Starting phenix.real_space_refine on Sun Jun 15 06:16:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e78_27937/06_2025/8e78_27937.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e78_27937/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8e78_27937/06_2025/8e78_27937.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e78_27937/06_2025/8e78_27937.map" model { file = "/net/cci-nas-00/data/ceres_data/8e78_27937/06_2025/8e78_27937.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e78_27937/06_2025/8e78_27937.cif" } resolution = 2.77 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= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, D Time building chain proxies: 9.04, per 1000 atoms: 0.52 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: 4.01 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.08 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: 5.86 Time building geometry restraints manager: 4.79 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 0.550 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: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 38.100 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.050 ------------------------------------------------------------------------------- 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 (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: -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 TRP 0.004 0.001 TRP D 127 HIS 0.006 0.001 HIS B 333 PHE 0.017 0.002 PHE D 445 TYR 0.016 0.002 TYR B 74 ARG 0.003 0.000 ARG B 105 Details of bonding type rmsd hydrogen bonds : bond 0.17196 ( 784) hydrogen bonds : angle 7.43357 ( 2160) covalent geometry : bond 0.00604 (17892) covalent geometry : angle 0.62515 (24240) *********************** 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 : 1.918 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: 1.3967 time to fit residues: 282.9162 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 : 1.862 ------------------------------------------------------------------------------- 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 185 optimal weight: 7.9990 chunk 166 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 89 optimal weight: 0.0370 chunk 172 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 199 optimal weight: 0.0470 overall best weight: 1.1760 ------------------------------------------------------------------------------- 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 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 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 = 0.3252 r_free = 0.3252 target = 0.060923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.041902 restraints weight = 58291.221| |-----------------------------------------------------------------------------| r_work (start): 0.2661 rms_B_bonded: 3.56 r_work: 0.2486 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17892 Z= 0.140 Angle : 0.622 6.621 24240 Z= 0.317 Chirality : 0.043 0.208 2712 Planarity : 0.004 0.043 3140 Dihedral : 4.697 20.958 2432 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.69 % Allowed : 9.57 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 (0.18), residues: 2216 helix: -0.06 (0.16), residues: 1028 sheet: -2.36 (0.38), residues: 180 loop : -1.44 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 319 HIS 0.005 0.001 HIS B 333 PHE 0.012 0.001 PHE D 445 TYR 0.013 0.002 TYR B 517 ARG 0.006 0.001 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.04086 ( 784) hydrogen bonds : angle 4.90009 ( 2160) covalent geometry : bond 0.00320 (17892) covalent geometry : angle 0.62157 (24240) *********************** 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 138 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 2 residues processed: 134 average time/residue: 1.2247 time to fit residues: 185.8614 Evaluate side-chains 114 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 112 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 123 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 204 optimal weight: 9.9990 chunk 172 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 chunk 150 optimal weight: 2.9990 chunk 208 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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** ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 GLN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 GLN ** C 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 GLN ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 554 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.060098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.040827 restraints weight = 58882.605| |-----------------------------------------------------------------------------| r_work (start): 0.2639 rms_B_bonded: 3.60 r_work: 0.2468 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17892 Z= 0.162 Angle : 0.604 7.017 24240 Z= 0.303 Chirality : 0.043 0.177 2712 Planarity : 0.004 0.047 3140 Dihedral : 4.432 20.509 2428 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.13 % Allowed : 11.28 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.71 (0.18), residues: 2216 helix: 0.53 (0.17), residues: 1056 sheet: -2.15 (0.39), residues: 180 loop : -1.18 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 319 HIS 0.006 0.001 HIS B 28 PHE 0.017 0.001 PHE D 341 TYR 0.012 0.002 TYR C 74 ARG 0.004 0.000 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.03790 ( 784) hydrogen bonds : angle 4.49110 ( 2160) covalent geometry : bond 0.00368 (17892) covalent geometry : angle 0.60432 (24240) *********************** 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 155 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 115 time to evaluate : 2.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 CYS cc_start: 0.8886 (t) cc_final: 0.8311 (t) REVERT: A 100 TYR cc_start: 0.7320 (OUTLIER) cc_final: 0.6349 (m-80) REVERT: A 551 MET cc_start: 0.8956 (ttm) cc_final: 0.8600 (mtm) REVERT: B 34 CYS cc_start: 0.8879 (t) cc_final: 0.8304 (t) REVERT: B 100 TYR cc_start: 0.7319 (OUTLIER) cc_final: 0.6349 (m-80) REVERT: B 551 MET cc_start: 0.8973 (ttm) cc_final: 0.8626 (mtm) REVERT: C 34 CYS cc_start: 0.8852 (t) cc_final: 0.8268 (t) REVERT: C 100 TYR cc_start: 0.7338 (OUTLIER) cc_final: 0.6338 (m-80) REVERT: C 551 MET cc_start: 0.8678 (ttm) cc_final: 0.8410 (mtm) REVERT: D 34 CYS cc_start: 0.8852 (t) cc_final: 0.8264 (t) REVERT: D 100 TYR cc_start: 0.7318 (OUTLIER) cc_final: 0.6318 (m-80) REVERT: D 551 MET cc_start: 0.8662 (ttm) cc_final: 0.8409 (mtm) outliers start: 40 outliers final: 13 residues processed: 143 average time/residue: 1.3332 time to fit residues: 216.3677 Evaluate side-chains 125 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 354 VAL 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 130 ASP Chi-restraints excluded: chain B residue 354 VAL 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 358 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 358 VAL 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 70 optimal weight: 8.9990 chunk 92 optimal weight: 20.0000 chunk 150 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 198 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 185 optimal weight: 8.9990 chunk 200 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3225 r_free = 0.3225 target = 0.059430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.039834 restraints weight = 61025.543| |-----------------------------------------------------------------------------| r_work (start): 0.2622 rms_B_bonded: 3.74 r_work: 0.2455 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17892 Z= 0.220 Angle : 0.642 7.983 24240 Z= 0.320 Chirality : 0.043 0.182 2712 Planarity : 0.004 0.050 3140 Dihedral : 4.372 17.004 2428 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.22 % Allowed : 13.09 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.44 (0.18), residues: 2216 helix: 0.74 (0.16), residues: 1060 sheet: -1.78 (0.40), residues: 168 loop : -1.13 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 319 HIS 0.003 0.001 HIS A 333 PHE 0.015 0.001 PHE B 445 TYR 0.014 0.002 TYR B 74 ARG 0.005 0.000 ARG D 387 Details of bonding type rmsd hydrogen bonds : bond 0.03523 ( 784) hydrogen bonds : angle 4.43313 ( 2160) covalent geometry : bond 0.00490 (17892) covalent geometry : angle 0.64243 (24240) *********************** 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 133 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 2.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 CYS cc_start: 0.8876 (t) cc_final: 0.8306 (t) REVERT: A 100 TYR cc_start: 0.7647 (OUTLIER) cc_final: 0.6697 (m-80) REVERT: A 416 ILE cc_start: 0.9247 (mm) cc_final: 0.8595 (pp) REVERT: A 551 MET cc_start: 0.9179 (ttp) cc_final: 0.8707 (mtm) REVERT: B 34 CYS cc_start: 0.8852 (t) cc_final: 0.8276 (t) REVERT: B 100 TYR cc_start: 0.7602 (OUTLIER) cc_final: 0.6655 (m-80) REVERT: B 416 ILE cc_start: 0.9262 (mm) cc_final: 0.8603 (pp) REVERT: C 34 CYS cc_start: 0.8854 (t) cc_final: 0.8271 (t) REVERT: C 100 TYR cc_start: 0.7512 (OUTLIER) cc_final: 0.6601 (m-80) REVERT: C 416 ILE cc_start: 0.9251 (mm) cc_final: 0.8601 (pp) REVERT: C 551 MET cc_start: 0.9090 (ttm) cc_final: 0.8614 (mtm) REVERT: D 34 CYS cc_start: 0.8865 (t) cc_final: 0.8281 (t) REVERT: D 100 TYR cc_start: 0.7606 (OUTLIER) cc_final: 0.6665 (m-80) REVERT: D 551 MET cc_start: 0.9086 (ttm) cc_final: 0.8622 (mtm) outliers start: 23 outliers final: 13 residues processed: 124 average time/residue: 1.5935 time to fit residues: 222.4229 Evaluate side-chains 117 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 302 MET 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 302 MET 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 174 optimal weight: 10.0000 chunk 152 optimal weight: 30.0000 chunk 36 optimal weight: 20.0000 chunk 38 optimal weight: 7.9990 chunk 185 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3220 r_free = 0.3220 target = 0.059101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.039489 restraints weight = 61593.389| |-----------------------------------------------------------------------------| r_work (start): 0.2616 rms_B_bonded: 3.76 r_work: 0.2448 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17892 Z= 0.220 Angle : 0.644 8.976 24240 Z= 0.316 Chirality : 0.043 0.184 2712 Planarity : 0.004 0.051 3140 Dihedral : 4.370 17.291 2428 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 2.02 % Allowed : 13.24 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.31 (0.18), residues: 2216 helix: 0.89 (0.16), residues: 1060 sheet: -1.66 (0.40), residues: 168 loop : -1.12 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 127 HIS 0.004 0.001 HIS A 333 PHE 0.015 0.001 PHE C 445 TYR 0.014 0.002 TYR B 74 ARG 0.007 0.000 ARG C 387 Details of bonding type rmsd hydrogen bonds : bond 0.03529 ( 784) hydrogen bonds : angle 4.39009 ( 2160) covalent geometry : bond 0.00494 (17892) covalent geometry : angle 0.64409 (24240) *********************** 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 138 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 100 time to evaluate : 2.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 CYS cc_start: 0.8856 (t) cc_final: 0.8277 (t) REVERT: A 100 TYR cc_start: 0.7705 (OUTLIER) cc_final: 0.6762 (m-80) REVERT: B 34 CYS cc_start: 0.8843 (t) cc_final: 0.8261 (t) REVERT: B 100 TYR cc_start: 0.7686 (OUTLIER) cc_final: 0.6751 (m-80) REVERT: B 381 MET cc_start: 0.9660 (tpt) cc_final: 0.9457 (tpt) REVERT: B 551 MET cc_start: 0.9044 (ttm) cc_final: 0.8645 (mtm) REVERT: C 34 CYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8265 (t) REVERT: C 100 TYR cc_start: 0.7664 (OUTLIER) cc_final: 0.6734 (m-80) REVERT: C 551 MET cc_start: 0.9213 (ttm) cc_final: 0.8650 (mtm) REVERT: D 34 CYS cc_start: 0.8861 (t) cc_final: 0.8271 (t) REVERT: D 100 TYR cc_start: 0.7656 (OUTLIER) cc_final: 0.6687 (m-80) REVERT: D 381 MET cc_start: 0.9654 (tpt) cc_final: 0.9435 (tpt) REVERT: D 551 MET cc_start: 0.9183 (ttm) cc_final: 0.8630 (mtm) outliers start: 38 outliers final: 21 residues processed: 126 average time/residue: 1.4973 time to fit residues: 215.4592 Evaluate side-chains 126 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 302 MET 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 113 THR Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 34 CYS Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 354 VAL 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 13 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 166 optimal weight: 7.9990 chunk 207 optimal weight: 20.0000 chunk 139 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.3242 r_free = 0.3242 target = 0.059966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.040472 restraints weight = 60473.568| |-----------------------------------------------------------------------------| r_work (start): 0.2652 rms_B_bonded: 3.75 r_work: 0.2481 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17892 Z= 0.145 Angle : 0.616 10.021 24240 Z= 0.301 Chirality : 0.042 0.182 2712 Planarity : 0.004 0.048 3140 Dihedral : 4.303 17.667 2428 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.07 % Allowed : 14.89 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.23 (0.18), residues: 2216 helix: 0.92 (0.16), residues: 1068 sheet: -1.44 (0.40), residues: 168 loop : -1.08 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 319 HIS 0.004 0.001 HIS A 333 PHE 0.016 0.001 PHE C 445 TYR 0.012 0.002 TYR A 74 ARG 0.006 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.03437 ( 784) hydrogen bonds : angle 4.28354 ( 2160) covalent geometry : bond 0.00336 (17892) covalent geometry : angle 0.61556 (24240) *********************** 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 143 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 104 time to evaluate : 2.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.9519 (tm-30) cc_final: 0.9112 (pp20) REVERT: A 100 TYR cc_start: 0.7793 (OUTLIER) cc_final: 0.6763 (m-80) REVERT: A 216 MET cc_start: 0.9553 (mmm) cc_final: 0.9276 (mtm) REVERT: A 551 MET cc_start: 0.8951 (ttm) cc_final: 0.8649 (mtm) REVERT: B 57 ASP cc_start: 0.9606 (OUTLIER) cc_final: 0.9384 (m-30) REVERT: B 82 GLU cc_start: 0.9513 (tm-30) cc_final: 0.9105 (pp20) REVERT: B 100 TYR cc_start: 0.7789 (OUTLIER) cc_final: 0.6764 (m-80) REVERT: B 216 MET cc_start: 0.9553 (mmm) cc_final: 0.9279 (mtm) REVERT: B 551 MET cc_start: 0.9008 (ttm) cc_final: 0.8611 (mtm) REVERT: C 57 ASP cc_start: 0.9607 (OUTLIER) cc_final: 0.9392 (m-30) REVERT: C 82 GLU cc_start: 0.9514 (tm-30) cc_final: 0.9106 (pp20) REVERT: C 100 TYR cc_start: 0.7768 (OUTLIER) cc_final: 0.6745 (m-80) REVERT: C 216 MET cc_start: 0.9553 (mmm) cc_final: 0.9279 (mtm) REVERT: D 100 TYR cc_start: 0.7787 (OUTLIER) cc_final: 0.6755 (m-80) REVERT: D 381 MET cc_start: 0.9659 (tpt) cc_final: 0.9428 (tpt) outliers start: 39 outliers final: 22 residues processed: 130 average time/residue: 1.7234 time to fit residues: 254.9679 Evaluate side-chains 132 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 3.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 CYS Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 302 MET 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 113 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 302 MET 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 113 THR Chi-restraints excluded: chain C residue 299 LEU 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 34 CYS Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 366 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 116 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 214 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 chunk 139 optimal weight: 0.8980 chunk 146 optimal weight: 20.0000 chunk 92 optimal weight: 7.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- 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 = 0.3228 r_free = 0.3228 target = 0.059192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.039748 restraints weight = 60631.309| |-----------------------------------------------------------------------------| r_work (start): 0.2634 rms_B_bonded: 3.76 r_work: 0.2466 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2549 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= 0.191 Angle : 0.638 10.783 24240 Z= 0.310 Chirality : 0.043 0.183 2712 Planarity : 0.004 0.048 3140 Dihedral : 4.288 18.137 2428 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.45 % Allowed : 15.00 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.02 (0.18), residues: 2216 helix: 1.10 (0.16), residues: 1060 sheet: -1.23 (0.41), residues: 168 loop : -0.99 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 319 HIS 0.003 0.001 HIS D 333 PHE 0.015 0.001 PHE B 445 TYR 0.013 0.002 TYR A 74 ARG 0.005 0.000 ARG C 387 Details of bonding type rmsd hydrogen bonds : bond 0.03445 ( 784) hydrogen bonds : angle 4.27903 ( 2160) covalent geometry : bond 0.00432 (17892) covalent geometry : angle 0.63780 (24240) *********************** 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 154 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 108 time to evaluate : 2.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.9617 (OUTLIER) cc_final: 0.9388 (m-30) REVERT: A 100 TYR cc_start: 0.7797 (OUTLIER) cc_final: 0.6678 (m-80) REVERT: A 216 MET cc_start: 0.9574 (mmm) cc_final: 0.9223 (mtm) REVERT: A 551 MET cc_start: 0.9115 (ttm) cc_final: 0.8751 (mtp) REVERT: B 57 ASP cc_start: 0.9621 (OUTLIER) cc_final: 0.9390 (m-30) REVERT: B 100 TYR cc_start: 0.7799 (OUTLIER) cc_final: 0.6680 (m-80) REVERT: B 216 MET cc_start: 0.9575 (mmm) cc_final: 0.9231 (mtm) REVERT: B 551 MET cc_start: 0.9198 (ttm) cc_final: 0.8902 (mtm) REVERT: C 57 ASP cc_start: 0.9616 (OUTLIER) cc_final: 0.9384 (m-30) REVERT: C 100 TYR cc_start: 0.7763 (OUTLIER) cc_final: 0.6647 (m-80) REVERT: C 216 MET cc_start: 0.9576 (mmm) cc_final: 0.9230 (mtm) REVERT: D 57 ASP cc_start: 0.9614 (OUTLIER) cc_final: 0.9386 (m-30) REVERT: D 82 GLU cc_start: 0.9446 (tm-30) cc_final: 0.9063 (pp20) REVERT: D 100 TYR cc_start: 0.7812 (OUTLIER) cc_final: 0.6711 (m-80) REVERT: D 216 MET cc_start: 0.9516 (mmm) cc_final: 0.9263 (mtm) outliers start: 46 outliers final: 34 residues processed: 135 average time/residue: 1.1316 time to fit residues: 175.1483 Evaluate side-chains 150 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 108 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 CYS Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 302 MET 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 34 CYS Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain C residue 34 CYS Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 299 LEU 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 C residue 486 LEU Chi-restraints excluded: chain D residue 34 CYS Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 302 MET 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 143 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 142 optimal weight: 8.9990 chunk 118 optimal weight: 0.8980 chunk 210 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 147 optimal weight: 20.0000 chunk 15 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 C 483 GLN D 282 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.060278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.041003 restraints weight = 59988.131| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 3.75 r_work: 0.2503 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2725 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= 0.121 Angle : 0.625 11.587 24240 Z= 0.304 Chirality : 0.042 0.181 2712 Planarity : 0.004 0.048 3140 Dihedral : 4.229 18.620 2428 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.23 % Allowed : 15.96 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.02 (0.18), residues: 2216 helix: 1.10 (0.16), residues: 1064 sheet: -1.09 (0.42), residues: 168 loop : -1.03 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 546 HIS 0.004 0.001 HIS D 333 PHE 0.016 0.001 PHE B 445 TYR 0.013 0.001 TYR D 208 ARG 0.004 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.03353 ( 784) hydrogen bonds : angle 4.21015 ( 2160) covalent geometry : bond 0.00282 (17892) covalent geometry : angle 0.62513 (24240) *********************** 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 147 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 105 time to evaluate : 2.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.9601 (OUTLIER) cc_final: 0.9382 (m-30) REVERT: A 100 TYR cc_start: 0.7840 (OUTLIER) cc_final: 0.6711 (m-80) REVERT: B 100 TYR cc_start: 0.7848 (OUTLIER) cc_final: 0.6721 (m-80) REVERT: B 551 MET cc_start: 0.9092 (ttm) cc_final: 0.8833 (mtm) REVERT: C 57 ASP cc_start: 0.9600 (OUTLIER) cc_final: 0.9389 (m-30) REVERT: C 100 TYR cc_start: 0.7809 (OUTLIER) cc_final: 0.6674 (m-80) REVERT: C 551 MET cc_start: 0.9186 (mtp) cc_final: 0.8960 (mtt) REVERT: D 57 ASP cc_start: 0.9597 (OUTLIER) cc_final: 0.9373 (m-30) REVERT: D 82 GLU cc_start: 0.9408 (tm-30) cc_final: 0.9003 (pp20) REVERT: D 100 TYR cc_start: 0.7817 (OUTLIER) cc_final: 0.6652 (m-80) REVERT: D 551 MET cc_start: 0.9180 (mtp) cc_final: 0.8951 (mtt) outliers start: 42 outliers final: 24 residues processed: 132 average time/residue: 1.0890 time to fit residues: 166.4939 Evaluate side-chains 131 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 2.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 113 THR 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 100 TYR Chi-restraints excluded: chain B residue 113 THR 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 B residue 486 LEU Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 184 THR 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 D residue 57 ASP Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 130 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 123 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 184 optimal weight: 0.0370 chunk 80 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 186 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 140 optimal weight: 8.9990 overall best weight: 1.9664 ------------------------------------------------------------------------------- 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 C 483 GLN D 282 HIS D 483 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.059964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.040794 restraints weight = 60895.741| |-----------------------------------------------------------------------------| r_work (start): 0.2666 rms_B_bonded: 3.74 r_work: 0.2501 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2784 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= 0.140 Angle : 0.631 12.327 24240 Z= 0.305 Chirality : 0.042 0.180 2712 Planarity : 0.004 0.048 3140 Dihedral : 4.172 18.358 2428 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.18 % Allowed : 15.69 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.08 (0.18), residues: 2216 helix: 1.11 (0.16), residues: 1068 sheet: -0.90 (0.43), residues: 168 loop : -0.93 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 546 HIS 0.003 0.001 HIS D 333 PHE 0.015 0.001 PHE B 445 TYR 0.013 0.001 TYR D 208 ARG 0.004 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.03250 ( 784) hydrogen bonds : angle 4.19300 ( 2160) covalent geometry : bond 0.00324 (17892) covalent geometry : angle 0.63148 (24240) *********************** 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 149 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 108 time to evaluate : 2.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.9605 (OUTLIER) cc_final: 0.9388 (m-30) REVERT: A 100 TYR cc_start: 0.7881 (OUTLIER) cc_final: 0.6699 (m-80) REVERT: A 551 MET cc_start: 0.8924 (mtm) cc_final: 0.8681 (mtm) REVERT: B 57 ASP cc_start: 0.9603 (OUTLIER) cc_final: 0.9386 (m-30) REVERT: B 100 TYR cc_start: 0.7877 (OUTLIER) cc_final: 0.6695 (m-80) REVERT: B 551 MET cc_start: 0.9150 (ttm) cc_final: 0.8892 (mtm) REVERT: C 57 ASP cc_start: 0.9600 (OUTLIER) cc_final: 0.9374 (m-30) REVERT: C 100 TYR cc_start: 0.7851 (OUTLIER) cc_final: 0.6678 (m-80) REVERT: C 551 MET cc_start: 0.9182 (mtp) cc_final: 0.8929 (mtt) REVERT: D 57 ASP cc_start: 0.9603 (OUTLIER) cc_final: 0.9374 (m-30) REVERT: D 100 TYR cc_start: 0.7850 (OUTLIER) cc_final: 0.6665 (m-80) REVERT: D 551 MET cc_start: 0.9177 (mtp) cc_final: 0.8923 (mtt) outliers start: 41 outliers final: 26 residues processed: 136 average time/residue: 1.1565 time to fit residues: 180.0609 Evaluate side-chains 141 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 113 THR 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 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 113 THR 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 85 MET Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 184 THR 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 85 MET Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 113 THR 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 Chi-restraints excluded: chain D residue 486 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 83 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 182 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 209 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 483 GLN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN ** C 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.058971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.039701 restraints weight = 61120.717| |-----------------------------------------------------------------------------| r_work (start): 0.2633 rms_B_bonded: 3.76 r_work: 0.2467 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17892 Z= 0.220 Angle : 0.679 12.787 24240 Z= 0.329 Chirality : 0.044 0.185 2712 Planarity : 0.004 0.054 3140 Dihedral : 4.242 19.273 2428 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.18 % Allowed : 15.85 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.19 (0.18), residues: 2216 helix: 1.26 (0.17), residues: 1060 sheet: -0.85 (0.43), residues: 168 loop : -0.92 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 546 HIS 0.003 0.001 HIS D 333 PHE 0.016 0.001 PHE C 215 TYR 0.014 0.002 TYR A 74 ARG 0.004 0.000 ARG C 387 Details of bonding type rmsd hydrogen bonds : bond 0.03410 ( 784) hydrogen bonds : angle 4.27272 ( 2160) covalent geometry : bond 0.00493 (17892) covalent geometry : angle 0.67924 (24240) ********************** 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 146 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 105 time to evaluate : 2.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.9623 (OUTLIER) cc_final: 0.9390 (m-30) REVERT: A 100 TYR cc_start: 0.7849 (OUTLIER) cc_final: 0.6753 (m-80) REVERT: B 57 ASP cc_start: 0.9629 (OUTLIER) cc_final: 0.9404 (m-30) REVERT: B 100 TYR cc_start: 0.7844 (OUTLIER) cc_final: 0.6752 (m-80) REVERT: B 551 MET cc_start: 0.9300 (ttm) cc_final: 0.8951 (mtm) REVERT: C 57 ASP cc_start: 0.9618 (OUTLIER) cc_final: 0.9380 (m-30) REVERT: C 100 TYR cc_start: 0.7791 (OUTLIER) cc_final: 0.6739 (m-80) REVERT: C 551 MET cc_start: 0.9221 (mtp) cc_final: 0.8962 (mtt) REVERT: D 57 ASP cc_start: 0.9620 (OUTLIER) cc_final: 0.9376 (m-30) REVERT: D 100 TYR cc_start: 0.7807 (OUTLIER) cc_final: 0.6691 (m-80) REVERT: D 416 ILE cc_start: 0.9248 (mp) cc_final: 0.8862 (pp) REVERT: D 551 MET cc_start: 0.9221 (mtp) cc_final: 0.8963 (mtt) outliers start: 41 outliers final: 23 residues processed: 136 average time/residue: 1.1369 time to fit residues: 177.3843 Evaluate side-chains 136 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 113 THR 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 113 THR 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 85 MET Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 184 THR 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 D residue 57 ASP Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 113 THR 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 144 optimal weight: 9.9990 chunk 109 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 193 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 181 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 212 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3242 r_free = 0.3242 target = 0.059563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.040387 restraints weight = 60863.377| |-----------------------------------------------------------------------------| r_work (start): 0.2658 rms_B_bonded: 3.75 r_work: 0.2491 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17892 Z= 0.155 Angle : 0.651 13.143 24240 Z= 0.317 Chirality : 0.043 0.185 2712 Planarity : 0.004 0.053 3140 Dihedral : 4.238 18.805 2428 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.86 % Allowed : 16.38 % 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 (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: 0.17 (0.18), residues: 2216 helix: 1.25 (0.17), residues: 1064 sheet: -0.84 (0.43), residues: 168 loop : -0.97 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 546 HIS 0.003 0.001 HIS D 333 PHE 0.017 0.001 PHE B 445 TYR 0.016 0.002 TYR D 208 ARG 0.004 0.000 ARG B 387 Details of bonding type rmsd hydrogen bonds : bond 0.03295 ( 784) hydrogen bonds : angle 4.22901 ( 2160) covalent geometry : bond 0.00356 (17892) covalent geometry : angle 0.65067 (24240) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9671.76 seconds wall clock time: 171 minutes 18.70 seconds (10278.70 seconds total)