Starting phenix.real_space_refine on Sun Aug 24 04:36:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e78_27937/08_2025/8e78_27937.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e78_27937/08_2025/8e78_27937.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8e78_27937/08_2025/8e78_27937.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e78_27937/08_2025/8e78_27937.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e78_27937/08_2025/8e78_27937.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e78_27937/08_2025/8e78_27937.map" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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 92 5.16 5 C 11200 2.51 5 N 3012 2.21 5 O 3208 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17512 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 4378 Classifications: {'peptide': 556} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 529} Restraints were copied for chains: B, C, D Time building chain proxies: 3.23, per 1000 atoms: 0.18 Number of scatterers: 17512 At special positions: 0 Unit cell: (134.16, 132.08, 80.08, 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 92 16.00 O 3208 8.00 N 3012 7.00 C 11200 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 718.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4112 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 12 sheets defined 55.9% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 removed outlier: 4.172A pdb=" N ASP A 4 " --> pdb=" O ARG A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 17 Processing helix chain 'A' and resid 18 through 25 Processing helix chain 'A' and resid 37 through 50 Processing helix chain 'A' and resid 54 through 69 Processing helix chain 'A' and resid 69 through 80 removed outlier: 3.675A pdb=" N ASP A 80 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 89 Proline residue: A 86 - end of helix Processing helix chain 'A' and resid 91 through 99 removed outlier: 3.561A pdb=" N LEU A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 119 through 125 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 154 through 167 Processing helix chain 'A' and resid 186 through 191 Processing helix chain 'A' and resid 205 through 224 Processing helix chain 'A' and resid 235 through 247 Processing helix chain 'A' and resid 257 through 276 removed outlier: 3.523A pdb=" N ALA A 261 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 282 Processing helix chain 'A' and resid 292 through 307 removed outlier: 3.952A pdb=" N ILE A 296 " --> pdb=" O ALA A 292 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 317 removed outlier: 3.876A pdb=" N LYS A 317 " --> pdb=" O GLU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 350 through 358 removed outlier: 3.747A pdb=" N VAL A 354 " --> pdb=" O SER A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 385 Processing helix chain 'A' and resid 396 through 400 removed outlier: 3.602A pdb=" N ALA A 400 " --> pdb=" O THR A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 411 Processing helix chain 'A' and resid 440 through 443 Processing helix chain 'A' and resid 444 through 456 Processing helix chain 'A' and resid 461 through 476 removed outlier: 3.725A pdb=" N PHE A 465 " --> pdb=" O PRO A 461 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL A 476 " --> pdb=" O ILE A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 483 Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 492 through 511 Processing helix chain 'A' and resid 522 through 529 Processing helix chain 'B' and resid 1 through 8 removed outlier: 4.172A pdb=" N ASP B 4 " --> pdb=" O ARG B 1 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 17 Processing helix chain 'B' and resid 18 through 25 Processing helix chain 'B' and resid 37 through 50 Processing helix chain 'B' and resid 54 through 69 Processing helix chain 'B' and resid 69 through 80 removed outlier: 3.675A pdb=" N ASP B 80 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 89 Proline residue: B 86 - end of helix Processing helix chain 'B' and resid 91 through 99 removed outlier: 3.561A pdb=" N LEU B 95 " --> pdb=" O PRO B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 154 through 167 Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 205 through 224 Processing helix chain 'B' and resid 235 through 247 Processing helix chain 'B' and resid 257 through 276 removed outlier: 3.524A pdb=" N ALA B 261 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 282 Processing helix chain 'B' and resid 292 through 307 removed outlier: 3.952A pdb=" N ILE B 296 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU B 307 " --> pdb=" O ALA B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 317 removed outlier: 3.876A pdb=" N LYS B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 350 through 358 removed outlier: 3.747A pdb=" N VAL B 354 " --> pdb=" O SER B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 385 Processing helix chain 'B' and resid 396 through 400 removed outlier: 3.602A pdb=" N ALA B 400 " --> pdb=" O THR B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 411 Processing helix chain 'B' and resid 440 through 443 Processing helix chain 'B' and resid 444 through 456 Processing helix chain 'B' and resid 461 through 476 removed outlier: 3.725A pdb=" N PHE B 465 " --> pdb=" O PRO B 461 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL B 476 " --> pdb=" O ILE B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 483 Processing helix chain 'B' and resid 489 through 491 No H-bonds generated for 'chain 'B' and resid 489 through 491' Processing helix chain 'B' and resid 492 through 511 Processing helix chain 'B' and resid 522 through 529 Processing helix chain 'C' and resid 1 through 8 removed outlier: 4.172A pdb=" N ASP C 4 " --> pdb=" O ARG C 1 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 17 Processing helix chain 'C' and resid 18 through 25 Processing helix chain 'C' and resid 37 through 50 Processing helix chain 'C' and resid 54 through 69 Processing helix chain 'C' and resid 69 through 80 removed outlier: 3.675A pdb=" N ASP C 80 " --> pdb=" O VAL C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 Proline residue: C 86 - end of helix Processing helix chain 'C' and resid 91 through 99 removed outlier: 3.562A pdb=" N LEU C 95 " --> pdb=" O PRO C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 119 through 125 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 154 through 167 Processing helix chain 'C' and resid 186 through 191 Processing helix chain 'C' and resid 205 through 224 Processing helix chain 'C' and resid 235 through 247 Processing helix chain 'C' and resid 257 through 276 removed outlier: 3.524A pdb=" N ALA C 261 " --> pdb=" O ILE C 257 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 274 " --> pdb=" O ALA C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 Processing helix chain 'C' and resid 292 through 307 removed outlier: 3.951A pdb=" N ILE C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU C 307 " --> pdb=" O ALA C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 317 removed outlier: 3.876A pdb=" N LYS C 317 " --> pdb=" O GLU C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 350 through 358 removed outlier: 3.748A pdb=" N VAL C 354 " --> pdb=" O SER C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 385 Processing helix chain 'C' and resid 396 through 400 removed outlier: 3.602A pdb=" N ALA C 400 " --> pdb=" O THR C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 411 Processing helix chain 'C' and resid 440 through 443 Processing helix chain 'C' and resid 444 through 456 Processing helix chain 'C' and resid 461 through 476 removed outlier: 3.725A pdb=" N PHE C 465 " --> pdb=" O PRO C 461 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL C 476 " --> pdb=" O ILE C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 483 Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 492 through 511 Processing helix chain 'C' and resid 522 through 529 Processing helix chain 'D' and resid 1 through 8 removed outlier: 4.173A pdb=" N ASP D 4 " --> pdb=" O ARG D 1 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 17 Processing helix chain 'D' and resid 18 through 25 Processing helix chain 'D' and resid 37 through 50 Processing helix chain 'D' and resid 54 through 69 Processing helix chain 'D' and resid 69 through 80 removed outlier: 3.675A pdb=" N ASP D 80 " --> pdb=" O VAL D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 89 Proline residue: D 86 - end of helix Processing helix chain 'D' and resid 91 through 99 removed outlier: 3.561A pdb=" N LEU D 95 " --> pdb=" O PRO D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 117 No H-bonds generated for 'chain 'D' and resid 115 through 117' Processing helix chain 'D' and resid 119 through 125 Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 154 through 167 Processing helix chain 'D' and resid 186 through 191 Processing helix chain 'D' and resid 205 through 224 Processing helix chain 'D' and resid 235 through 247 Processing helix chain 'D' and resid 257 through 276 removed outlier: 3.524A pdb=" N ALA D 261 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG D 273 " --> pdb=" O LEU D 269 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE D 274 " --> pdb=" O ALA D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 282 Processing helix chain 'D' and resid 292 through 307 removed outlier: 3.951A pdb=" N ILE D 296 " --> pdb=" O ALA D 292 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU D 307 " --> pdb=" O ALA D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 317 removed outlier: 3.877A pdb=" N LYS D 317 " --> pdb=" O GLU D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 342 Processing helix chain 'D' and resid 350 through 358 removed outlier: 3.748A pdb=" N VAL D 354 " --> pdb=" O SER D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 385 Processing helix chain 'D' and resid 396 through 400 removed outlier: 3.601A pdb=" N ALA D 400 " --> pdb=" O THR D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 411 Processing helix chain 'D' and resid 440 through 443 Processing helix chain 'D' and resid 444 through 456 Processing helix chain 'D' and resid 461 through 476 removed outlier: 3.724A pdb=" N PHE D 465 " --> pdb=" O PRO D 461 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL D 476 " --> pdb=" O ILE D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 483 Processing helix chain 'D' and resid 489 through 491 No H-bonds generated for 'chain 'D' and resid 489 through 491' Processing helix chain 'D' and resid 492 through 511 Processing helix chain 'D' and resid 522 through 529 Processing sheet with id=AA1, first strand: chain 'A' and resid 110 through 113 removed outlier: 6.428A pdb=" N LEU A 110 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASP A 181 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE A 112 " --> pdb=" O ASP A 181 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA A 134 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL A 178 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL A 136 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LEU A 180 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR A 138 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 318 through 320 removed outlier: 6.401A pdb=" N VAL A 285 " --> pdb=" O ILE A 364 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLY A 437 " --> pdb=" O PHE A 417 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 426 through 427 Processing sheet with id=AA4, first strand: chain 'B' and resid 110 through 113 removed outlier: 6.428A pdb=" N LEU B 110 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASP B 181 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE B 112 " --> pdb=" O ASP B 181 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA B 134 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL B 178 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N VAL B 136 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU B 180 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR B 138 " --> pdb=" O LEU B 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 318 through 320 removed outlier: 6.402A pdb=" N VAL B 285 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY B 437 " --> pdb=" O PHE B 417 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 426 through 427 Processing sheet with id=AA7, first strand: chain 'C' and resid 110 through 113 removed outlier: 6.428A pdb=" N LEU C 110 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ASP C 181 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE C 112 " --> pdb=" O ASP C 181 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA C 134 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL C 178 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL C 136 " --> pdb=" O VAL C 178 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU C 180 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR C 138 " --> pdb=" O LEU C 180 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 318 through 320 removed outlier: 6.402A pdb=" N VAL C 285 " --> pdb=" O ILE C 364 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLY C 437 " --> pdb=" O PHE C 417 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 426 through 427 Processing sheet with id=AB1, first strand: chain 'D' and resid 110 through 113 removed outlier: 6.428A pdb=" N LEU D 110 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ASP D 181 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE D 112 " --> pdb=" O ASP D 181 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA D 134 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL D 178 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N VAL D 136 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU D 180 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR D 138 " --> pdb=" O LEU D 180 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 318 through 320 removed outlier: 6.402A pdb=" N VAL D 285 " --> pdb=" O ILE D 364 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLY D 437 " --> pdb=" O PHE D 417 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 426 through 427 784 hydrogen bonds defined for protein. 2160 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.15 Time building geometry restraints manager: 1.68 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: 5760 1.34 - 1.46: 3094 1.46 - 1.57: 8890 1.57 - 1.69: 0 1.69 - 1.81: 148 Bond restraints: 17892 Sorted by residual: bond pdb=" C LEU C 176 " pdb=" O LEU C 176 " ideal model delta sigma weight residual 1.249 1.234 0.015 8.50e-03 1.38e+04 3.11e+00 bond pdb=" C LEU B 176 " pdb=" O LEU B 176 " ideal model delta sigma weight residual 1.249 1.234 0.015 8.50e-03 1.38e+04 3.11e+00 bond pdb=" C LEU A 176 " pdb=" O LEU A 176 " ideal model delta sigma weight residual 1.249 1.234 0.015 8.50e-03 1.38e+04 2.92e+00 bond pdb=" C LEU D 176 " pdb=" O LEU D 176 " ideal model delta sigma weight residual 1.249 1.235 0.014 8.50e-03 1.38e+04 2.76e+00 bond pdb=" CG LEU B 120 " pdb=" CD2 LEU B 120 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.19e+00 ... (remaining 17887 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 23041 1.26 - 2.52: 956 2.52 - 3.78: 179 3.78 - 5.04: 52 5.04 - 6.29: 12 Bond angle restraints: 24240 Sorted by residual: angle pdb=" N GLN A 173 " pdb=" CA GLN A 173 " pdb=" C GLN A 173 " ideal model delta sigma weight residual 114.56 111.55 3.01 1.27e+00 6.20e-01 5.62e+00 angle pdb=" N GLN C 173 " pdb=" CA GLN C 173 " pdb=" C GLN C 173 " ideal model delta sigma weight residual 114.56 111.55 3.01 1.27e+00 6.20e-01 5.61e+00 angle pdb=" N GLN D 173 " pdb=" CA GLN D 173 " pdb=" C GLN D 173 " ideal model delta sigma weight residual 114.56 111.57 2.99 1.27e+00 6.20e-01 5.54e+00 angle pdb=" N GLN B 173 " pdb=" CA GLN B 173 " pdb=" C GLN B 173 " ideal model delta sigma weight residual 114.56 111.62 2.94 1.27e+00 6.20e-01 5.37e+00 angle pdb=" C CYS B 175 " pdb=" N LEU B 176 " pdb=" CA LEU B 176 " ideal model delta sigma weight residual 122.64 120.09 2.55 1.25e+00 6.40e-01 4.15e+00 ... (remaining 24235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 9551 17.51 - 35.02: 1021 35.02 - 52.53: 140 52.53 - 70.04: 32 70.04 - 87.56: 4 Dihedral angle restraints: 10748 sinusoidal: 4324 harmonic: 6424 Sorted by residual: dihedral pdb=" CA PRO D 547 " pdb=" C PRO D 547 " pdb=" N LYS D 548 " pdb=" CA LYS D 548 " ideal model delta harmonic sigma weight residual 180.00 158.31 21.69 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA PRO A 547 " pdb=" C PRO A 547 " pdb=" N LYS A 548 " pdb=" CA LYS A 548 " ideal model delta harmonic sigma weight residual 180.00 158.32 21.68 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA PRO B 547 " pdb=" C PRO B 547 " pdb=" N LYS B 548 " pdb=" CA LYS B 548 " ideal model delta harmonic sigma weight residual 180.00 158.32 21.68 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 10745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1486 0.033 - 0.066: 884 0.066 - 0.099: 239 0.099 - 0.132: 87 0.132 - 0.165: 16 Chirality restraints: 2712 Sorted by residual: chirality pdb=" CA PHE D 445 " pdb=" N PHE D 445 " pdb=" C PHE D 445 " pdb=" CB PHE D 445 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.77e-01 chirality pdb=" CA PHE A 445 " pdb=" N PHE A 445 " pdb=" C PHE A 445 " pdb=" CB PHE A 445 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" CA PHE B 445 " pdb=" N PHE B 445 " pdb=" C PHE B 445 " pdb=" CB PHE B 445 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.69e-01 ... (remaining 2709 not shown) Planarity restraints: 3140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP D 546 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO D 547 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 547 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 547 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 546 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO A 547 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 547 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 547 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 546 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO B 547 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 547 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 547 " 0.026 5.00e-02 4.00e+02 ... (remaining 3137 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2868 2.75 - 3.29: 17689 3.29 - 3.83: 30938 3.83 - 4.36: 39442 4.36 - 4.90: 63429 Nonbonded interactions: 154366 Sorted by model distance: nonbonded pdb=" OD1 ASP A 116 " pdb=" OH TYR C 544 " model vdw 2.218 3.040 nonbonded pdb=" O CYS C 407 " pdb=" OG1 THR C 411 " model vdw 2.221 3.040 nonbonded pdb=" O CYS D 407 " pdb=" OG1 THR D 411 " model vdw 2.222 3.040 nonbonded pdb=" OD1 ASP B 116 " pdb=" OH TYR D 544 " model vdw 2.222 3.040 nonbonded pdb=" O CYS A 407 " pdb=" OG1 THR A 411 " model vdw 2.222 3.040 ... (remaining 154361 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.220 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:6.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5961 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 : 0.006 0.049 17892 Z= 0.259 Angle : 0.625 6.295 24240 Z= 0.345 Chirality : 0.045 0.165 2712 Planarity : 0.004 0.047 3140 Dihedral : 14.264 87.556 6636 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.00 (0.16), residues: 2216 helix: -1.90 (0.13), residues: 1024 sheet: -2.70 (0.35), residues: 180 loop : -1.80 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 105 TYR 0.016 0.002 TYR B 74 PHE 0.017 0.002 PHE D 445 TRP 0.004 0.001 TRP D 127 HIS 0.006 0.001 HIS B 333 Details of bonding type rmsd covalent geometry : bond 0.00604 (17892) covalent geometry : angle 0.62515 (24240) hydrogen bonds : bond 0.17196 ( 784) hydrogen bonds : angle 7.43357 ( 2160) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 2 residues processed: 181 average time/residue: 0.5616 time to fit residues: 113.4262 Evaluate side-chains 111 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain D residue 130 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 30.0000 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 chunk 212 optimal weight: 9.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 115 HIS A 125 ASN A 226 ASN A 258 GLN ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN A 385 HIS B 52 GLN B 115 HIS B 125 ASN B 226 ASN B 258 GLN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 GLN B 385 HIS C 52 GLN C 115 HIS C 125 ASN C 226 ASN C 258 GLN ** C 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN C 385 HIS D 52 GLN D 115 HIS D 125 ASN D 226 ASN D 258 GLN ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 GLN D 385 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.059764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.040682 restraints weight = 58886.574| |-----------------------------------------------------------------------------| r_work (start): 0.2625 rms_B_bonded: 3.54 r_work: 0.2454 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17892 Z= 0.195 Angle : 0.643 6.686 24240 Z= 0.326 Chirality : 0.044 0.189 2712 Planarity : 0.004 0.044 3140 Dihedral : 4.705 21.689 2432 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.69 % Allowed : 9.31 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.18), residues: 2216 helix: -0.01 (0.16), residues: 1036 sheet: -2.35 (0.38), residues: 180 loop : -1.34 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 356 TYR 0.014 0.002 TYR B 517 PHE 0.012 0.001 PHE A 445 TRP 0.004 0.001 TRP C 319 HIS 0.005 0.001 HIS B 333 Details of bonding type rmsd covalent geometry : bond 0.00437 (17892) covalent geometry : angle 0.64268 (24240) hydrogen bonds : bond 0.04109 ( 784) hydrogen bonds : angle 4.87431 ( 2160) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 4 residues processed: 125 average time/residue: 0.4628 time to fit residues: 65.8394 Evaluate side-chains 108 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 354 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 190 optimal weight: 5.9990 chunk 146 optimal weight: 0.9990 chunk 152 optimal weight: 20.0000 chunk 95 optimal weight: 30.0000 chunk 215 optimal weight: 2.9990 chunk 133 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 138 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 chunk 139 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 HIS ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 HIS ** C 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 HIS ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 333 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.059472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.040025 restraints weight = 60193.272| |-----------------------------------------------------------------------------| r_work (start): 0.2617 rms_B_bonded: 3.66 r_work: 0.2449 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17892 Z= 0.174 Angle : 0.594 6.915 24240 Z= 0.299 Chirality : 0.043 0.181 2712 Planarity : 0.004 0.047 3140 Dihedral : 4.468 20.728 2428 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 1.70 % Allowed : 11.86 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.18), residues: 2216 helix: 0.56 (0.16), residues: 1056 sheet: -2.13 (0.39), residues: 180 loop : -1.12 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 356 TYR 0.013 0.002 TYR C 74 PHE 0.016 0.001 PHE C 445 TRP 0.003 0.001 TRP A 546 HIS 0.006 0.001 HIS B 28 Details of bonding type rmsd covalent geometry : bond 0.00394 (17892) covalent geometry : angle 0.59441 (24240) hydrogen bonds : bond 0.03757 ( 784) hydrogen bonds : angle 4.50470 ( 2160) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 TYR cc_start: 0.7421 (OUTLIER) cc_final: 0.6399 (m-80) REVERT: A 551 MET cc_start: 0.9063 (ttp) cc_final: 0.8632 (mtm) REVERT: B 100 TYR cc_start: 0.7426 (OUTLIER) cc_final: 0.6407 (m-80) REVERT: B 551 MET cc_start: 0.9056 (ttm) cc_final: 0.8646 (mtm) REVERT: C 100 TYR cc_start: 0.7390 (OUTLIER) cc_final: 0.6374 (m-80) REVERT: C 551 MET cc_start: 0.8899 (ttm) cc_final: 0.8492 (mtm) REVERT: D 100 TYR cc_start: 0.7369 (OUTLIER) cc_final: 0.6341 (m-80) REVERT: D 551 MET cc_start: 0.8798 (ttm) cc_final: 0.8585 (mtm) outliers start: 32 outliers final: 5 residues processed: 141 average time/residue: 0.4775 time to fit residues: 76.4466 Evaluate side-chains 111 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 366 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 219 optimal weight: 8.9990 chunk 111 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 chunk 201 optimal weight: 10.0000 chunk 143 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 183 optimal weight: 8.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.059079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.039912 restraints weight = 60458.025| |-----------------------------------------------------------------------------| r_work (start): 0.2614 rms_B_bonded: 3.59 r_work: 0.2445 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17892 Z= 0.196 Angle : 0.622 8.090 24240 Z= 0.308 Chirality : 0.043 0.181 2712 Planarity : 0.004 0.047 3140 Dihedral : 4.427 20.746 2428 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.33 % Allowed : 12.50 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.18), residues: 2216 helix: 0.74 (0.16), residues: 1060 sheet: -2.16 (0.38), residues: 180 loop : -0.99 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 108 TYR 0.013 0.002 TYR B 74 PHE 0.015 0.001 PHE B 445 TRP 0.002 0.001 TRP C 319 HIS 0.005 0.001 HIS A 28 Details of bonding type rmsd covalent geometry : bond 0.00441 (17892) covalent geometry : angle 0.62151 (24240) hydrogen bonds : bond 0.03507 ( 784) hydrogen bonds : angle 4.40829 ( 2160) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 TYR cc_start: 0.7518 (OUTLIER) cc_final: 0.6511 (m-80) REVERT: A 416 ILE cc_start: 0.9225 (mm) cc_final: 0.8570 (pp) REVERT: A 551 MET cc_start: 0.9128 (ttp) cc_final: 0.8707 (mtm) REVERT: B 100 TYR cc_start: 0.7495 (OUTLIER) cc_final: 0.6487 (m-80) REVERT: C 100 TYR cc_start: 0.7462 (OUTLIER) cc_final: 0.6406 (m-80) REVERT: C 416 ILE cc_start: 0.9245 (mm) cc_final: 0.8598 (pp) REVERT: D 100 TYR cc_start: 0.7462 (OUTLIER) cc_final: 0.6424 (m-80) REVERT: D 416 ILE cc_start: 0.9244 (mm) cc_final: 0.8604 (pp) REVERT: D 551 MET cc_start: 0.9091 (ttm) cc_final: 0.8720 (mtm) outliers start: 25 outliers final: 9 residues processed: 126 average time/residue: 0.7127 time to fit residues: 100.3535 Evaluate side-chains 109 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 366 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 19 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 106 optimal weight: 7.9990 chunk 202 optimal weight: 20.0000 chunk 133 optimal weight: 3.9990 chunk 161 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 162 optimal weight: 0.0270 chunk 187 optimal weight: 0.7980 chunk 84 optimal weight: 8.9990 chunk 211 optimal weight: 3.9990 overall best weight: 1.3440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.060508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.040944 restraints weight = 60279.036| |-----------------------------------------------------------------------------| r_work (start): 0.2661 rms_B_bonded: 3.74 r_work: 0.2492 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17892 Z= 0.123 Angle : 0.613 9.058 24240 Z= 0.302 Chirality : 0.042 0.180 2712 Planarity : 0.004 0.052 3140 Dihedral : 4.321 19.460 2428 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.44 % Allowed : 13.40 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.18), residues: 2216 helix: 0.84 (0.16), residues: 1064 sheet: -1.55 (0.40), residues: 168 loop : -1.02 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 387 TYR 0.011 0.001 TYR C 208 PHE 0.016 0.001 PHE C 445 TRP 0.005 0.001 TRP B 546 HIS 0.005 0.001 HIS A 28 Details of bonding type rmsd covalent geometry : bond 0.00285 (17892) covalent geometry : angle 0.61344 (24240) hydrogen bonds : bond 0.03371 ( 784) hydrogen bonds : angle 4.26824 ( 2160) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.9518 (tm-30) cc_final: 0.9122 (pp20) REVERT: A 100 TYR cc_start: 0.7711 (OUTLIER) cc_final: 0.6561 (m-80) REVERT: B 82 GLU cc_start: 0.9513 (tm-30) cc_final: 0.9124 (pp20) REVERT: B 100 TYR cc_start: 0.7699 (OUTLIER) cc_final: 0.6549 (m-80) REVERT: B 551 MET cc_start: 0.8903 (ttm) cc_final: 0.8673 (mtp) REVERT: C 82 GLU cc_start: 0.9514 (tm-30) cc_final: 0.9124 (pp20) REVERT: C 100 TYR cc_start: 0.7671 (OUTLIER) cc_final: 0.6516 (m-80) REVERT: D 82 GLU cc_start: 0.9515 (tm-30) cc_final: 0.9126 (pp20) REVERT: D 100 TYR cc_start: 0.7678 (OUTLIER) cc_final: 0.6544 (m-80) outliers start: 27 outliers final: 9 residues processed: 130 average time/residue: 0.6021 time to fit residues: 88.9822 Evaluate side-chains 116 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 366 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 156 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 185 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 160 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.059905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.040604 restraints weight = 59838.757| |-----------------------------------------------------------------------------| r_work (start): 0.2644 rms_B_bonded: 3.65 r_work: 0.2476 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17892 Z= 0.145 Angle : 0.610 9.747 24240 Z= 0.299 Chirality : 0.042 0.178 2712 Planarity : 0.004 0.054 3140 Dihedral : 4.242 17.346 2428 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 1.49 % Allowed : 14.84 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.18), residues: 2216 helix: 0.99 (0.16), residues: 1068 sheet: -1.27 (0.42), residues: 168 loop : -0.99 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 387 TYR 0.011 0.001 TYR A 74 PHE 0.014 0.001 PHE B 445 TRP 0.009 0.001 TRP C 546 HIS 0.004 0.001 HIS B 28 Details of bonding type rmsd covalent geometry : bond 0.00332 (17892) covalent geometry : angle 0.60979 (24240) hydrogen bonds : bond 0.03308 ( 784) hydrogen bonds : angle 4.21714 ( 2160) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.9615 (OUTLIER) cc_final: 0.9385 (m-30) REVERT: A 100 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.6561 (m-80) REVERT: B 100 TYR cc_start: 0.7771 (OUTLIER) cc_final: 0.6591 (m-80) REVERT: B 551 MET cc_start: 0.8926 (ttm) cc_final: 0.8595 (mtm) REVERT: C 57 ASP cc_start: 0.9619 (OUTLIER) cc_final: 0.9405 (m-30) REVERT: C 100 TYR cc_start: 0.7726 (OUTLIER) cc_final: 0.6541 (m-80) REVERT: C 551 MET cc_start: 0.8520 (mtm) cc_final: 0.8284 (mtm) REVERT: D 57 ASP cc_start: 0.9615 (OUTLIER) cc_final: 0.9389 (m-30) REVERT: D 100 TYR cc_start: 0.7743 (OUTLIER) cc_final: 0.6565 (m-80) outliers start: 28 outliers final: 12 residues processed: 126 average time/residue: 0.6063 time to fit residues: 86.7259 Evaluate side-chains 126 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 486 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 14 optimal weight: 0.6980 chunk 46 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 150 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN D 282 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.059506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.040255 restraints weight = 59570.025| |-----------------------------------------------------------------------------| r_work (start): 0.2645 rms_B_bonded: 3.69 r_work: 0.2474 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17892 Z= 0.148 Angle : 0.617 10.749 24240 Z= 0.301 Chirality : 0.042 0.182 2712 Planarity : 0.004 0.054 3140 Dihedral : 4.198 17.525 2428 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.91 % Allowed : 15.27 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.18), residues: 2216 helix: 1.06 (0.16), residues: 1068 sheet: -1.13 (0.42), residues: 168 loop : -0.96 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 387 TYR 0.011 0.001 TYR C 208 PHE 0.015 0.001 PHE B 445 TRP 0.012 0.001 TRP A 546 HIS 0.004 0.001 HIS A 28 Details of bonding type rmsd covalent geometry : bond 0.00341 (17892) covalent geometry : angle 0.61714 (24240) hydrogen bonds : bond 0.03267 ( 784) hydrogen bonds : angle 4.19375 ( 2160) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 111 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.9126 (mtm) cc_final: 0.8808 (mtp) REVERT: A 57 ASP cc_start: 0.9608 (OUTLIER) cc_final: 0.9372 (m-30) REVERT: A 100 TYR cc_start: 0.7814 (OUTLIER) cc_final: 0.6567 (m-80) REVERT: A 216 MET cc_start: 0.9520 (mmm) cc_final: 0.9262 (mtm) REVERT: A 551 MET cc_start: 0.8533 (mtm) cc_final: 0.8146 (mtm) REVERT: B 15 MET cc_start: 0.9131 (mtm) cc_final: 0.8813 (mtp) REVERT: B 57 ASP cc_start: 0.9611 (OUTLIER) cc_final: 0.9377 (m-30) REVERT: B 100 TYR cc_start: 0.7799 (OUTLIER) cc_final: 0.6548 (m-80) REVERT: B 216 MET cc_start: 0.9516 (mmm) cc_final: 0.9258 (mtm) REVERT: B 551 MET cc_start: 0.8982 (ttm) cc_final: 0.8740 (mtm) REVERT: C 57 ASP cc_start: 0.9613 (OUTLIER) cc_final: 0.9382 (m-30) REVERT: C 82 GLU cc_start: 0.9505 (tm-30) cc_final: 0.9102 (pp20) REVERT: C 100 TYR cc_start: 0.7766 (OUTLIER) cc_final: 0.6518 (m-80) REVERT: C 551 MET cc_start: 0.8667 (mtm) cc_final: 0.8440 (mtm) REVERT: D 57 ASP cc_start: 0.9608 (OUTLIER) cc_final: 0.9375 (m-30) REVERT: D 82 GLU cc_start: 0.9508 (tm-30) cc_final: 0.9102 (pp20) REVERT: D 100 TYR cc_start: 0.7761 (OUTLIER) cc_final: 0.6521 (m-80) REVERT: D 216 MET cc_start: 0.9532 (mmm) cc_final: 0.9291 (mtm) REVERT: D 551 MET cc_start: 0.8577 (mtm) cc_final: 0.8312 (mtm) outliers start: 36 outliers final: 15 residues processed: 135 average time/residue: 0.5745 time to fit residues: 88.4896 Evaluate side-chains 129 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 486 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 94 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 212 optimal weight: 0.9990 chunk 176 optimal weight: 0.0570 chunk 4 optimal weight: 3.9990 chunk 190 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 207 optimal weight: 20.0000 chunk 158 optimal weight: 0.0020 overall best weight: 0.8110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 HIS A 483 GLN B 282 HIS B 483 GLN C 282 HIS D 282 HIS D 483 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.060459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.041295 restraints weight = 59425.334| |-----------------------------------------------------------------------------| r_work (start): 0.2678 rms_B_bonded: 3.69 r_work: 0.2509 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17892 Z= 0.109 Angle : 0.611 11.600 24240 Z= 0.298 Chirality : 0.042 0.179 2712 Planarity : 0.004 0.051 3140 Dihedral : 4.158 17.686 2428 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.86 % Allowed : 15.74 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.18), residues: 2216 helix: 1.08 (0.16), residues: 1064 sheet: -1.04 (0.42), residues: 168 loop : -0.93 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 387 TYR 0.013 0.001 TYR D 208 PHE 0.016 0.001 PHE D 445 TRP 0.014 0.001 TRP D 546 HIS 0.003 0.001 HIS C 333 Details of bonding type rmsd covalent geometry : bond 0.00254 (17892) covalent geometry : angle 0.61071 (24240) hydrogen bonds : bond 0.03246 ( 784) hydrogen bonds : angle 4.13995 ( 2160) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 111 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.9162 (mtm) cc_final: 0.8841 (mtp) REVERT: A 57 ASP cc_start: 0.9597 (OUTLIER) cc_final: 0.9367 (m-30) REVERT: A 82 GLU cc_start: 0.9439 (tm-30) cc_final: 0.9030 (pp20) REVERT: A 100 TYR cc_start: 0.7798 (OUTLIER) cc_final: 0.6501 (m-80) REVERT: A 551 MET cc_start: 0.8570 (mtm) cc_final: 0.8343 (mtm) REVERT: B 15 MET cc_start: 0.9160 (mtm) cc_final: 0.8816 (mtp) REVERT: B 57 ASP cc_start: 0.9599 (OUTLIER) cc_final: 0.9372 (m-30) REVERT: B 82 GLU cc_start: 0.9430 (tm-30) cc_final: 0.8979 (OUTLIER) REVERT: B 100 TYR cc_start: 0.7778 (OUTLIER) cc_final: 0.6479 (m-80) REVERT: B 551 MET cc_start: 0.8960 (ttm) cc_final: 0.8579 (mtm) REVERT: C 15 MET cc_start: 0.9169 (mtm) cc_final: 0.8850 (mtp) REVERT: C 57 ASP cc_start: 0.9603 (OUTLIER) cc_final: 0.9384 (m-30) REVERT: C 100 TYR cc_start: 0.7752 (OUTLIER) cc_final: 0.6456 (m-80) REVERT: C 551 MET cc_start: 0.8697 (mtm) cc_final: 0.8483 (mtm) REVERT: D 57 ASP cc_start: 0.9601 (OUTLIER) cc_final: 0.9376 (m-30) REVERT: D 100 TYR cc_start: 0.7749 (OUTLIER) cc_final: 0.6453 (m-80) REVERT: D 216 MET cc_start: 0.9525 (mmm) cc_final: 0.9267 (mtm) REVERT: D 551 MET cc_start: 0.8616 (mtm) cc_final: 0.8354 (mtm) outliers start: 35 outliers final: 20 residues processed: 138 average time/residue: 0.5390 time to fit residues: 84.9577 Evaluate side-chains 137 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 486 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 65 optimal weight: 9.9990 chunk 212 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 HIS B 282 HIS C 282 HIS D 282 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.060331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.041179 restraints weight = 60094.866| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 3.73 r_work: 0.2504 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17892 Z= 0.125 Angle : 0.610 11.989 24240 Z= 0.297 Chirality : 0.042 0.178 2712 Planarity : 0.004 0.051 3140 Dihedral : 4.094 17.797 2428 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 1.81 % Allowed : 16.17 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.18), residues: 2216 helix: 1.13 (0.16), residues: 1068 sheet: -0.88 (0.43), residues: 168 loop : -0.85 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 387 TYR 0.013 0.001 TYR B 208 PHE 0.015 0.001 PHE B 445 TRP 0.010 0.001 TRP D 546 HIS 0.003 0.001 HIS A 333 Details of bonding type rmsd covalent geometry : bond 0.00291 (17892) covalent geometry : angle 0.60979 (24240) hydrogen bonds : bond 0.03158 ( 784) hydrogen bonds : angle 4.12718 ( 2160) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.9124 (mtm) cc_final: 0.8778 (mtp) REVERT: A 57 ASP cc_start: 0.9601 (OUTLIER) cc_final: 0.9369 (m-30) REVERT: A 100 TYR cc_start: 0.7837 (OUTLIER) cc_final: 0.6678 (m-80) REVERT: B 15 MET cc_start: 0.9119 (mtm) cc_final: 0.8765 (mtp) REVERT: B 57 ASP cc_start: 0.9606 (OUTLIER) cc_final: 0.9380 (m-30) REVERT: B 100 TYR cc_start: 0.7818 (OUTLIER) cc_final: 0.6651 (m-80) REVERT: B 551 MET cc_start: 0.9068 (ttm) cc_final: 0.8807 (mtm) REVERT: C 15 MET cc_start: 0.9183 (mtm) cc_final: 0.8847 (mtp) REVERT: C 57 ASP cc_start: 0.9612 (OUTLIER) cc_final: 0.9390 (m-30) REVERT: C 100 TYR cc_start: 0.7807 (OUTLIER) cc_final: 0.6647 (m-80) REVERT: C 551 MET cc_start: 0.8749 (mtm) cc_final: 0.8507 (mtm) REVERT: D 15 MET cc_start: 0.9190 (mtm) cc_final: 0.8864 (mtp) REVERT: D 57 ASP cc_start: 0.9605 (OUTLIER) cc_final: 0.9374 (m-30) REVERT: D 100 TYR cc_start: 0.7805 (OUTLIER) cc_final: 0.6640 (m-80) REVERT: D 551 MET cc_start: 0.8728 (mtm) cc_final: 0.8502 (mtm) outliers start: 34 outliers final: 13 residues processed: 134 average time/residue: 0.5387 time to fit residues: 82.6147 Evaluate side-chains 131 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 366 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 202 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 209 optimal weight: 0.9990 chunk 204 optimal weight: 0.7980 chunk 78 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 205 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.059512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.040459 restraints weight = 59303.169| |-----------------------------------------------------------------------------| r_work (start): 0.2660 rms_B_bonded: 3.65 r_work: 0.2488 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17892 Z= 0.160 Angle : 0.635 13.195 24240 Z= 0.309 Chirality : 0.043 0.182 2712 Planarity : 0.004 0.053 3140 Dihedral : 4.116 18.160 2428 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.70 % Allowed : 16.54 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.18), residues: 2216 helix: 1.19 (0.17), residues: 1068 sheet: -0.82 (0.44), residues: 168 loop : -0.85 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 387 TYR 0.013 0.002 TYR C 208 PHE 0.015 0.001 PHE B 445 TRP 0.007 0.001 TRP D 319 HIS 0.003 0.001 HIS D 282 Details of bonding type rmsd covalent geometry : bond 0.00366 (17892) covalent geometry : angle 0.63469 (24240) hydrogen bonds : bond 0.03228 ( 784) hydrogen bonds : angle 4.14747 ( 2160) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.9136 (mtm) cc_final: 0.8785 (mtp) REVERT: A 57 ASP cc_start: 0.9612 (OUTLIER) cc_final: 0.9380 (m-30) REVERT: A 100 TYR cc_start: 0.7912 (OUTLIER) cc_final: 0.6704 (m-80) REVERT: A 551 MET cc_start: 0.8510 (mtm) cc_final: 0.8303 (mtm) REVERT: B 57 ASP cc_start: 0.9608 (OUTLIER) cc_final: 0.9376 (m-30) REVERT: B 100 TYR cc_start: 0.7897 (OUTLIER) cc_final: 0.6688 (m-80) REVERT: B 551 MET cc_start: 0.9121 (ttm) cc_final: 0.8852 (mtm) REVERT: C 15 MET cc_start: 0.9192 (mtm) cc_final: 0.8836 (mtp) REVERT: C 57 ASP cc_start: 0.9614 (OUTLIER) cc_final: 0.9388 (m-30) REVERT: C 100 TYR cc_start: 0.7886 (OUTLIER) cc_final: 0.6705 (m-80) REVERT: C 551 MET cc_start: 0.8835 (mtm) cc_final: 0.8579 (mtm) REVERT: D 15 MET cc_start: 0.9190 (mtm) cc_final: 0.8836 (mtp) REVERT: D 57 ASP cc_start: 0.9608 (OUTLIER) cc_final: 0.9377 (m-30) REVERT: D 100 TYR cc_start: 0.7914 (OUTLIER) cc_final: 0.6727 (m-80) REVERT: D 551 MET cc_start: 0.8776 (mtm) cc_final: 0.8550 (mtm) outliers start: 32 outliers final: 15 residues processed: 132 average time/residue: 0.5368 time to fit residues: 81.2839 Evaluate side-chains 129 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 366 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 123 optimal weight: 10.0000 chunk 135 optimal weight: 6.9990 chunk 110 optimal weight: 0.7980 chunk 179 optimal weight: 0.0670 chunk 214 optimal weight: 2.9990 chunk 3 optimal weight: 0.0770 chunk 217 optimal weight: 0.0570 chunk 89 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 194 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 HIS B 282 HIS C 282 HIS D 282 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.060727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.041772 restraints weight = 59277.788| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 3.67 r_work: 0.2525 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17892 Z= 0.112 Angle : 0.624 13.269 24240 Z= 0.305 Chirality : 0.042 0.181 2712 Planarity : 0.004 0.053 3140 Dihedral : 4.092 17.638 2428 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.54 % Allowed : 16.54 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.18), residues: 2216 helix: 1.20 (0.16), residues: 1064 sheet: -0.76 (0.44), residues: 168 loop : -0.87 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 106 TYR 0.016 0.001 TYR C 208 PHE 0.017 0.001 PHE B 445 TRP 0.009 0.001 TRP D 546 HIS 0.003 0.001 HIS A 333 Details of bonding type rmsd covalent geometry : bond 0.00259 (17892) covalent geometry : angle 0.62415 (24240) hydrogen bonds : bond 0.03123 ( 784) hydrogen bonds : angle 4.08705 ( 2160) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4232.99 seconds wall clock time: 73 minutes 40.31 seconds (4420.31 seconds total)