Starting phenix.real_space_refine on Wed Sep 17 10:08:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zd0_11172/09_2025/6zd0_11172.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zd0_11172/09_2025/6zd0_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6zd0_11172/09_2025/6zd0_11172.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zd0_11172/09_2025/6zd0_11172.map" model { file = "/net/cci-nas-00/data/ceres_data/6zd0_11172/09_2025/6zd0_11172.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zd0_11172/09_2025/6zd0_11172.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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-2.0-5805/lib/python3.9/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: 2.38, per 1000 atoms: 0.30 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: 0.81 Conformation dependent library (CDL) restraints added in 493.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.44 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: 1.16 Time building geometry restraints manager: 1.03 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: 0.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.500 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5769 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 aren 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 covalent geometry : bond 0.00355 ( 7950) covalent geometry : angle 0.90517 (11067) hydrogen bonds : bond 0.19691 ( 483) hydrogen bonds : angle 10.36223 ( 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 : 0.086 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0181 time to fit residues: 0.2095 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 : 0.053 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: 0.0220 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=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... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- 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: 0.5772 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 aren 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 covalent geometry : bond 0.00556 ( 7950) covalent geometry : angle 0.99448 (11067) hydrogen bonds : bond 0.07574 ( 483) hydrogen bonds : angle 10.23000 ( 1272) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 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 : 0.081 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0108 time to fit residues: 0.1807 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 : 0.009 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0137 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=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: 9.9990 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: 16.0072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.077837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.065730 restraints weight = 24492.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.066110 restraints weight = 22612.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.066333 restraints weight = 21121.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.066558 restraints weight = 20212.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.066720 restraints weight = 19454.738| |-----------------------------------------------------------------------------| r_work (final): 0.3588 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.050562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.037222 restraints weight = 5091.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.037222 restraints weight = 5264.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.037222 restraints weight = 5264.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.037222 restraints weight = 5264.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.037222 restraints weight = 5264.556| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5771 moved from start: 1.1392 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= 0.254 Angle : 0.780 9.217 11067 Z= 0.493 Chirality : 0.043 0.134 1530 Planarity : 0.004 0.037 1599 Dihedral : 6.984 35.470 1599 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.76 % Allowed : 9.64 % Favored : 89.60 % 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 aren not related in a simple way. whole: -3.76 (0.19), residues: 1587 helix: -1.71 (0.23), residues: 363 sheet: -2.60 (0.23), residues: 435 loop : -2.79 (0.21), residues: 789 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 covalent geometry : bond 0.00343 ( 7950) covalent geometry : angle 0.77969 (11067) hydrogen bonds : bond 0.05371 ( 483) hydrogen bonds : angle 9.02861 ( 1272) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 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 : 0.062 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0075 time to fit residues: 0.1347 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 : 0.083 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: 0.0225 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 128 optimal weight: 8.9990 chunk 108 optimal weight: 40.0000 chunk 141 optimal weight: 40.0000 chunk 90 optimal weight: 50.0000 chunk 45 optimal weight: 50.0000 chunk 37 optimal weight: 30.0000 chunk 31 optimal weight: 50.0000 chunk 73 optimal weight: 40.0000 chunk 75 optimal weight: 6.9990 chunk 44 optimal weight: 50.0000 chunk 124 optimal weight: 50.0000 overall best weight: 25.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.072291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.060927 restraints weight = 25309.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 14)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.061148 restraints weight = 22828.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.061608 restraints weight = 21201.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.061794 restraints weight = 19859.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.061921 restraints weight = 19076.575| |-----------------------------------------------------------------------------| r_work (final): 0.3505 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.046261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.033308 restraints weight = 5396.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.033308 restraints weight = 5414.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.033308 restraints weight = 5414.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.033308 restraints weight = 5414.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.033308 restraints weight = 5414.948| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5966 moved from start: 1.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 7950 Z= 0.378 Angle : 0.966 7.469 11067 Z= 0.615 Chirality : 0.047 0.185 1530 Planarity : 0.005 0.031 1599 Dihedral : 9.058 35.021 1599 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.38 % Allowed : 19.28 % 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 aren not related in a simple way. whole: -4.81 (0.18), residues: 1587 helix: -2.34 (0.23), residues: 357 sheet: -3.40 (0.27), residues: 285 loop : -3.64 (0.17), residues: 945 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 covalent geometry : bond 0.00512 ( 7950) covalent geometry : angle 0.96634 (11067) hydrogen bonds : bond 0.07126 ( 483) hydrogen bonds : angle 12.21762 ( 1272) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 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 : 0.094 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0104 time to fit residues: 0.1789 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 : 0.016 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0226 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 154 optimal weight: 40.0000 chunk 139 optimal weight: 10.0000 chunk 54 optimal weight: 30.0000 chunk 76 optimal weight: 50.0000 chunk 38 optimal weight: 0.0070 chunk 152 optimal weight: 2.9990 chunk 3 optimal weight: 40.0000 chunk 102 optimal weight: 50.0000 chunk 65 optimal weight: 50.0000 chunk 63 optimal weight: 0.0870 chunk 4 optimal weight: 50.0000 overall best weight: 8.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.075317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.063821 restraints weight = 24245.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.064027 restraints weight = 22031.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.064437 restraints weight = 20648.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.064675 restraints weight = 19497.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.064789 restraints weight = 18652.209| |-----------------------------------------------------------------------------| r_work (final): 0.3631 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.047936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.037573 restraints weight = 5380.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.037549 restraints weight = 5452.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 14)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.037546 restraints weight = 5495.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.037546 restraints weight = 5499.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.037546 restraints weight = 5499.088| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5817 moved from start: 1.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 7950 Z= 0.187 Angle : 0.703 7.365 11067 Z= 0.444 Chirality : 0.043 0.133 1530 Planarity : 0.004 0.029 1599 Dihedral : 6.766 31.876 1599 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.53 % Favored : 88.28 % 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 aren not related in a simple way. whole: -4.14 (0.19), residues: 1587 helix: -1.42 (0.24), residues: 384 sheet: -2.71 (0.26), residues: 360 loop : -3.51 (0.19), residues: 843 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 covalent geometry : bond 0.00254 ( 7950) covalent geometry : angle 0.70287 (11067) hydrogen bonds : bond 0.04087 ( 483) hydrogen bonds : angle 9.58542 ( 1272) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 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 : 0.088 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0120 time to fit residues: 0.1975 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 : 0.090 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 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0257 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: 3.9990 chunk 4 optimal weight: 50.0000 chunk 101 optimal weight: 50.0000 chunk 151 optimal weight: 40.0000 chunk 62 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 35 optimal weight: 50.0000 chunk 51 optimal weight: 0.9990 chunk 77 optimal weight: 30.0000 chunk 70 optimal weight: 40.0000 chunk 119 optimal weight: 50.0000 overall best weight: 8.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.075375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.063958 restraints weight = 24508.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.064240 restraints weight = 22694.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.064494 restraints weight = 21310.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.064611 restraints weight = 20263.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.064777 restraints weight = 19552.589| |-----------------------------------------------------------------------------| r_work (final): 0.3568 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.043746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.029457 restraints weight = 7399.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.029457 restraints weight = 8551.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.029452 restraints weight = 8553.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.029452 restraints weight = 8570.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.029452 restraints weight = 8570.025| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5622 moved from start: 1.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 7950 Z= 0.184 Angle : 0.671 7.401 11067 Z= 0.425 Chirality : 0.042 0.132 1530 Planarity : 0.003 0.028 1599 Dihedral : 6.247 31.210 1599 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.50 % Favored : 84.31 % 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 aren not related in a simple way. whole: -3.74 (0.20), residues: 1587 helix: -0.78 (0.26), residues: 390 sheet: -2.71 (0.26), residues: 381 loop : -3.30 (0.21), residues: 816 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 covalent geometry : bond 0.00251 ( 7950) covalent geometry : angle 0.67137 (11067) hydrogen bonds : bond 0.04026 ( 483) hydrogen bonds : angle 9.09222 ( 1272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 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 : 0.102 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0119 time to fit residues: 0.2117 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 : 0.100 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 : 0.020 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0276 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: 30.0000 chunk 65 optimal weight: 40.0000 chunk 69 optimal weight: 50.0000 chunk 97 optimal weight: 30.0000 chunk 50 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 126 optimal weight: 40.0000 chunk 34 optimal weight: 0.7980 chunk 100 optimal weight: 40.0000 overall best weight: 8.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.075721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.064072 restraints weight = 24696.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.064342 restraints weight = 22622.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.064648 restraints weight = 21285.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.064783 restraints weight = 20191.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.064866 restraints weight = 19506.264| |-----------------------------------------------------------------------------| r_work (final): 0.3563 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.049087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.035913 restraints weight = 4900.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.035700 restraints weight = 5243.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.035699 restraints weight = 5468.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.035699 restraints weight = 5470.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.035699 restraints weight = 5470.108| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5832 moved from start: 1.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 7950 Z= 0.175 Angle : 0.643 4.824 11067 Z= 0.411 Chirality : 0.042 0.134 1530 Planarity : 0.003 0.029 1599 Dihedral : 6.032 30.215 1599 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.48 % Favored : 87.52 % 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 aren not related in a simple way. whole: -3.42 (0.20), residues: 1587 helix: -0.47 (0.27), residues: 390 sheet: -2.68 (0.27), residues: 324 loop : -3.06 (0.20), 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 covalent geometry : bond 0.00240 ( 7950) covalent geometry : angle 0.64329 (11067) hydrogen bonds : bond 0.03827 ( 483) hydrogen bonds : angle 8.77721 ( 1272) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 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 : 0.086 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0120 time to fit residues: 0.1964 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 : 0.014 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 : 0.015 ------------------------------------------------------------------------------- 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: 50.0000 chunk 97 optimal weight: 40.0000 chunk 49 optimal weight: 50.0000 chunk 133 optimal weight: 0.5980 chunk 23 optimal weight: 0.0270 chunk 66 optimal weight: 70.0000 chunk 119 optimal weight: 50.0000 chunk 8 optimal weight: 30.0000 chunk 134 optimal weight: 50.0000 chunk 82 optimal weight: 20.0000 chunk 44 optimal weight: 40.0000 overall best weight: 18.1250 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.070959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.057844 restraints weight = 24787.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.057793 restraints weight = 27037.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.057515 restraints weight = 27558.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.057515 restraints weight = 29157.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.057515 restraints weight = 29157.922| |-----------------------------------------------------------------------------| r_work (final): 0.3751 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.054286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.035305 restraints weight = 4899.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.035305 restraints weight = 5657.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.035305 restraints weight = 5657.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.035305 restraints weight = 5657.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.035305 restraints weight = 5657.172| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5856 moved from start: 1.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 7950 Z= 0.275 Angle : 0.769 5.517 11067 Z= 0.494 Chirality : 0.043 0.151 1530 Planarity : 0.004 0.030 1599 Dihedral : 7.247 30.511 1599 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.42 % Favored : 79.58 % 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 aren not related in a simple way. whole: -3.95 (0.20), residues: 1587 helix: -1.02 (0.26), residues: 378 sheet: -3.03 (0.28), residues: 285 loop : -3.34 (0.19), residues: 924 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 covalent geometry : bond 0.00373 ( 7950) covalent geometry : angle 0.76897 (11067) hydrogen bonds : bond 0.05378 ( 483) hydrogen bonds : angle 10.57781 ( 1272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 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 : 0.086 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0120 time to fit residues: 0.1930 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 : 0.015 ------------------------------------------------------------------------------- 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: 50.0000 chunk 88 optimal weight: 40.0000 chunk 147 optimal weight: 0.0770 chunk 34 optimal weight: 40.0000 chunk 4 optimal weight: 50.0000 chunk 68 optimal weight: 50.0000 chunk 156 optimal weight: 50.0000 chunk 85 optimal weight: 50.0000 chunk 82 optimal weight: 0.9980 chunk 20 optimal weight: 40.0000 chunk 80 optimal weight: 0.6980 overall best weight: 16.3546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.072639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.061648 restraints weight = 25436.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.062014 restraints weight = 23251.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.062191 restraints weight = 21631.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.062509 restraints weight = 20524.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.062693 restraints weight = 19670.408| |-----------------------------------------------------------------------------| r_work (final): 0.3528 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.048556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.037336 restraints weight = 6056.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.037336 restraints weight = 6385.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.037336 restraints weight = 6385.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.037336 restraints weight = 6385.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.037336 restraints weight = 6385.941| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5922 moved from start: 1.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7950 Z= 0.250 Angle : 0.732 5.505 11067 Z= 0.470 Chirality : 0.043 0.146 1530 Planarity : 0.004 0.031 1599 Dihedral : 7.054 29.798 1599 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.39 % Favored : 82.61 % 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 aren not related in a simple way. whole: -4.12 (0.19), residues: 1587 helix: -1.07 (0.25), residues: 381 sheet: -3.36 (0.26), residues: 285 loop : -3.41 (0.19), residues: 921 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 covalent geometry : bond 0.00341 ( 7950) covalent geometry : angle 0.73201 (11067) hydrogen bonds : bond 0.04874 ( 483) hydrogen bonds : angle 10.34891 ( 1272) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 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: 0.0116 time to fit residues: 0.1877 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 : 0.015 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0223 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 62 optimal weight: 0.0670 chunk 15 optimal weight: 50.0000 chunk 98 optimal weight: 3.9990 chunk 73 optimal weight: 50.0000 chunk 95 optimal weight: 0.0670 chunk 118 optimal weight: 50.0000 chunk 29 optimal weight: 30.0000 chunk 135 optimal weight: 0.1980 chunk 77 optimal weight: 40.0000 chunk 142 optimal weight: 50.0000 chunk 75 optimal weight: 0.4980 overall best weight: 0.9658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.077433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.065902 restraints weight = 24003.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.066345 restraints weight = 21740.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.066650 restraints weight = 20099.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.066805 restraints weight = 18892.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 14)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.066806 restraints weight = 17989.367| |-----------------------------------------------------------------------------| r_work (final): 0.3685 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.043283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.029699 restraints weight = 7570.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.029495 restraints weight = 8310.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.029495 restraints weight = 8913.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.029495 restraints weight = 8913.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.029495 restraints weight = 8913.853| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5481 moved from start: 1.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 7950 Z= 0.130 Angle : 0.590 5.773 11067 Z= 0.377 Chirality : 0.041 0.123 1530 Planarity : 0.003 0.029 1599 Dihedral : 5.391 27.870 1599 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % 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 : 0.00 % 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 aren not related in a simple way. whole: -3.42 (0.20), residues: 1587 helix: 0.08 (0.27), residues: 387 sheet: -2.88 (0.25), residues: 357 loop : -3.24 (0.19), residues: 843 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 covalent geometry : bond 0.00179 ( 7950) covalent geometry : angle 0.59006 (11067) hydrogen bonds : bond 0.03190 ( 483) hydrogen bonds : angle 7.91319 ( 1272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 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: 0.0117 time to fit residues: 0.1927 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: 0.0226 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 25 optimal weight: 50.0000 chunk 63 optimal weight: 0.9980 chunk 115 optimal weight: 40.0000 chunk 99 optimal weight: 40.0000 chunk 52 optimal weight: 4.9990 chunk 157 optimal weight: 50.0000 chunk 106 optimal weight: 60.0000 chunk 14 optimal weight: 4.9990 chunk 45 optimal weight: 0.0970 chunk 39 optimal weight: 0.0030 chunk 88 optimal weight: 0.0770 overall best weight: 1.2348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.078048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.066236 restraints weight = 24425.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.066689 restraints weight = 22137.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.066910 restraints weight = 20368.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.067311 restraints weight = 19222.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.067439 restraints weight = 18183.826| |-----------------------------------------------------------------------------| r_work (final): 0.3680 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.049048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.037447 restraints weight = 5254.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.037447 restraints weight = 5599.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.037447 restraints weight = 5599.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.037447 restraints weight = 5599.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.037447 restraints weight = 5599.837| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5686 moved from start: 1.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 7950 Z= 0.121 Angle : 0.554 5.295 11067 Z= 0.355 Chirality : 0.041 0.125 1530 Planarity : 0.003 0.030 1599 Dihedral : 4.577 26.272 1599 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % 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 aren not related in a simple way. whole: -2.68 (0.21), residues: 1587 helix: 1.37 (0.29), residues: 369 sheet: -2.80 (0.24), residues: 393 loop : -2.82 (0.20), residues: 825 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 covalent geometry : bond 0.00168 ( 7950) covalent geometry : angle 0.55390 (11067) hydrogen bonds : bond 0.02865 ( 483) hydrogen bonds : angle 6.73166 ( 1272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 870.93 seconds wall clock time: 15 minutes 50.23 seconds (950.23 seconds total)