Starting phenix.real_space_refine on Tue Sep 24 11:36:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zd0_11172/09_2024/6zd0_11172.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zd0_11172/09_2024/6zd0_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zd0_11172/09_2024/6zd0_11172.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zd0_11172/09_2024/6zd0_11172.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zd0_11172/09_2024/6zd0_11172.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zd0_11172/09_2024/6zd0_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-5461/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: 5.59, per 1000 atoms: 0.70 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: 2.27 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: 1.41 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: 2.63 Time building geometry restraints manager: 2.54 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: 0.00 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: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.560 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.290 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.276 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0481 time to fit residues: 0.6240 Evaluate side-chains 3 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.272 Evaluate side-chains 0 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.050 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0777 Evaluate side-chains 0 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.048 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6126 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 fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.273 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0230 time to fit residues: 0.4794 Evaluate side-chains 3 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.270 Evaluate side-chains 0 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.048 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0753 Evaluate side-chains 0 residues out of total 72 non-(ALA, GLY, PRO) need fitting. 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 80 optimal weight: 0.1980 chunk 44 optimal weight: 50.0000 chunk 120 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 39 optimal weight: 20.0000 chunk 144 optimal weight: 0.5980 chunk 156 optimal weight: 40.0000 chunk 128 optimal weight: 5.9990 chunk 143 optimal weight: 30.0000 chunk 49 optimal weight: 50.0000 chunk 116 optimal weight: 50.0000 overall best weight: 2.0784 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5907 moved from start: 1.0496 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= 0.147 Angle : 0.644 9.403 11067 Z= 0.403 Chirality : 0.042 0.124 1530 Planarity : 0.003 0.035 1599 Dihedral : 5.580 33.127 1599 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.29 % Favored : 94.33 % 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: -2.94 (0.20), residues: 1587 helix: -0.46 (0.26), residues: 369 sheet: -1.96 (0.24), residues: 447 loop : -2.71 (0.21), residues: 771 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) ************************************************ 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 fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.257 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0240 time to fit residues: 0.5256 Evaluate side-chains 3 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.254 Evaluate side-chains 0 residues out of total 72 non-(ALA, GLY, PRO) need fitting. 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: 0.0709 Evaluate side-chains 0 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 50.0000 chunk 108 optimal weight: 50.0000 chunk 75 optimal weight: 6.9990 chunk 16 optimal weight: 50.0000 chunk 69 optimal weight: 40.0000 chunk 97 optimal weight: 50.0000 chunk 145 optimal weight: 0.0170 chunk 153 optimal weight: 40.0000 chunk 137 optimal weight: 50.0000 chunk 41 optimal weight: 40.0000 chunk 127 optimal weight: 50.0000 overall best weight: 25.4032 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6206 moved from start: 1.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 7950 Z= 0.350 Angle : 0.887 8.564 11067 Z= 0.568 Chirality : 0.045 0.144 1530 Planarity : 0.005 0.028 1599 Dihedral : 7.784 33.518 1599 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.95 % Allowed : 13.80 % 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: -4.05 (0.19), residues: 1587 helix: -1.88 (0.24), residues: 372 sheet: -2.71 (0.24), residues: 393 loop : -3.11 (0.19), residues: 822 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) ************************************************ 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 fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.237 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0280 time to fit residues: 0.5357 Evaluate side-chains 3 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.263 Evaluate side-chains 0 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.049 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0763 Evaluate side-chains 0 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 4.9990 chunk 2 optimal weight: 0.0070 chunk 114 optimal weight: 50.0000 chunk 63 optimal weight: 0.5980 chunk 131 optimal weight: 0.1980 chunk 106 optimal weight: 60.0000 chunk 0 optimal weight: 50.0000 chunk 78 optimal weight: 20.0000 chunk 137 optimal weight: 40.0000 chunk 38 optimal weight: 0.9990 chunk 51 optimal weight: 40.0000 overall best weight: 1.3602 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5996 moved from start: 1.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 7950 Z= 0.141 Angle : 0.621 7.631 11067 Z= 0.391 Chirality : 0.042 0.123 1530 Planarity : 0.003 0.029 1599 Dihedral : 5.412 30.376 1599 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.32 % Favored : 91.49 % 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: -3.05 (0.20), residues: 1587 helix: -0.24 (0.26), residues: 384 sheet: -2.33 (0.25), residues: 393 loop : -2.81 (0.20), residues: 810 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) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 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 fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.229 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0363 time to fit residues: 0.5321 Evaluate side-chains 3 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.220 Evaluate side-chains 0 residues out of total 72 non-(ALA, GLY, PRO) need fitting. 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: 0.0703 Evaluate side-chains 0 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 40.0000 chunk 30 optimal weight: 50.0000 chunk 90 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 153 optimal weight: 30.0000 chunk 127 optimal weight: 50.0000 chunk 71 optimal weight: 40.0000 chunk 12 optimal weight: 50.0000 chunk 50 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 148 optimal weight: 30.0000 overall best weight: 17.9998 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6209 moved from start: 1.2799 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= 0.256 Angle : 0.743 6.952 11067 Z= 0.473 Chirality : 0.043 0.145 1530 Planarity : 0.004 0.027 1599 Dihedral : 6.765 30.875 1599 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.57 % Allowed : 16.45 % Favored : 82.99 % 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: -3.94 (0.19), residues: 1587 helix: -1.63 (0.24), residues: 393 sheet: -2.53 (0.26), residues: 345 loop : -3.23 (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 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 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 fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.237 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0232 time to fit residues: 0.4977 Evaluate side-chains 3 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.233 Evaluate side-chains 0 residues out of total 72 non-(ALA, GLY, PRO) need fitting. 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: 0.0699 Evaluate side-chains 0 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 40.0000 chunk 87 optimal weight: 30.0000 chunk 112 optimal weight: 20.0000 chunk 129 optimal weight: 0.0270 chunk 85 optimal weight: 50.0000 chunk 153 optimal weight: 20.0000 chunk 95 optimal weight: 50.0000 chunk 93 optimal weight: 0.9990 chunk 70 optimal weight: 40.0000 chunk 94 optimal weight: 10.0000 chunk 61 optimal weight: 50.0000 overall best weight: 10.2052 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6182 moved from start: 1.2966 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= 0.185 Angle : 0.645 5.186 11067 Z= 0.414 Chirality : 0.042 0.130 1530 Planarity : 0.003 0.025 1599 Dihedral : 5.943 27.258 1599 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.19 % Allowed : 17.20 % 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 (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: -4.24 (0.19), residues: 1587 helix: -1.72 (0.24), residues: 399 sheet: -2.86 (0.25), residues: 339 loop : -3.44 (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 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 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 fitting. 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: 0.5250 Evaluate side-chains 3 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.256 Evaluate side-chains 0 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.044 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0721 Evaluate side-chains 0 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 0.8980 chunk 46 optimal weight: 40.0000 chunk 30 optimal weight: 50.0000 chunk 29 optimal weight: 30.0000 chunk 97 optimal weight: 30.0000 chunk 104 optimal weight: 50.0000 chunk 75 optimal weight: 7.9990 chunk 14 optimal weight: 40.0000 chunk 120 optimal weight: 40.0000 chunk 139 optimal weight: 20.0000 chunk 146 optimal weight: 0.0020 overall best weight: 11.7798 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6234 moved from start: 1.3827 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= 0.206 Angle : 0.670 5.499 11067 Z= 0.430 Chirality : 0.042 0.135 1530 Planarity : 0.003 0.027 1599 Dihedral : 6.132 26.431 1599 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.19 % Allowed : 20.42 % Favored : 79.40 % 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: -4.56 (0.19), residues: 1587 helix: -1.87 (0.24), residues: 405 sheet: -3.62 (0.26), residues: 264 loop : -3.53 (0.19), residues: 918 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) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 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 fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.264 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0251 time to fit residues: 0.5403 Evaluate side-chains 3 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.267 Evaluate side-chains 0 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.048 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0730 Evaluate side-chains 0 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 2.9990 chunk 142 optimal weight: 40.0000 chunk 146 optimal weight: 8.9990 chunk 85 optimal weight: 50.0000 chunk 62 optimal weight: 40.0000 chunk 112 optimal weight: 0.5980 chunk 43 optimal weight: 20.0000 chunk 129 optimal weight: 5.9990 chunk 135 optimal weight: 30.0000 chunk 93 optimal weight: 8.9990 chunk 151 optimal weight: 0.6980 overall best weight: 3.8586 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6132 moved from start: 1.3526 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= 0.135 Angle : 0.582 5.246 11067 Z= 0.373 Chirality : 0.041 0.121 1530 Planarity : 0.003 0.026 1599 Dihedral : 4.963 24.092 1599 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.37 % Favored : 85.63 % 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: -4.06 (0.19), residues: 1587 helix: -0.88 (0.26), residues: 369 sheet: -3.43 (0.23), residues: 360 loop : -3.27 (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 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 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 fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.253 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0239 time to fit residues: 0.5116 Evaluate side-chains 3 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.246 Evaluate side-chains 0 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.049 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0717 Evaluate side-chains 0 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 40.0000 chunk 71 optimal weight: 40.0000 chunk 104 optimal weight: 50.0000 chunk 158 optimal weight: 0.0980 chunk 145 optimal weight: 40.0000 chunk 126 optimal weight: 40.0000 chunk 13 optimal weight: 70.0000 chunk 97 optimal weight: 50.0000 chunk 77 optimal weight: 50.0000 chunk 100 optimal weight: 50.0000 chunk 134 optimal weight: 50.0000 overall best weight: 32.0196 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6372 moved from start: 1.5623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7950 Z= 0.400 Angle : 0.908 5.884 11067 Z= 0.587 Chirality : 0.045 0.174 1530 Planarity : 0.005 0.029 1599 Dihedral : 8.351 28.160 1599 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 24.35 Ramachandran Plot: Outliers : 2.08 % Allowed : 27.41 % Favored : 70.51 % 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: -6.01 (0.17), residues: 1587 helix: -3.24 (0.19), residues: 342 sheet: -4.99 (0.21), residues: 285 loop : -4.15 (0.17), residues: 960 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 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 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 fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.198 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0205 time to fit residues: 0.4235 Evaluate side-chains 3 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.262 Evaluate side-chains 0 residues out of total 72 non-(ALA, GLY, PRO) need fitting. 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: 0.0732 Evaluate side-chains 0 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 50.0000 chunk 116 optimal weight: 0.0970 chunk 18 optimal weight: 30.0000 chunk 35 optimal weight: 40.0000 chunk 126 optimal weight: 50.0000 chunk 52 optimal weight: 0.1980 chunk 129 optimal weight: 50.0000 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 50.0000 chunk 110 optimal weight: 9.9990 chunk 7 optimal weight: 0.2980 overall best weight: 2.2780 ------------------------------------------------------------------------------- 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 = 0.3971 r_free = 0.3971 target = 0.073472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.060796 restraints weight = 25347.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.060796 restraints weight = 24538.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.060796 restraints weight = 24538.408| |-----------------------------------------------------------------------------| r_work (final): 0.3566 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.041028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.028017 restraints weight = 7495.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.028015 restraints weight = 8006.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.028015 restraints weight = 8016.947| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5695 moved from start: 1.4659 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= 0.143 Angle : 0.608 4.983 11067 Z= 0.388 Chirality : 0.042 0.127 1530 Planarity : 0.003 0.026 1599 Dihedral : 5.487 23.470 1599 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.69 % Favored : 84.12 % 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: -4.88 (0.18), residues: 1587 helix: -1.59 (0.24), residues: 384 sheet: -3.99 (0.26), residues: 285 loop : -3.91 (0.18), residues: 918 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1206.42 seconds wall clock time: 22 minutes 4.93 seconds (1324.93 seconds total)