Starting phenix.real_space_refine on Fri Dec 8 09:38:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zd0_11172/12_2023/6zd0_11172.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zd0_11172/12_2023/6zd0_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_11172/12_2023/6zd0_11172.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zd0_11172/12_2023/6zd0_11172.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zd0_11172/12_2023/6zd0_11172.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zd0_11172/12_2023/6zd0_11172.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 5.50, per 1000 atoms: 0.69 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 - 3.50 Amino acid : False - 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: 3.36 Conformation dependent library (CDL) restraints added in 2.3 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: 1.46 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: 2.93 Time building geometry restraints manager: 3.60 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: 102.15 - 107.72: 194 107.72 - 113.30: 4366 113.30 - 118.87: 1715 118.87 - 124.45: 4762 124.45 - 130.02: 30 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 2.520 nonbonded pdb=" O GLU A 84 " pdb=" N ASP A 407 " model vdw 2.217 2.520 nonbonded pdb=" N HIS E 81 " pdb=" O GLN E 403 " model vdw 2.237 2.520 nonbonded pdb=" N GLY E 153 " pdb=" O LEU E 271 " model vdw 2.252 2.520 nonbonded pdb=" O LEU E 118 " pdb=" N TYR E 389 " model vdw 2.258 2.520 ... (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 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: 0.240 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: 1.260 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 28.490 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.410 ------------------------------------------------------------------------------- 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 : 0.264 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0477 time to fit residues: 0.6281 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3416 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: 0.0788 Evaluate side-chains 0 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.054 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0605 ------------------------------------------------------------------------------- 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: 30.0000 chunk 81 optimal weight: 40.0000 chunk 64 optimal weight: 40.0000 chunk 124 optimal weight: 40.0000 chunk 48 optimal weight: 50.0000 chunk 75 optimal weight: 8.9990 chunk 92 optimal weight: 0.0060 chunk 144 optimal weight: 40.0000 overall best weight: 23.8010 ------------------------------------------------------------------------------- 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: 0.6074 moved from start: 1.0670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 7950 Z= 0.386 Angle : 0.944 6.912 11067 Z= 0.601 Chirality : 0.045 0.145 1530 Planarity : 0.006 0.029 1599 Dihedral : 8.438 43.606 1599 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 1.13 % Allowed : 9.45 % Favored : 89.41 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.59 % 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: -3.84 (0.18), residues: 1587 helix: -2.29 (0.22), residues: 357 sheet: -2.22 (0.23), residues: 438 loop : -2.86 (0.19), residues: 792 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 : 0.269 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0308 time to fit residues: 0.6210 Evaluate side-chains 3 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.282 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3758 Evaluate side-chains 0 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.055 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0854 Evaluate side-chains 0 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.053 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0664 ------------------------------------------------------------------------------- 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: 0.7980 chunk 44 optimal weight: 30.0000 chunk 120 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 144 optimal weight: 0.0040 chunk 156 optimal weight: 50.0000 chunk 128 optimal weight: 7.9990 chunk 143 optimal weight: 50.0000 chunk 49 optimal weight: 40.0000 chunk 116 optimal weight: 50.0000 overall best weight: 2.3396 ------------------------------------------------------------------------------- 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: 0.5897 moved from start: 1.0287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 7950 Z= 0.146 Angle : 0.636 9.267 11067 Z= 0.399 Chirality : 0.042 0.121 1530 Planarity : 0.003 0.034 1599 Dihedral : 5.567 32.654 1599 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.62 % Favored : 93.01 % 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: -2.81 (0.20), residues: 1587 helix: -0.50 (0.26), residues: 366 sheet: -1.81 (0.24), residues: 456 loop : -2.59 (0.21), residues: 765 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 fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.280 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0257 time to fit residues: 0.5747 Evaluate side-chains 3 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.279 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3535 Evaluate side-chains 0 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.053 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0809 Evaluate side-chains 0 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.052 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0645 ------------------------------------------------------------------------------- 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: 5.9990 chunk 16 optimal weight: 50.0000 chunk 69 optimal weight: 50.0000 chunk 97 optimal weight: 8.9990 chunk 145 optimal weight: 0.0050 chunk 153 optimal weight: 30.0000 chunk 137 optimal weight: 50.0000 chunk 41 optimal weight: 50.0000 chunk 127 optimal weight: 50.0000 overall best weight: 19.0006 ------------------------------------------------------------------------------- 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: 0.6173 moved from start: 1.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 7950 Z= 0.292 Angle : 0.825 8.510 11067 Z= 0.526 Chirality : 0.044 0.140 1530 Planarity : 0.004 0.026 1599 Dihedral : 7.542 32.900 1599 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 21.23 Ramachandran Plot: Outliers : 1.32 % Allowed : 12.85 % Favored : 85.82 % 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: -3.47 (0.20), residues: 1587 helix: -1.63 (0.24), residues: 378 sheet: -2.18 (0.26), residues: 375 loop : -2.72 (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 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 fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.267 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0242 time to fit residues: 0.5366 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3300 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: 0.0735 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0590 ------------------------------------------------------------------------------- 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: 30.0000 chunk 2 optimal weight: 0.0000 chunk 114 optimal weight: 50.0000 chunk 63 optimal weight: 50.0000 chunk 131 optimal weight: 0.0970 chunk 106 optimal weight: 60.0000 chunk 0 optimal weight: 50.0000 chunk 78 optimal weight: 30.0000 chunk 137 optimal weight: 50.0000 chunk 38 optimal weight: 50.0000 chunk 51 optimal weight: 40.0000 overall best weight: 20.0194 ------------------------------------------------------------------------------- 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: 0.6230 moved from start: 1.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 7950 Z= 0.290 Angle : 0.820 7.176 11067 Z= 0.524 Chirality : 0.044 0.149 1530 Planarity : 0.004 0.028 1599 Dihedral : 7.784 32.002 1599 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.76 % Allowed : 16.64 % 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 : 0.20 % 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: -4.33 (0.18), residues: 1587 helix: -1.94 (0.23), residues: 369 sheet: -2.98 (0.24), residues: 354 loop : -3.33 (0.19), 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) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 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 : 0.510 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0433 time to fit residues: 0.8373 Evaluate side-chains 3 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.326 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3966 Evaluate side-chains 0 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.065 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1086 Evaluate side-chains 0 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.065 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0828 ------------------------------------------------------------------------------- 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: 40.0000 chunk 90 optimal weight: 40.0000 chunk 37 optimal weight: 40.0000 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: 5.9990 chunk 80 optimal weight: 0.9980 chunk 148 optimal weight: 40.0000 overall best weight: 23.3994 ------------------------------------------------------------------------------- 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: 0.6340 moved from start: 1.5184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 7950 Z= 0.343 Angle : 0.907 7.366 11067 Z= 0.580 Chirality : 0.044 0.159 1530 Planarity : 0.005 0.030 1599 Dihedral : 8.580 32.475 1599 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 27.64 Ramachandran Plot: Outliers : 1.32 % Allowed : 23.44 % Favored : 75.24 % 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 : 0.39 % 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: -5.05 (0.18), residues: 1587 helix: -2.19 (0.24), residues: 324 sheet: -3.67 (0.24), residues: 327 loop : -3.84 (0.17), residues: 936 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) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 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 : 0.289 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0289 time to fit residues: 0.6761 Evaluate side-chains 3 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.285 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3517 Evaluate side-chains 0 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.052 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0766 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0610 ------------------------------------------------------------------------------- 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: 0.2980 chunk 112 optimal weight: 0.0010 chunk 129 optimal weight: 30.0000 chunk 85 optimal weight: 50.0000 chunk 153 optimal weight: 40.0000 chunk 95 optimal weight: 40.0000 chunk 93 optimal weight: 3.9990 chunk 70 optimal weight: 40.0000 chunk 94 optimal weight: 40.0000 chunk 61 optimal weight: 30.0000 overall best weight: 12.8596 ------------------------------------------------------------------------------- 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: 0.6275 moved from start: 1.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 7950 Z= 0.217 Angle : 0.706 6.237 11067 Z= 0.452 Chirality : 0.043 0.132 1530 Planarity : 0.004 0.026 1599 Dihedral : 6.916 26.930 1599 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 1.13 % Allowed : 21.17 % Favored : 77.69 % 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: -5.02 (0.18), residues: 1587 helix: -2.04 (0.24), residues: 354 sheet: -4.01 (0.25), residues: 285 loop : -3.81 (0.18), residues: 948 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) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 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: 0.0249 time to fit residues: 0.5598 Evaluate side-chains 3 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.268 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4325 Evaluate side-chains 0 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.052 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0741 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0589 ------------------------------------------------------------------------------- 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: 0.0010 chunk 46 optimal weight: 50.0000 chunk 30 optimal weight: 50.0000 chunk 29 optimal weight: 40.0000 chunk 97 optimal weight: 0.2980 chunk 104 optimal weight: 40.0000 chunk 75 optimal weight: 0.7980 chunk 14 optimal weight: 50.0000 chunk 120 optimal weight: 50.0000 chunk 139 optimal weight: 40.0000 chunk 146 optimal weight: 1.9990 overall best weight: 8.6192 ------------------------------------------------------------------------------- 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: 0.6243 moved from start: 1.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 7950 Z= 0.176 Angle : 0.645 5.353 11067 Z= 0.413 Chirality : 0.042 0.124 1530 Planarity : 0.003 0.027 1599 Dihedral : 6.095 25.537 1599 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.57 % Allowed : 20.60 % Favored : 78.83 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 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: -4.71 (0.19), residues: 1587 helix: -1.47 (0.26), residues: 339 sheet: -3.94 (0.23), residues: 315 loop : -3.63 (0.18), residues: 933 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) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 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 : 0.275 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0253 time to fit residues: 0.5629 Evaluate side-chains 3 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.277 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3468 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: 0.0765 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0610 ------------------------------------------------------------------------------- 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: 10.0000 chunk 142 optimal weight: 30.0000 chunk 146 optimal weight: 6.9990 chunk 85 optimal weight: 40.0000 chunk 62 optimal weight: 50.0000 chunk 112 optimal weight: 0.0670 chunk 43 optimal weight: 0.3980 chunk 129 optimal weight: 30.0000 chunk 135 optimal weight: 30.0000 chunk 93 optimal weight: 6.9990 chunk 151 optimal weight: 30.0000 overall best weight: 4.8926 ------------------------------------------------------------------------------- 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: 0.6183 moved from start: 1.4746 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= 0.144 Angle : 0.595 4.831 11067 Z= 0.381 Chirality : 0.041 0.123 1530 Planarity : 0.003 0.027 1599 Dihedral : 5.285 24.395 1599 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.38 % Allowed : 16.26 % Favored : 83.36 % 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: -4.35 (0.19), residues: 1587 helix: -0.96 (0.26), residues: 378 sheet: -3.72 (0.24), residues: 309 loop : -3.59 (0.19), residues: 900 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) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 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 : 0.275 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0274 time to fit residues: 0.5740 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3484 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: 0.0766 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0621 ------------------------------------------------------------------------------- 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: 30.0000 chunk 104 optimal weight: 40.0000 chunk 158 optimal weight: 40.0000 chunk 145 optimal weight: 40.0000 chunk 126 optimal weight: 40.0000 chunk 13 optimal weight: 70.0000 chunk 97 optimal weight: 0.0030 chunk 77 optimal weight: 50.0000 chunk 100 optimal weight: 30.0000 chunk 134 optimal weight: 50.0000 overall best weight: 28.0006 ------------------------------------------------------------------------------- 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: 0.6374 moved from start: 1.6504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 7950 Z= 0.368 Angle : 0.871 7.045 11067 Z= 0.563 Chirality : 0.044 0.154 1530 Planarity : 0.005 0.031 1599 Dihedral : 7.869 27.180 1599 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 29.20 Ramachandran Plot: Outliers : 3.21 % Allowed : 27.03 % Favored : 69.75 % 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: -5.85 (0.16), residues: 1587 helix: -3.10 (0.19), residues: 339 sheet: -4.53 (0.29), residues: 189 loop : -4.34 (0.16), residues: 1059 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) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 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 : 0.301 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0258 time to fit residues: 0.5763 Evaluate side-chains 3 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.258 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3375 Evaluate side-chains 0 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.051 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0754 Evaluate side-chains 0 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.051 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0594 ------------------------------------------------------------------------------- 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: 40.0000 chunk 116 optimal weight: 0.8980 chunk 18 optimal weight: 40.0000 chunk 35 optimal weight: 50.0000 chunk 126 optimal weight: 40.0000 chunk 52 optimal weight: 0.0970 chunk 129 optimal weight: 0.0970 chunk 15 optimal weight: 0.0000 chunk 23 optimal weight: 0.0970 chunk 110 optimal weight: 0.0010 chunk 7 optimal weight: 0.9990 overall best weight: 0.0584 ------------------------------------------------------------------------------- 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 = 0.3860 r_free = 0.3860 target = 0.071932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.059068 restraints weight = 36167.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.059412 restraints weight = 30765.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.059412 restraints weight = 28005.949| |-----------------------------------------------------------------------------| r_work (final): 0.3952 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.042799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.032304 restraints weight = 7337.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.032304 restraints weight = 7408.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.032304 restraints weight = 7408.942| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5751 moved from start: 1.5465 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= 0.141 Angle : 0.614 5.493 11067 Z= 0.391 Chirality : 0.041 0.127 1530 Planarity : 0.003 0.026 1599 Dihedral : 5.381 23.750 1599 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.38 % Allowed : 14.93 % Favored : 84.69 % 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: -4.68 (0.19), residues: 1587 helix: -1.16 (0.24), residues: 381 sheet: -3.86 (0.27), residues: 279 loop : -3.91 (0.18), residues: 927 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: 1303.29 seconds wall clock time: 24 minutes 33.48 seconds (1473.48 seconds total)