Starting phenix.real_space_refine on Mon May 19 03:40:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yeg_39194/05_2025/8yeg_39194.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yeg_39194/05_2025/8yeg_39194.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yeg_39194/05_2025/8yeg_39194.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yeg_39194/05_2025/8yeg_39194.map" model { file = "/net/cci-nas-00/data/ceres_data/8yeg_39194/05_2025/8yeg_39194.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yeg_39194/05_2025/8yeg_39194.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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: 4 Type Number sf(0) Gaussians S 113 5.16 5 C 11547 2.51 5 N 3076 2.21 5 O 3485 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 18221 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 925 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "F" Number of atoms: 3283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3283 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 395} Chain breaks: 1 Chain: "L" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 881 Classifications: {'peptide': 113} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 105} Chain: "B" Number of atoms: 3283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3283 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 395} Chain breaks: 1 Chain: "C" Number of atoms: 3283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3283 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 395} Chain breaks: 1 Chain: "D" Number of atoms: 3283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3283 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 395} Chain breaks: 1 Chain: "E" Number of atoms: 3283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3283 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 395} Chain breaks: 1 Time building chain proxies: 10.27, per 1000 atoms: 0.56 Number of scatterers: 18221 At special positions: 0 Unit cell: (131.61, 119.84, 144.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 113 16.00 O 3485 8.00 N 3076 7.00 C 11547 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 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: 4.31 Conformation dependent library (CDL) restraints added in 2.2 seconds 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4272 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 28 sheets defined 14.3% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 83 through 87 removed outlier: 3.936A pdb=" N THR A 87 " --> pdb=" O ALA A 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 27 removed outlier: 4.117A pdb=" N TYR F 26 " --> pdb=" O ALA F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 211 removed outlier: 3.678A pdb=" N GLN F 211 " --> pdb=" O PHE F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 237 Processing helix chain 'F' and resid 269 through 273 removed outlier: 3.587A pdb=" N LEU F 273 " --> pdb=" O ASP F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 281 removed outlier: 3.859A pdb=" N SER F 281 " --> pdb=" O ASN F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 354 No H-bonds generated for 'chain 'F' and resid 352 through 354' Processing helix chain 'F' and resid 380 through 391 Processing helix chain 'F' and resid 391 through 398 removed outlier: 4.056A pdb=" N LEU F 395 " --> pdb=" O ASN F 391 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TRP F 398 " --> pdb=" O VAL F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 439 removed outlier: 3.681A pdb=" N ASP F 439 " --> pdb=" O PRO F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 457 Processing helix chain 'F' and resid 458 through 469 Processing helix chain 'L' and resid 85 through 89 removed outlier: 3.643A pdb=" N VAL L 89 " --> pdb=" O PRO L 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 235 Processing helix chain 'B' and resid 277 through 281 Processing helix chain 'B' and resid 352 through 354 No H-bonds generated for 'chain 'B' and resid 352 through 354' Processing helix chain 'B' and resid 380 through 391 Processing helix chain 'B' and resid 391 through 398 removed outlier: 3.938A pdb=" N LEU B 395 " --> pdb=" O ASN B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 457 Processing helix chain 'B' and resid 458 through 469 removed outlier: 3.638A pdb=" N LYS B 463 " --> pdb=" O PRO B 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 26 Processing helix chain 'C' and resid 230 through 236 Processing helix chain 'C' and resid 269 through 273 removed outlier: 3.718A pdb=" N LEU C 273 " --> pdb=" O ASP C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 removed outlier: 3.970A pdb=" N SER C 282 " --> pdb=" O ASN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 391 Processing helix chain 'C' and resid 391 through 398 removed outlier: 4.119A pdb=" N LEU C 395 " --> pdb=" O ASN C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 440 removed outlier: 4.096A pdb=" N ASP C 439 " --> pdb=" O PRO C 436 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET C 440 " --> pdb=" O TYR C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 457 Processing helix chain 'C' and resid 458 through 469 removed outlier: 3.533A pdb=" N GLY C 469 " --> pdb=" O LEU C 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 27 removed outlier: 4.200A pdb=" N TYR D 26 " --> pdb=" O ALA D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.894A pdb=" N PHE D 88 " --> pdb=" O SER D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 237 Processing helix chain 'D' and resid 269 through 273 removed outlier: 3.961A pdb=" N LEU D 273 " --> pdb=" O ASP D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 354 No H-bonds generated for 'chain 'D' and resid 352 through 354' Processing helix chain 'D' and resid 380 through 391 Processing helix chain 'D' and resid 391 through 398 removed outlier: 4.079A pdb=" N LEU D 395 " --> pdb=" O ASN D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 440 removed outlier: 3.962A pdb=" N ASP D 439 " --> pdb=" O PRO D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 457 removed outlier: 3.683A pdb=" N GLN D 457 " --> pdb=" O GLU D 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 454 through 457' Processing helix chain 'D' and resid 458 through 469 removed outlier: 3.580A pdb=" N ARG D 462 " --> pdb=" O PHE D 458 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS D 463 " --> pdb=" O PRO D 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 27 removed outlier: 4.201A pdb=" N TYR E 26 " --> pdb=" O ALA E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 236 Processing helix chain 'E' and resid 277 through 281 Processing helix chain 'E' and resid 300 through 302 No H-bonds generated for 'chain 'E' and resid 300 through 302' Processing helix chain 'E' and resid 352 through 354 No H-bonds generated for 'chain 'E' and resid 352 through 354' Processing helix chain 'E' and resid 380 through 391 Processing helix chain 'E' and resid 391 through 398 removed outlier: 4.136A pdb=" N LEU E 395 " --> pdb=" O ASN E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 440 removed outlier: 3.795A pdb=" N ASP E 439 " --> pdb=" O PRO E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 457 removed outlier: 3.534A pdb=" N GLN E 457 " --> pdb=" O GLU E 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 454 through 457' Processing helix chain 'E' and resid 458 through 469 removed outlier: 3.838A pdb=" N GLY E 469 " --> pdb=" O LEU E 465 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 5.954A pdb=" N GLY A 10 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N MET A 34 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 28 through 37 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 28 through 37 current: chain 'F' and resid 308 through 309 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 308 through 309 current: chain 'F' and resid 356 through 378 removed outlier: 3.574A pdb=" N THR B 263 " --> pdb=" O TYR F 356 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 51 through 52 Processing sheet with id=AA5, first strand: chain 'F' and resid 68 through 73 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 68 through 73 current: chain 'F' and resid 245 through 259 removed outlier: 5.626A pdb=" N ALA F 254 " --> pdb=" O SER F 293 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N SER F 293 " --> pdb=" O ALA F 254 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N HIS F 256 " --> pdb=" O THR F 291 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 115 through 121 removed outlier: 4.168A pdb=" N LEU F 119 " --> pdb=" O VAL F 142 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N VAL F 142 " --> pdb=" O LEU F 119 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 185 through 191 removed outlier: 5.838A pdb=" N TRP F 166 " --> pdb=" O CYS F 226 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N CYS F 226 " --> pdb=" O TRP F 166 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N MET F 197 " --> pdb=" O LYS F 227 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 263 through 264 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 263 through 264 current: chain 'C' and resid 308 through 309 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 308 through 309 current: chain 'C' and resid 356 through 378 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 297 through 298 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 297 through 298 current: chain 'B' and resid 245 through 258 removed outlier: 5.276A pdb=" N ALA B 254 " --> pdb=" O SER B 293 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N SER B 293 " --> pdb=" O ALA B 254 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N HIS B 256 " --> pdb=" O THR B 291 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AB2, first strand: chain 'L' and resid 11 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 11 through 13 current: chain 'L' and resid 51 through 55 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 59 through 60 current: chain 'L' and resid 103 through 104 Processing sheet with id=AB3, first strand: chain 'B' and resid 27 through 45 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 27 through 45 current: chain 'B' and resid 308 through 309 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 308 through 309 current: chain 'B' and resid 356 through 378 No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 115 through 121 removed outlier: 4.020A pdb=" N LEU B 119 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL B 142 " --> pdb=" O LEU B 119 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 185 through 191 removed outlier: 5.840A pdb=" N TRP B 166 " --> pdb=" O CYS B 226 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N CYS B 226 " --> pdb=" O TRP B 166 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N MET B 197 " --> pdb=" O LYS B 227 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 297 through 298 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 297 through 298 current: chain 'E' and resid 245 through 259 removed outlier: 5.219A pdb=" N ALA E 254 " --> pdb=" O SER E 293 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N SER E 293 " --> pdb=" O ALA E 254 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N HIS E 256 " --> pdb=" O THR E 291 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 51 through 52 Processing sheet with id=AB8, first strand: chain 'C' and resid 68 through 73 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 68 through 73 current: chain 'C' and resid 245 through 259 removed outlier: 6.541A pdb=" N THR C 291 " --> pdb=" O ARG C 255 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N PHE C 257 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL C 289 " --> pdb=" O PHE C 257 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 115 through 120 removed outlier: 4.071A pdb=" N LEU C 119 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL C 142 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 185 through 191 removed outlier: 5.608A pdb=" N TRP C 166 " --> pdb=" O CYS C 226 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N CYS C 226 " --> pdb=" O TRP C 166 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N MET C 197 " --> pdb=" O LYS C 227 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 263 through 264 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 263 through 264 current: chain 'D' and resid 308 through 309 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 308 through 309 current: chain 'D' and resid 356 through 378 No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 51 through 52 Processing sheet with id=AC4, first strand: chain 'D' and resid 68 through 73 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 68 through 73 current: chain 'D' and resid 245 through 258 removed outlier: 6.426A pdb=" N THR D 291 " --> pdb=" O ARG D 255 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N PHE D 257 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL D 289 " --> pdb=" O PHE D 257 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 115 through 120 removed outlier: 5.059A pdb=" N GLY D 116 " --> pdb=" O MET D 146 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N MET D 146 " --> pdb=" O GLY D 116 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N VAL D 144 " --> pdb=" O PRO D 118 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 185 through 191 removed outlier: 5.859A pdb=" N TRP D 166 " --> pdb=" O CYS D 226 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N CYS D 226 " --> pdb=" O TRP D 166 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N MET D 197 " --> pdb=" O LYS D 227 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 263 through 264 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 263 through 264 current: chain 'E' and resid 308 through 309 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 308 through 309 current: chain 'E' and resid 356 through 378 No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'E' and resid 51 through 52 Processing sheet with id=AC9, first strand: chain 'E' and resid 114 through 121 removed outlier: 4.281A pdb=" N LEU E 119 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N VAL E 142 " --> pdb=" O LEU E 119 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 185 through 191 removed outlier: 6.082A pdb=" N TRP E 166 " --> pdb=" O CYS E 226 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N CYS E 226 " --> pdb=" O TRP E 166 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N MET E 197 " --> pdb=" O LYS E 227 " (cutoff:3.500A) 262 hydrogen bonds defined for protein. 663 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: 4.37 Time building geometry restraints manager: 4.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5931 1.34 - 1.46: 4583 1.46 - 1.58: 7997 1.58 - 1.71: 0 1.71 - 1.83: 172 Bond restraints: 18683 Sorted by residual: bond pdb=" CA GLY F 131 " pdb=" C GLY F 131 " ideal model delta sigma weight residual 1.516 1.506 0.010 8.10e-03 1.52e+04 1.50e+00 bond pdb=" C VAL F 73 " pdb=" N LEU F 74 " ideal model delta sigma weight residual 1.339 1.272 0.067 5.57e-02 3.22e+02 1.47e+00 bond pdb=" CA ARG D 335 " pdb=" CB ARG D 335 " ideal model delta sigma weight residual 1.527 1.497 0.030 2.48e-02 1.63e+03 1.45e+00 bond pdb=" CB ASN C 259 " pdb=" CG ASN C 259 " ideal model delta sigma weight residual 1.516 1.486 0.030 2.50e-02 1.60e+03 1.42e+00 bond pdb=" CA GLY E 105 " pdb=" C GLY E 105 " ideal model delta sigma weight residual 1.520 1.512 0.008 7.30e-03 1.88e+04 1.28e+00 ... (remaining 18678 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 24605 1.61 - 3.21: 667 3.21 - 4.82: 81 4.82 - 6.43: 14 6.43 - 8.03: 11 Bond angle restraints: 25378 Sorted by residual: angle pdb=" C GLY F 130 " pdb=" N GLY F 131 " pdb=" CA GLY F 131 " ideal model delta sigma weight residual 122.33 118.89 3.44 7.30e-01 1.88e+00 2.22e+01 angle pdb=" CG ARG D 68 " pdb=" CD ARG D 68 " pdb=" NE ARG D 68 " ideal model delta sigma weight residual 112.00 119.46 -7.46 2.20e+00 2.07e-01 1.15e+01 angle pdb=" CA ARG D 68 " pdb=" CB ARG D 68 " pdb=" CG ARG D 68 " ideal model delta sigma weight residual 114.10 120.11 -6.01 2.00e+00 2.50e-01 9.04e+00 angle pdb=" CA ARG B 361 " pdb=" CB ARG B 361 " pdb=" CG ARG B 361 " ideal model delta sigma weight residual 114.10 119.91 -5.81 2.00e+00 2.50e-01 8.44e+00 angle pdb=" C TRP L 56 " pdb=" N ALA L 57 " pdb=" CA ALA L 57 " ideal model delta sigma weight residual 121.54 126.89 -5.35 1.91e+00 2.74e-01 7.84e+00 ... (remaining 25373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 10023 17.91 - 35.83: 816 35.83 - 53.74: 143 53.74 - 71.66: 33 71.66 - 89.57: 14 Dihedral angle restraints: 11029 sinusoidal: 4320 harmonic: 6709 Sorted by residual: dihedral pdb=" CA PHE E 370 " pdb=" C PHE E 370 " pdb=" N ILE E 371 " pdb=" CA ILE E 371 " ideal model delta harmonic sigma weight residual 180.00 158.87 21.13 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA PHE D 244 " pdb=" C PHE D 244 " pdb=" N PHE D 245 " pdb=" CA PHE D 245 " ideal model delta harmonic sigma weight residual -180.00 -159.29 -20.71 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA PHE C 370 " pdb=" C PHE C 370 " pdb=" N ILE C 371 " pdb=" CA ILE C 371 " ideal model delta harmonic sigma weight residual 180.00 160.23 19.77 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 11026 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1512 0.031 - 0.061: 785 0.061 - 0.092: 237 0.092 - 0.123: 164 0.123 - 0.153: 34 Chirality restraints: 2732 Sorted by residual: chirality pdb=" CA VAL E 289 " pdb=" N VAL E 289 " pdb=" C VAL E 289 " pdb=" CB VAL E 289 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CA VAL F 289 " pdb=" N VAL F 289 " pdb=" C VAL F 289 " pdb=" CB VAL F 289 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.60e-01 chirality pdb=" CA VAL B 289 " pdb=" N VAL B 289 " pdb=" C VAL B 289 " pdb=" CB VAL B 289 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.30e-01 ... (remaining 2729 not shown) Planarity restraints: 3308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 132 " 0.036 2.00e-02 2.50e+03 2.62e-02 1.38e+01 pdb=" CG TYR B 132 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR B 132 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR B 132 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 132 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 132 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 132 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 132 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 391 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO C 392 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 392 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 392 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 135 " 0.033 5.00e-02 4.00e+02 5.04e-02 4.06e+00 pdb=" N PRO D 136 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO D 136 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 136 " 0.028 5.00e-02 4.00e+02 ... (remaining 3305 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 107 2.62 - 3.19: 14731 3.19 - 3.76: 25291 3.76 - 4.33: 37434 4.33 - 4.90: 65426 Nonbonded interactions: 142989 Sorted by model distance: nonbonded pdb=" O PRO F 118 " pdb=" OH TYR B 132 " model vdw 2.047 3.040 nonbonded pdb=" O LEU B 303 " pdb=" OH TYR B 308 " model vdw 2.093 3.040 nonbonded pdb=" O PRO B 118 " pdb=" OH TYR E 132 " model vdw 2.125 3.040 nonbonded pdb=" O LEU D 303 " pdb=" OH TYR D 308 " model vdw 2.187 3.040 nonbonded pdb=" O LEU C 303 " pdb=" OH TYR C 308 " model vdw 2.195 3.040 ... (remaining 142984 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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=1.00 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: 0.480 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: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 37.750 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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 : 0.005 0.067 18685 Z= 0.218 Angle : 0.647 8.035 25382 Z= 0.345 Chirality : 0.046 0.153 2732 Planarity : 0.005 0.054 3308 Dihedral : 13.912 89.573 6751 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.16), residues: 2306 helix: -0.95 (0.35), residues: 225 sheet: 0.07 (0.19), residues: 732 loop : -1.43 (0.15), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 398 HIS 0.007 0.002 HIS E 165 PHE 0.022 0.002 PHE B 80 TYR 0.064 0.002 TYR B 132 ARG 0.012 0.001 ARG D 68 Details of bonding type rmsd hydrogen bonds : bond 0.16588 ( 262) hydrogen bonds : angle 6.45637 ( 663) SS BOND : bond 0.00953 ( 2) SS BOND : angle 1.80212 ( 4) covalent geometry : bond 0.00518 (18683) covalent geometry : angle 0.64634 (25378) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 1.878 Fit side-chains REVERT: B 358 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7772 (mm-30) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.2946 time to fit residues: 103.7034 Evaluate side-chains 200 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.9980 chunk 172 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 178 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 133 optimal weight: 10.0000 chunk 207 optimal weight: 0.4980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.140993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.115421 restraints weight = 24989.110| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.27 r_work: 0.3267 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.0694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18685 Z= 0.135 Angle : 0.527 7.509 25382 Z= 0.271 Chirality : 0.044 0.177 2732 Planarity : 0.004 0.050 3308 Dihedral : 4.619 19.396 2524 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.74 % Allowed : 5.16 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.16), residues: 2306 helix: -0.59 (0.35), residues: 225 sheet: -0.01 (0.18), residues: 741 loop : -1.28 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 104 HIS 0.005 0.001 HIS E 165 PHE 0.013 0.001 PHE B 80 TYR 0.035 0.001 TYR B 132 ARG 0.004 0.000 ARG F 248 Details of bonding type rmsd hydrogen bonds : bond 0.03458 ( 262) hydrogen bonds : angle 5.38722 ( 663) SS BOND : bond 0.00693 ( 2) SS BOND : angle 1.22478 ( 4) covalent geometry : bond 0.00323 (18683) covalent geometry : angle 0.52692 (25378) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 209 time to evaluate : 1.927 Fit side-chains REVERT: A 97 MET cc_start: 0.7774 (mmt) cc_final: 0.7565 (mmm) REVERT: F 31 ASN cc_start: 0.8461 (p0) cc_final: 0.8097 (t0) REVERT: L 87 GLU cc_start: 0.8523 (pt0) cc_final: 0.7834 (tm-30) REVERT: C 308 TYR cc_start: 0.8213 (m-80) cc_final: 0.7901 (m-80) REVERT: E 246 TYR cc_start: 0.8707 (p90) cc_final: 0.8269 (p90) REVERT: E 440 MET cc_start: 0.7930 (mtt) cc_final: 0.7567 (mtt) outliers start: 15 outliers final: 10 residues processed: 219 average time/residue: 0.2882 time to fit residues: 96.5600 Evaluate side-chains 212 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 202 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain E residue 358 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 222 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 142 optimal weight: 20.0000 chunk 220 optimal weight: 9.9990 chunk 153 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 HIS E 35 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.135895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.110475 restraints weight = 25464.330| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.14 r_work: 0.3163 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 18685 Z= 0.191 Angle : 0.563 7.247 25382 Z= 0.290 Chirality : 0.045 0.185 2732 Planarity : 0.004 0.049 3308 Dihedral : 4.717 21.562 2524 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.24 % Allowed : 8.92 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.16), residues: 2306 helix: -0.56 (0.35), residues: 225 sheet: -0.16 (0.18), residues: 742 loop : -1.34 (0.16), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 104 HIS 0.007 0.001 HIS E 165 PHE 0.015 0.002 PHE B 80 TYR 0.019 0.002 TYR C 132 ARG 0.005 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.03474 ( 262) hydrogen bonds : angle 5.27724 ( 663) SS BOND : bond 0.00866 ( 2) SS BOND : angle 1.41172 ( 4) covalent geometry : bond 0.00467 (18683) covalent geometry : angle 0.56276 (25378) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 209 time to evaluate : 1.892 Fit side-chains revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8908 (m-80) cc_final: 0.8691 (m-80) REVERT: F 31 ASN cc_start: 0.8311 (p0) cc_final: 0.8099 (t0) REVERT: F 396 GLU cc_start: 0.7111 (tm-30) cc_final: 0.6591 (pt0) REVERT: L 87 GLU cc_start: 0.8526 (pt0) cc_final: 0.7971 (tm-30) REVERT: B 132 TYR cc_start: 0.8822 (OUTLIER) cc_final: 0.7054 (m-80) REVERT: B 146 MET cc_start: 0.8720 (ptp) cc_final: 0.8473 (ptp) REVERT: C 308 TYR cc_start: 0.8173 (m-80) cc_final: 0.7713 (m-80) REVERT: D 384 MET cc_start: 0.6728 (OUTLIER) cc_final: 0.6370 (mpp) REVERT: D 466 LEU cc_start: 0.8716 (mt) cc_final: 0.8510 (mp) REVERT: E 246 TYR cc_start: 0.8708 (p90) cc_final: 0.8353 (p90) REVERT: E 440 MET cc_start: 0.8207 (mtt) cc_final: 0.7768 (mtt) outliers start: 25 outliers final: 19 residues processed: 224 average time/residue: 0.2784 time to fit residues: 96.2078 Evaluate side-chains 215 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 194 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 353 ASN Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 325 HIS Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain E residue 358 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 137 optimal weight: 0.9990 chunk 28 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 227 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 162 optimal weight: 9.9990 chunk 161 optimal weight: 7.9990 chunk 181 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 HIS D 325 HIS D 467 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.135742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.110358 restraints weight = 25451.018| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.14 r_work: 0.3160 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 18685 Z= 0.186 Angle : 0.553 7.136 25382 Z= 0.285 Chirality : 0.045 0.185 2732 Planarity : 0.004 0.049 3308 Dihedral : 4.703 21.309 2524 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.74 % Allowed : 10.21 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.16), residues: 2306 helix: -0.52 (0.34), residues: 225 sheet: -0.26 (0.18), residues: 742 loop : -1.35 (0.16), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 104 HIS 0.006 0.001 HIS E 165 PHE 0.014 0.002 PHE D 253 TYR 0.016 0.002 TYR C 132 ARG 0.004 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.03306 ( 262) hydrogen bonds : angle 5.19374 ( 663) SS BOND : bond 0.00865 ( 2) SS BOND : angle 1.33889 ( 4) covalent geometry : bond 0.00455 (18683) covalent geometry : angle 0.55328 (25378) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 202 time to evaluate : 2.039 Fit side-chains REVERT: F 396 GLU cc_start: 0.6930 (tm-30) cc_final: 0.6467 (pt0) REVERT: L 87 GLU cc_start: 0.8597 (pt0) cc_final: 0.8079 (tm-30) REVERT: B 132 TYR cc_start: 0.8829 (OUTLIER) cc_final: 0.7312 (m-80) REVERT: B 146 MET cc_start: 0.8733 (ptp) cc_final: 0.8467 (ptp) REVERT: C 308 TYR cc_start: 0.8134 (m-80) cc_final: 0.7627 (m-80) REVERT: D 146 MET cc_start: 0.8755 (ptp) cc_final: 0.8531 (ptp) REVERT: D 384 MET cc_start: 0.6717 (OUTLIER) cc_final: 0.6357 (mpp) REVERT: D 466 LEU cc_start: 0.8827 (mt) cc_final: 0.8599 (mp) REVERT: E 246 TYR cc_start: 0.8694 (p90) cc_final: 0.8342 (p90) REVERT: E 440 MET cc_start: 0.8281 (mtt) cc_final: 0.7844 (mtt) outliers start: 35 outliers final: 24 residues processed: 225 average time/residue: 0.2980 time to fit residues: 102.5592 Evaluate side-chains 220 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 353 ASN Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 358 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 158 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 chunk 102 optimal weight: 0.0970 chunk 69 optimal weight: 8.9990 chunk 148 optimal weight: 9.9990 chunk 192 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 HIS D 325 HIS D 467 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.133872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.109230 restraints weight = 25401.344| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.04 r_work: 0.3123 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18685 Z= 0.133 Angle : 0.505 6.513 25382 Z= 0.260 Chirality : 0.043 0.181 2732 Planarity : 0.004 0.047 3308 Dihedral : 4.465 19.965 2524 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.93 % Allowed : 10.91 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.17), residues: 2306 helix: -0.40 (0.35), residues: 225 sheet: -0.26 (0.18), residues: 742 loop : -1.28 (0.16), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 104 HIS 0.005 0.001 HIS E 165 PHE 0.013 0.001 PHE D 253 TYR 0.012 0.001 TYR F 246 ARG 0.004 0.000 ARG F 248 Details of bonding type rmsd hydrogen bonds : bond 0.02929 ( 262) hydrogen bonds : angle 4.99974 ( 663) SS BOND : bond 0.00787 ( 2) SS BOND : angle 1.11312 ( 4) covalent geometry : bond 0.00322 (18683) covalent geometry : angle 0.50526 (25378) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 213 time to evaluate : 1.890 Fit side-chains REVERT: F 396 GLU cc_start: 0.6945 (tm-30) cc_final: 0.6423 (pt0) REVERT: B 132 TYR cc_start: 0.8822 (OUTLIER) cc_final: 0.7393 (m-80) REVERT: B 164 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8207 (pt0) REVERT: C 308 TYR cc_start: 0.8099 (m-80) cc_final: 0.7605 (m-80) REVERT: C 365 GLU cc_start: 0.7999 (tt0) cc_final: 0.7649 (mt-10) REVERT: D 384 MET cc_start: 0.6773 (OUTLIER) cc_final: 0.6407 (mpp) REVERT: D 466 LEU cc_start: 0.8792 (mt) cc_final: 0.8569 (mp) REVERT: D 470 TYR cc_start: 0.3411 (OUTLIER) cc_final: 0.2554 (m-80) REVERT: E 246 TYR cc_start: 0.8716 (p90) cc_final: 0.8462 (p90) REVERT: E 440 MET cc_start: 0.8233 (mtt) cc_final: 0.7755 (mtt) outliers start: 39 outliers final: 27 residues processed: 238 average time/residue: 0.2723 time to fit residues: 100.5649 Evaluate side-chains 229 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 353 ASN Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 470 TYR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 245 PHE Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 358 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 106 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 123 optimal weight: 7.9990 chunk 218 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 ASN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 HIS D 325 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.130889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.106652 restraints weight = 25789.314| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.02 r_work: 0.3083 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 18685 Z= 0.258 Angle : 0.629 12.420 25382 Z= 0.323 Chirality : 0.047 0.186 2732 Planarity : 0.005 0.047 3308 Dihedral : 4.915 22.647 2524 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.63 % Allowed : 11.60 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.16), residues: 2306 helix: -0.50 (0.34), residues: 225 sheet: -0.45 (0.18), residues: 742 loop : -1.46 (0.16), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 104 HIS 0.008 0.002 HIS C 165 PHE 0.017 0.002 PHE B 80 TYR 0.019 0.002 TYR C 132 ARG 0.005 0.001 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.03680 ( 262) hydrogen bonds : angle 5.33174 ( 663) SS BOND : bond 0.00996 ( 2) SS BOND : angle 2.03815 ( 4) covalent geometry : bond 0.00630 (18683) covalent geometry : angle 0.62836 (25378) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 199 time to evaluate : 2.101 Fit side-chains REVERT: F 220 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.8303 (p0) REVERT: B 132 TYR cc_start: 0.8916 (OUTLIER) cc_final: 0.7627 (m-80) REVERT: B 164 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8175 (pt0) REVERT: B 339 MET cc_start: 0.8744 (ptp) cc_final: 0.8503 (ptp) REVERT: C 52 LYS cc_start: 0.7967 (mttp) cc_final: 0.7472 (tptp) REVERT: C 308 TYR cc_start: 0.8130 (m-80) cc_final: 0.7599 (m-80) REVERT: D 384 MET cc_start: 0.6743 (OUTLIER) cc_final: 0.6352 (mpp) REVERT: D 466 LEU cc_start: 0.8853 (mt) cc_final: 0.8553 (mp) REVERT: D 470 TYR cc_start: 0.3638 (OUTLIER) cc_final: 0.2689 (m-80) REVERT: E 246 TYR cc_start: 0.8776 (p90) cc_final: 0.8544 (p90) REVERT: E 440 MET cc_start: 0.8343 (mtt) cc_final: 0.7810 (mtt) outliers start: 53 outliers final: 38 residues processed: 228 average time/residue: 0.2878 time to fit residues: 102.0545 Evaluate side-chains 236 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 193 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 31 ASN Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain F residue 270 ASP Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 353 ASN Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 470 TYR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 390 MET Chi-restraints excluded: chain E residue 447 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 5 optimal weight: 6.9990 chunk 146 optimal weight: 0.0670 chunk 206 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 200 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 195 optimal weight: 10.0000 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 ASN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 HIS D 325 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.133315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.108917 restraints weight = 25446.002| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.03 r_work: 0.3118 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18685 Z= 0.136 Angle : 0.526 12.274 25382 Z= 0.270 Chirality : 0.044 0.182 2732 Planarity : 0.004 0.047 3308 Dihedral : 4.536 20.876 2524 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.33 % Allowed : 12.59 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.17), residues: 2306 helix: -0.38 (0.35), residues: 225 sheet: -0.38 (0.18), residues: 742 loop : -1.34 (0.16), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 104 HIS 0.004 0.001 HIS E 165 PHE 0.013 0.001 PHE D 253 TYR 0.012 0.001 TYR B 132 ARG 0.003 0.000 ARG C 40 Details of bonding type rmsd hydrogen bonds : bond 0.02931 ( 262) hydrogen bonds : angle 5.01918 ( 663) SS BOND : bond 0.00682 ( 2) SS BOND : angle 1.48195 ( 4) covalent geometry : bond 0.00328 (18683) covalent geometry : angle 0.52556 (25378) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 209 time to evaluate : 2.069 Fit side-chains REVERT: B 132 TYR cc_start: 0.8831 (OUTLIER) cc_final: 0.7390 (m-80) REVERT: B 164 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8211 (pt0) REVERT: C 52 LYS cc_start: 0.7967 (mttp) cc_final: 0.7490 (tptp) REVERT: C 308 TYR cc_start: 0.8044 (m-80) cc_final: 0.7409 (m-80) REVERT: C 365 GLU cc_start: 0.8026 (tt0) cc_final: 0.7573 (mt-10) REVERT: D 384 MET cc_start: 0.6770 (OUTLIER) cc_final: 0.6350 (mpp) REVERT: D 466 LEU cc_start: 0.8845 (mt) cc_final: 0.8591 (mp) REVERT: D 470 TYR cc_start: 0.3455 (OUTLIER) cc_final: 0.2571 (m-80) REVERT: E 246 TYR cc_start: 0.8735 (p90) cc_final: 0.8490 (p90) REVERT: E 440 MET cc_start: 0.8344 (mtt) cc_final: 0.7862 (mtt) outliers start: 47 outliers final: 34 residues processed: 238 average time/residue: 0.2699 time to fit residues: 99.7305 Evaluate side-chains 241 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 203 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 31 ASN Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 353 ASN Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 470 TYR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 245 PHE Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 390 MET Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 460 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 64 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 chunk 117 optimal weight: 0.1980 chunk 29 optimal weight: 8.9990 chunk 131 optimal weight: 9.9990 chunk 151 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 157 optimal weight: 8.9990 chunk 120 optimal weight: 0.0980 chunk 8 optimal weight: 5.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 ASN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 HIS D 325 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.133089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.108561 restraints weight = 25428.922| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.05 r_work: 0.3114 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18685 Z= 0.146 Angle : 0.528 11.202 25382 Z= 0.270 Chirality : 0.044 0.182 2732 Planarity : 0.004 0.047 3308 Dihedral : 4.470 20.208 2524 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.33 % Allowed : 13.09 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.17), residues: 2306 helix: -0.33 (0.35), residues: 225 sheet: -0.34 (0.19), residues: 747 loop : -1.31 (0.16), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 104 HIS 0.005 0.001 HIS E 165 PHE 0.013 0.001 PHE D 253 TYR 0.013 0.001 TYR F 246 ARG 0.003 0.000 ARG C 40 Details of bonding type rmsd hydrogen bonds : bond 0.02955 ( 262) hydrogen bonds : angle 4.98294 ( 663) SS BOND : bond 0.00703 ( 2) SS BOND : angle 1.52350 ( 4) covalent geometry : bond 0.00352 (18683) covalent geometry : angle 0.52780 (25378) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 208 time to evaluate : 1.935 Fit side-chains REVERT: F 102 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8700 (pp) REVERT: B 132 TYR cc_start: 0.8834 (OUTLIER) cc_final: 0.7406 (m-80) REVERT: B 164 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8228 (pt0) REVERT: C 52 LYS cc_start: 0.7889 (mttp) cc_final: 0.7466 (tptp) REVERT: C 308 TYR cc_start: 0.8060 (m-80) cc_final: 0.7427 (m-80) REVERT: C 365 GLU cc_start: 0.8028 (tt0) cc_final: 0.7559 (mt-10) REVERT: D 384 MET cc_start: 0.6721 (OUTLIER) cc_final: 0.6295 (mpp) REVERT: D 470 TYR cc_start: 0.3525 (OUTLIER) cc_final: 0.2630 (m-80) REVERT: E 246 TYR cc_start: 0.8742 (p90) cc_final: 0.8524 (p90) REVERT: E 440 MET cc_start: 0.8282 (mtt) cc_final: 0.7805 (mtt) outliers start: 47 outliers final: 36 residues processed: 238 average time/residue: 0.2741 time to fit residues: 101.0918 Evaluate side-chains 242 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 201 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 353 ASN Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 470 TYR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 245 PHE Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 390 MET Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 460 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 222 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 48 optimal weight: 20.0000 chunk 97 optimal weight: 0.6980 chunk 182 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 HIS D 325 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.133426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.108980 restraints weight = 25555.879| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.04 r_work: 0.3120 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18685 Z= 0.139 Angle : 0.518 10.526 25382 Z= 0.263 Chirality : 0.043 0.181 2732 Planarity : 0.004 0.047 3308 Dihedral : 4.398 19.456 2524 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.23 % Allowed : 13.73 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.17), residues: 2306 helix: -0.27 (0.35), residues: 225 sheet: -0.33 (0.19), residues: 747 loop : -1.28 (0.16), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 104 HIS 0.005 0.001 HIS E 165 PHE 0.013 0.001 PHE D 253 TYR 0.013 0.001 TYR A 79 ARG 0.004 0.000 ARG C 40 Details of bonding type rmsd hydrogen bonds : bond 0.02883 ( 262) hydrogen bonds : angle 4.92161 ( 663) SS BOND : bond 0.00714 ( 2) SS BOND : angle 1.44565 ( 4) covalent geometry : bond 0.00335 (18683) covalent geometry : angle 0.51725 (25378) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 208 time to evaluate : 1.944 Fit side-chains REVERT: F 102 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8691 (pp) REVERT: F 178 GLN cc_start: 0.7497 (mp10) cc_final: 0.6844 (tt0) REVERT: B 132 TYR cc_start: 0.8826 (OUTLIER) cc_final: 0.7398 (m-80) REVERT: B 164 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8207 (pt0) REVERT: C 52 LYS cc_start: 0.7890 (mttp) cc_final: 0.7499 (tptp) REVERT: D 384 MET cc_start: 0.6723 (OUTLIER) cc_final: 0.6229 (mpp) REVERT: D 466 LEU cc_start: 0.8773 (mp) cc_final: 0.8404 (mp) REVERT: D 470 TYR cc_start: 0.3416 (OUTLIER) cc_final: 0.2533 (m-80) REVERT: E 147 ASP cc_start: 0.8642 (p0) cc_final: 0.8422 (p0) REVERT: E 440 MET cc_start: 0.8224 (mtt) cc_final: 0.7730 (mtt) outliers start: 45 outliers final: 38 residues processed: 238 average time/residue: 0.2783 time to fit residues: 103.1201 Evaluate side-chains 246 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 203 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 270 ASP Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 353 ASN Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 470 TYR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 245 PHE Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 390 MET Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 460 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 80 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 150 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 HIS D 325 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.131881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.107468 restraints weight = 25641.404| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.05 r_work: 0.3094 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 18685 Z= 0.202 Angle : 0.572 10.061 25382 Z= 0.292 Chirality : 0.045 0.183 2732 Planarity : 0.004 0.047 3308 Dihedral : 4.645 21.091 2524 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.28 % Allowed : 14.13 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.17), residues: 2306 helix: -0.32 (0.35), residues: 225 sheet: -0.46 (0.19), residues: 742 loop : -1.38 (0.16), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 104 HIS 0.006 0.001 HIS E 165 PHE 0.015 0.002 PHE B 80 TYR 0.021 0.002 TYR A 79 ARG 0.003 0.000 ARG B 106 Details of bonding type rmsd hydrogen bonds : bond 0.03272 ( 262) hydrogen bonds : angle 5.13200 ( 663) SS BOND : bond 0.00864 ( 2) SS BOND : angle 1.72522 ( 4) covalent geometry : bond 0.00492 (18683) covalent geometry : angle 0.57201 (25378) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 195 time to evaluate : 1.993 Fit side-chains REVERT: F 102 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8715 (pp) REVERT: B 132 TYR cc_start: 0.8899 (OUTLIER) cc_final: 0.7565 (m-80) REVERT: B 164 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8213 (pt0) REVERT: C 308 TYR cc_start: 0.8112 (m-10) cc_final: 0.7526 (m-80) REVERT: D 384 MET cc_start: 0.6776 (OUTLIER) cc_final: 0.6293 (mpp) REVERT: D 470 TYR cc_start: 0.3476 (OUTLIER) cc_final: 0.2548 (m-80) REVERT: E 147 ASP cc_start: 0.8678 (p0) cc_final: 0.8440 (p0) REVERT: E 440 MET cc_start: 0.8334 (mtt) cc_final: 0.7882 (mtt) outliers start: 46 outliers final: 39 residues processed: 223 average time/residue: 0.2884 time to fit residues: 99.1993 Evaluate side-chains 237 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 193 time to evaluate : 2.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 270 ASP Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 353 ASN Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 470 TYR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 245 PHE Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 390 MET Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 460 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 180 optimal weight: 3.9990 chunk 56 optimal weight: 0.0770 chunk 201 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 157 optimal weight: 7.9990 chunk 131 optimal weight: 9.9990 chunk 53 optimal weight: 0.0050 overall best weight: 1.8158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 HIS D 325 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.134380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.109952 restraints weight = 25493.946| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.04 r_work: 0.3131 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18685 Z= 0.112 Angle : 0.499 9.929 25382 Z= 0.254 Chirality : 0.043 0.179 2732 Planarity : 0.003 0.047 3308 Dihedral : 4.289 18.681 2524 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.18 % Allowed : 14.43 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.17), residues: 2306 helix: -0.18 (0.35), residues: 225 sheet: -0.36 (0.19), residues: 749 loop : -1.23 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 104 HIS 0.004 0.001 HIS C 165 PHE 0.012 0.001 PHE D 253 TYR 0.013 0.001 TYR E 246 ARG 0.004 0.000 ARG C 40 Details of bonding type rmsd hydrogen bonds : bond 0.02714 ( 262) hydrogen bonds : angle 4.86551 ( 663) SS BOND : bond 0.00625 ( 2) SS BOND : angle 1.18024 ( 4) covalent geometry : bond 0.00266 (18683) covalent geometry : angle 0.49858 (25378) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8750.03 seconds wall clock time: 152 minutes 0.37 seconds (9120.37 seconds total)