Starting phenix.real_space_refine on Tue Aug 26 22:58:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dgz_46853/08_2025/9dgz_46853.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dgz_46853/08_2025/9dgz_46853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dgz_46853/08_2025/9dgz_46853.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dgz_46853/08_2025/9dgz_46853.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dgz_46853/08_2025/9dgz_46853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dgz_46853/08_2025/9dgz_46853.map" } resolution = 2.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians S 117 5.16 5 C 13650 2.51 5 N 3720 2.21 5 O 4539 1.98 5 H 21701 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43727 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7209 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 458, 7201 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 440} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 458, 7201 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 440} Chain breaks: 1 bond proxies already assigned to first conformer: 7257 Chain: "B" Number of atoms: 7184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 7184 Classifications: {'peptide': 457} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 439} Chain breaks: 1 Chain: "C" Number of atoms: 7217 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 457, 7180 Classifications: {'peptide': 457} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 439} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 457, 7180 Classifications: {'peptide': 457} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 439} Chain breaks: 1 bond proxies already assigned to first conformer: 7204 Chain: "D" Number of atoms: 7238 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 459, 7214 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 441} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 459, 7214 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 441} Chain breaks: 1 bond proxies already assigned to first conformer: 7253 Chain: "E" Number of atoms: 7185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 7185 Classifications: {'peptide': 457} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 439} Chain breaks: 1 Chain: "F" Number of atoms: 7224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 7224 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 442} Chain breaks: 1 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 75 Classifications: {'water': 75} Link IDs: {None: 74} Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 84 Classifications: {'water': 84} Link IDs: {None: 83} Chain: "C" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "D" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "E" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "F" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Time building chain proxies: 12.14, per 1000 atoms: 0.28 Number of scatterers: 43727 At special positions: 0 Unit cell: (129.94, 137.24, 100.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 117 16.00 O 4539 8.00 N 3720 7.00 C 13650 6.00 H 21701 1.00 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: 4.06 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 953.7 nanoseconds 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5172 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 18 sheets defined 53.5% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 15 through 27 Processing helix chain 'A' and resid 38 through 46 Processing helix chain 'A' and resid 56 through 63 Processing helix chain 'A' and resid 74 through 82 Processing helix chain 'A' and resid 106 through 119 Processing helix chain 'A' and resid 135 through 147 removed outlier: 3.680A pdb=" N SER A 139 " --> pdb=" O ARG A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'A' and resid 185 through 200 Processing helix chain 'A' and resid 204 through 206 No H-bonds generated for 'chain 'A' and resid 204 through 206' Processing helix chain 'A' and resid 212 through 245 removed outlier: 3.577A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN A 224 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 257 Processing helix chain 'A' and resid 276 through 291 Processing helix chain 'A' and resid 293 through 322 removed outlier: 4.284A pdb=" N VAL A 303 " --> pdb=" O TYR A 299 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE A 304 " --> pdb=" O TRP A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 360 removed outlier: 3.746A pdb=" N TYR A 352 " --> pdb=" O SER A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 381 Processing helix chain 'A' and resid 391 through 394 No H-bonds generated for 'chain 'A' and resid 391 through 394' Processing helix chain 'A' and resid 400 through 406 Processing helix chain 'A' and resid 417 through 423 removed outlier: 3.506A pdb=" N LEU A 423 " --> pdb=" O PHE A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 432 removed outlier: 3.819A pdb=" N LYS A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 456 Processing helix chain 'B' and resid 15 through 27 Processing helix chain 'B' and resid 38 through 46 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 74 through 82 Processing helix chain 'B' and resid 106 through 120 Processing helix chain 'B' and resid 135 through 147 removed outlier: 3.582A pdb=" N SER B 139 " --> pdb=" O ARG B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 185 through 200 Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 212 through 245 removed outlier: 3.555A pdb=" N LEU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN B 224 " --> pdb=" O LYS B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 257 Processing helix chain 'B' and resid 276 through 291 Processing helix chain 'B' and resid 293 through 322 removed outlier: 3.540A pdb=" N GLN B 302 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL B 303 " --> pdb=" O TYR B 299 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE B 304 " --> pdb=" O TRP B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 360 removed outlier: 3.800A pdb=" N TYR B 352 " --> pdb=" O SER B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'B' and resid 391 through 394 No H-bonds generated for 'chain 'B' and resid 391 through 394' Processing helix chain 'B' and resid 400 through 406 Processing helix chain 'B' and resid 417 through 422 removed outlier: 4.182A pdb=" N LYS B 421 " --> pdb=" O TRP B 417 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU B 422 " --> pdb=" O ASP B 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 417 through 422' Processing helix chain 'B' and resid 424 through 432 removed outlier: 3.860A pdb=" N LYS B 431 " --> pdb=" O ARG B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 456 Processing helix chain 'C' and resid 15 through 27 Processing helix chain 'C' and resid 38 through 46 Processing helix chain 'C' and resid 56 through 65 Processing helix chain 'C' and resid 74 through 82 Processing helix chain 'C' and resid 106 through 120 Processing helix chain 'C' and resid 135 through 147 removed outlier: 3.603A pdb=" N SER C 139 " --> pdb=" O ARG C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 174 Processing helix chain 'C' and resid 185 through 200 Processing helix chain 'C' and resid 204 through 206 No H-bonds generated for 'chain 'C' and resid 204 through 206' Processing helix chain 'C' and resid 212 through 245 removed outlier: 3.629A pdb=" N LEU C 221 " --> pdb=" O GLU C 217 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN C 224 " --> pdb=" O LYS C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 257 Processing helix chain 'C' and resid 276 through 291 Processing helix chain 'C' and resid 293 through 322 removed outlier: 4.312A pdb=" N VAL C 303 " --> pdb=" O TYR C 299 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE C 304 " --> pdb=" O TRP C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 360 removed outlier: 3.741A pdb=" N TYR C 352 " --> pdb=" O SER C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 381 Processing helix chain 'C' and resid 390 through 394 Processing helix chain 'C' and resid 400 through 406 Processing helix chain 'C' and resid 417 through 423 removed outlier: 3.555A pdb=" N LEU C 423 " --> pdb=" O PHE C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 432 removed outlier: 3.855A pdb=" N LYS C 431 " --> pdb=" O ARG C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 456 Processing helix chain 'D' and resid 15 through 27 Processing helix chain 'D' and resid 38 through 46 Processing helix chain 'D' and resid 56 through 65 Processing helix chain 'D' and resid 74 through 82 Processing helix chain 'D' and resid 106 through 120 Processing helix chain 'D' and resid 135 through 147 removed outlier: 3.632A pdb=" N SER D 139 " --> pdb=" O ARG D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 174 Processing helix chain 'D' and resid 185 through 200 Processing helix chain 'D' and resid 204 through 206 No H-bonds generated for 'chain 'D' and resid 204 through 206' Processing helix chain 'D' and resid 212 through 245 removed outlier: 3.555A pdb=" N LEU D 221 " --> pdb=" O GLU D 217 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN D 224 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 257 Processing helix chain 'D' and resid 276 through 291 Processing helix chain 'D' and resid 293 through 322 removed outlier: 3.541A pdb=" N GLN D 302 " --> pdb=" O ARG D 298 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL D 303 " --> pdb=" O TYR D 299 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE D 304 " --> pdb=" O TRP D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 360 removed outlier: 3.803A pdb=" N TYR D 352 " --> pdb=" O SER D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 381 Processing helix chain 'D' and resid 390 through 394 Processing helix chain 'D' and resid 400 through 406 Processing helix chain 'D' and resid 417 through 422 removed outlier: 4.178A pdb=" N LYS D 421 " --> pdb=" O TRP D 417 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU D 422 " --> pdb=" O ASP D 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 417 through 422' Processing helix chain 'D' and resid 424 through 432 removed outlier: 3.858A pdb=" N LYS D 431 " --> pdb=" O ARG D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 456 Processing helix chain 'E' and resid 15 through 27 Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 56 through 63 Processing helix chain 'E' and resid 74 through 82 Processing helix chain 'E' and resid 106 through 120 Processing helix chain 'E' and resid 135 through 147 removed outlier: 3.663A pdb=" N SER E 139 " --> pdb=" O ARG E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 174 Processing helix chain 'E' and resid 185 through 200 Processing helix chain 'E' and resid 204 through 206 No H-bonds generated for 'chain 'E' and resid 204 through 206' Processing helix chain 'E' and resid 212 through 245 removed outlier: 3.627A pdb=" N LEU E 221 " --> pdb=" O GLU E 217 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN E 224 " --> pdb=" O LYS E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 257 Processing helix chain 'E' and resid 276 through 291 Processing helix chain 'E' and resid 293 through 322 removed outlier: 3.503A pdb=" N GLN E 302 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL E 303 " --> pdb=" O TYR E 299 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE E 304 " --> pdb=" O TRP E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 360 removed outlier: 3.742A pdb=" N TYR E 352 " --> pdb=" O SER E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 381 removed outlier: 3.508A pdb=" N ILE E 376 " --> pdb=" O PRO E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 394 No H-bonds generated for 'chain 'E' and resid 391 through 394' Processing helix chain 'E' and resid 400 through 406 Processing helix chain 'E' and resid 417 through 423 removed outlier: 3.555A pdb=" N LEU E 423 " --> pdb=" O PHE E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 432 removed outlier: 3.859A pdb=" N LYS E 431 " --> pdb=" O ARG E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 456 Processing helix chain 'F' and resid 15 through 27 Processing helix chain 'F' and resid 38 through 46 Processing helix chain 'F' and resid 56 through 65 Processing helix chain 'F' and resid 74 through 82 Processing helix chain 'F' and resid 106 through 119 Processing helix chain 'F' and resid 135 through 147 removed outlier: 3.674A pdb=" N SER F 139 " --> pdb=" O ARG F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 174 Processing helix chain 'F' and resid 185 through 200 Processing helix chain 'F' and resid 204 through 206 No H-bonds generated for 'chain 'F' and resid 204 through 206' Processing helix chain 'F' and resid 212 through 245 removed outlier: 3.570A pdb=" N LEU F 221 " --> pdb=" O GLU F 217 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 257 Processing helix chain 'F' and resid 276 through 291 Processing helix chain 'F' and resid 293 through 322 removed outlier: 4.285A pdb=" N VAL F 303 " --> pdb=" O TYR F 299 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE F 304 " --> pdb=" O TRP F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 348 through 360 removed outlier: 3.743A pdb=" N TYR F 352 " --> pdb=" O SER F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 381 removed outlier: 3.500A pdb=" N ILE F 376 " --> pdb=" O PRO F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 394 Processing helix chain 'F' and resid 400 through 406 Processing helix chain 'F' and resid 417 through 423 Processing helix chain 'F' and resid 424 through 432 removed outlier: 3.818A pdb=" N LYS F 431 " --> pdb=" O ARG F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 456 Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 72 removed outlier: 6.565A pdb=" N LYS A 6 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N PHE A 86 " --> pdb=" O LYS A 6 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N CYS A 8 " --> pdb=" O PHE A 86 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 181 removed outlier: 6.150A pdb=" N VAL A 178 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR A 211 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE A 180 " --> pdb=" O THR A 211 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 395 through 397 removed outlier: 6.077A pdb=" N LEU A 364 " --> pdb=" O THR A 396 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE A 331 " --> pdb=" O HIS A 365 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N TYR A 367 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE A 333 " --> pdb=" O TYR A 367 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA A 410 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL A 411 " --> pdb=" O PHE A 439 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ILE A 438 " --> pdb=" O GLU A 460 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 69 through 72 removed outlier: 6.557A pdb=" N LYS B 6 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N PHE B 86 " --> pdb=" O LYS B 6 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N CYS B 8 " --> pdb=" O PHE B 86 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 178 through 181 removed outlier: 6.147A pdb=" N VAL B 178 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N THR B 211 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE B 180 " --> pdb=" O THR B 211 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 395 through 397 removed outlier: 6.096A pdb=" N LEU B 364 " --> pdb=" O THR B 396 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE B 331 " --> pdb=" O HIS B 365 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N TYR B 367 " --> pdb=" O ILE B 331 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE B 333 " --> pdb=" O TYR B 367 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA B 410 " --> pdb=" O LYS B 330 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL B 411 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA B 436 " --> pdb=" O GLN B 458 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N GLU B 460 " --> pdb=" O ALA B 436 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ILE B 438 " --> pdb=" O GLU B 460 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 69 through 72 removed outlier: 6.550A pdb=" N LYS C 6 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N PHE C 86 " --> pdb=" O LYS C 6 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N CYS C 8 " --> pdb=" O PHE C 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 178 through 181 removed outlier: 6.133A pdb=" N VAL C 178 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N THR C 211 " --> pdb=" O VAL C 178 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE C 180 " --> pdb=" O THR C 211 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 395 through 397 removed outlier: 6.027A pdb=" N LEU C 364 " --> pdb=" O THR C 396 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE C 331 " --> pdb=" O HIS C 365 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N TYR C 367 " --> pdb=" O ILE C 331 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE C 333 " --> pdb=" O TYR C 367 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA C 410 " --> pdb=" O LYS C 330 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL C 411 " --> pdb=" O PHE C 439 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA C 436 " --> pdb=" O GLN C 458 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLU C 460 " --> pdb=" O ALA C 436 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ILE C 438 " --> pdb=" O GLU C 460 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 69 through 72 removed outlier: 6.566A pdb=" N LYS D 6 " --> pdb=" O LEU D 84 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N PHE D 86 " --> pdb=" O LYS D 6 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N CYS D 8 " --> pdb=" O PHE D 86 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 178 through 181 removed outlier: 6.141A pdb=" N VAL D 178 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N THR D 211 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE D 180 " --> pdb=" O THR D 211 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 395 through 397 removed outlier: 6.055A pdb=" N LEU D 364 " --> pdb=" O THR D 396 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE D 331 " --> pdb=" O HIS D 365 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N TYR D 367 " --> pdb=" O ILE D 331 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE D 333 " --> pdb=" O TYR D 367 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA D 410 " --> pdb=" O LYS D 330 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL D 411 " --> pdb=" O PHE D 439 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA D 436 " --> pdb=" O GLN D 458 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N GLU D 460 " --> pdb=" O ALA D 436 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE D 438 " --> pdb=" O GLU D 460 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 69 through 72 removed outlier: 6.569A pdb=" N LYS E 6 " --> pdb=" O LEU E 84 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N PHE E 86 " --> pdb=" O LYS E 6 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N CYS E 8 " --> pdb=" O PHE E 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 178 through 181 removed outlier: 6.132A pdb=" N VAL E 178 " --> pdb=" O LEU E 209 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N THR E 211 " --> pdb=" O VAL E 178 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE E 180 " --> pdb=" O THR E 211 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 395 through 397 removed outlier: 6.195A pdb=" N LEU E 364 " --> pdb=" O THR E 396 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE E 331 " --> pdb=" O HIS E 365 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N TYR E 367 " --> pdb=" O ILE E 331 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE E 333 " --> pdb=" O TYR E 367 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA E 410 " --> pdb=" O LYS E 330 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL E 411 " --> pdb=" O PHE E 439 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA E 436 " --> pdb=" O GLN E 458 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N GLU E 460 " --> pdb=" O ALA E 436 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE E 438 " --> pdb=" O GLU E 460 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 69 through 72 removed outlier: 6.561A pdb=" N LYS F 6 " --> pdb=" O LEU F 84 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N PHE F 86 " --> pdb=" O LYS F 6 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N CYS F 8 " --> pdb=" O PHE F 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 178 through 181 removed outlier: 6.150A pdb=" N VAL F 178 " --> pdb=" O LEU F 209 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N THR F 211 " --> pdb=" O VAL F 178 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE F 180 " --> pdb=" O THR F 211 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'F' and resid 395 through 397 removed outlier: 6.078A pdb=" N LEU F 364 " --> pdb=" O THR F 396 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE F 331 " --> pdb=" O HIS F 365 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N TYR F 367 " --> pdb=" O ILE F 331 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE F 333 " --> pdb=" O TYR F 367 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA F 410 " --> pdb=" O LYS F 330 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL F 411 " --> pdb=" O PHE F 439 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA F 436 " --> pdb=" O GLN F 458 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N GLU F 460 " --> pdb=" O ALA F 436 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ILE F 438 " --> pdb=" O GLU F 460 " (cutoff:3.500A) 1053 hydrogen bonds defined for protein. 3118 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: 12.25 Time building geometry restraints manager: 5.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 21626 1.03 - 1.23: 112 1.23 - 1.42: 8931 1.42 - 1.62: 12822 1.62 - 1.81: 159 Bond restraints: 43650 Sorted by residual: bond pdb=" C ASN C 159 " pdb=" O ASN C 159 " ideal model delta sigma weight residual 1.236 1.198 0.039 1.15e-02 7.56e+03 1.14e+01 bond pdb=" N VAL D 326 " pdb=" CA VAL D 326 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.35e+00 bond pdb=" N VAL F 281 " pdb=" CA VAL F 281 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 7.75e+00 bond pdb=" N ILE A 459 " pdb=" CA ILE A 459 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.24e-02 6.50e+03 7.60e+00 bond pdb=" N ILE A 455 " pdb=" CA ILE A 455 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.27e+00 ... (remaining 43645 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 76244 1.33 - 2.66: 2641 2.66 - 3.99: 149 3.99 - 5.33: 9 5.33 - 6.66: 3 Bond angle restraints: 79046 Sorted by residual: angle pdb=" N ASP B 359 " pdb=" CA ASP B 359 " pdb=" C ASP B 359 " ideal model delta sigma weight residual 111.82 107.10 4.72 1.16e+00 7.43e-01 1.65e+01 angle pdb=" CA ASN C 159 " pdb=" C ASN C 159 " pdb=" O ASN C 159 " ideal model delta sigma weight residual 121.28 117.18 4.10 1.10e+00 8.26e-01 1.39e+01 angle pdb=" N ILE F 455 " pdb=" CA ILE F 455 " pdb=" C ILE F 455 " ideal model delta sigma weight residual 111.05 106.70 4.35 1.25e+00 6.40e-01 1.21e+01 angle pdb=" CA ASN C 159 " pdb=" C ASN C 159 " pdb=" N PRO C 160 " ideal model delta sigma weight residual 117.44 120.63 -3.19 9.20e-01 1.18e+00 1.20e+01 angle pdb=" C ASN C 159 " pdb=" CA ASN C 159 " pdb=" CB ASN C 159 " ideal model delta sigma weight residual 111.27 116.27 -5.00 1.47e+00 4.63e-01 1.16e+01 ... (remaining 79041 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 19223 17.46 - 34.92: 892 34.92 - 52.37: 220 52.37 - 69.83: 66 69.83 - 87.29: 20 Dihedral angle restraints: 20421 sinusoidal: 11224 harmonic: 9197 Sorted by residual: dihedral pdb=" CA PHE D 457 " pdb=" C PHE D 457 " pdb=" N GLN D 458 " pdb=" CA GLN D 458 " ideal model delta harmonic sigma weight residual 180.00 160.37 19.63 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA PHE B 457 " pdb=" C PHE B 457 " pdb=" N GLN B 458 " pdb=" CA GLN B 458 " ideal model delta harmonic sigma weight residual 180.00 160.43 19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA PHE E 457 " pdb=" C PHE E 457 " pdb=" N GLN E 458 " pdb=" CA GLN E 458 " ideal model delta harmonic sigma weight residual 180.00 160.51 19.49 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 20418 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2602 0.049 - 0.097: 625 0.097 - 0.146: 159 0.146 - 0.194: 2 0.194 - 0.243: 4 Chirality restraints: 3392 Sorted by residual: chirality pdb=" CA ILE F 455 " pdb=" N ILE F 455 " pdb=" C ILE F 455 " pdb=" CB ILE F 455 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA ILE A 455 " pdb=" N ILE A 455 " pdb=" C ILE A 455 " pdb=" CB ILE A 455 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA GLU B 360 " pdb=" N GLU B 360 " pdb=" C GLU B 360 " pdb=" CB GLU B 360 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.78e-01 ... (remaining 3389 not shown) Planarity restraints: 6468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 159 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C ASN C 159 " 0.056 2.00e-02 2.50e+03 pdb=" O ASN C 159 " -0.021 2.00e-02 2.50e+03 pdb=" N PRO C 160 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 361 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.62e+00 pdb=" N ALA B 362 " -0.050 2.00e-02 2.50e+03 pdb=" CA ALA B 362 " 0.013 2.00e-02 2.50e+03 pdb=" H ALA B 362 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 360 " 0.006 2.00e-02 2.50e+03 1.29e-02 1.65e+00 pdb=" C GLU B 360 " -0.022 2.00e-02 2.50e+03 pdb=" O GLU B 360 " 0.008 2.00e-02 2.50e+03 pdb=" N GLY B 361 " 0.008 2.00e-02 2.50e+03 ... (remaining 6465 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 2831 2.20 - 2.80: 94123 2.80 - 3.40: 131249 3.40 - 4.00: 176716 4.00 - 4.60: 266870 Nonbonded interactions: 671789 Sorted by model distance: nonbonded pdb=" O THR E 95 " pdb=" HZ2 LYS E 100 " model vdw 1.602 2.450 nonbonded pdb=" HZ3 LYS B 330 " pdb=" O ASP B 406 " model vdw 1.603 2.450 nonbonded pdb=" HZ3 LYS B 329 " pdb=" O HOH B 503 " model vdw 1.605 2.450 nonbonded pdb=" O VAL B 377 " pdb=" HG SER B 381 " model vdw 1.607 2.450 nonbonded pdb=" O ASN D 235 " pdb=" HG SER D 238 " model vdw 1.607 2.450 ... (remaining 671784 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' and (resid 2 through 239 or resid 241 through 269 or resid 271 throug \ h 275 or resid 277 through 381 or resid 390 through 465)) selection = (chain 'B' and (resid 2 through 239 or resid 241 through 269 or resid 271 throug \ h 275 or resid 277 through 465)) selection = (chain 'C' and (resid 2 through 239 or resid 241 through 269 or resid 271 throug \ h 275 or resid 277 through 381 or (resid 390 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name OE1 or name NE2 or name HA or n \ ame HB2 or name HB3 or name HG2 or name HG3 or name HE21 or name HE22)) or resid \ 391 through 465)) selection = (chain 'D' and (resid 2 through 200 or (resid 201 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 202 through 239 or resid 241 through 269 or resid 271 through 275 \ or resid 277 through 381 or (resid 390 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name OE1 or name NE2 or name HA or name H \ B2 or name HB3 or name HG2 or name HG3 or name HE21 or name HE22)) or resid 391 \ through 465)) selection = (chain 'E' and (resid 2 through 200 or (resid 201 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 202 through 239 or resid 241 through 269 or resid 271 through 275 \ or resid 277 through 465)) selection = (chain 'F' and (resid 2 through 239 or resid 241 through 269 or resid 271 throug \ h 275 or resid 277 through 381 or (resid 390 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name OE1 or name NE2 or name HA or n \ ame HB2 or name HB3 or name HG2 or name HG3 or name HE21 or name HE22)) or resid \ 391 through 465)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.580 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: 0.360 Extract box with map and model: 0.820 Check model and map are aligned: 0.150 Set scattering table: 0.160 Process input model: 48.720 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:9.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5963 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 : 0.003 0.039 21949 Z= 0.145 Angle : 0.497 6.658 29706 Z= 0.282 Chirality : 0.044 0.243 3392 Planarity : 0.003 0.032 3828 Dihedral : 10.940 87.288 8186 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.51 % Allowed : 2.07 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.15), residues: 2730 helix: 1.58 (0.14), residues: 1339 sheet: 0.14 (0.24), residues: 420 loop : -0.24 (0.18), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 115 TYR 0.011 0.002 TYR E 402 PHE 0.017 0.002 PHE F 272 TRP 0.014 0.002 TRP A 300 HIS 0.003 0.001 HIS A 365 Details of bonding type rmsd covalent geometry : bond 0.00280 (21949) covalent geometry : angle 0.49694 (29706) hydrogen bonds : bond 0.19728 ( 1053) hydrogen bonds : angle 5.68948 ( 3118) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 413 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.6051 (mmtp) cc_final: 0.5479 (mtpt) REVERT: A 29 GLU cc_start: 0.5001 (pt0) cc_final: 0.4611 (pm20) REVERT: A 65 ARG cc_start: 0.5873 (ttp-170) cc_final: 0.5635 (ttp-170) REVERT: A 74 ASN cc_start: 0.5954 (t0) cc_final: 0.5699 (t0) REVERT: A 77 ASP cc_start: 0.4839 (t0) cc_final: 0.4395 (m-30) REVERT: A 80 LYS cc_start: 0.5227 (tttm) cc_final: 0.4910 (ttpt) REVERT: A 112 CYS cc_start: 0.5671 (t) cc_final: 0.5348 (m) REVERT: A 138 GLU cc_start: 0.5240 (tt0) cc_final: 0.4047 (tp30) REVERT: A 142 ARG cc_start: 0.5164 (mtt180) cc_final: 0.4293 (mmm160) REVERT: A 161 GLU cc_start: 0.5817 (tp30) cc_final: 0.4573 (pp20) REVERT: A 170 LYS cc_start: 0.5427 (ttpp) cc_final: 0.4877 (tppp) REVERT: A 187 GLU cc_start: 0.4696 (mt-10) cc_final: 0.4239 (mp0) REVERT: A 190 ARG cc_start: 0.4968 (mtp-110) cc_final: 0.4594 (ttp80) REVERT: A 193 GLN cc_start: 0.5190 (mm-40) cc_final: 0.4857 (mm-40) REVERT: A 259 GLN cc_start: 0.5214 (mt0) cc_final: 0.4551 (mm-40) REVERT: A 328 ASP cc_start: 0.5885 (m-30) cc_final: 0.5584 (m-30) REVERT: A 352 TYR cc_start: 0.6489 (m-80) cc_final: 0.6194 (m-80) REVERT: A 373 ARG cc_start: 0.5559 (ttm170) cc_final: 0.5202 (ptm-80) REVERT: A 421 LYS cc_start: 0.5853 (tttt) cc_final: 0.5429 (mtmm) REVERT: A 451 GLU cc_start: 0.4829 (tt0) cc_final: 0.4076 (tp30) REVERT: B 5 LYS cc_start: 0.5826 (mmtp) cc_final: 0.5161 (mtpt) REVERT: B 29 GLU cc_start: 0.5021 (mt-10) cc_final: 0.4721 (pm20) REVERT: B 74 ASN cc_start: 0.5800 (t0) cc_final: 0.5241 (t0) REVERT: B 77 ASP cc_start: 0.4921 (t0) cc_final: 0.4376 (m-30) REVERT: B 100 LYS cc_start: 0.5242 (tttt) cc_final: 0.5029 (tttp) REVERT: B 135 ARG cc_start: 0.3647 (mtm-85) cc_final: 0.3267 (mmm160) REVERT: B 138 GLU cc_start: 0.5535 (tt0) cc_final: 0.5135 (tt0) REVERT: B 170 LYS cc_start: 0.5531 (ttpp) cc_final: 0.4977 (ttmm) REVERT: B 171 ASP cc_start: 0.5352 (m-30) cc_final: 0.5018 (m-30) REVERT: B 190 ARG cc_start: 0.4941 (mtp-110) cc_final: 0.4384 (ttm110) REVERT: B 205 ARG cc_start: 0.5283 (ttm170) cc_final: 0.4797 (tpt90) REVERT: B 206 GLU cc_start: 0.5552 (mt-10) cc_final: 0.5243 (mp0) REVERT: B 259 GLN cc_start: 0.5385 (mt0) cc_final: 0.4737 (mm-40) REVERT: B 267 LYS cc_start: 0.5995 (mttp) cc_final: 0.5454 (mmmt) REVERT: B 373 ARG cc_start: 0.4927 (mtp180) cc_final: 0.4702 (ptm-80) REVERT: B 421 LYS cc_start: 0.5842 (mttt) cc_final: 0.5611 (mtmm) REVERT: B 430 LYS cc_start: 0.5790 (mttt) cc_final: 0.5570 (mttp) REVERT: B 431 LYS cc_start: 0.5709 (mttt) cc_final: 0.5197 (mptt) REVERT: B 464 LYS cc_start: 0.5879 (tttt) cc_final: 0.5665 (ttmp) REVERT: C 5 LYS cc_start: 0.5898 (mmtp) cc_final: 0.5316 (mtpt) REVERT: C 31 ARG cc_start: 0.5684 (ttt90) cc_final: 0.5373 (ttt90) REVERT: C 80 LYS cc_start: 0.4910 (tttm) cc_final: 0.4602 (ttpt) REVERT: C 100 LYS cc_start: 0.5330 (tttt) cc_final: 0.5060 (tttt) REVERT: C 112 CYS cc_start: 0.5356 (t) cc_final: 0.5018 (t) REVERT: C 135 ARG cc_start: 0.3816 (mtm-85) cc_final: 0.3353 (mpt-90) REVERT: C 138 GLU cc_start: 0.5104 (tp30) cc_final: 0.4647 (tt0) REVERT: C 142 ARG cc_start: 0.5125 (mtt180) cc_final: 0.4122 (mmm-85) REVERT: C 170 LYS cc_start: 0.5666 (ttpp) cc_final: 0.5107 (tppp) REVERT: C 171 ASP cc_start: 0.5302 (m-30) cc_final: 0.4986 (m-30) REVERT: C 187 GLU cc_start: 0.4864 (mt-10) cc_final: 0.4354 (mp0) REVERT: C 200 GLU cc_start: 0.5898 (mt-10) cc_final: 0.5439 (mm-30) REVERT: C 205 ARG cc_start: 0.5501 (ttm-80) cc_final: 0.5002 (tpt90) REVERT: C 214 TRP cc_start: 0.6203 (m-90) cc_final: 0.5063 (m100) REVERT: C 259 GLN cc_start: 0.5172 (mt0) cc_final: 0.4520 (mm110) REVERT: C 267 LYS cc_start: 0.6006 (mmtm) cc_final: 0.5608 (mmmt) REVERT: C 320 ASP cc_start: 0.5751 (t70) cc_final: 0.5065 (m-30) REVERT: C 328 ASP cc_start: 0.6089 (m-30) cc_final: 0.5703 (m-30) REVERT: C 431 LYS cc_start: 0.5627 (mttt) cc_final: 0.5080 (mmtm) REVERT: C 451 GLU cc_start: 0.4876 (tt0) cc_final: 0.4099 (tp30) REVERT: D 5 LYS cc_start: 0.5852 (mmtp) cc_final: 0.5181 (mtpt) REVERT: D 77 ASP cc_start: 0.4780 (t0) cc_final: 0.4324 (m-30) REVERT: D 80 LYS cc_start: 0.5108 (tttm) cc_final: 0.4898 (ttpp) REVERT: D 98 MET cc_start: 0.4989 (mtp) cc_final: 0.4598 (mmm) REVERT: D 142 ARG cc_start: 0.4868 (ttp-110) cc_final: 0.4507 (mtp180) REVERT: D 170 LYS cc_start: 0.5564 (ttpp) cc_final: 0.5003 (ttmm) REVERT: D 171 ASP cc_start: 0.5338 (m-30) cc_final: 0.5020 (m-30) REVERT: D 205 ARG cc_start: 0.5318 (ptp-110) cc_final: 0.4772 (tpt90) REVERT: D 206 GLU cc_start: 0.5204 (mp0) cc_final: 0.4914 (mp0) REVERT: D 259 GLN cc_start: 0.5245 (mt0) cc_final: 0.4591 (mm-40) REVERT: D 267 LYS cc_start: 0.6008 (mmtm) cc_final: 0.5494 (tttm) REVERT: D 373 ARG cc_start: 0.5075 (mtt180) cc_final: 0.4700 (ptm-80) REVERT: D 421 LYS cc_start: 0.5815 (mttt) cc_final: 0.5565 (mtmm) REVERT: D 430 LYS cc_start: 0.5656 (mttt) cc_final: 0.5437 (mttp) REVERT: D 431 LYS cc_start: 0.5634 (mttt) cc_final: 0.5116 (mptt) REVERT: D 451 GLU cc_start: 0.5039 (tt0) cc_final: 0.4256 (tp30) REVERT: D 464 LYS cc_start: 0.5734 (tttt) cc_final: 0.5499 (ttmp) REVERT: E 31 ARG cc_start: 0.5767 (ttt90) cc_final: 0.5535 (ttt90) REVERT: E 80 LYS cc_start: 0.5036 (tttm) cc_final: 0.4733 (ttpt) REVERT: E 93 THR cc_start: 0.6271 (m) cc_final: 0.5963 (t) REVERT: E 112 CYS cc_start: 0.5438 (t) cc_final: 0.5144 (t) REVERT: E 138 GLU cc_start: 0.5276 (tt0) cc_final: 0.4860 (tt0) REVERT: E 142 ARG cc_start: 0.4975 (mtp180) cc_final: 0.4526 (mtp180) REVERT: E 170 LYS cc_start: 0.5826 (tttt) cc_final: 0.5131 (tptp) REVERT: E 190 ARG cc_start: 0.5294 (mtp-110) cc_final: 0.4992 (ttp80) REVERT: E 200 GLU cc_start: 0.5807 (mt-10) cc_final: 0.5270 (mm-30) REVERT: E 205 ARG cc_start: 0.5131 (ttp-110) cc_final: 0.4653 (tpt90) REVERT: E 206 GLU cc_start: 0.5496 (mt-10) cc_final: 0.5262 (mp0) REVERT: E 259 GLN cc_start: 0.5169 (mt0) cc_final: 0.4517 (mm110) REVERT: E 267 LYS cc_start: 0.6024 (mmtm) cc_final: 0.5621 (mmmt) REVERT: E 279 LYS cc_start: 0.5612 (tttm) cc_final: 0.5355 (ttpp) REVERT: E 320 ASP cc_start: 0.5794 (t70) cc_final: 0.5111 (m-30) REVERT: E 328 ASP cc_start: 0.6123 (m-30) cc_final: 0.5758 (m-30) REVERT: E 403 GLU cc_start: 0.5457 (tt0) cc_final: 0.5131 (tt0) REVERT: E 431 LYS cc_start: 0.5687 (mttt) cc_final: 0.5137 (mmtm) REVERT: E 451 GLU cc_start: 0.4967 (tt0) cc_final: 0.4217 (tp30) REVERT: F 5 LYS cc_start: 0.5975 (mmtp) cc_final: 0.5228 (mtpt) REVERT: F 80 LYS cc_start: 0.5386 (tttm) cc_final: 0.5088 (ttpt) REVERT: F 93 THR cc_start: 0.6249 (m) cc_final: 0.5965 (t) REVERT: F 100 LYS cc_start: 0.5225 (tttt) cc_final: 0.5024 (tttp) REVERT: F 138 GLU cc_start: 0.5471 (tp30) cc_final: 0.4936 (tt0) REVERT: F 142 ARG cc_start: 0.5163 (ttp-110) cc_final: 0.4541 (mmm160) REVERT: F 161 GLU cc_start: 0.5835 (tp30) cc_final: 0.4586 (pp20) REVERT: F 170 LYS cc_start: 0.5501 (ttpp) cc_final: 0.4956 (tppp) REVERT: F 187 GLU cc_start: 0.4697 (mt-10) cc_final: 0.4221 (mp0) REVERT: F 193 GLN cc_start: 0.5137 (mm-40) cc_final: 0.4829 (mm-40) REVERT: F 205 ARG cc_start: 0.5028 (ttp-110) cc_final: 0.4738 (tpt90) REVERT: F 259 GLN cc_start: 0.5248 (mt0) cc_final: 0.4586 (mm-40) REVERT: F 267 LYS cc_start: 0.5998 (mttp) cc_final: 0.5459 (mmmt) REVERT: F 328 ASP cc_start: 0.5921 (m-30) cc_final: 0.5616 (m-30) REVERT: F 373 ARG cc_start: 0.5627 (ttm-80) cc_final: 0.5305 (ttt-90) REVERT: F 421 LYS cc_start: 0.5856 (tttt) cc_final: 0.5362 (mtmm) REVERT: F 451 GLU cc_start: 0.4804 (tt0) cc_final: 0.4055 (tp30) REVERT: F 458 GLN cc_start: 0.5554 (OUTLIER) cc_final: 0.5229 (tt0) outliers start: 11 outliers final: 4 residues processed: 422 average time/residue: 2.2571 time to fit residues: 1045.2984 Evaluate side-chains 353 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 348 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 458 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.0870 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 overall best weight: 2.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 458 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.162844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.147530 restraints weight = 55825.571| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 0.56 r_work: 0.3381 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 1.79 restraints_weight: 0.2500 r_work: 0.3124 rms_B_bonded: 4.82 restraints_weight: 0.1250 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21949 Z= 0.165 Angle : 0.537 3.843 29706 Z= 0.301 Chirality : 0.045 0.149 3392 Planarity : 0.004 0.054 3828 Dihedral : 4.821 57.739 2992 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.72 % Allowed : 4.86 % Favored : 94.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.15), residues: 2730 helix: 1.64 (0.13), residues: 1382 sheet: -0.35 (0.23), residues: 445 loop : -0.39 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 31 TYR 0.012 0.002 TYR D 367 PHE 0.012 0.002 PHE F 338 TRP 0.015 0.002 TRP A 300 HIS 0.003 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00332 (21949) covalent geometry : angle 0.53663 (29706) hydrogen bonds : bond 0.06898 ( 1053) hydrogen bonds : angle 4.40267 ( 3118) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 350 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7001 (ttp-170) cc_final: 0.6757 (ttp-170) REVERT: B 171 ASP cc_start: 0.7431 (m-30) cc_final: 0.7106 (m-30) REVERT: C 171 ASP cc_start: 0.7361 (m-30) cc_final: 0.7045 (m-30) REVERT: C 214 TRP cc_start: 0.8595 (m-90) cc_final: 0.8230 (m100) REVERT: C 328 ASP cc_start: 0.8164 (m-30) cc_final: 0.7943 (m-30) REVERT: D 171 ASP cc_start: 0.7303 (m-30) cc_final: 0.6969 (m-30) REVERT: D 206 GLU cc_start: 0.7091 (mp0) cc_final: 0.6885 (pm20) REVERT: E 98 MET cc_start: 0.7423 (mtp) cc_final: 0.7013 (mmm) REVERT: E 328 ASP cc_start: 0.8208 (m-30) cc_final: 0.7917 (m-30) REVERT: F 426 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6958 (tt0) outliers start: 16 outliers final: 7 residues processed: 355 average time/residue: 2.2467 time to fit residues: 877.2979 Evaluate side-chains 324 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 316 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 398 SER Chi-restraints excluded: chain F residue 426 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 218 optimal weight: 6.9990 chunk 242 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 217 optimal weight: 3.9990 chunk 70 optimal weight: 0.0870 chunk 109 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 246 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN B 365 HIS E 458 GLN F 118 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.160603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.144955 restraints weight = 52286.166| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 0.55 r_work: 0.3343 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 1.76 restraints_weight: 0.2500 r_work: 0.3110 rms_B_bonded: 4.49 restraints_weight: 0.1250 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21949 Z= 0.217 Angle : 0.602 4.379 29706 Z= 0.339 Chirality : 0.046 0.151 3392 Planarity : 0.005 0.055 3828 Dihedral : 4.979 47.658 2989 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.93 % Allowed : 6.77 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.15), residues: 2730 helix: 1.18 (0.13), residues: 1386 sheet: -0.75 (0.23), residues: 413 loop : -0.49 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 31 TYR 0.015 0.003 TYR E 402 PHE 0.016 0.003 PHE F 338 TRP 0.017 0.003 TRP D 214 HIS 0.003 0.001 HIS D 429 Details of bonding type rmsd covalent geometry : bond 0.00450 (21949) covalent geometry : angle 0.60162 (29706) hydrogen bonds : bond 0.07389 ( 1053) hydrogen bonds : angle 4.49835 ( 3118) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 306 time to evaluate : 1.272 Fit side-chains REVERT: A 426 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6941 (tt0) REVERT: B 171 ASP cc_start: 0.7409 (m-30) cc_final: 0.7065 (m-30) REVERT: B 200 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7945 (mm-30) REVERT: C 171 ASP cc_start: 0.7221 (m-30) cc_final: 0.6897 (m-30) REVERT: C 214 TRP cc_start: 0.8525 (m-90) cc_final: 0.8204 (m100) REVERT: C 328 ASP cc_start: 0.8183 (m-30) cc_final: 0.7878 (m-30) REVERT: D 135 ARG cc_start: 0.6465 (mmm160) cc_final: 0.6020 (mmt90) REVERT: D 171 ASP cc_start: 0.7333 (m-30) cc_final: 0.6992 (m-30) outliers start: 21 outliers final: 12 residues processed: 315 average time/residue: 1.9679 time to fit residues: 685.0849 Evaluate side-chains 305 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 292 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 398 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 203 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 241 optimal weight: 7.9990 chunk 172 optimal weight: 0.2980 chunk 57 optimal weight: 9.9990 chunk 142 optimal weight: 7.9990 chunk 218 optimal weight: 8.9990 chunk 164 optimal weight: 0.8980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 365 HIS F 118 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.162015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.146605 restraints weight = 56393.702| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 0.56 r_work: 0.3371 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 1.86 restraints_weight: 0.2500 r_work: 0.3144 rms_B_bonded: 4.39 restraints_weight: 0.1250 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21949 Z= 0.163 Angle : 0.526 3.977 29706 Z= 0.294 Chirality : 0.044 0.145 3392 Planarity : 0.004 0.046 3828 Dihedral : 4.757 47.508 2989 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.85 % Allowed : 7.53 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.15), residues: 2730 helix: 1.37 (0.13), residues: 1386 sheet: -0.91 (0.23), residues: 430 loop : -0.56 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 31 TYR 0.013 0.002 TYR E 402 PHE 0.015 0.002 PHE F 338 TRP 0.015 0.002 TRP A 300 HIS 0.002 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00331 (21949) covalent geometry : angle 0.52610 (29706) hydrogen bonds : bond 0.06423 ( 1053) hydrogen bonds : angle 4.28786 ( 3118) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 306 time to evaluate : 1.254 Fit side-chains REVERT: B 171 ASP cc_start: 0.7288 (m-30) cc_final: 0.6924 (m-30) REVERT: C 171 ASP cc_start: 0.7227 (m-30) cc_final: 0.6875 (m-30) REVERT: C 214 TRP cc_start: 0.8542 (m-90) cc_final: 0.8202 (m100) REVERT: C 328 ASP cc_start: 0.8219 (m-30) cc_final: 0.7985 (m-30) REVERT: D 135 ARG cc_start: 0.6465 (mmm160) cc_final: 0.6041 (mmt90) REVERT: D 171 ASP cc_start: 0.7239 (m-30) cc_final: 0.6878 (m-30) outliers start: 19 outliers final: 11 residues processed: 315 average time/residue: 1.7121 time to fit residues: 600.2664 Evaluate side-chains 310 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 299 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 130 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 191 optimal weight: 6.9990 chunk 219 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 114 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 238 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 242 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN F 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.161344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.144061 restraints weight = 52987.720| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 0.60 r_work: 0.3352 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work: 0.3108 rms_B_bonded: 4.73 restraints_weight: 0.1250 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21949 Z= 0.183 Angle : 0.553 4.032 29706 Z= 0.311 Chirality : 0.045 0.146 3392 Planarity : 0.005 0.063 3828 Dihedral : 4.865 49.523 2989 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.72 % Allowed : 7.95 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.15), residues: 2730 helix: 1.28 (0.13), residues: 1386 sheet: -0.96 (0.23), residues: 425 loop : -0.59 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 31 TYR 0.014 0.002 TYR E 402 PHE 0.016 0.002 PHE E 338 TRP 0.015 0.003 TRP A 300 HIS 0.003 0.001 HIS A 365 Details of bonding type rmsd covalent geometry : bond 0.00375 (21949) covalent geometry : angle 0.55300 (29706) hydrogen bonds : bond 0.06754 ( 1053) hydrogen bonds : angle 4.34771 ( 3118) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 295 time to evaluate : 1.217 Fit side-chains REVERT: B 171 ASP cc_start: 0.7341 (m-30) cc_final: 0.7002 (m-30) REVERT: C 171 ASP cc_start: 0.7227 (m-30) cc_final: 0.6888 (m-30) REVERT: C 214 TRP cc_start: 0.8569 (m-90) cc_final: 0.8211 (m100) REVERT: C 328 ASP cc_start: 0.8247 (m-30) cc_final: 0.8031 (m-30) REVERT: C 422 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7657 (mm-30) REVERT: D 135 ARG cc_start: 0.6522 (mmm160) cc_final: 0.6034 (mmt90) REVERT: D 171 ASP cc_start: 0.7284 (m-30) cc_final: 0.6921 (m-30) REVERT: D 200 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7945 (mm-30) REVERT: E 328 ASP cc_start: 0.8254 (m-30) cc_final: 0.8034 (m-30) outliers start: 16 outliers final: 12 residues processed: 303 average time/residue: 1.6721 time to fit residues: 565.3147 Evaluate side-chains 303 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 291 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 130 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 238 optimal weight: 5.9990 chunk 205 optimal weight: 7.9990 chunk 160 optimal weight: 8.9990 chunk 235 optimal weight: 6.9990 chunk 191 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 147 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 chunk 210 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN F 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.160203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.144460 restraints weight = 52104.473| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 0.56 r_work: 0.3347 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 1.78 restraints_weight: 0.2500 r_work: 0.3086 rms_B_bonded: 4.84 restraints_weight: 0.1250 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 21949 Z= 0.243 Angle : 0.629 4.399 29706 Z= 0.355 Chirality : 0.046 0.149 3392 Planarity : 0.006 0.068 3828 Dihedral : 5.139 51.340 2989 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.97 % Allowed : 7.99 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.15), residues: 2730 helix: 1.01 (0.13), residues: 1386 sheet: -0.89 (0.23), residues: 413 loop : -0.68 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 135 TYR 0.017 0.003 TYR E 402 PHE 0.019 0.003 PHE F 338 TRP 0.016 0.003 TRP F 300 HIS 0.004 0.001 HIS D 429 Details of bonding type rmsd covalent geometry : bond 0.00509 (21949) covalent geometry : angle 0.62922 (29706) hydrogen bonds : bond 0.07447 ( 1053) hydrogen bonds : angle 4.54373 ( 3118) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 285 time to evaluate : 1.049 Fit side-chains REVERT: B 98 MET cc_start: 0.7177 (OUTLIER) cc_final: 0.6936 (mmm) REVERT: B 171 ASP cc_start: 0.7380 (m-30) cc_final: 0.7039 (m-30) REVERT: C 171 ASP cc_start: 0.7249 (m-30) cc_final: 0.6931 (m-30) REVERT: C 214 TRP cc_start: 0.8570 (m-90) cc_final: 0.8209 (m100) REVERT: C 328 ASP cc_start: 0.8231 (m-30) cc_final: 0.8018 (m-30) REVERT: D 135 ARG cc_start: 0.6534 (mmm160) cc_final: 0.6041 (mmt90) REVERT: D 171 ASP cc_start: 0.7329 (m-30) cc_final: 0.6967 (m-30) REVERT: D 200 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8016 (mm-30) outliers start: 22 outliers final: 19 residues processed: 298 average time/residue: 1.7138 time to fit residues: 568.6490 Evaluate side-chains 302 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 282 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 112 CYS Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 130 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 209 optimal weight: 0.9990 chunk 179 optimal weight: 0.8980 chunk 219 optimal weight: 8.9990 chunk 250 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 202 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 chunk 212 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN F 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.162506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.147175 restraints weight = 53414.209| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 0.55 r_work: 0.3380 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 1.75 restraints_weight: 0.2500 r_work: 0.3162 rms_B_bonded: 4.22 restraints_weight: 0.1250 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21949 Z= 0.144 Angle : 0.507 4.428 29706 Z= 0.283 Chirality : 0.043 0.142 3392 Planarity : 0.004 0.047 3828 Dihedral : 4.741 49.085 2989 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.68 % Allowed : 8.54 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.15), residues: 2730 helix: 1.44 (0.13), residues: 1385 sheet: -0.99 (0.22), residues: 451 loop : -0.68 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 135 TYR 0.012 0.002 TYR B 367 PHE 0.017 0.002 PHE F 338 TRP 0.015 0.002 TRP A 300 HIS 0.002 0.000 HIS A 365 Details of bonding type rmsd covalent geometry : bond 0.00290 (21949) covalent geometry : angle 0.50673 (29706) hydrogen bonds : bond 0.06098 ( 1053) hydrogen bonds : angle 4.20898 ( 3118) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 300 time to evaluate : 1.271 Fit side-chains REVERT: B 98 MET cc_start: 0.7100 (OUTLIER) cc_final: 0.6868 (mmm) REVERT: B 171 ASP cc_start: 0.7267 (m-30) cc_final: 0.6938 (m-30) REVERT: C 171 ASP cc_start: 0.7245 (m-30) cc_final: 0.6884 (m-30) REVERT: C 214 TRP cc_start: 0.8461 (m-90) cc_final: 0.8195 (m100) REVERT: C 328 ASP cc_start: 0.8204 (m-30) cc_final: 0.7970 (m-30) REVERT: D 135 ARG cc_start: 0.6457 (mmm160) cc_final: 0.6058 (mmt90) REVERT: D 171 ASP cc_start: 0.7196 (m-30) cc_final: 0.6842 (m-30) REVERT: D 200 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7791 (mm-30) REVERT: E 328 ASP cc_start: 0.8221 (m-30) cc_final: 0.7991 (m-30) outliers start: 15 outliers final: 12 residues processed: 307 average time/residue: 2.0189 time to fit residues: 692.4934 Evaluate side-chains 306 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 293 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 130 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 161 optimal weight: 7.9990 chunk 228 optimal weight: 9.9990 chunk 139 optimal weight: 7.9990 chunk 174 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 179 optimal weight: 3.9990 chunk 156 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN F 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.161499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.144748 restraints weight = 52977.894| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 0.59 r_work: 0.3355 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 2.01 restraints_weight: 0.2500 r_work: 0.3114 rms_B_bonded: 4.68 restraints_weight: 0.1250 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21949 Z= 0.175 Angle : 0.545 4.511 29706 Z= 0.306 Chirality : 0.044 0.143 3392 Planarity : 0.005 0.080 3828 Dihedral : 4.847 50.247 2989 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.80 % Allowed : 8.46 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.15), residues: 2730 helix: 1.33 (0.13), residues: 1385 sheet: -0.99 (0.23), residues: 426 loop : -0.63 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 135 TYR 0.015 0.002 TYR E 402 PHE 0.017 0.002 PHE E 338 TRP 0.015 0.002 TRP D 300 HIS 0.003 0.001 HIS D 429 Details of bonding type rmsd covalent geometry : bond 0.00360 (21949) covalent geometry : angle 0.54499 (29706) hydrogen bonds : bond 0.06585 ( 1053) hydrogen bonds : angle 4.30318 ( 3118) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 293 time to evaluate : 1.327 Fit side-chains REVERT: B 98 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6890 (mmm) REVERT: B 171 ASP cc_start: 0.7324 (m-30) cc_final: 0.6988 (m-30) REVERT: C 171 ASP cc_start: 0.7234 (m-30) cc_final: 0.6889 (m-30) REVERT: C 214 TRP cc_start: 0.8507 (m-90) cc_final: 0.8175 (m100) REVERT: C 328 ASP cc_start: 0.8248 (m-30) cc_final: 0.8026 (m-30) REVERT: D 135 ARG cc_start: 0.6509 (mmm160) cc_final: 0.6076 (mmt90) REVERT: D 171 ASP cc_start: 0.7262 (m-30) cc_final: 0.6894 (m-30) REVERT: D 200 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7850 (mm-30) REVERT: F 257 MET cc_start: 0.8861 (mtp) cc_final: 0.8631 (mtp) outliers start: 18 outliers final: 14 residues processed: 303 average time/residue: 1.8996 time to fit residues: 644.6835 Evaluate side-chains 305 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 290 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 130 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 57 optimal weight: 4.9990 chunk 238 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 241 optimal weight: 4.9990 chunk 229 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 chunk 184 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN F 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.161776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.146608 restraints weight = 50316.282| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 0.53 r_work: 0.3376 rms_B_bonded: 1.11 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 1.67 restraints_weight: 0.2500 r_work: 0.3165 rms_B_bonded: 3.99 restraints_weight: 0.1250 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21949 Z= 0.168 Angle : 0.537 4.929 29706 Z= 0.301 Chirality : 0.044 0.143 3392 Planarity : 0.004 0.047 3828 Dihedral : 4.807 50.219 2989 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.80 % Allowed : 8.38 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.15), residues: 2730 helix: 1.37 (0.13), residues: 1385 sheet: -0.99 (0.23), residues: 426 loop : -0.65 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 205 TYR 0.013 0.002 TYR E 402 PHE 0.017 0.002 PHE F 338 TRP 0.015 0.002 TRP A 300 HIS 0.002 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00343 (21949) covalent geometry : angle 0.53700 (29706) hydrogen bonds : bond 0.06437 ( 1053) hydrogen bonds : angle 4.27045 ( 3118) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 291 time to evaluate : 1.653 Fit side-chains REVERT: B 77 ASP cc_start: 0.6761 (m-30) cc_final: 0.6492 (m-30) REVERT: B 98 MET cc_start: 0.7041 (OUTLIER) cc_final: 0.6811 (mmm) REVERT: B 171 ASP cc_start: 0.7239 (m-30) cc_final: 0.6914 (m-30) REVERT: C 135 ARG cc_start: 0.6709 (mmm-85) cc_final: 0.6390 (mmt90) REVERT: C 171 ASP cc_start: 0.7217 (m-30) cc_final: 0.6864 (m-30) REVERT: C 214 TRP cc_start: 0.8414 (m-90) cc_final: 0.8132 (m100) REVERT: C 328 ASP cc_start: 0.8206 (m-30) cc_final: 0.7963 (m-30) REVERT: D 77 ASP cc_start: 0.6759 (m-30) cc_final: 0.6489 (m-30) REVERT: D 135 ARG cc_start: 0.6458 (mmm160) cc_final: 0.6048 (mmt90) REVERT: D 171 ASP cc_start: 0.7220 (m-30) cc_final: 0.6867 (m-30) REVERT: D 200 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7775 (mm-30) outliers start: 18 outliers final: 15 residues processed: 301 average time/residue: 1.5332 time to fit residues: 516.9997 Evaluate side-chains 304 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 288 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 130 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 264 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 38 optimal weight: 0.0470 chunk 200 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 176 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 138 optimal weight: 0.0980 chunk 75 optimal weight: 0.4980 chunk 49 optimal weight: 0.6980 chunk 158 optimal weight: 3.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN F 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.166219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.151457 restraints weight = 62621.706| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 0.58 r_work: 0.3427 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 1.93 restraints_weight: 0.2500 r_work: 0.3192 rms_B_bonded: 4.77 restraints_weight: 0.1250 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21949 Z= 0.107 Angle : 0.462 5.472 29706 Z= 0.253 Chirality : 0.042 0.137 3392 Planarity : 0.003 0.030 3828 Dihedral : 4.300 42.674 2989 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.21 % Allowed : 8.97 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.16), residues: 2730 helix: 1.73 (0.14), residues: 1400 sheet: -1.04 (0.22), residues: 451 loop : -0.59 (0.19), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 205 TYR 0.011 0.001 TYR D 367 PHE 0.014 0.001 PHE B 338 TRP 0.015 0.002 TRP C 300 HIS 0.002 0.000 HIS E 409 Details of bonding type rmsd covalent geometry : bond 0.00218 (21949) covalent geometry : angle 0.46177 (29706) hydrogen bonds : bond 0.05031 ( 1053) hydrogen bonds : angle 3.99242 ( 3118) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 309 time to evaluate : 0.759 Fit side-chains REVERT: B 77 ASP cc_start: 0.6674 (m-30) cc_final: 0.6396 (m-30) REVERT: B 98 MET cc_start: 0.7056 (OUTLIER) cc_final: 0.6850 (mmm) REVERT: B 171 ASP cc_start: 0.7298 (m-30) cc_final: 0.6960 (m-30) REVERT: C 98 MET cc_start: 0.7142 (mtp) cc_final: 0.6880 (mmm) REVERT: C 135 ARG cc_start: 0.6526 (mmm-85) cc_final: 0.6207 (mmt90) REVERT: C 214 TRP cc_start: 0.8483 (m-90) cc_final: 0.8136 (m100) REVERT: C 328 ASP cc_start: 0.8186 (m-30) cc_final: 0.7892 (m-30) REVERT: D 77 ASP cc_start: 0.6631 (m-30) cc_final: 0.6383 (m-30) REVERT: D 135 ARG cc_start: 0.6489 (mmm160) cc_final: 0.6132 (mmt90) REVERT: D 171 ASP cc_start: 0.7206 (m-30) cc_final: 0.6840 (m-30) REVERT: D 200 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7658 (mm-30) REVERT: D 306 MET cc_start: 0.9220 (tpp) cc_final: 0.8989 (tpp) REVERT: E 98 MET cc_start: 0.7185 (mtp) cc_final: 0.6904 (mmm) REVERT: E 328 ASP cc_start: 0.8209 (m-30) cc_final: 0.7968 (m-30) REVERT: F 242 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8280 (mt-10) outliers start: 4 outliers final: 3 residues processed: 310 average time/residue: 1.4646 time to fit residues: 508.2485 Evaluate side-chains 296 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 292 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain F residue 130 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 139 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 chunk 259 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 220 optimal weight: 6.9990 chunk 181 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN F 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.160652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.145534 restraints weight = 48741.297| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 0.52 r_work: 0.3361 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 1.66 restraints_weight: 0.2500 r_work: 0.3143 rms_B_bonded: 4.08 restraints_weight: 0.1250 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 21949 Z= 0.231 Angle : 0.613 4.563 29706 Z= 0.346 Chirality : 0.046 0.145 3392 Planarity : 0.005 0.057 3828 Dihedral : 4.817 48.212 2987 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.25 % Allowed : 9.31 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.15), residues: 2730 helix: 1.29 (0.13), residues: 1385 sheet: -0.92 (0.23), residues: 423 loop : -0.59 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 114 TYR 0.020 0.003 TYR E 402 PHE 0.018 0.003 PHE F 338 TRP 0.016 0.003 TRP D 300 HIS 0.004 0.001 HIS D 429 Details of bonding type rmsd covalent geometry : bond 0.00485 (21949) covalent geometry : angle 0.61261 (29706) hydrogen bonds : bond 0.07138 ( 1053) hydrogen bonds : angle 4.42681 ( 3118) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20025.12 seconds wall clock time: 339 minutes 1.24 seconds (20341.24 seconds total)