLU E 492 " pdb=" O GLU E 492 " ideal model delta sigma weight residual 1.238 1.220 0.017 1.28e-02 6.10e+03 1.87e+00 ... (remaining 7945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 10078 1.50 - 3.00: 872 3.00 - 4.50: 93 4.50 - 6.00: 20 6.00 - 7.50: 4 Bond angle restraints: 11067 Sorted by residual: angle pdb=" N GLY C 446 " pdb=" CA GLY C 446 " pdb=" C GLY C 446 " ideal model delta sigma weight residual 115.64 108.64 7.00 1.46e+00 4.69e-01 2.30e+01 angle pdb=" N TYR E 257 " pdb=" CA TYR E 257 " pdb=" C TYR E 257 " ideal model delta sigma weight residual 113.88 108.08 5.80 1.23e+00 6.61e-01 2.22e+01 angle pdb=" N ARG B 55 " pdb=" CA ARG B 55 " pdb=" CB ARG B 55 " ideal model delta sigma weight residual 114.17 109.47 4.70 1.14e+00 7.69e-01 1.70e+01 angle pdb=" N GLY A 301 " pdb=" CA GLY A 301 " pdb=" C GLY A 301 " ideal model delta sigma weight residual 110.38 115.66 -5.28 1.42e+00 4.96e-01 1.38e+01 angle pdb=" C PHE C 378 " pdb=" CA PHE C 378 " pdb=" CB PHE C 378 " ideal model delta sigma weight residual 109.90 115.45 -5.55 1.56e+00 4.11e-01 1.27e+01 ... (remaining 11062 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.31: 4051 6.31 - 12.62: 450 12.62 - 18.93: 130 18.93 - 25.24: 23 25.24 - 31.55: 5 Dihedral angle restraints: 4659 sinusoidal: 0 harmonic: 4659 Sorted by residual: dihedral pdb=" CA SER A 314 " pdb=" C SER A 314 " pdb=" N THR A 315 " pdb=" CA THR A 315 " ideal model delta harmonic sigma weight residual -180.00 -148.45 -31.55 0 5.00e+00 4.00e-02 3.98e+01 dihedral pdb=" CA ASP C 443 " pdb=" C ASP C 443 " pdb=" N ALA C 444 " pdb=" CA ALA C 444 " ideal model delta harmonic sigma weight residual 180.00 148.91 31.09 0 5.00e+00 4.00e-02 3.87e+01 dihedral pdb=" CA PHE F 23 " pdb=" C PHE F 23 " pdb=" N ASP F 24 " pdb=" CA ASP F 24 " ideal model delta harmonic sigma weight residual 180.00 152.47 27.53 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 4656 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 868 0.033 - 0.067: 435 0.067 - 0.100: 163 0.100 - 0.133: 59 0.133 - 0.167: 5 Chirality restraints: 1530 Sorted by residual: chirality pdb=" CA VAL E 248 " pdb=" N VAL E 248 " pdb=" C VAL E 248 " pdb=" CB VAL E 248 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CA VAL C 348 " pdb=" N VAL C 348 " pdb=" C VAL C 348 " pdb=" CB VAL C 348 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CA ASN A 166 " pdb=" N ASN A 166 " pdb=" C ASN A 166 " pdb=" CB ASN A 166 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.88e-01 ... (remaining 1527 not shown) Planarity restraints: 1599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 443 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.64e+00 pdb=" C ASP C 443 " -0.041 2.00e-02 2.50e+03 pdb=" O ASP C 443 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA C 444 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 98 " 0.006 2.00e-02 2.50e+03 1.24e-02 1.55e+00 pdb=" C PRO A 98 " -0.022 2.00e-02 2.50e+03 pdb=" O PRO A 98 " 0.008 2.00e-02 2.50e+03 pdb=" N GLY A 99 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 214 " 0.006 2.00e-02 2.50e+03 1.22e-02 1.49e+00 pdb=" C GLN A 214 " -0.021 2.00e-02 2.50e+03 pdb=" O GLN A 214 " 0.008 2.00e-02 2.50e+03 pdb=" N SER A 215 " 0.007 2.00e-02 2.50e+03 ... (remaining 1596 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1064 2.75 - 3.28: 7930 3.28 - 3.82: 11606 3.82 - 4.36: 11125 4.36 - 4.90: 19995 Nonbonded interactions: 51720 Sorted by model distance: nonbonded pdb=" O SER A 314 " pdb=" N LYS A 316 " model vdw 2.207 3.120 nonbonded pdb=" O GLU A 84 " pdb=" N ASP A 407 " model vdw 2.217 3.120 nonbonded pdb=" N HIS E 81 " pdb=" O GLN E 403 " model vdw 2.237 3.120 nonbonded pdb=" N GLY E 153 " pdb=" O LEU E 271 " model vdw 2.252 3.120 nonbonded pdb=" O LEU E 118 " pdb=" N TYR E 389 " model vdw 2.258 3.120 ... (remaining 51715 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.080 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5846 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 : 0.004 0.058 7950 Z= 0.261 Angle : 0.905 7.500 11067 Z= 0.591 Chirality : 0.046 0.167 1530 Planarity : 0.003 0.024 1599 Dihedral : 7.553 31.545 1599 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.08 % Favored : 89.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -4.73 (0.17), residues: 1587 helix: -3.45 (0.18), residues: 312 sheet: -2.56 (0.22), residues: 447 loop : -3.39 (0.17), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 67 PHE 0.000 0.000 PHE A 95 TRP 0.000 0.000 TRP A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.26 ( 7950) covalent geometry : angle 0.90517 / 0.59 (11067) hydrogen bonds : bond 0.19691 / 14.95 ( 483) hydrogen bonds : angle 10.36223 / 7.76 ( 1272) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.049 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0110 time to fit residues: 0.1223 Evaluate side-chains 3 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.064 Evaluate side-chains 0 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0132 Evaluate side-chains 0 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 0.0670 chunk 107 optimal weight: 50.0000 chunk 10 optimal weight: 50.0000 chunk 66 optimal weight: 60.0000 chunk 130 optimal weight: 50.0000 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 50.0000 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 50.0000 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 50.0000 overall best weight: 25.8132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.077372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.064743 restraints weight = 24433.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.064949 restraints weight = 22666.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.065245 restraints weight = 21557.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.065388 restraints weight = 20634.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.065388 restraints weight = 19799.132| |-----------------------------------------------------------------------------| r_work (final): 0.3633 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.054386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.039123 restraints weight = 4940.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.038923 restraints weight = 5226.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.038663 restraints weight = 5534.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.038662 restraints weight = 5788.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.038624 restraints weight = 5788.688| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5826 moved from start: 1.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 7950 Z= 0.419 Angle : 0.994 7.880 11067 Z= 0.633 Chirality : 0.046 0.144 1530 Planarity : 0.006 0.032 1599 Dihedral : 8.739 44.551 1599 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 1.32 % Allowed : 9.64 % Favored : 89.04 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.59 % 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: -3.92 (0.19), residues: 1587 helix: -2.31 (0.22), residues: 357 sheet: -2.28 (0.23), residues: 444 loop : -2.93 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 67 PHE 0.000 0.000 PHE A 95 TRP 0.000 0.000 TRP A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.42 ( 7950) covalent geometry : angle 0.99448 / 0.63 (11067) hydrogen bonds : bond 0.07574 / 5.71 ( 483) hydrogen bonds : angle 10.23000 / 7.58 ( 1272) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.082 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0104 time to fit residues: 0.1727 Evaluate side-chains 3 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.050 Evaluate side-chains 0 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0149 Evaluate side-chains 0 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 58 optimal weight: 50.0000 chunk 102 optimal weight: 30.0000 chunk 51 optimal weight: 50.0000 chunk 155 optimal weight: 50.0000 chunk 112 optimal weight: 20.0000 chunk 89 optimal weight: 50.0000 chunk 40 optimal weight: 0.0370 chunk 68 optimal weight: 50.0000 chunk 140 optimal weight: 50.0000 chunk 55 optimal weight: 20.0000 chunk 119 optimal weight: 50.0000 overall best weight: 24.0074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.073733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.062274 restraints weight = 25228.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.062471 restraints weight = 23428.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.062815 restraints weight = 22236.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.063014 restraints weight = 21100.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.063124 restraints weight = 20265.611| |-----------------------------------------------------------------------------| r_work (final): 0.3520 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.046647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.034534 restraints weight = 5528.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.034551 restraints weight = 5446.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.034596 restraints weight = 5430.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.034596 restraints weight = 5359.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.034596 restraints weight = 5359.601| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5971 moved from start: 1.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 7950 Z= 0.361 Angle : 0.956 9.733 11067 Z= 0.604 Chirality : 0.046 0.154 1530 Planarity : 0.005 0.020 1599 Dihedral : 8.542 36.195 1599 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.76 % Allowed : 13.80 % Favored : 85.44 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.39 % 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: -4.33 (0.18), residues: 1587 helix: -2.22 (0.23), residues: 354 sheet: -2.96 (0.25), residues: 360 loop : -3.19 (0.18), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 67 PHE 0.000 0.000 PHE A 95 TRP 0.000 0.000 TRP A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.36 ( 7950) covalent geometry : angle 0.95646 / 0.60 (11067) hydrogen bonds : bond 0.07310 / 5.51 ( 483) hydrogen bonds : angle 11.04043 / 8.15 ( 1272) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.069 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0074 time to fit residues: 0.1302 Evaluate side-chains 3 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.073 Evaluate side-chains 0 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.015 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0230 Evaluate side-chains 0 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 128 optimal weight: 9.9990 chunk 108 optimal weight: 40.0000 chunk 141 optimal weight: 40.0000 chunk 90 optimal weight: 40.0000 chunk 45 optimal weight: 50.0000 chunk 37 optimal weight: 30.0000 chunk 31 optimal weight: 40.0000 chunk 73 optimal weight: 40.0000 chunk 75 optimal weight: 7.9990 chunk 44 optimal weight: 50.0000 chunk 124 optimal weight: 50.0000 overall best weight: 25.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.067697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.053335 restraints weight = 18220.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.053275 restraints weight = 18788.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.053275 restraints weight = 18983.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.053275 restraints weight = 18983.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.053275 restraints weight = 18983.619| |-----------------------------------------------------------------------------| r_work (final): 0.3565 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.046100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.033919 restraints weight = 5454.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.033916 restraints weight = 5569.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.033916 restraints weight = 5574.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.033916 restraints weight = 5574.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.033916 restraints weight = 5574.225| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5997 moved from start: 1.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 7950 Z= 0.370 Angle : 0.950 7.635 11067 Z= 0.603 Chirality : 0.046 0.175 1530 Planarity : 0.005 0.020 1599 Dihedral : 8.800 34.414 1599 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.76 % Allowed : 18.90 % Favored : 80.34 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -5.04 (0.17), residues: 1587 helix: -2.48 (0.22), residues: 342 sheet: -3.49 (0.25), residues: 312 loop : -3.80 (0.17), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 67 PHE 0.000 0.000 PHE A 95 TRP 0.000 0.000 TRP A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.37 ( 7950) covalent geometry : angle 0.94990 / 0.60 (11067) hydrogen bonds : bond 0.06787 / 5.12 ( 483) hydrogen bonds : angle 12.09412 / 8.97 ( 1272) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.075 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0084 time to fit residues: 0.1431 Evaluate side-chains 3 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.081 Evaluate side-chains 0 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.014 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0219 Evaluate side-chains 0 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 154 optimal weight: 40.0000 chunk 139 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 76 optimal weight: 0.0070 chunk 38 optimal weight: 8.9990 chunk 152 optimal weight: 30.0000 chunk 3 optimal weight: 40.0000 chunk 102 optimal weight: 40.0000 chunk 65 optimal weight: 50.0000 chunk 63 optimal weight: 40.0000 chunk 4 optimal weight: 2.9990 overall best weight: 10.4010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.074037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.062622 restraints weight = 23847.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.063013 restraints weight = 21789.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.063158 restraints weight = 20350.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.063463 restraints weight = 19368.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.063554 restraints weight = 18560.634| |-----------------------------------------------------------------------------| r_work (final): 0.3612 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.048292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.037098 restraints weight = 5675.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.037098 restraints weight = 5713.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.037098 restraints weight = 5713.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.037098 restraints weight = 5713.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.037097 restraints weight = 5713.739| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5907 moved from start: 1.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 7950 Z= 0.204 Angle : 0.731 7.598 11067 Z= 0.460 Chirality : 0.043 0.141 1530 Planarity : 0.003 0.016 1599 Dihedral : 7.012 31.204 1599 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.19 % Allowed : 13.23 % Favored : 86.58 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -4.54 (0.19), residues: 1587 helix: -1.68 (0.23), residues: 378 sheet: -3.22 (0.24), residues: 363 loop : -3.64 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 67 PHE 0.000 0.000 PHE A 95 TRP 0.000 0.000 TRP A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.20 ( 7950) covalent geometry : angle 0.73141 / 0.46 (11067) hydrogen bonds : bond 0.04396 / 3.35 ( 483) hydrogen bonds : angle 10.24165 / 7.62 ( 1272) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.079 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0109 time to fit residues: 0.1816 Evaluate side-chains 3 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.079 Evaluate side-chains 0 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.015 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0219 Evaluate side-chains 0 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 40 optimal weight: 0.1980 chunk 4 optimal weight: 30.0000 chunk 101 optimal weight: 50.0000 chunk 151 optimal weight: 30.0000 chunk 62 optimal weight: 0.6980 chunk 27 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 chunk 51 optimal weight: 50.0000 chunk 77 optimal weight: 40.0000 chunk 70 optimal weight: 50.0000 chunk 119 optimal weight: 50.0000 overall best weight: 8.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.075044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.063486 restraints weight = 24274.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.063694 restraints weight = 22403.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.064064 restraints weight = 21173.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.064272 restraints weight = 20065.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.064272 restraints weight = 19206.391| |-----------------------------------------------------------------------------| r_work (final): 0.3618 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.044357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.027853 restraints weight = 6713.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.027681 restraints weight = 7691.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.027253 restraints weight = 8251.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.026969 restraints weight = 9246.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.026969 restraints weight = 10156.420| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5600 moved from start: 1.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 7950 Z= 0.177 Angle : 0.667 7.296 11067 Z= 0.420 Chirality : 0.042 0.137 1530 Planarity : 0.003 0.016 1599 Dihedral : 6.080 30.240 1599 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 13.42 % Favored : 86.39 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -3.93 (0.20), residues: 1587 helix: -1.03 (0.25), residues: 408 sheet: -3.10 (0.24), residues: 366 loop : -3.26 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 67 PHE 0.000 0.000 PHE A 95 TRP 0.000 0.000 TRP A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.18 ( 7950) covalent geometry : angle 0.66729 / 0.42 (11067) hydrogen bonds : bond 0.03845 / 2.92 ( 483) hydrogen bonds : angle 9.17799 / 6.82 ( 1272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.080 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0073 time to fit residues: 0.1284 Evaluate side-chains 3 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.078 Evaluate side-chains 0 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.014 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0224 Evaluate side-chains 0 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 127 optimal weight: 50.0000 chunk 99 optimal weight: 10.0000 chunk 65 optimal weight: 40.0000 chunk 69 optimal weight: 50.0000 chunk 97 optimal weight: 50.0000 chunk 50 optimal weight: 50.0000 chunk 144 optimal weight: 0.0050 chunk 2 optimal weight: 30.0000 chunk 126 optimal weight: 40.0000 chunk 34 optimal weight: 40.0000 chunk 100 optimal weight: 40.0000 overall best weight: 24.0010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.070718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.059669 restraints weight = 24648.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.059833 restraints weight = 22942.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.060121 restraints weight = 21846.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.060215 restraints weight = 20859.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.060422 restraints weight = 20204.664| |-----------------------------------------------------------------------------| r_work (final): 0.3486 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.049606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.038408 restraints weight = 5013.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.038408 restraints weight = 5284.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.038408 restraints weight = 5284.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.038408 restraints weight = 5284.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.038408 restraints weight = 5284.361| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6034 moved from start: 1.5374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 7950 Z= 0.338 Angle : 0.868 6.533 11067 Z= 0.555 Chirality : 0.044 0.166 1530 Planarity : 0.004 0.018 1599 Dihedral : 8.076 31.339 1599 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.74 % Favored : 78.26 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -4.59 (0.19), residues: 1587 helix: -1.62 (0.24), residues: 378 sheet: -3.75 (0.23), residues: 321 loop : -3.53 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 67 PHE 0.000 0.000 PHE A 95 TRP 0.000 0.000 TRP A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.34 ( 7950) covalent geometry : angle 0.86798 / 0.55 (11067) hydrogen bonds : bond 0.06197 / 4.64 ( 483) hydrogen bonds : angle 11.75654 / 8.71 ( 1272) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.082 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0073 time to fit residues: 0.1185 Evaluate side-chains 3 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.086 Evaluate side-chains 0 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0134 Evaluate side-chains 0 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 65 optimal weight: 40.0000 chunk 97 optimal weight: 40.0000 chunk 49 optimal weight: 50.0000 chunk 133 optimal weight: 40.0000 chunk 23 optimal weight: 40.0000 chunk 66 optimal weight: 70.0000 chunk 119 optimal weight: 50.0000 chunk 8 optimal weight: 40.0000 chunk 134 optimal weight: 40.0000 chunk 82 optimal weight: 50.0000 chunk 44 optimal weight: 30.0000 overall best weight: 38.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.068308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.057879 restraints weight = 25778.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.058040 restraints weight = 23737.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.058394 restraints weight = 22541.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.058525 restraints weight = 21269.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.058734 restraints weight = 20484.883| |-----------------------------------------------------------------------------| r_work (final): 0.3453 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.038057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.025778 restraints weight = 7435.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.025639 restraints weight = 7767.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.025639 restraints weight = 8082.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.025639 restraints weight = 8082.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.025639 restraints weight = 8082.779| |-----------------------------------------------------------------------------| r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5827 moved from start: 1.7671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 7950 Z= 0.491 Angle : 1.148 7.456 11067 Z= 0.732 Chirality : 0.048 0.170 1530 Planarity : 0.006 0.032 1599 Dihedral : 10.489 38.462 1599 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 30.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 27.98 % Favored : 71.83 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.17 % 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: -5.51 (0.17), residues: 1587 helix: -2.73 (0.21), residues: 372 sheet: -4.23 (0.30), residues: 177 loop : -4.19 (0.16), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 67 PHE 0.000 0.000 PHE A 95 TRP 0.000 0.000 TRP A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00668 / 0.49 ( 7950) covalent geometry : angle 1.14773 / 0.73 (11067) hydrogen bonds : bond 0.08526 / 6.41 ( 483) hydrogen bonds : angle 14.27322 / 10.60 ( 1272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.082 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0110 time to fit residues: 0.1811 Evaluate side-chains 3 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.081 Evaluate side-chains 0 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0136 Evaluate side-chains 0 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 42 optimal weight: 6.9990 chunk 88 optimal weight: 0.2980 chunk 147 optimal weight: 2.9990 chunk 34 optimal weight: 50.0000 chunk 4 optimal weight: 6.9990 chunk 68 optimal weight: 50.0000 chunk 156 optimal weight: 50.0000 chunk 85 optimal weight: 50.0000 chunk 82 optimal weight: 0.3980 chunk 20 optimal weight: 50.0000 chunk 80 optimal weight: 30.0000 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.074334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.062971 restraints weight = 24914.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.063418 restraints weight = 22690.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.063641 restraints weight = 21086.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.064003 restraints weight = 19658.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.064123 restraints weight = 18750.913| |-----------------------------------------------------------------------------| r_work (final): 0.3599 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.053453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.034901 restraints weight = 4853.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.034900 restraints weight = 5800.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.034900 restraints weight = 5801.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.034900 restraints weight = 5801.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.034900 restraints weight = 5801.797| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5840 moved from start: 1.6225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 7950 Z= 0.169 Angle : 0.697 9.258 11067 Z= 0.440 Chirality : 0.043 0.146 1530 Planarity : 0.003 0.016 1599 Dihedral : 6.811 28.115 1599 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.79 (0.18), residues: 1587 helix: -1.50 (0.25), residues: 402 sheet: -3.95 (0.24), residues: 321 loop : -3.83 (0.17), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 67 PHE 0.000 0.000 PHE A 95 TRP 0.000 0.000 TRP A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.17 ( 7950) covalent geometry : angle 0.69712 / 0.44 (11067) hydrogen bonds : bond 0.03863 / 2.96 ( 483) hydrogen bonds : angle 10.19045 / 7.66 ( 1272) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.087 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0115 time to fit residues: 0.1936 Evaluate side-chains 3 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.095 Evaluate side-chains 0 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.028 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0500 Evaluate side-chains 0 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 62 optimal weight: 9.9990 chunk 15 optimal weight: 0.6980 chunk 98 optimal weight: 20.0000 chunk 73 optimal weight: 50.0000 chunk 95 optimal weight: 30.0000 chunk 118 optimal weight: 40.0000 chunk 29 optimal weight: 40.0000 chunk 135 optimal weight: 30.0000 chunk 77 optimal weight: 50.0000 chunk 142 optimal weight: 40.0000 chunk 75 optimal weight: 6.9990 overall best weight: 13.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.071926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.060966 restraints weight = 24717.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.061172 restraints weight = 22893.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.061172 restraints weight = 21673.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.061172 restraints weight = 21673.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.061172 restraints weight = 21673.718| |-----------------------------------------------------------------------------| r_work (final): 0.3524 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.046401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.034348 restraints weight = 5566.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.034348 restraints weight = 6071.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.034348 restraints weight = 6071.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.034348 restraints weight = 6071.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.034348 restraints weight = 6071.677| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6009 moved from start: 1.6499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7950 Z= 0.229 Angle : 0.724 7.255 11067 Z= 0.461 Chirality : 0.043 0.152 1530 Planarity : 0.004 0.015 1599 Dihedral : 7.023 28.709 1599 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.77 % Favored : 82.23 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.40 (0.19), residues: 1587 helix: -1.14 (0.26), residues: 378 sheet: -3.74 (0.28), residues: 267 loop : -3.61 (0.18), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 67 PHE 0.000 0.000 PHE A 95 TRP 0.000 0.000 TRP A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.23 ( 7950) covalent geometry : angle 0.72355 / 0.46 (11067) hydrogen bonds : bond 0.04717 / 3.54 ( 483) hydrogen bonds : angle 10.87643 / 8.13 ( 1272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.085 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0112 time to fit residues: 0.1897 Evaluate side-chains 3 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.084 Evaluate side-chains 0 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.015 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0231 Evaluate side-chains 0 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 25 optimal weight: 40.0000 chunk 63 optimal weight: 40.0000 chunk 115 optimal weight: 40.0000 chunk 99 optimal weight: 0.9990 chunk 52 optimal weight: 30.0000 chunk 157 optimal weight: 40.0000 chunk 106 optimal weight: 50.0000 chunk 14 optimal weight: 0.0570 chunk 45 optimal weight: 0.5980 chunk 39 optimal weight: 50.0000 chunk 88 optimal weight: 50.0000 overall best weight: 14.3308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.072363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.060405 restraints weight = 24516.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.060631 restraints weight = 22257.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.060929 restraints weight = 20946.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.061344 restraints weight = 19527.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.061506 restraints weight = 18635.104| |-----------------------------------------------------------------------------| r_work (final): 0.3545 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.045998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.035082 restraints weight = 5533.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.034946 restraints weight = 5696.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.034937 restraints weight = 6002.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.034936 restraints weight = 6005.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.034936 restraints weight = 6005.763| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6010 moved from start: 1.6729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 7950 Z= 0.236 Angle : 0.726 7.039 11067 Z= 0.464 Chirality : 0.043 0.153 1530 Planarity : 0.004 0.017 1599 Dihedral : 7.001 27.964 1599 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.58 % Favored : 82.42 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.35 (0.20), residues: 1587 helix: -1.09 (0.27), residues: 378 sheet: -3.64 (0.29), residues: 249 loop : -3.63 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 67 PHE 0.000 0.000 PHE A 95 TRP 0.000 0.000 TRP A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.24 ( 7950) covalent geometry : angle 0.72618 / 0.46 (11067) hydrogen bonds : bond 0.04713 / 3.54 ( 483) hydrogen bonds : angle 11.05290 / 8.27 ( 1272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 794.84 seconds wall clock time: 14 minutes 16.20 seconds (856.20 seconds total)