Starting phenix.real_space_refine on Sun Jun 15 23:38:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yeg_39194/06_2025/8yeg_39194.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yeg_39194/06_2025/8yeg_39194.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yeg_39194/06_2025/8yeg_39194.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yeg_39194/06_2025/8yeg_39194.map" model { file = "/net/cci-nas-00/data/ceres_data/8yeg_39194/06_2025/8yeg_39194.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yeg_39194/06_2025/8yeg_39194.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 113 5.16 5 C 11547 2.51 5 N 3076 2.21 5 O 3485 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18221 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 925 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "F" Number of atoms: 3283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3283 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 395} Chain breaks: 1 Chain: "L" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 881 Classifications: {'peptide': 113} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 105} Chain: "B" Number of atoms: 3283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3283 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 395} Chain breaks: 1 Chain: "C" Number of atoms: 3283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3283 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 395} Chain breaks: 1 Chain: "D" Number of atoms: 3283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3283 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 395} Chain breaks: 1 Chain: "E" Number of atoms: 3283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3283 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 395} Chain breaks: 1 Time building chain proxies: 10.48, per 1000 atoms: 0.58 Number of scatterers: 18221 At special positions: 0 Unit cell: (131.61, 119.84, 144.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 113 16.00 O 3485 8.00 N 3076 7.00 C 11547 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.18 Conformation dependent library (CDL) restraints added in 2.3 seconds 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4272 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 28 sheets defined 14.3% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'A' and resid 83 through 87 removed outlier: 3.936A pdb=" N THR A 87 " --> pdb=" O ALA A 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 27 removed outlier: 4.117A pdb=" N TYR F 26 " --> pdb=" O ALA F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 211 removed outlier: 3.678A pdb=" N GLN F 211 " --> pdb=" O PHE F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 237 Processing helix chain 'F' and resid 269 through 273 removed outlier: 3.587A pdb=" N LEU F 273 " --> pdb=" O ASP F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 281 removed outlier: 3.859A pdb=" N SER F 281 " --> pdb=" O ASN F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 354 No H-bonds generated for 'chain 'F' and resid 352 through 354' Processing helix chain 'F' and resid 380 through 391 Processing helix chain 'F' and resid 391 through 398 removed outlier: 4.056A pdb=" N LEU F 395 " --> pdb=" O ASN F 391 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TRP F 398 " --> pdb=" O VAL F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 439 removed outlier: 3.681A pdb=" N ASP F 439 " --> pdb=" O PRO F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 457 Processing helix chain 'F' and resid 458 through 469 Processing helix chain 'L' and resid 85 through 89 removed outlier: 3.643A pdb=" N VAL L 89 " --> pdb=" O PRO L 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 235 Processing helix chain 'B' and resid 277 through 281 Processing helix chain 'B' and resid 352 through 354 No H-bonds generated for 'chain 'B' and resid 352 through 354' Processing helix chain 'B' and resid 380 through 391 Processing helix chain 'B' and resid 391 through 398 removed outlier: 3.938A pdb=" N LEU B 395 " --> pdb=" O ASN B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 457 Processing helix chain 'B' and resid 458 through 469 removed outlier: 3.638A pdb=" N LYS B 463 " --> pdb=" O PRO B 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 26 Processing helix chain 'C' and resid 230 through 236 Processing helix chain 'C' and resid 269 through 273 removed outlier: 3.718A pdb=" N LEU C 273 " --> pdb=" O ASP C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 removed outlier: 3.970A pdb=" N SER C 282 " --> pdb=" O ASN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 391 Processing helix chain 'C' and resid 391 through 398 removed outlier: 4.119A pdb=" N LEU C 395 " --> pdb=" O ASN C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 440 removed outlier: 4.096A pdb=" N ASP C 439 " --> pdb=" O PRO C 436 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET C 440 " --> pdb=" O TYR C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 457 Processing helix chain 'C' and resid 458 through 469 removed outlier: 3.533A pdb=" N GLY C 469 " --> pdb=" O LEU C 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 27 removed outlier: 4.200A pdb=" N TYR D 26 " --> pdb=" O ALA D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.894A pdb=" N PHE D 88 " --> pdb=" O SER D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 237 Processing helix chain 'D' and resid 269 through 273 removed outlier: 3.961A pdb=" N LEU D 273 " --> pdb=" O ASP D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 354 No H-bonds generated for 'chain 'D' and resid 352 through 354' Processing helix chain 'D' and resid 380 through 391 Processing helix chain 'D' and resid 391 through 398 removed outlier: 4.079A pdb=" N LEU D 395 " --> pdb=" O ASN D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 440 removed outlier: 3.962A pdb=" N ASP D 439 " --> pdb=" O PRO D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 457 removed outlier: 3.683A pdb=" N GLN D 457 " --> pdb=" O GLU D 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 454 through 457' Processing helix chain 'D' and resid 458 through 469 removed outlier: 3.580A pdb=" N ARG D 462 " --> pdb=" O PHE D 458 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS D 463 " --> pdb=" O PRO D 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 27 removed outlier: 4.201A pdb=" N TYR E 26 " --> pdb=" O ALA E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 236 Processing helix chain 'E' and resid 277 through 281 Processing helix chain 'E' and resid 300 through 302 No H-bonds generated for 'chain 'E' and resid 300 through 302' Processing helix chain 'E' and resid 352 through 354 No H-bonds generated for 'chain 'E' and resid 352 through 354' Processing helix chain 'E' and resid 380 through 391 Processing helix chain 'E' and resid 391 through 398 removed outlier: 4.136A pdb=" N LEU E 395 " --> pdb=" O ASN E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 440 removed outlier: 3.795A pdb=" N ASP E 439 " --> pdb=" O PRO E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 457 removed outlier: 3.534A pdb=" N GLN E 457 " --> pdb=" O GLU E 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 454 through 457' Processing helix chain 'E' and resid 458 through 469 removed outlier: 3.838A pdb=" N GLY E 469 " --> pdb=" O LEU E 465 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 5.954A pdb=" N GLY A 10 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N MET A 34 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 28 through 37 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 28 through 37 current: chain 'F' and resid 308 through 309 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 308 through 309 current: chain 'F' and resid 356 through 378 removed outlier: 3.574A pdb=" N THR B 263 " --> pdb=" O TYR F 356 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 51 through 52 Processing sheet with id=AA5, first strand: chain 'F' and resid 68 through 73 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 68 through 73 current: chain 'F' and resid 245 through 259 removed outlier: 5.626A pdb=" N ALA F 254 " --> pdb=" O SER F 293 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N SER F 293 " --> pdb=" O ALA F 254 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N HIS F 256 " --> pdb=" O THR F 291 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 115 through 121 removed outlier: 4.168A pdb=" N LEU F 119 " --> pdb=" O VAL F 142 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N VAL F 142 " --> pdb=" O LEU F 119 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 185 through 191 removed outlier: 5.838A pdb=" N TRP F 166 " --> pdb=" O CYS F 226 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N CYS F 226 " --> pdb=" O TRP F 166 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N MET F 197 " --> pdb=" O LYS F 227 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 263 through 264 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 263 through 264 current: chain 'C' and resid 308 through 309 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 308 through 309 current: chain 'C' and resid 356 through 378 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 297 through 298 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 297 through 298 current: chain 'B' and resid 245 through 258 removed outlier: 5.276A pdb=" N ALA B 254 " --> pdb=" O SER B 293 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N SER B 293 " --> pdb=" O ALA B 254 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N HIS B 256 " --> pdb=" O THR B 291 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AB2, first strand: chain 'L' and resid 11 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 11 through 13 current: chain 'L' and resid 51 through 55 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 59 through 60 current: chain 'L' and resid 103 through 104 Processing sheet with id=AB3, first strand: chain 'B' and resid 27 through 45 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 27 through 45 current: chain 'B' and resid 308 through 309 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 308 through 309 current: chain 'B' and resid 356 through 378 No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 115 through 121 removed outlier: 4.020A pdb=" N LEU B 119 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL B 142 " --> pdb=" O LEU B 119 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 185 through 191 removed outlier: 5.840A pdb=" N TRP B 166 " --> pdb=" O CYS B 226 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N CYS B 226 " --> pdb=" O TRP B 166 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N MET B 197 " --> pdb=" O LYS B 227 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 297 through 298 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 297 through 298 current: chain 'E' and resid 245 through 259 removed outlier: 5.219A pdb=" N ALA E 254 " --> pdb=" O SER E 293 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N SER E 293 " --> pdb=" O ALA E 254 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N HIS E 256 " --> pdb=" O THR E 291 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 51 through 52 Processing sheet with id=AB8, first strand: chain 'C' and resid 68 through 73 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 68 through 73 current: chain 'C' and resid 245 through 259 removed outlier: 6.541A pdb=" N THR C 291 " --> pdb=" O ARG C 255 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N PHE C 257 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL C 289 " --> pdb=" O PHE C 257 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 115 through 120 removed outlier: 4.071A pdb=" N LEU C 119 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL C 142 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 185 through 191 removed outlier: 5.608A pdb=" N TRP C 166 " --> pdb=" O CYS C 226 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N CYS C 226 " --> pdb=" O TRP C 166 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N MET C 197 " --> pdb=" O LYS C 227 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 263 through 264 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 263 through 264 current: chain 'D' and resid 308 through 309 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 308 through 309 current: chain 'D' and resid 356 through 378 No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 51 through 52 Processing sheet with id=AC4, first strand: chain 'D' and resid 68 through 73 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 68 through 73 current: chain 'D' and resid 245 through 258 removed outlier: 6.426A pdb=" N THR D 291 " --> pdb=" O ARG D 255 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N PHE D 257 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL D 289 " --> pdb=" O PHE D 257 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 115 through 120 removed outlier: 5.059A pdb=" N GLY D 116 " --> pdb=" O MET D 146 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N MET D 146 " --> pdb=" O GLY D 116 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N VAL D 144 " --> pdb=" O PRO D 118 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 185 through 191 removed outlier: 5.859A pdb=" N TRP D 166 " --> pdb=" O CYS D 226 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N CYS D 226 " --> pdb=" O TRP D 166 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N MET D 197 " --> pdb=" O LYS D 227 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 263 through 264 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 263 through 264 current: chain 'E' and resid 308 through 309 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 308 through 309 current: chain 'E' and resid 356 through 378 No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'E' and resid 51 through 52 Processing sheet with id=AC9, first strand: chain 'E' and resid 114 through 121 removed outlier: 4.281A pdb=" N LEU E 119 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N VAL E 142 " --> pdb=" O LEU E 119 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 185 through 191 removed outlier: 6.082A pdb=" N TRP E 166 " --> pdb=" O CYS E 226 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N CYS E 226 " --> pdb=" O TRP E 166 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N MET E 197 " --> pdb=" O LYS E 227 " (cutoff:3.500A) 262 hydrogen bonds defined for protein. 663 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.65 Time building geometry restraints manager: 4.98 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: 0.460 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: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 39.430 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 18685 Z= 0.218 Angle : 0.647 8.035 25382 Z= 0.345 Chirality : 0.046 0.153 2732 Planarity : 0.005 0.054 3308 Dihedral : 13.912 89.573 6751 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.16), residues: 2306 helix: -0.95 (0.35), residues: 225 sheet: 0.07 (0.19), residues: 732 loop : -1.43 (0.15), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 398 HIS 0.007 0.002 HIS E 165 PHE 0.022 0.002 PHE B 80 TYR 0.064 0.002 TYR B 132 ARG 0.012 0.001 ARG D 68 Details of bonding type rmsd hydrogen bonds : bond 0.16588 ( 262) hydrogen bonds : angle 6.45637 ( 663) SS BOND : bond 0.00953 ( 2) SS BOND : angle 1.80212 ( 4) covalent geometry : bond 0.00518 (18683) covalent geometry : angle 0.64634 (25378) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 2.084 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: 0.2954 time to fit residues: 103.8397 Evaluate side-chains 200 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.9980 chunk 172 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 178 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 133 optimal weight: 10.0000 chunk 207 optimal weight: 0.4980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.140993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.115406 restraints weight = 24989.112| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.27 r_work: 0.3267 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.0694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18685 Z= 0.135 Angle : 0.527 7.509 25382 Z= 0.271 Chirality : 0.044 0.177 2732 Planarity : 0.004 0.050 3308 Dihedral : 4.619 19.396 2524 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.74 % Allowed : 5.16 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.16), residues: 2306 helix: -0.59 (0.35), residues: 225 sheet: -0.01 (0.18), residues: 741 loop : -1.28 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 104 HIS 0.005 0.001 HIS E 165 PHE 0.013 0.001 PHE B 80 TYR 0.035 0.001 TYR B 132 ARG 0.004 0.000 ARG F 248 Details of bonding type rmsd hydrogen bonds : bond 0.03458 ( 262) hydrogen bonds : angle 5.38722 ( 663) SS BOND : bond 0.00693 ( 2) SS BOND : angle 1.22478 ( 4) covalent geometry : bond 0.00323 (18683) covalent geometry : angle 0.52692 (25378) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 209 time to evaluate : 1.908 Fit side-chains REVERT: A 97 MET cc_start: 0.7770 (mmt) cc_final: 0.7560 (mmm) REVERT: F 31 ASN cc_start: 0.8455 (p0) cc_final: 0.8097 (t0) REVERT: L 87 GLU cc_start: 0.8522 (pt0) cc_final: 0.7829 (tm-30) REVERT: C 308 TYR cc_start: 0.8214 (m-80) cc_final: 0.7904 (m-80) REVERT: E 246 TYR cc_start: 0.8707 (p90) cc_final: 0.8268 (p90) REVERT: E 440 MET cc_start: 0.7930 (mtt) cc_final: 0.7565 (mtt) outliers start: 15 outliers final: 10 residues processed: 219 average time/residue: 0.2985 time to fit residues: 100.0133 Evaluate side-chains 212 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 202 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain E residue 358 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 222 optimal weight: 2.9990 chunk 154 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 142 optimal weight: 20.0000 chunk 220 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 HIS E 35 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.134025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.108772 restraints weight = 25640.082| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.12 r_work: 0.3141 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 18685 Z= 0.267 Angle : 0.634 8.122 25382 Z= 0.327 Chirality : 0.047 0.188 2732 Planarity : 0.005 0.049 3308 Dihedral : 5.012 23.287 2524 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 1.54 % Allowed : 9.12 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.16), residues: 2306 helix: -0.68 (0.34), residues: 225 sheet: -0.28 (0.18), residues: 742 loop : -1.46 (0.16), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 104 HIS 0.009 0.002 HIS E 165 PHE 0.018 0.002 PHE E 451 TYR 0.025 0.002 TYR C 132 ARG 0.006 0.001 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.03948 ( 262) hydrogen bonds : angle 5.50122 ( 663) SS BOND : bond 0.01044 ( 2) SS BOND : angle 1.72867 ( 4) covalent geometry : bond 0.00657 (18683) covalent geometry : angle 0.63392 (25378) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 202 time to evaluate : 2.160 Fit side-chains REVERT: A 79 TYR cc_start: 0.8918 (m-80) cc_final: 0.8692 (m-80) REVERT: F 396 GLU cc_start: 0.7216 (tm-30) cc_final: 0.6647 (pt0) REVERT: L 87 GLU cc_start: 0.8535 (pt0) cc_final: 0.7980 (tm-30) REVERT: B 132 TYR cc_start: 0.8883 (OUTLIER) cc_final: 0.7307 (m-80) REVERT: B 146 MET cc_start: 0.8743 (ptp) cc_final: 0.8477 (ptp) REVERT: C 308 TYR cc_start: 0.8227 (m-80) cc_final: 0.7824 (m-80) REVERT: D 384 MET cc_start: 0.6730 (OUTLIER) cc_final: 0.6384 (mpp) REVERT: D 466 LEU cc_start: 0.8792 (mt) cc_final: 0.8558 (mp) REVERT: E 246 TYR cc_start: 0.8706 (p90) cc_final: 0.8366 (p90) REVERT: E 440 MET cc_start: 0.8315 (mtt) cc_final: 0.7833 (mtt) outliers start: 31 outliers final: 22 residues processed: 223 average time/residue: 0.2926 time to fit residues: 100.4026 Evaluate side-chains 217 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 2.195 ------------------------------------------------------------------------------- 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 38 SER Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 353 ASN Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 325 HIS Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 358 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 137 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 111 optimal weight: 0.0470 chunk 53 optimal weight: 10.0000 chunk 227 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 162 optimal weight: 3.9990 chunk 161 optimal weight: 6.9990 chunk 181 optimal weight: 3.9990 overall best weight: 1.9884 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.136225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.111094 restraints weight = 25146.940| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.09 r_work: 0.3189 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18685 Z= 0.120 Angle : 0.501 6.578 25382 Z= 0.259 Chirality : 0.043 0.183 2732 Planarity : 0.004 0.050 3308 Dihedral : 4.544 20.540 2524 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.44 % Allowed : 10.51 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.17), residues: 2306 helix: -0.50 (0.35), residues: 225 sheet: -0.24 (0.18), residues: 744 loop : -1.30 (0.16), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 104 HIS 0.008 0.001 HIS C 325 PHE 0.013 0.001 PHE D 253 TYR 0.011 0.001 TYR B 132 ARG 0.003 0.000 ARG C 40 Details of bonding type rmsd hydrogen bonds : bond 0.02945 ( 262) hydrogen bonds : angle 5.07471 ( 663) SS BOND : bond 0.00694 ( 2) SS BOND : angle 1.09535 ( 4) covalent geometry : bond 0.00288 (18683) covalent geometry : angle 0.50111 (25378) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 216 time to evaluate : 1.861 Fit side-chains REVERT: F 31 ASN cc_start: 0.8328 (p0) cc_final: 0.8073 (t0) REVERT: F 396 GLU cc_start: 0.6886 (tm-30) cc_final: 0.6449 (pt0) REVERT: B 132 TYR cc_start: 0.8790 (OUTLIER) cc_final: 0.7282 (m-80) REVERT: C 308 TYR cc_start: 0.8095 (m-80) cc_final: 0.7569 (m-80) REVERT: D 384 MET cc_start: 0.6703 (OUTLIER) cc_final: 0.6353 (mpp) REVERT: D 466 LEU cc_start: 0.8867 (mt) cc_final: 0.8625 (mp) REVERT: E 246 TYR cc_start: 0.8637 (p90) cc_final: 0.8289 (p90) REVERT: E 440 MET cc_start: 0.8217 (mtt) cc_final: 0.7777 (mtt) outliers start: 29 outliers final: 20 residues processed: 234 average time/residue: 0.2910 time to fit residues: 104.3051 Evaluate side-chains 221 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 199 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 353 ASN Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain 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 E residue 358 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 158 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 102 optimal weight: 0.0470 chunk 69 optimal weight: 10.0000 chunk 148 optimal weight: 9.9990 chunk 192 optimal weight: 0.9990 chunk 67 optimal weight: 7.9990 chunk 167 optimal weight: 0.9990 chunk 184 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 overall best weight: 3.6086 ------------------------------------------------------------------------------- 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 = 0.3530 r_free = 0.3530 target = 0.132479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.108048 restraints weight = 25507.696| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.03 r_work: 0.3106 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 18685 Z= 0.186 Angle : 0.549 7.166 25382 Z= 0.282 Chirality : 0.045 0.184 2732 Planarity : 0.004 0.048 3308 Dihedral : 4.645 21.116 2524 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.13 % Allowed : 11.30 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.17), residues: 2306 helix: -0.45 (0.35), residues: 225 sheet: -0.33 (0.19), residues: 742 loop : -1.35 (0.16), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 104 HIS 0.006 0.001 HIS C 165 PHE 0.015 0.002 PHE B 80 TYR 0.015 0.002 TYR F 246 ARG 0.003 0.000 ARG C 40 Details of bonding type rmsd hydrogen bonds : bond 0.03251 ( 262) hydrogen bonds : angle 5.14584 ( 663) SS BOND : bond 0.00901 ( 2) SS BOND : angle 1.34870 ( 4) covalent geometry : bond 0.00454 (18683) covalent geometry : angle 0.54905 (25378) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 203 time to evaluate : 2.140 Fit side-chains REVERT: B 132 TYR cc_start: 0.8867 (OUTLIER) cc_final: 0.7441 (m-80) REVERT: B 164 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8151 (pt0) REVERT: C 308 TYR cc_start: 0.8116 (m-80) cc_final: 0.7598 (m-80) REVERT: D 384 MET cc_start: 0.6791 (OUTLIER) cc_final: 0.6422 (mpp) REVERT: D 466 LEU cc_start: 0.8836 (mt) cc_final: 0.8577 (mp) REVERT: D 470 TYR cc_start: 0.3515 (OUTLIER) cc_final: 0.2615 (m-80) REVERT: E 246 TYR cc_start: 0.8742 (p90) cc_final: 0.8503 (p90) REVERT: E 440 MET cc_start: 0.8356 (mtt) cc_final: 0.7857 (mtt) outliers start: 43 outliers final: 33 residues processed: 230 average time/residue: 0.2937 time to fit residues: 104.9095 Evaluate side-chains 233 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 196 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 270 ASP Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 353 ASN Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 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 198 VAL Chi-restraints excluded: chain E residue 245 PHE Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 358 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 106 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 140 optimal weight: 0.9990 chunk 135 optimal weight: 8.9990 chunk 139 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 123 optimal weight: 8.9990 chunk 218 optimal weight: 0.0570 overall best weight: 1.8106 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.134011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.109619 restraints weight = 25326.646| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.02 r_work: 0.3138 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18685 Z= 0.110 Angle : 0.496 14.806 25382 Z= 0.253 Chirality : 0.043 0.180 2732 Planarity : 0.003 0.047 3308 Dihedral : 4.315 18.982 2524 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.88 % Allowed : 12.25 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.17), residues: 2306 helix: -0.30 (0.35), residues: 225 sheet: -0.25 (0.19), residues: 734 loop : -1.20 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 104 HIS 0.004 0.001 HIS B 165 PHE 0.012 0.001 PHE D 253 TYR 0.011 0.001 TYR B 132 ARG 0.004 0.000 ARG C 40 Details of bonding type rmsd hydrogen bonds : bond 0.02723 ( 262) hydrogen bonds : angle 4.88398 ( 663) SS BOND : bond 0.00914 ( 2) SS BOND : angle 1.10190 ( 4) covalent geometry : bond 0.00260 (18683) covalent geometry : angle 0.49571 (25378) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 214 time to evaluate : 1.903 Fit side-chains REVERT: B 132 TYR cc_start: 0.8788 (OUTLIER) cc_final: 0.7368 (m-80) REVERT: B 164 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8198 (pt0) REVERT: C 52 LYS cc_start: 0.7974 (mttp) cc_final: 0.7517 (tptp) REVERT: C 308 TYR cc_start: 0.8014 (m-80) cc_final: 0.7401 (m-80) REVERT: D 384 MET cc_start: 0.6790 (OUTLIER) cc_final: 0.6381 (mpp) REVERT: D 466 LEU cc_start: 0.8722 (mt) cc_final: 0.8504 (mp) REVERT: D 470 TYR cc_start: 0.3492 (OUTLIER) cc_final: 0.2514 (m-80) REVERT: E 246 TYR cc_start: 0.8697 (p90) cc_final: 0.8447 (p90) REVERT: E 440 MET cc_start: 0.8225 (mtt) cc_final: 0.7767 (mtt) outliers start: 38 outliers final: 26 residues processed: 239 average time/residue: 0.2948 time to fit residues: 109.7116 Evaluate side-chains 231 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 201 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 353 ASN Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 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 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 390 MET Chi-restraints excluded: chain E residue 447 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 5 optimal weight: 10.0000 chunk 146 optimal weight: 0.6980 chunk 206 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 200 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 165 optimal weight: 9.9990 chunk 195 optimal weight: 10.0000 overall best weight: 5.3388 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.130874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.106599 restraints weight = 25701.078| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.02 r_work: 0.3083 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 18685 Z= 0.262 Angle : 0.628 11.866 25382 Z= 0.322 Chirality : 0.047 0.184 2732 Planarity : 0.005 0.047 3308 Dihedral : 4.852 20.586 2524 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.58 % Allowed : 12.64 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.16), residues: 2306 helix: -0.43 (0.34), residues: 225 sheet: -0.45 (0.18), residues: 742 loop : -1.43 (0.16), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 166 HIS 0.008 0.002 HIS C 165 PHE 0.017 0.002 PHE B 80 TYR 0.018 0.002 TYR C 132 ARG 0.004 0.001 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.03630 ( 262) hydrogen bonds : angle 5.28923 ( 663) SS BOND : bond 0.00974 ( 2) SS BOND : angle 2.10253 ( 4) covalent geometry : bond 0.00644 (18683) covalent geometry : angle 0.62726 (25378) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 196 time to evaluate : 2.144 Fit side-chains REVERT: F 220 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.8325 (p0) REVERT: F 390 MET cc_start: 0.6866 (ttm) cc_final: 0.6608 (ttm) REVERT: B 132 TYR cc_start: 0.8922 (OUTLIER) cc_final: 0.7643 (m-80) REVERT: B 164 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8203 (pt0) REVERT: B 339 MET cc_start: 0.8732 (ptp) cc_final: 0.8486 (ptp) REVERT: C 308 TYR cc_start: 0.8122 (m-80) cc_final: 0.7569 (m-80) REVERT: D 384 MET cc_start: 0.6728 (OUTLIER) cc_final: 0.6335 (mpp) REVERT: D 466 LEU cc_start: 0.8876 (mt) cc_final: 0.8571 (mp) REVERT: D 470 TYR cc_start: 0.3615 (OUTLIER) cc_final: 0.2696 (m-80) REVERT: E 246 TYR cc_start: 0.8825 (p90) cc_final: 0.8544 (p90) REVERT: E 440 MET cc_start: 0.8329 (mtt) cc_final: 0.7810 (mtt) outliers start: 52 outliers final: 39 residues processed: 226 average time/residue: 0.3211 time to fit residues: 113.0235 Evaluate side-chains 236 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 192 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 31 ASN Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 270 ASP Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 353 ASN Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 470 TYR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 245 PHE Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 390 MET Chi-restraints excluded: chain E residue 447 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 64 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 151 optimal weight: 4.9990 chunk 103 optimal weight: 0.0020 chunk 84 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 120 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 ASN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 HIS D 325 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.133597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.109017 restraints weight = 25387.308| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.06 r_work: 0.3119 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18685 Z= 0.127 Angle : 0.516 10.704 25382 Z= 0.265 Chirality : 0.044 0.182 2732 Planarity : 0.004 0.047 3308 Dihedral : 4.481 19.141 2524 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.13 % Allowed : 13.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.17), residues: 2306 helix: -0.30 (0.35), residues: 225 sheet: -0.40 (0.18), residues: 744 loop : -1.30 (0.16), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 104 HIS 0.004 0.001 HIS B 165 PHE 0.013 0.001 PHE D 253 TYR 0.012 0.001 TYR B 132 ARG 0.003 0.000 ARG C 40 Details of bonding type rmsd hydrogen bonds : bond 0.02867 ( 262) hydrogen bonds : angle 4.96439 ( 663) SS BOND : bond 0.00660 ( 2) SS BOND : angle 1.34265 ( 4) covalent geometry : bond 0.00306 (18683) covalent geometry : angle 0.51541 (25378) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 204 time to evaluate : 1.877 Fit side-chains REVERT: A 81 GLN cc_start: 0.8073 (tp40) cc_final: 0.7855 (tp40) REVERT: F 102 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8692 (pp) REVERT: F 178 GLN cc_start: 0.7464 (mp10) cc_final: 0.6819 (tt0) REVERT: B 132 TYR cc_start: 0.8825 (OUTLIER) cc_final: 0.7360 (m-80) REVERT: B 164 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8190 (pt0) REVERT: D 384 MET cc_start: 0.6710 (OUTLIER) cc_final: 0.6283 (mpp) REVERT: D 470 TYR cc_start: 0.3533 (OUTLIER) cc_final: 0.2641 (m-80) REVERT: E 246 TYR cc_start: 0.8735 (p90) cc_final: 0.8518 (p90) REVERT: E 440 MET cc_start: 0.8257 (mtt) cc_final: 0.7793 (mtt) outliers start: 43 outliers final: 34 residues processed: 232 average time/residue: 0.2806 time to fit residues: 100.7867 Evaluate side-chains 238 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 199 time to evaluate : 2.118 ------------------------------------------------------------------------------- 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 102 LEU Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 353 ASN Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain 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 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 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 Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 460 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 181 optimal weight: 2.9990 chunk 222 optimal weight: 10.0000 chunk 110 optimal weight: 0.1980 chunk 134 optimal weight: 8.9990 chunk 48 optimal weight: 20.0000 chunk 97 optimal weight: 0.0570 chunk 182 optimal weight: 5.9990 chunk 135 optimal weight: 0.6980 chunk 130 optimal weight: 5.9990 overall best weight: 1.9902 ------------------------------------------------------------------------------- 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 = 0.3549 r_free = 0.3549 target = 0.134001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.109317 restraints weight = 25519.618| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.07 r_work: 0.3120 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18685 Z= 0.119 Angle : 0.506 10.186 25382 Z= 0.259 Chirality : 0.043 0.181 2732 Planarity : 0.003 0.047 3308 Dihedral : 4.354 18.229 2524 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.08 % Allowed : 13.88 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.17), residues: 2306 helix: -0.24 (0.35), residues: 225 sheet: -0.37 (0.19), residues: 742 loop : -1.25 (0.16), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 104 HIS 0.007 0.001 HIS C 325 PHE 0.013 0.001 PHE D 253 TYR 0.012 0.001 TYR A 79 ARG 0.004 0.000 ARG C 40 Details of bonding type rmsd hydrogen bonds : bond 0.02786 ( 262) hydrogen bonds : angle 4.89922 ( 663) SS BOND : bond 0.00621 ( 2) SS BOND : angle 1.33807 ( 4) covalent geometry : bond 0.00283 (18683) covalent geometry : angle 0.50576 (25378) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 205 time to evaluate : 2.054 Fit side-chains REVERT: F 102 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8693 (pp) REVERT: B 132 TYR cc_start: 0.8812 (OUTLIER) cc_final: 0.7364 (m-80) REVERT: B 164 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8216 (pt0) REVERT: C 365 GLU cc_start: 0.8140 (tt0) cc_final: 0.7617 (mt-10) REVERT: D 384 MET cc_start: 0.6688 (OUTLIER) cc_final: 0.6235 (mpp) REVERT: D 466 LEU cc_start: 0.8729 (mp) cc_final: 0.8352 (mp) REVERT: D 470 TYR cc_start: 0.3193 (OUTLIER) cc_final: 0.2376 (m-80) REVERT: E 246 TYR cc_start: 0.8729 (p90) cc_final: 0.8499 (p90) REVERT: E 440 MET cc_start: 0.8253 (mtt) cc_final: 0.7779 (mtt) outliers start: 42 outliers final: 35 residues processed: 231 average time/residue: 0.2914 time to fit residues: 104.2757 Evaluate side-chains 239 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 199 time to evaluate : 2.069 ------------------------------------------------------------------------------- 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 102 LEU Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 353 ASN Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain 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 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 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 Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 460 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 80 optimal weight: 0.0970 chunk 120 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 133 optimal weight: 9.9990 chunk 150 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 141 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 ASN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 HIS D 325 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.132358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.108063 restraints weight = 25585.626| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.03 r_work: 0.3104 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 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 : 0.005 0.061 18685 Z= 0.187 Angle : 0.560 9.714 25382 Z= 0.287 Chirality : 0.045 0.183 2732 Planarity : 0.004 0.047 3308 Dihedral : 4.554 19.050 2524 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.33 % Allowed : 13.78 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.17), residues: 2306 helix: -0.29 (0.35), residues: 225 sheet: -0.41 (0.19), residues: 747 loop : -1.32 (0.16), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 104 HIS 0.006 0.001 HIS C 165 PHE 0.014 0.002 PHE D 253 TYR 0.024 0.002 TYR A 79 ARG 0.004 0.000 ARG C 40 Details of bonding type rmsd hydrogen bonds : bond 0.03173 ( 262) hydrogen bonds : angle 5.07833 ( 663) SS BOND : bond 0.00826 ( 2) SS BOND : angle 1.65521 ( 4) covalent geometry : bond 0.00457 (18683) covalent geometry : angle 0.55974 (25378) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 197 time to evaluate : 2.550 Fit side-chains REVERT: F 102 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8716 (pp) REVERT: F 178 GLN cc_start: 0.7512 (mp10) cc_final: 0.6835 (tt0) REVERT: B 132 TYR cc_start: 0.8868 (OUTLIER) cc_final: 0.7432 (m-80) REVERT: B 164 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8209 (pt0) REVERT: C 308 TYR cc_start: 0.8053 (m-10) cc_final: 0.7435 (m-80) REVERT: D 384 MET cc_start: 0.6769 (OUTLIER) cc_final: 0.6291 (mpp) REVERT: D 470 TYR cc_start: 0.3504 (OUTLIER) cc_final: 0.2569 (m-80) REVERT: E 147 ASP cc_start: 0.8654 (p0) cc_final: 0.8424 (p0) REVERT: E 246 TYR cc_start: 0.8790 (p90) cc_final: 0.8568 (p90) REVERT: E 440 MET cc_start: 0.8321 (mtt) cc_final: 0.7864 (mtt) outliers start: 47 outliers final: 36 residues processed: 224 average time/residue: 0.3564 time to fit residues: 125.9476 Evaluate side-chains 234 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 193 time to evaluate : 3.717 ------------------------------------------------------------------------------- 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 102 LEU Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 353 ASN Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 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 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 456 ASP Chi-restraints excluded: chain D residue 466 LEU 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 Chi-restraints excluded: chain E residue 447 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 180 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 127 optimal weight: 8.9990 chunk 157 optimal weight: 8.9990 chunk 131 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 HIS D 325 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.133427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.109056 restraints weight = 25532.888| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.03 r_work: 0.3120 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18685 Z= 0.134 Angle : 0.518 9.471 25382 Z= 0.265 Chirality : 0.044 0.181 2732 Planarity : 0.004 0.046 3308 Dihedral : 4.401 18.409 2524 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.08 % Allowed : 14.08 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.17), residues: 2306 helix: -0.22 (0.35), residues: 225 sheet: -0.38 (0.19), residues: 732 loop : -1.23 (0.16), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 104 HIS 0.004 0.001 HIS E 165 PHE 0.013 0.001 PHE D 253 TYR 0.012 0.001 TYR B 132 ARG 0.003 0.000 ARG C 40 Details of bonding type rmsd hydrogen bonds : bond 0.02879 ( 262) hydrogen bonds : angle 4.96673 ( 663) SS BOND : bond 0.00705 ( 2) SS BOND : angle 1.36609 ( 4) covalent geometry : bond 0.00322 (18683) covalent geometry : angle 0.51762 (25378) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9277.72 seconds wall clock time: 162 minutes 54.04 seconds (9774.04 seconds total)