Starting phenix.real_space_refine on Thu Sep 18 15:28:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yeg_39194/09_2025/8yeg_39194.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yeg_39194/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8yeg_39194/09_2025/8yeg_39194.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yeg_39194/09_2025/8yeg_39194.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yeg_39194/09_2025/8yeg_39194.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yeg_39194/09_2025/8yeg_39194.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 5.03, per 1000 atoms: 0.28 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: 1.75 Conformation dependent library (CDL) restraints added in 952.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.70 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: 2.92 Time building geometry restraints manager: 2.26 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.830 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.550 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (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 ARG 0.012 0.001 ARG D 68 TYR 0.064 0.002 TYR B 132 PHE 0.022 0.002 PHE B 80 TRP 0.017 0.002 TRP D 398 HIS 0.007 0.002 HIS E 165 Details of bonding type rmsd covalent geometry : bond 0.00518 (18683) covalent geometry : angle 0.64634 (25378) SS BOND : bond 0.00953 ( 2) SS BOND : angle 1.80212 ( 4) hydrogen bonds : bond 0.16588 ( 262) hydrogen bonds : angle 6.45637 ( 663) *********************** 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 : 0.481 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: 0.1356 time to fit residues: 47.9366 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 : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 0.1980 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 0.8980 overall best weight: 2.6186 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.140654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.115028 restraints weight = 24890.552| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.27 r_work: 0.3261 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.0689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18685 Z= 0.148 Angle : 0.538 7.413 25382 Z= 0.276 Chirality : 0.044 0.182 2732 Planarity : 0.004 0.050 3308 Dihedral : 4.671 19.896 2524 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.74 % Allowed : 5.50 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.16), residues: 2306 helix: -0.62 (0.35), residues: 225 sheet: -0.02 (0.18), residues: 735 loop : -1.31 (0.16), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 248 TYR 0.037 0.001 TYR B 132 PHE 0.013 0.002 PHE B 80 TRP 0.018 0.001 TRP A 104 HIS 0.006 0.001 HIS E 165 Details of bonding type rmsd covalent geometry : bond 0.00359 (18683) covalent geometry : angle 0.53761 (25378) SS BOND : bond 0.00737 ( 2) SS BOND : angle 1.28075 ( 4) hydrogen bonds : bond 0.03579 ( 262) hydrogen bonds : angle 5.41897 ( 663) *********************** 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 : 0.840 Fit side-chains REVERT: A 97 MET cc_start: 0.7798 (mmt) cc_final: 0.7588 (mmm) REVERT: F 31 ASN cc_start: 0.8440 (p0) cc_final: 0.8084 (t0) REVERT: L 87 GLU cc_start: 0.8521 (pt0) cc_final: 0.7835 (tm-30) REVERT: C 308 TYR cc_start: 0.8205 (m-80) cc_final: 0.7897 (m-80) REVERT: E 246 TYR cc_start: 0.8722 (p90) cc_final: 0.8285 (p90) REVERT: E 440 MET cc_start: 0.7966 (mtt) cc_final: 0.7602 (mtt) outliers start: 15 outliers final: 10 residues processed: 219 average time/residue: 0.1361 time to fit residues: 45.8446 Evaluate side-chains 211 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 201 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 139 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 152 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 168 optimal weight: 10.0000 chunk 67 optimal weight: 0.6980 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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** E 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.137023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.111665 restraints weight = 25545.419| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.14 r_work: 0.3180 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18685 Z= 0.147 Angle : 0.521 6.671 25382 Z= 0.268 Chirality : 0.044 0.183 2732 Planarity : 0.004 0.049 3308 Dihedral : 4.518 19.877 2524 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.19 % Allowed : 8.58 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.17), residues: 2306 helix: -0.53 (0.35), residues: 225 sheet: -0.09 (0.18), residues: 742 loop : -1.28 (0.16), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.015 0.001 TYR C 132 PHE 0.013 0.001 PHE D 253 TRP 0.017 0.001 TRP A 104 HIS 0.005 0.001 HIS E 165 Details of bonding type rmsd covalent geometry : bond 0.00358 (18683) covalent geometry : angle 0.52049 (25378) SS BOND : bond 0.00745 ( 2) SS BOND : angle 1.27160 ( 4) hydrogen bonds : bond 0.03180 ( 262) hydrogen bonds : angle 5.13637 ( 663) *********************** 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 237 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: F 396 GLU cc_start: 0.7086 (tm-30) cc_final: 0.6710 (pt0) REVERT: L 87 GLU cc_start: 0.8514 (pt0) cc_final: 0.7965 (tm-30) REVERT: B 132 TYR cc_start: 0.8713 (OUTLIER) cc_final: 0.6844 (m-80) REVERT: C 308 TYR cc_start: 0.8152 (m-80) cc_final: 0.7751 (m-80) REVERT: D 384 MET cc_start: 0.6822 (OUTLIER) cc_final: 0.6465 (mpp) REVERT: E 246 TYR cc_start: 0.8681 (p90) cc_final: 0.8316 (p90) REVERT: E 440 MET cc_start: 0.8136 (mtt) cc_final: 0.7711 (mtt) outliers start: 24 outliers final: 17 residues processed: 228 average time/residue: 0.1376 time to fit residues: 48.4042 Evaluate side-chains 220 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 201 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 D residue 21 VAL Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain D residue 384 MET 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 50 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 204 optimal weight: 10.0000 chunk 225 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 207 optimal weight: 0.9990 chunk 186 optimal weight: 9.9990 chunk 161 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 201 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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** D 325 HIS D 467 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.135736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.110542 restraints weight = 25499.139| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.10 r_work: 0.3181 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18685 Z= 0.160 Angle : 0.528 6.735 25382 Z= 0.271 Chirality : 0.044 0.183 2732 Planarity : 0.004 0.047 3308 Dihedral : 4.522 20.104 2524 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.78 % Allowed : 10.01 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.17), residues: 2306 helix: -0.45 (0.35), residues: 225 sheet: -0.17 (0.18), residues: 742 loop : -1.29 (0.16), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.014 0.001 TYR C 132 PHE 0.013 0.001 PHE B 80 TRP 0.016 0.001 TRP A 104 HIS 0.006 0.001 HIS E 165 Details of bonding type rmsd covalent geometry : bond 0.00391 (18683) covalent geometry : angle 0.52788 (25378) SS BOND : bond 0.00823 ( 2) SS BOND : angle 1.18196 ( 4) hydrogen bonds : bond 0.03126 ( 262) hydrogen bonds : angle 5.07238 ( 663) *********************** 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 242 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 206 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: F 396 GLU cc_start: 0.6882 (tm-30) cc_final: 0.6464 (pt0) REVERT: B 132 TYR cc_start: 0.8797 (OUTLIER) cc_final: 0.7144 (m-80) REVERT: B 146 MET cc_start: 0.8696 (ptp) cc_final: 0.8444 (ptp) REVERT: C 308 TYR cc_start: 0.8101 (m-80) cc_final: 0.7588 (m-80) REVERT: D 384 MET cc_start: 0.6748 (OUTLIER) cc_final: 0.6367 (mpp) REVERT: D 466 LEU cc_start: 0.8859 (mt) cc_final: 0.8632 (mp) REVERT: E 246 TYR cc_start: 0.8651 (p90) cc_final: 0.8298 (p90) REVERT: E 440 MET cc_start: 0.8176 (mtt) cc_final: 0.7703 (mtt) outliers start: 36 outliers final: 25 residues processed: 228 average time/residue: 0.1368 time to fit residues: 48.4368 Evaluate side-chains 223 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 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 L residue 108 THR 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 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 456 ASP 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 209 optimal weight: 10.0000 chunk 182 optimal weight: 0.8980 chunk 107 optimal weight: 8.9990 chunk 181 optimal weight: 2.9990 chunk 203 optimal weight: 0.7980 chunk 71 optimal weight: 8.9990 chunk 216 optimal weight: 9.9990 chunk 109 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 187 optimal weight: 5.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- 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 D 467 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.137295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.111882 restraints weight = 25429.498| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.14 r_work: 0.3184 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18685 Z= 0.130 Angle : 0.496 6.312 25382 Z= 0.255 Chirality : 0.043 0.180 2732 Planarity : 0.004 0.047 3308 Dihedral : 4.360 19.186 2524 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.93 % Allowed : 10.81 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.17), residues: 2306 helix: -0.33 (0.35), residues: 225 sheet: -0.19 (0.18), residues: 744 loop : -1.25 (0.16), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 40 TYR 0.011 0.001 TYR B 132 PHE 0.013 0.001 PHE D 253 TRP 0.016 0.001 TRP A 104 HIS 0.005 0.001 HIS E 165 Details of bonding type rmsd covalent geometry : bond 0.00315 (18683) covalent geometry : angle 0.49538 (25378) SS BOND : bond 0.00756 ( 2) SS BOND : angle 1.08787 ( 4) hydrogen bonds : bond 0.02848 ( 262) hydrogen bonds : angle 4.91930 ( 663) *********************** 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 258 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 219 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: F 396 GLU cc_start: 0.6871 (tm-30) cc_final: 0.6318 (pt0) REVERT: B 132 TYR cc_start: 0.8801 (OUTLIER) cc_final: 0.7173 (m-80) REVERT: C 308 TYR cc_start: 0.8080 (m-80) cc_final: 0.7549 (m-80) REVERT: C 365 GLU cc_start: 0.8053 (tt0) cc_final: 0.7594 (mt-10) REVERT: D 384 MET cc_start: 0.6669 (OUTLIER) cc_final: 0.6284 (mpp) REVERT: D 466 LEU cc_start: 0.8796 (mt) cc_final: 0.8552 (mp) REVERT: D 470 TYR cc_start: 0.3451 (OUTLIER) cc_final: 0.2538 (m-80) REVERT: E 246 TYR cc_start: 0.8681 (p90) cc_final: 0.8371 (p90) REVERT: E 440 MET cc_start: 0.8154 (mtt) cc_final: 0.7738 (mtt) outliers start: 39 outliers final: 27 residues processed: 241 average time/residue: 0.1376 time to fit residues: 51.3737 Evaluate side-chains 233 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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 353 ASN Chi-restraints excluded: chain L residue 89 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 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 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 390 MET Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 470 TYR 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 169 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 168 optimal weight: 8.9990 chunk 204 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 overall best weight: 9.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 ASN ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 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 = 0.3479 r_free = 0.3479 target = 0.128319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.104281 restraints weight = 25989.536| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.00 r_work: 0.3049 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.138 18685 Z= 0.449 Angle : 0.803 12.747 25382 Z= 0.414 Chirality : 0.053 0.194 2732 Planarity : 0.006 0.083 3308 Dihedral : 5.455 24.885 2524 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.53 % Allowed : 11.80 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.16), residues: 2306 helix: -0.79 (0.34), residues: 225 sheet: -0.60 (0.18), residues: 747 loop : -1.69 (0.15), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 106 TYR 0.031 0.003 TYR C 132 PHE 0.023 0.003 PHE B 80 TRP 0.019 0.003 TRP F 166 HIS 0.011 0.003 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.01102 (18683) covalent geometry : angle 0.80227 (25378) SS BOND : bond 0.01434 ( 2) SS BOND : angle 2.78563 ( 4) hydrogen bonds : bond 0.04763 ( 262) hydrogen bonds : angle 5.74872 ( 663) *********************** 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 240 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 189 time to evaluate : 0.725 Fit side-chains REVERT: F 220 ASP cc_start: 0.8539 (OUTLIER) cc_final: 0.8319 (p0) REVERT: B 132 TYR cc_start: 0.9019 (OUTLIER) cc_final: 0.7797 (m-80) REVERT: B 233 GLN cc_start: 0.8796 (tt0) cc_final: 0.8593 (tt0) REVERT: B 339 MET cc_start: 0.8786 (ptp) cc_final: 0.8524 (ptp) REVERT: D 123 TYR cc_start: 0.8807 (t80) cc_final: 0.8583 (t80) REVERT: D 384 MET cc_start: 0.6785 (OUTLIER) cc_final: 0.6375 (mpp) REVERT: D 466 LEU cc_start: 0.8860 (mt) cc_final: 0.8560 (mp) REVERT: D 470 TYR cc_start: 0.3697 (OUTLIER) cc_final: 0.2755 (m-80) REVERT: E 246 TYR cc_start: 0.8859 (p90) cc_final: 0.8591 (p90) REVERT: E 440 MET cc_start: 0.8449 (mtt) cc_final: 0.7888 (mtt) outliers start: 51 outliers final: 37 residues processed: 223 average time/residue: 0.1362 time to fit residues: 47.4483 Evaluate side-chains 220 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 179 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 31 ASN Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 155 MET 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 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 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 234 MET 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 358 GLU 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 140 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 156 optimal weight: 0.6980 chunk 1 optimal weight: 9.9990 chunk 138 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 163 optimal weight: 4.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 ASN F 325 HIS L 22 ASN B 305 ASN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 HIS D 325 HIS ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.135217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.110807 restraints weight = 25366.749| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.04 r_work: 0.3145 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18685 Z= 0.086 Angle : 0.492 12.370 25382 Z= 0.254 Chirality : 0.043 0.182 2732 Planarity : 0.004 0.048 3308 Dihedral : 4.423 20.302 2524 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.83 % Allowed : 13.34 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.17), residues: 2306 helix: -0.40 (0.35), residues: 225 sheet: -0.41 (0.18), residues: 744 loop : -1.34 (0.16), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 29 TYR 0.010 0.001 TYR E 351 PHE 0.014 0.001 PHE F 366 TRP 0.020 0.001 TRP A 104 HIS 0.005 0.001 HIS F 325 Details of bonding type rmsd covalent geometry : bond 0.00189 (18683) covalent geometry : angle 0.49174 (25378) SS BOND : bond 0.00482 ( 2) SS BOND : angle 0.91831 ( 4) hydrogen bonds : bond 0.02626 ( 262) hydrogen bonds : angle 4.91289 ( 663) *********************** 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 254 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 217 time to evaluate : 0.791 Fit side-chains REVERT: A 34 MET cc_start: 0.8815 (mtm) cc_final: 0.8455 (mtp) REVERT: F 102 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8598 (pp) REVERT: B 132 TYR cc_start: 0.8780 (OUTLIER) cc_final: 0.7421 (m-80) REVERT: C 52 LYS cc_start: 0.7972 (mttp) cc_final: 0.7493 (tptp) REVERT: C 234 MET cc_start: 0.9280 (mtm) cc_final: 0.9071 (mtm) REVERT: C 365 GLU cc_start: 0.8029 (tt0) cc_final: 0.7567 (mt-10) REVERT: E 246 TYR cc_start: 0.8744 (p90) cc_final: 0.8530 (p90) REVERT: E 440 MET cc_start: 0.8296 (mtt) cc_final: 0.7858 (mtt) outliers start: 37 outliers final: 27 residues processed: 240 average time/residue: 0.1355 time to fit residues: 51.0839 Evaluate side-chains 231 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 202 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 102 LEU 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 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 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 325 HIS Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain E residue 245 PHE 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 12 optimal weight: 4.9990 chunk 178 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 202 optimal weight: 0.0770 chunk 67 optimal weight: 0.2980 chunk 73 optimal weight: 8.9990 chunk 90 optimal weight: 9.9990 chunk 216 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 146 optimal weight: 0.0060 overall best weight: 1.0758 ------------------------------------------------------------------------------- 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** D 325 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.134710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.110309 restraints weight = 25289.320| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.03 r_work: 0.3149 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18685 Z= 0.089 Angle : 0.485 11.245 25382 Z= 0.247 Chirality : 0.042 0.178 2732 Planarity : 0.003 0.047 3308 Dihedral : 4.136 17.421 2524 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.64 % Allowed : 14.18 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.17), residues: 2306 helix: -0.16 (0.35), residues: 225 sheet: -0.26 (0.19), residues: 749 loop : -1.20 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 40 TYR 0.010 0.001 TYR A 79 PHE 0.012 0.001 PHE F 366 TRP 0.019 0.001 TRP A 104 HIS 0.013 0.001 HIS C 325 Details of bonding type rmsd covalent geometry : bond 0.00204 (18683) covalent geometry : angle 0.48448 (25378) SS BOND : bond 0.00516 ( 2) SS BOND : angle 1.05624 ( 4) hydrogen bonds : bond 0.02544 ( 262) hydrogen bonds : angle 4.79599 ( 663) *********************** 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 245 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 0.853 Fit side-chains REVERT: F 102 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8596 (pp) REVERT: F 178 GLN cc_start: 0.7465 (mp10) cc_final: 0.6836 (tt0) REVERT: B 132 TYR cc_start: 0.8761 (OUTLIER) cc_final: 0.7168 (m-80) REVERT: C 52 LYS cc_start: 0.7884 (mttp) cc_final: 0.7482 (tptp) REVERT: C 365 GLU cc_start: 0.8061 (tt0) cc_final: 0.7614 (mt-10) REVERT: D 466 LEU cc_start: 0.8591 (mp) cc_final: 0.8319 (mp) REVERT: E 246 TYR cc_start: 0.8741 (p90) cc_final: 0.8510 (p90) outliers start: 33 outliers final: 28 residues processed: 235 average time/residue: 0.1363 time to fit residues: 50.2785 Evaluate side-chains 235 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 102 LEU 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 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 371 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain E residue 245 PHE Chi-restraints excluded: chain E residue 252 MET 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 53 optimal weight: 0.0970 chunk 202 optimal weight: 0.1980 chunk 121 optimal weight: 0.9980 chunk 147 optimal weight: 8.9990 chunk 135 optimal weight: 7.9990 chunk 215 optimal weight: 0.0020 chunk 197 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 16 optimal weight: 0.3980 chunk 131 optimal weight: 20.0000 overall best weight: 0.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 325 HIS B 317 ASN C 140 ASN D 325 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.138317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.114117 restraints weight = 25081.822| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.00 r_work: 0.3192 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18685 Z= 0.074 Angle : 0.457 10.651 25382 Z= 0.235 Chirality : 0.042 0.176 2732 Planarity : 0.003 0.046 3308 Dihedral : 3.789 17.294 2524 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.29 % Allowed : 14.53 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.17), residues: 2306 helix: 0.01 (0.36), residues: 225 sheet: -0.08 (0.19), residues: 738 loop : -1.05 (0.16), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 40 TYR 0.017 0.001 TYR A 79 PHE 0.013 0.001 PHE F 33 TRP 0.022 0.001 TRP A 104 HIS 0.006 0.000 HIS F 325 Details of bonding type rmsd covalent geometry : bond 0.00162 (18683) covalent geometry : angle 0.45692 (25378) SS BOND : bond 0.00398 ( 2) SS BOND : angle 0.72719 ( 4) hydrogen bonds : bond 0.02230 ( 262) hydrogen bonds : angle 4.61587 ( 663) *********************** 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 247 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 221 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: F 102 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8573 (pp) REVERT: B 132 TYR cc_start: 0.8685 (OUTLIER) cc_final: 0.7019 (m-80) REVERT: C 52 LYS cc_start: 0.7844 (mttp) cc_final: 0.7539 (tptp) REVERT: C 365 GLU cc_start: 0.7999 (tt0) cc_final: 0.7561 (mt-10) REVERT: D 466 LEU cc_start: 0.8510 (mp) cc_final: 0.8287 (mp) REVERT: E 246 TYR cc_start: 0.8670 (p90) cc_final: 0.8450 (p90) REVERT: E 360 MET cc_start: 0.8441 (mtp) cc_final: 0.8123 (mmm) outliers start: 26 outliers final: 20 residues processed: 235 average time/residue: 0.1323 time to fit residues: 48.6280 Evaluate side-chains 229 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 102 LEU 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 B residue 58 VAL Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 224 THR 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 D residue 21 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain E residue 245 PHE 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 141 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 ASN C 140 ASN C 325 HIS D 325 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.131883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.107554 restraints weight = 25616.223| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.03 r_work: 0.3097 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 18685 Z= 0.223 Angle : 0.600 10.207 25382 Z= 0.307 Chirality : 0.046 0.183 2732 Planarity : 0.004 0.046 3308 Dihedral : 4.580 18.154 2524 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.54 % Allowed : 14.72 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.17), residues: 2306 helix: -0.17 (0.35), residues: 225 sheet: -0.34 (0.19), residues: 742 loop : -1.28 (0.16), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 248 TYR 0.016 0.002 TYR L 97 PHE 0.020 0.002 PHE F 245 TRP 0.012 0.002 TRP D 398 HIS 0.007 0.002 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00550 (18683) covalent geometry : angle 0.59934 (25378) SS BOND : bond 0.00890 ( 2) SS BOND : angle 1.90243 ( 4) hydrogen bonds : bond 0.03441 ( 262) hydrogen bonds : angle 5.18670 ( 663) ********************** 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 228 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 197 time to evaluate : 0.722 Fit side-chains REVERT: A 34 MET cc_start: 0.8837 (mtm) cc_final: 0.8616 (mtp) REVERT: F 31 ASN cc_start: 0.8130 (OUTLIER) cc_final: 0.7880 (t0) REVERT: F 102 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8741 (pp) REVERT: F 178 GLN cc_start: 0.7518 (mp10) cc_final: 0.6855 (tt0) REVERT: B 132 TYR cc_start: 0.8920 (OUTLIER) cc_final: 0.7523 (m-80) REVERT: E 246 TYR cc_start: 0.8734 (p90) cc_final: 0.8521 (p90) outliers start: 31 outliers final: 25 residues processed: 215 average time/residue: 0.1274 time to fit residues: 42.6685 Evaluate side-chains 218 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 31 ASN 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 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 125 ASP Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain C residue 51 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 325 HIS 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 456 ASP Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 245 PHE 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 110 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 164 optimal weight: 7.9990 chunk 213 optimal weight: 5.9990 chunk 210 optimal weight: 0.0060 chunk 124 optimal weight: 0.8980 chunk 59 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 159 optimal weight: 0.9990 chunk 142 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 ASN F 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 = 0.3526 r_free = 0.3526 target = 0.132247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.108099 restraints weight = 25676.533| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.02 r_work: 0.3101 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.147 18685 Z= 0.240 Angle : 0.873 59.198 25382 Z= 0.522 Chirality : 0.048 0.785 2732 Planarity : 0.006 0.210 3308 Dihedral : 4.624 21.977 2524 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.54 % Allowed : 14.97 % Favored : 83.49 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.17), residues: 2306 helix: -0.16 (0.35), residues: 225 sheet: -0.34 (0.19), residues: 747 loop : -1.27 (0.16), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 248 TYR 0.015 0.001 TYR B 132 PHE 0.019 0.002 PHE F 245 TRP 0.011 0.001 TRP D 398 HIS 0.351 0.005 HIS C 325 Details of bonding type rmsd covalent geometry : bond 0.00441 (18683) covalent geometry : angle 0.87260 (25378) SS BOND : bond 0.00811 ( 2) SS BOND : angle 1.83090 ( 4) hydrogen bonds : bond 0.03285 ( 262) hydrogen bonds : angle 5.18046 ( 663) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4512.03 seconds wall clock time: 77 minutes 55.47 seconds (4675.47 seconds total)