Starting phenix.real_space_refine on Wed Mar 12 13:54:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zd0_11172/03_2025/6zd0_11172.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zd0_11172/03_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_11172/03_2025/6zd0_11172.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zd0_11172/03_2025/6zd0_11172.map" model { file = "/net/cci-nas-00/data/ceres_data/6zd0_11172/03_2025/6zd0_11172.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zd0_11172/03_2025/6zd0_11172.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 17, 'ARG:plan': 18, 'TYR:plan': 20, 'ASN:plan1': 36, 'TRP:plan': 7, 'ASP:plan': 20, 'PHE:plan': 15, 'GLU:plan': 21, 'HIS:plan': 9} 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, 'ARG:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 5, 'HIS:plan': 1} 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: {'GLN:plan1': 17, 'ARG:plan': 18, 'TYR:plan': 20, 'ASN:plan1': 36, 'TRP:plan': 7, 'ASP:plan': 20, 'PHE:plan': 15, 'GLU:plan': 21, 'HIS:plan': 9} 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, 'ARG:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 5, 'HIS:plan': 1} 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: {'GLN:plan1': 17, 'ARG:plan': 18, 'TYR:plan': 20, 'ASN:plan1': 36, 'TRP:plan': 7, 'ASP:plan': 20, 'PHE:plan': 15, 'GLU:plan': 21, 'HIS:plan': 9} 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, 'ARG:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 153 Time building chain proxies: 5.74, per 1000 atoms: 0.72 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: 2.31 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.30 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: 3.12 Time building geometry restraints manager: 2.66 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: 0.150 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 24.470 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.670 ------------------------------------------------------------------------------- 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= 0.259 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 95 TYR 0.000 0.000 TYR A 67 *********************** 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 : 0.231 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0436 time to fit residues: 0.5510 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 : 0.226 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 : 0.040 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0639 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 : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 50.0000 chunk 120 optimal weight: 50.0000 chunk 66 optimal weight: 60.0000 chunk 41 optimal weight: 50.0000 chunk 81 optimal weight: 40.0000 chunk 64 optimal weight: 50.0000 chunk 124 optimal weight: 40.0000 chunk 48 optimal weight: 50.0000 chunk 75 optimal weight: 9.9990 chunk 92 optimal weight: 0.0470 chunk 144 optimal weight: 50.0000 overall best weight: 28.0092 ------------------------------------------------------------------------------- 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 = 0.3919 r_free = 0.3919 target = 0.076832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.064046 restraints weight = 24034.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.064310 restraints weight = 22391.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.064466 restraints weight = 21130.524| |-----------------------------------------------------------------------------| r_work (final): 0.3619 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.053918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.038959 restraints weight = 4631.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.038955 restraints weight = 4988.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.038955 restraints weight = 4992.244| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5803 moved from start: 1.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 7950 Z= 0.432 Angle : 1.025 8.285 11067 Z= 0.652 Chirality : 0.047 0.146 1530 Planarity : 0.006 0.031 1599 Dihedral : 9.090 44.556 1599 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 1.13 % Allowed : 10.59 % 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 : 0.78 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.09 (0.18), residues: 1587 helix: -2.41 (0.22), residues: 351 sheet: -2.34 (0.23), residues: 456 loop : -3.09 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 95 TYR 0.000 0.000 TYR A 67 *********************** 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 : 0.227 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0238 time to fit residues: 0.4968 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 : 0.232 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 : 0.041 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0727 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 : 0.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 26 optimal weight: 50.0000 chunk 139 optimal weight: 20.0000 chunk 143 optimal weight: 30.0000 chunk 51 optimal weight: 20.0000 chunk 3 optimal weight: 30.0000 chunk 75 optimal weight: 7.9990 chunk 125 optimal weight: 40.0000 chunk 111 optimal weight: 7.9990 chunk 107 optimal weight: 50.0000 chunk 16 optimal weight: 50.0000 chunk 115 optimal weight: 40.0000 overall best weight: 17.1996 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.077108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.065281 restraints weight = 24213.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.065638 restraints weight = 22052.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.065897 restraints weight = 20614.550| |-----------------------------------------------------------------------------| r_work (final): 0.3655 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.049261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.036973 restraints weight = 4836.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.036973 restraints weight = 5065.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.036973 restraints weight = 5065.162| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5796 moved from start: 1.1752 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= 0.270 Angle : 0.802 9.341 11067 Z= 0.508 Chirality : 0.043 0.138 1530 Planarity : 0.005 0.035 1599 Dihedral : 7.334 34.301 1599 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.76 % Allowed : 10.21 % 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 : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.19), residues: 1587 helix: -1.84 (0.23), residues: 363 sheet: -2.72 (0.24), residues: 390 loop : -2.90 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 95 TYR 0.000 0.000 TYR A 67 *********************** 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 : 0.249 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0232 time to fit residues: 0.5016 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 : 0.232 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 : 0.046 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0682 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 : 0.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 49 optimal weight: 5.9990 chunk 11 optimal weight: 50.0000 chunk 9 optimal weight: 50.0000 chunk 12 optimal weight: 40.0000 chunk 35 optimal weight: 50.0000 chunk 93 optimal weight: 0.8980 chunk 5 optimal weight: 20.0000 chunk 133 optimal weight: 0.7980 chunk 149 optimal weight: 50.0000 chunk 53 optimal weight: 50.0000 chunk 131 optimal weight: 20.0000 overall best weight: 9.5390 ------------------------------------------------------------------------------- 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 = 0.3936 r_free = 0.3936 target = 0.077449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.065654 restraints weight = 24410.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.066061 restraints weight = 22126.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.066376 restraints weight = 20454.685| |-----------------------------------------------------------------------------| r_work (final): 0.3661 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.049273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.037900 restraints weight = 5123.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.037900 restraints weight = 5487.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.037900 restraints weight = 5487.351| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5659 moved from start: 1.1962 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= 0.194 Angle : 0.687 8.180 11067 Z= 0.434 Chirality : 0.042 0.128 1530 Planarity : 0.003 0.030 1599 Dihedral : 6.269 32.148 1599 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.78 % 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 : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.20), residues: 1587 helix: -1.20 (0.25), residues: 381 sheet: -2.43 (0.26), residues: 357 loop : -2.74 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 95 TYR 0.000 0.000 TYR A 67 *********************** 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 : 0.255 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0239 time to fit residues: 0.5326 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 : 0.248 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 : 0.046 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0728 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 : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 63 optimal weight: 0.0370 chunk 49 optimal weight: 30.0000 chunk 81 optimal weight: 50.0000 chunk 93 optimal weight: 0.7980 chunk 9 optimal weight: 50.0000 chunk 48 optimal weight: 7.9990 chunk 24 optimal weight: 50.0000 chunk 30 optimal weight: 40.0000 chunk 69 optimal weight: 50.0000 chunk 106 optimal weight: 50.0000 chunk 144 optimal weight: 0.0870 overall best weight: 7.7842 ------------------------------------------------------------------------------- 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 = 0.077428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.065580 restraints weight = 24218.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.065810 restraints weight = 21963.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.066252 restraints weight = 20549.635| |-----------------------------------------------------------------------------| r_work (final): 0.3647 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.048706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.037023 restraints weight = 5180.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.037023 restraints weight = 5402.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.037023 restraints weight = 5402.680| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5669 moved from start: 1.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 7950 Z= 0.172 Angle : 0.659 8.154 11067 Z= 0.416 Chirality : 0.042 0.126 1530 Planarity : 0.003 0.030 1599 Dihedral : 5.885 31.189 1599 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.91 % Favored : 87.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.20), residues: 1587 helix: -0.54 (0.27), residues: 366 sheet: -2.55 (0.26), residues: 357 loop : -2.51 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 95 TYR 0.000 0.000 TYR A 67 *********************** 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 : 0.225 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0231 time to fit residues: 0.4936 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 : 0.241 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 : 0.047 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0672 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 : 0.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 51 optimal weight: 0.2980 chunk 22 optimal weight: 4.9990 chunk 84 optimal weight: 40.0000 chunk 72 optimal weight: 50.0000 chunk 32 optimal weight: 30.0000 chunk 110 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 25 optimal weight: 30.0000 chunk 157 optimal weight: 40.0000 chunk 17 optimal weight: 50.0000 chunk 87 optimal weight: 0.0050 overall best weight: 7.0602 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.077497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.065555 restraints weight = 24784.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.065928 restraints weight = 22599.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.066093 restraints weight = 21111.690| |-----------------------------------------------------------------------------| r_work (final): 0.3643 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.047967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.036611 restraints weight = 5043.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.036611 restraints weight = 5254.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.036611 restraints weight = 5254.179| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5778 moved from start: 1.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 7950 Z= 0.160 Angle : 0.636 7.884 11067 Z= 0.402 Chirality : 0.042 0.122 1530 Planarity : 0.003 0.029 1599 Dihedral : 5.499 29.959 1599 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.19 % Allowed : 12.10 % Favored : 87.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.21), residues: 1587 helix: 0.03 (0.28), residues: 369 sheet: -2.39 (0.26), residues: 363 loop : -2.59 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 95 TYR 0.000 0.000 TYR A 67 *********************** 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 : 0.227 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0249 time to fit residues: 0.4917 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 : 0.229 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 : 0.041 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0638 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 : 0.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 51 optimal weight: 0.4980 chunk 48 optimal weight: 8.9990 chunk 138 optimal weight: 50.0000 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 30.0000 chunk 81 optimal weight: 40.0000 chunk 156 optimal weight: 50.0000 chunk 9 optimal weight: 50.0000 chunk 17 optimal weight: 40.0000 chunk 44 optimal weight: 40.0000 chunk 74 optimal weight: 50.0000 overall best weight: 16.2992 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.074179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.062724 restraints weight = 25392.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.063033 restraints weight = 23290.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.063034 restraints weight = 21909.889| |-----------------------------------------------------------------------------| r_work (final): 0.3514 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.047978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.037173 restraints weight = 5526.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.037173 restraints weight = 5486.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.037173 restraints weight = 5486.514| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5931 moved from start: 1.3423 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= 0.264 Angle : 0.749 5.753 11067 Z= 0.481 Chirality : 0.043 0.149 1530 Planarity : 0.004 0.029 1599 Dihedral : 6.840 31.314 1599 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.74 % Favored : 85.26 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.20), residues: 1587 helix: -0.88 (0.26), residues: 396 sheet: -2.58 (0.29), residues: 288 loop : -3.08 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 95 TYR 0.000 0.000 TYR A 67 *********************** REFINEMENT MACRO_CYCLE 7 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 : 0.233 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0237 time to fit residues: 0.5055 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 : 0.235 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 : 0.045 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0636 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 : 0.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 21 optimal weight: 50.0000 chunk 34 optimal weight: 30.0000 chunk 156 optimal weight: 50.0000 chunk 93 optimal weight: 4.9990 chunk 134 optimal weight: 50.0000 chunk 145 optimal weight: 9.9990 chunk 77 optimal weight: 40.0000 chunk 75 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 107 optimal weight: 50.0000 chunk 149 optimal weight: 30.0000 overall best weight: 14.9996 ------------------------------------------------------------------------------- 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 = 0.3850 r_free = 0.3850 target = 0.073521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.062219 restraints weight = 24341.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.062429 restraints weight = 22404.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.062749 restraints weight = 21309.322| |-----------------------------------------------------------------------------| r_work (final): 0.3508 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.048247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.037232 restraints weight = 5362.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.037289 restraints weight = 5312.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.037289 restraints weight = 5262.370| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5908 moved from start: 1.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 7950 Z= 0.234 Angle : 0.712 5.549 11067 Z= 0.458 Chirality : 0.043 0.141 1530 Planarity : 0.004 0.029 1599 Dihedral : 6.651 30.431 1599 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.07 % Favored : 83.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.20), residues: 1587 helix: -0.79 (0.26), residues: 381 sheet: -3.04 (0.24), residues: 348 loop : -3.32 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 95 TYR 0.000 0.000 TYR A 67 *********************** REFINEMENT MACRO_CYCLE 8 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 : 0.232 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0260 time to fit residues: 0.5018 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 : 0.231 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 : 0.041 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0723 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 : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 801, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.2501 > 50: distance: 0 - 37: 16.162 distance: 1 - 2: 24.557 distance: 1 - 4: 22.435 distance: 2 - 3: 26.125 distance: 2 - 5: 21.822 distance: 3 - 34: 30.908 distance: 5 - 6: 13.362 distance: 6 - 7: 13.254 distance: 6 - 9: 13.826 distance: 7 - 8: 16.598 distance: 7 - 10: 31.295 distance: 10 - 11: 12.156 distance: 10 - 27: 43.717 distance: 11 - 12: 14.624 distance: 11 - 14: 22.077 distance: 12 - 13: 12.846 distance: 12 - 15: 32.515 distance: 13 - 24: 33.068 distance: 15 - 16: 22.118 distance: 16 - 17: 34.964 distance: 16 - 19: 20.407 distance: 17 - 18: 13.045 distance: 17 - 20: 35.011 distance: 20 - 21: 39.818 distance: 21 - 22: 25.983 distance: 22 - 23: 27.935 distance: 22 - 24: 29.732 distance: 24 - 25: 27.671 distance: 25 - 26: 43.114 distance: 25 - 28: 26.244 distance: 26 - 27: 25.900 distance: 26 - 29: 28.068 distance: 29 - 30: 28.815 distance: 30 - 31: 10.528 distance: 30 - 33: 27.011 distance: 31 - 32: 23.427 distance: 31 - 34: 26.696 distance: 34 - 35: 24.115 distance: 35 - 36: 20.833 distance: 35 - 38: 26.055 distance: 36 - 37: 29.884 distance: 36 - 39: 22.864 distance: 39 - 40: 13.395 distance: 40 - 41: 13.491 distance: 40 - 43: 19.047 distance: 41 - 44: 15.172 distance: 44 - 45: 10.403 distance: 45 - 46: 11.516 distance: 45 - 48: 20.478 distance: 46 - 47: 19.051