Starting phenix.real_space_refine on Sat Jul 4 09:23:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ekr_28211/07_2026/8ekr_28211.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ekr_28211/07_2026/8ekr_28211.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ekr_28211/07_2026/8ekr_28211.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ekr_28211/07_2026/8ekr_28211.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ekr_28211/07_2026/8ekr_28211.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ekr_28211/07_2026/8ekr_28211.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ekr_28211/07_2026/8ekr_28211.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ekr_28211/07_2026/8ekr_28211.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 112 5.16 5 C 12940 2.51 5 N 3288 2.21 5 O 3368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19712 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4893 Classifications: {'peptide': 613} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 591} Chain breaks: 4 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 97 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 12, 'ARG:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 95 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'PEX': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 4.98, per 1000 atoms: 0.25 Number of scatterers: 19712 At special positions: 0 Unit cell: (137.97, 137.97, 113.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 112 16.00 P 4 15.00 O 3368 8.00 N 3288 7.00 C 12940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 955.0 milliseconds 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4632 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 4 sheets defined 61.0% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 76 through 84 Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 94 through 102 Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.771A pdb=" N ASN A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 146 Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 166 through 174 removed outlier: 3.574A pdb=" N ILE A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 186 removed outlier: 4.075A pdb=" N ASN A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 219 Processing helix chain 'A' and resid 223 through 231 Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 260 through 282 removed outlier: 3.587A pdb=" N LEU A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG A 280 " --> pdb=" O GLN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 308 through 316 removed outlier: 3.754A pdb=" N HIS A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 377 through 413 removed outlier: 5.247A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 459 Processing helix chain 'A' and resid 459 through 466 removed outlier: 4.165A pdb=" N ILE A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N TRP A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 470 Processing helix chain 'A' and resid 471 through 492 removed outlier: 4.046A pdb=" N ALA A 480 " --> pdb=" O PHE A 476 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN A 487 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 511 removed outlier: 3.638A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 518 Processing helix chain 'A' and resid 519 through 529 removed outlier: 3.617A pdb=" N VAL A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N MET A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE A 529 " --> pdb=" O TYR A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 559 removed outlier: 4.071A pdb=" N ASP A 536 " --> pdb=" O VAL A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 602 Processing helix chain 'A' and resid 619 through 650 removed outlier: 3.568A pdb=" N ASN A 650 " --> pdb=" O SER A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 672 Processing helix chain 'B' and resid 76 through 84 Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 94 through 102 Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.770A pdb=" N ASN B 127 " --> pdb=" O LYS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 146 Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 166 through 174 removed outlier: 3.574A pdb=" N ILE B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 186 removed outlier: 4.075A pdb=" N ASN B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'B' and resid 223 through 231 Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 260 through 282 removed outlier: 3.587A pdb=" N LEU B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG B 280 " --> pdb=" O GLN B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 308 through 316 removed outlier: 3.754A pdb=" N HIS B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 377 through 413 removed outlier: 5.247A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 459 Processing helix chain 'B' and resid 459 through 466 removed outlier: 4.165A pdb=" N ILE B 463 " --> pdb=" O ARG B 459 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TRP B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 470 Processing helix chain 'B' and resid 471 through 492 removed outlier: 4.047A pdb=" N ALA B 480 " --> pdb=" O PHE B 476 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN B 487 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 511 removed outlier: 3.638A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 518 Processing helix chain 'B' and resid 519 through 529 removed outlier: 3.617A pdb=" N VAL B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET B 528 " --> pdb=" O ILE B 524 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE B 529 " --> pdb=" O TYR B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 559 removed outlier: 4.072A pdb=" N ASP B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 602 Processing helix chain 'B' and resid 619 through 650 removed outlier: 3.567A pdb=" N ASN B 650 " --> pdb=" O SER B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 672 Processing helix chain 'C' and resid 76 through 84 Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 94 through 102 Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.769A pdb=" N ASN C 127 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 146 Processing helix chain 'C' and resid 151 through 155 Processing helix chain 'C' and resid 166 through 174 removed outlier: 3.573A pdb=" N ILE C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 186 removed outlier: 4.075A pdb=" N ASN C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 219 Processing helix chain 'C' and resid 223 through 231 Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 260 through 282 removed outlier: 3.587A pdb=" N LEU C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 308 through 316 removed outlier: 3.754A pdb=" N HIS C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 363 Processing helix chain 'C' and resid 369 through 373 Processing helix chain 'C' and resid 377 through 413 removed outlier: 5.246A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 459 Processing helix chain 'C' and resid 459 through 466 removed outlier: 4.165A pdb=" N ILE C 463 " --> pdb=" O ARG C 459 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TRP C 464 " --> pdb=" O ARG C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 470 Processing helix chain 'C' and resid 471 through 492 removed outlier: 4.046A pdb=" N ALA C 480 " --> pdb=" O PHE C 476 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN C 487 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 511 removed outlier: 3.639A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 518 Processing helix chain 'C' and resid 519 through 529 removed outlier: 3.616A pdb=" N VAL C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE C 529 " --> pdb=" O TYR C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 559 removed outlier: 4.071A pdb=" N ASP C 536 " --> pdb=" O VAL C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 602 Processing helix chain 'C' and resid 619 through 650 removed outlier: 3.567A pdb=" N ASN C 650 " --> pdb=" O SER C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 672 Processing helix chain 'D' and resid 76 through 84 Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 94 through 102 Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.770A pdb=" N ASN D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 146 Processing helix chain 'D' and resid 151 through 155 Processing helix chain 'D' and resid 166 through 174 removed outlier: 3.574A pdb=" N ILE D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 186 removed outlier: 4.075A pdb=" N ASN D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 219 Processing helix chain 'D' and resid 223 through 231 Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 260 through 282 removed outlier: 3.587A pdb=" N LEU D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG D 280 " --> pdb=" O GLN D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 308 through 316 removed outlier: 3.754A pdb=" N HIS D 313 " --> pdb=" O GLU D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 363 Processing helix chain 'D' and resid 369 through 373 Processing helix chain 'D' and resid 377 through 413 removed outlier: 5.247A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 459 Processing helix chain 'D' and resid 459 through 466 removed outlier: 4.165A pdb=" N ILE D 463 " --> pdb=" O ARG D 459 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TRP D 464 " --> pdb=" O ARG D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 470 Processing helix chain 'D' and resid 471 through 492 removed outlier: 4.047A pdb=" N ALA D 480 " --> pdb=" O PHE D 476 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN D 487 " --> pdb=" O THR D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 511 removed outlier: 3.637A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 518 Processing helix chain 'D' and resid 519 through 529 removed outlier: 3.617A pdb=" N VAL D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET D 528 " --> pdb=" O ILE D 524 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE D 529 " --> pdb=" O TYR D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 559 removed outlier: 4.071A pdb=" N ASP D 536 " --> pdb=" O VAL D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 602 Processing helix chain 'D' and resid 619 through 650 removed outlier: 3.567A pdb=" N ASN D 650 " --> pdb=" O SER D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 672 Processing sheet with id=AA1, first strand: chain 'A' and resid 330 through 335 removed outlier: 5.008A pdb=" N THR A 331 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU A 342 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASP A 700 " --> pdb=" O VAL A 691 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 330 through 335 removed outlier: 5.009A pdb=" N THR B 331 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU B 342 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ASP B 700 " --> pdb=" O VAL B 691 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 330 through 335 removed outlier: 5.008A pdb=" N THR C 331 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU C 342 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASP C 700 " --> pdb=" O VAL C 691 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 330 through 335 removed outlier: 5.009A pdb=" N THR D 331 " --> pdb=" O LEU D 342 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU D 342 " --> pdb=" O THR D 331 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ASP D 700 " --> pdb=" O VAL D 691 " (cutoff:3.500A) 1056 hydrogen bonds defined for protein. 3012 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: 3.15 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2980 1.31 - 1.44: 5712 1.44 - 1.56: 11320 1.56 - 1.69: 8 1.69 - 1.82: 172 Bond restraints: 20192 Sorted by residual: bond pdb=" C4 PEX A 801 " pdb=" O4 PEX A 801 " ideal model delta sigma weight residual 1.327 1.401 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C4 PEX D 801 " pdb=" O4 PEX D 801 " ideal model delta sigma weight residual 1.327 1.401 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C4 PEX B 801 " pdb=" O4 PEX B 801 " ideal model delta sigma weight residual 1.327 1.401 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C4 PEX C 801 " pdb=" O4 PEX C 801 " ideal model delta sigma weight residual 1.327 1.401 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C14 PEX D 801 " pdb=" O6 PEX D 801 " ideal model delta sigma weight residual 1.331 1.401 -0.070 2.00e-02 2.50e+03 1.23e+01 ... (remaining 20187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 27074 3.22 - 6.43: 278 6.43 - 9.65: 36 9.65 - 12.87: 4 12.87 - 16.08: 4 Bond angle restraints: 27396 Sorted by residual: angle pdb=" C ASN B 259 " pdb=" N SER B 260 " pdb=" CA SER B 260 " ideal model delta sigma weight residual 120.49 129.47 -8.98 1.42e+00 4.96e-01 4.00e+01 angle pdb=" C ASN A 259 " pdb=" N SER A 260 " pdb=" CA SER A 260 " ideal model delta sigma weight residual 120.49 129.45 -8.96 1.42e+00 4.96e-01 3.98e+01 angle pdb=" C ASN D 259 " pdb=" N SER D 260 " pdb=" CA SER D 260 " ideal model delta sigma weight residual 120.49 129.45 -8.96 1.42e+00 4.96e-01 3.98e+01 angle pdb=" C ASN C 259 " pdb=" N SER C 260 " pdb=" CA SER C 260 " ideal model delta sigma weight residual 120.49 129.42 -8.93 1.42e+00 4.96e-01 3.95e+01 angle pdb=" O3 PEX D 801 " pdb=" P1 PEX D 801 " pdb=" O8 PEX D 801 " ideal model delta sigma weight residual 93.74 109.82 -16.08 3.00e+00 1.11e-01 2.87e+01 ... (remaining 27391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 10819 17.88 - 35.77: 829 35.77 - 53.65: 132 53.65 - 71.54: 44 71.54 - 89.42: 16 Dihedral angle restraints: 11840 sinusoidal: 4676 harmonic: 7164 Sorted by residual: dihedral pdb=" CA PHE D 161 " pdb=" C PHE D 161 " pdb=" N TYR D 162 " pdb=" CA TYR D 162 " ideal model delta harmonic sigma weight residual -180.00 -159.72 -20.28 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA PHE C 161 " pdb=" C PHE C 161 " pdb=" N TYR C 162 " pdb=" CA TYR C 162 " ideal model delta harmonic sigma weight residual -180.00 -159.72 -20.28 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA PHE B 161 " pdb=" C PHE B 161 " pdb=" N TYR B 162 " pdb=" CA TYR B 162 " ideal model delta harmonic sigma weight residual 180.00 -159.74 -20.26 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 11837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2076 0.036 - 0.072: 760 0.072 - 0.107: 221 0.107 - 0.143: 52 0.143 - 0.179: 23 Chirality restraints: 3132 Sorted by residual: chirality pdb=" CB VAL B 184 " pdb=" CA VAL B 184 " pdb=" CG1 VAL B 184 " pdb=" CG2 VAL B 184 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.01e-01 chirality pdb=" CB VAL D 184 " pdb=" CA VAL D 184 " pdb=" CG1 VAL D 184 " pdb=" CG2 VAL D 184 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" CB VAL A 184 " pdb=" CA VAL A 184 " pdb=" CG1 VAL A 184 " pdb=" CG2 VAL A 184 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.78e-01 ... (remaining 3129 not shown) Planarity restraints: 3352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 725 " 0.053 5.00e-02 4.00e+02 8.08e-02 1.04e+01 pdb=" N PRO D 726 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO D 726 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 726 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 725 " -0.053 5.00e-02 4.00e+02 8.05e-02 1.04e+01 pdb=" N PRO B 726 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 726 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 726 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 725 " -0.053 5.00e-02 4.00e+02 8.05e-02 1.04e+01 pdb=" N PRO C 726 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO C 726 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 726 " -0.044 5.00e-02 4.00e+02 ... (remaining 3349 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5451 2.81 - 3.33: 18085 3.33 - 3.86: 32646 3.86 - 4.38: 36887 4.38 - 4.90: 64293 Nonbonded interactions: 157362 Sorted by model distance: nonbonded pdb=" O LEU B 513 " pdb=" OG1 THR B 516 " model vdw 2.292 3.040 nonbonded pdb=" O LEU A 513 " pdb=" OG1 THR A 516 " model vdw 2.292 3.040 nonbonded pdb=" O LEU C 513 " pdb=" OG1 THR C 516 " model vdw 2.292 3.040 nonbonded pdb=" O LEU D 513 " pdb=" OG1 THR D 516 " model vdw 2.293 3.040 nonbonded pdb=" O TRP C 223 " pdb=" OG1 THR C 227 " model vdw 2.304 3.040 ... (remaining 157357 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.210 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 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 : 0.004 0.074 20192 Z= 0.174 Angle : 0.804 16.085 27396 Z= 0.390 Chirality : 0.043 0.179 3132 Planarity : 0.006 0.081 3352 Dihedral : 13.745 89.422 7208 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.38 % Allowed : 0.57 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.15), residues: 2412 helix: -0.08 (0.13), residues: 1368 sheet: -0.04 (0.43), residues: 108 loop : -1.79 (0.16), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 371 TYR 0.034 0.002 TYR D 162 PHE 0.015 0.001 PHE D 75 TRP 0.012 0.001 TRP D 333 HIS 0.005 0.001 HIS D 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 (20192) covalent geometry : angle 0.80409 / 0.39 (27396) hydrogen bonds : bond 0.16438 / 10.55 ( 1056) hydrogen bonds : angle 5.86447 / 4.09 ( 3012) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 481 time to evaluate : 0.499 Fit side-chains REVERT: A 123 LYS cc_start: 0.8090 (tptm) cc_final: 0.7870 (tptm) REVERT: A 189 ASP cc_start: 0.7588 (t0) cc_final: 0.7268 (t0) REVERT: B 123 LYS cc_start: 0.8095 (tptm) cc_final: 0.7876 (tptm) REVERT: B 189 ASP cc_start: 0.7591 (t0) cc_final: 0.7268 (t0) REVERT: C 123 LYS cc_start: 0.8092 (tptm) cc_final: 0.7862 (tptm) REVERT: C 189 ASP cc_start: 0.7582 (t0) cc_final: 0.7267 (t0) REVERT: D 123 LYS cc_start: 0.8085 (tptm) cc_final: 0.7861 (tptm) REVERT: D 189 ASP cc_start: 0.7592 (t0) cc_final: 0.7271 (t0) outliers start: 8 outliers final: 0 residues processed: 489 average time/residue: 0.5083 time to fit residues: 286.5708 Evaluate side-chains 347 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.0970 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 ASN A 156 GLN A 247 ASN A 487 GLN B 148 ASN B 156 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN B 487 GLN C 148 ASN C 156 GLN C 247 ASN C 487 GLN D 148 ASN D 156 GLN D 191 HIS ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN D 487 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.155887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.123960 restraints weight = 23670.964| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.87 r_work: 0.3239 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20192 Z= 0.129 Angle : 0.541 9.158 27396 Z= 0.271 Chirality : 0.038 0.169 3132 Planarity : 0.004 0.060 3352 Dihedral : 5.280 47.920 2748 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.26 % Allowed : 11.30 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.16), residues: 2412 helix: 1.09 (0.13), residues: 1456 sheet: 2.65 (0.51), residues: 68 loop : -1.62 (0.17), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 539 TYR 0.029 0.001 TYR A 162 PHE 0.009 0.001 PHE D 75 TRP 0.006 0.001 TRP B 676 HIS 0.005 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (20192) covalent geometry : angle 0.54080 / 0.27 (27396) hydrogen bonds : bond 0.03772 / 2.62 ( 1056) hydrogen bonds : angle 3.71457 / 2.55 ( 3012) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 350 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 ASP cc_start: 0.7807 (t0) cc_final: 0.7528 (t0) REVERT: A 269 HIS cc_start: 0.6745 (m90) cc_final: 0.6463 (t-90) REVERT: A 371 ARG cc_start: 0.8072 (mmt90) cc_final: 0.7163 (mmp-170) REVERT: A 388 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7733 (ttp-170) REVERT: A 433 MET cc_start: 0.7748 (tpt) cc_final: 0.7458 (tpp) REVERT: A 520 GLN cc_start: 0.6902 (pm20) cc_final: 0.6567 (pm20) REVERT: A 637 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8449 (mt) REVERT: A 640 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8097 (ttp) REVERT: B 189 ASP cc_start: 0.7797 (t0) cc_final: 0.7522 (t0) REVERT: B 255 MET cc_start: 0.8621 (tpt) cc_final: 0.8418 (mmm) REVERT: B 269 HIS cc_start: 0.6748 (m90) cc_final: 0.6471 (t-90) REVERT: B 371 ARG cc_start: 0.8071 (mmt90) cc_final: 0.7161 (mmp-170) REVERT: B 388 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7680 (tpp-160) REVERT: B 468 MET cc_start: 0.6523 (ppp) cc_final: 0.6301 (ppp) REVERT: B 538 LEU cc_start: 0.8132 (mm) cc_final: 0.7882 (mm) REVERT: B 539 ARG cc_start: 0.7024 (OUTLIER) cc_final: 0.6330 (ptt90) REVERT: B 636 LEU cc_start: 0.8614 (mp) cc_final: 0.8410 (mt) REVERT: B 637 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8448 (mt) REVERT: B 640 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8080 (ttp) REVERT: B 708 GLU cc_start: 0.8648 (tt0) cc_final: 0.8394 (mt-10) REVERT: C 189 ASP cc_start: 0.7795 (t0) cc_final: 0.7518 (t0) REVERT: C 255 MET cc_start: 0.8629 (tpt) cc_final: 0.8428 (mmm) REVERT: C 269 HIS cc_start: 0.6746 (m90) cc_final: 0.6470 (t-90) REVERT: C 371 ARG cc_start: 0.8075 (mmt90) cc_final: 0.7163 (mmp-170) REVERT: C 388 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7704 (ttp-170) REVERT: C 538 LEU cc_start: 0.8132 (mm) cc_final: 0.7882 (mm) REVERT: C 636 LEU cc_start: 0.8615 (mp) cc_final: 0.8415 (mt) REVERT: C 637 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8461 (mt) REVERT: C 640 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8107 (ttp) REVERT: C 708 GLU cc_start: 0.8656 (tt0) cc_final: 0.8404 (mt-10) REVERT: D 189 ASP cc_start: 0.7796 (t0) cc_final: 0.7521 (t0) REVERT: D 191 HIS cc_start: 0.8205 (m170) cc_final: 0.7937 (m-70) REVERT: D 269 HIS cc_start: 0.6759 (m90) cc_final: 0.6479 (t-90) REVERT: D 371 ARG cc_start: 0.8073 (mmt90) cc_final: 0.7164 (mmp-170) REVERT: D 388 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7676 (tpp-160) REVERT: D 538 LEU cc_start: 0.8138 (mm) cc_final: 0.7886 (mm) REVERT: D 539 ARG cc_start: 0.7027 (OUTLIER) cc_final: 0.6318 (ptt90) REVERT: D 637 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8451 (mt) REVERT: D 640 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8097 (ttp) outliers start: 68 outliers final: 41 residues processed: 378 average time/residue: 0.4926 time to fit residues: 216.7816 Evaluate side-chains 379 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 324 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 615 GLN Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 539 ARG Chi-restraints excluded: chain B residue 615 GLN Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 539 ARG Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 727 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 539 ARG Chi-restraints excluded: chain D residue 615 GLN Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 640 MET Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 648 THR Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain D residue 727 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 70 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 169 optimal weight: 0.9990 chunk 62 optimal weight: 0.0570 chunk 78 optimal weight: 0.0870 chunk 242 optimal weight: 0.4980 chunk 219 optimal weight: 0.7980 chunk 28 optimal weight: 0.1980 chunk 18 optimal weight: 0.0870 chunk 94 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.1854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 191 HIS ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.158684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.127706 restraints weight = 23823.006| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.76 r_work: 0.3262 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 20192 Z= 0.095 Angle : 0.491 9.005 27396 Z= 0.243 Chirality : 0.035 0.172 3132 Planarity : 0.004 0.047 3352 Dihedral : 4.639 35.740 2748 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.92 % Allowed : 14.42 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.17), residues: 2412 helix: 1.74 (0.14), residues: 1440 sheet: 2.61 (0.49), residues: 68 loop : -1.44 (0.18), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 539 TYR 0.016 0.001 TYR D 162 PHE 0.012 0.001 PHE B 612 TRP 0.008 0.001 TRP D 333 HIS 0.005 0.001 HIS D 521 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.09 (20192) covalent geometry : angle 0.49131 / 0.24 (27396) hydrogen bonds : bond 0.03115 / 2.18 ( 1056) hydrogen bonds : angle 3.38095 / 2.33 ( 3012) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 325 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ASP cc_start: 0.7779 (t0) cc_final: 0.7462 (t0) REVERT: A 191 HIS cc_start: 0.8190 (m170) cc_final: 0.7940 (m-70) REVERT: A 269 HIS cc_start: 0.6782 (m90) cc_final: 0.6504 (OUTLIER) REVERT: A 371 ARG cc_start: 0.7992 (mmt90) cc_final: 0.7096 (mmp-170) REVERT: A 388 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7634 (ttp-170) REVERT: A 468 MET cc_start: 0.6564 (ppp) cc_final: 0.6200 (tmm) REVERT: A 473 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7706 (mm-30) REVERT: A 520 GLN cc_start: 0.6726 (pm20) cc_final: 0.6516 (pm20) REVERT: A 528 MET cc_start: 0.5649 (mpt) cc_final: 0.5147 (mpp) REVERT: A 640 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.8090 (ttp) REVERT: A 708 GLU cc_start: 0.8624 (tt0) cc_final: 0.8367 (mt-10) REVERT: B 189 ASP cc_start: 0.7770 (t0) cc_final: 0.7456 (t0) REVERT: B 269 HIS cc_start: 0.6781 (m90) cc_final: 0.6520 (t70) REVERT: B 371 ARG cc_start: 0.7991 (mmt90) cc_final: 0.7102 (mmp-170) REVERT: B 388 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7657 (ttp-170) REVERT: B 468 MET cc_start: 0.6572 (ppp) cc_final: 0.6336 (tmm) REVERT: B 473 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7708 (mm-30) REVERT: B 520 GLN cc_start: 0.6823 (pm20) cc_final: 0.6512 (pm20) REVERT: B 528 MET cc_start: 0.5651 (mpt) cc_final: 0.5146 (mpp) REVERT: B 640 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.8050 (ttp) REVERT: C 189 ASP cc_start: 0.7721 (t0) cc_final: 0.7397 (t0) REVERT: C 269 HIS cc_start: 0.6775 (m90) cc_final: 0.6495 (t70) REVERT: C 327 SER cc_start: 0.8847 (m) cc_final: 0.8645 (t) REVERT: C 371 ARG cc_start: 0.8003 (mmt90) cc_final: 0.7107 (mmp-170) REVERT: C 388 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7908 (ttt180) REVERT: C 473 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7747 (mm-30) REVERT: C 520 GLN cc_start: 0.6754 (pm20) cc_final: 0.6421 (pm20) REVERT: C 528 MET cc_start: 0.5617 (mpt) cc_final: 0.5111 (mpp) REVERT: C 640 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.8054 (ttp) REVERT: D 189 ASP cc_start: 0.7726 (t0) cc_final: 0.7411 (t0) REVERT: D 191 HIS cc_start: 0.8173 (m170) cc_final: 0.7907 (m-70) REVERT: D 269 HIS cc_start: 0.6782 (m90) cc_final: 0.6490 (t70) REVERT: D 371 ARG cc_start: 0.7997 (mmt90) cc_final: 0.7111 (mmp-170) REVERT: D 388 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7617 (ttp-170) REVERT: D 473 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7702 (mm-30) REVERT: D 520 GLN cc_start: 0.6826 (pm20) cc_final: 0.6505 (pm20) REVERT: D 528 MET cc_start: 0.5658 (mpt) cc_final: 0.5165 (mpp) REVERT: D 640 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.8090 (ttp) REVERT: D 708 GLU cc_start: 0.8611 (tt0) cc_final: 0.8350 (mt-10) outliers start: 61 outliers final: 31 residues processed: 360 average time/residue: 0.5708 time to fit residues: 234.8834 Evaluate side-chains 340 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 298 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 539 ARG Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 539 ARG Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 539 ARG Chi-restraints excluded: chain D residue 640 MET Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 88 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 214 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 240 optimal weight: 0.6980 chunk 201 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 191 HIS C 191 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.153441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.122103 restraints weight = 23796.166| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.75 r_work: 0.3186 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20192 Z= 0.117 Angle : 0.509 8.554 27396 Z= 0.254 Chirality : 0.036 0.183 3132 Planarity : 0.004 0.042 3352 Dihedral : 4.631 38.661 2748 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.07 % Allowed : 16.24 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.17), residues: 2412 helix: 1.88 (0.13), residues: 1444 sheet: 2.53 (0.50), residues: 68 loop : -1.29 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 539 TYR 0.019 0.001 TYR A 162 PHE 0.026 0.001 PHE C 161 TRP 0.008 0.001 TRP B 223 HIS 0.005 0.001 HIS D 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (20192) covalent geometry : angle 0.50936 / 0.25 (27396) hydrogen bonds : bond 0.03412 / 2.38 ( 1056) hydrogen bonds : angle 3.31799 / 2.28 ( 3012) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 338 time to evaluate : 0.824 Fit side-chains revert: symmetry clash REVERT: A 189 ASP cc_start: 0.7741 (t0) cc_final: 0.7367 (t0) REVERT: A 191 HIS cc_start: 0.8233 (m170) cc_final: 0.8014 (m-70) REVERT: A 371 ARG cc_start: 0.8029 (mmt90) cc_final: 0.7157 (mmp-170) REVERT: A 388 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7934 (ttt180) REVERT: A 468 MET cc_start: 0.6640 (ppp) cc_final: 0.6290 (tmm) REVERT: A 640 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.8123 (ttp) REVERT: B 189 ASP cc_start: 0.7733 (t0) cc_final: 0.7367 (t0) REVERT: B 191 HIS cc_start: 0.8208 (m170) cc_final: 0.7949 (m-70) REVERT: B 269 HIS cc_start: 0.6931 (m90) cc_final: 0.6589 (t-90) REVERT: B 371 ARG cc_start: 0.8016 (mmt90) cc_final: 0.7158 (mmp-170) REVERT: B 388 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7927 (ttt180) REVERT: B 520 GLN cc_start: 0.6737 (pm20) cc_final: 0.6393 (pm20) REVERT: B 538 LEU cc_start: 0.7991 (mm) cc_final: 0.7687 (mm) REVERT: B 539 ARG cc_start: 0.7029 (OUTLIER) cc_final: 0.6318 (ptt90) REVERT: B 640 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.8133 (ttp) REVERT: B 708 GLU cc_start: 0.8666 (tt0) cc_final: 0.8395 (mt-10) REVERT: C 189 ASP cc_start: 0.7736 (t0) cc_final: 0.7367 (t0) REVERT: C 191 HIS cc_start: 0.8200 (m170) cc_final: 0.7937 (m-70) REVERT: C 371 ARG cc_start: 0.8024 (mmt90) cc_final: 0.7173 (mmp-170) REVERT: C 388 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7937 (ttt180) REVERT: C 520 GLN cc_start: 0.6736 (pm20) cc_final: 0.6382 (pm20) REVERT: C 538 LEU cc_start: 0.8000 (mm) cc_final: 0.7704 (mm) REVERT: C 539 ARG cc_start: 0.7054 (OUTLIER) cc_final: 0.6369 (ptt90) REVERT: C 640 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.8112 (ttp) REVERT: C 708 GLU cc_start: 0.8664 (tt0) cc_final: 0.8412 (mt-10) REVERT: D 189 ASP cc_start: 0.7731 (t0) cc_final: 0.7372 (t0) REVERT: D 191 HIS cc_start: 0.8231 (m170) cc_final: 0.7972 (m-70) REVERT: D 371 ARG cc_start: 0.8035 (mmt90) cc_final: 0.7175 (mmp-170) REVERT: D 388 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7924 (ttt180) REVERT: D 520 GLN cc_start: 0.6734 (pm20) cc_final: 0.6366 (pm20) REVERT: D 538 LEU cc_start: 0.8005 (mm) cc_final: 0.7712 (mm) REVERT: D 539 ARG cc_start: 0.7043 (OUTLIER) cc_final: 0.6354 (ptt90) REVERT: D 624 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8530 (mp) REVERT: D 640 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.8119 (ttp) outliers start: 64 outliers final: 41 residues processed: 374 average time/residue: 0.5218 time to fit residues: 225.8658 Evaluate side-chains 360 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 307 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 539 ARG Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 539 ARG Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 727 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 539 ARG Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 640 MET Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain D residue 727 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 37 optimal weight: 0.0980 chunk 22 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 185 optimal weight: 6.9990 chunk 221 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 220 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.154438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.122692 restraints weight = 23645.026| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.87 r_work: 0.3182 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20192 Z= 0.100 Angle : 0.483 8.422 27396 Z= 0.241 Chirality : 0.036 0.194 3132 Planarity : 0.003 0.037 3352 Dihedral : 4.483 36.530 2748 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.30 % Allowed : 17.48 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.17), residues: 2412 helix: 2.01 (0.13), residues: 1448 sheet: 2.86 (0.47), residues: 68 loop : -1.20 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 539 TYR 0.015 0.001 TYR A 162 PHE 0.017 0.001 PHE C 161 TRP 0.010 0.001 TRP D 223 HIS 0.004 0.001 HIS D 521 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (20192) covalent geometry : angle 0.48331 / 0.24 (27396) hydrogen bonds : bond 0.03183 / 2.23 ( 1056) hydrogen bonds : angle 3.25635 / 2.24 ( 3012) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 331 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ASP cc_start: 0.7772 (t0) cc_final: 0.7337 (t0) REVERT: A 191 HIS cc_start: 0.8300 (m170) cc_final: 0.8026 (m-70) REVERT: A 371 ARG cc_start: 0.7996 (mmt90) cc_final: 0.7121 (mmp-170) REVERT: A 388 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7972 (ttt180) REVERT: A 433 MET cc_start: 0.7693 (tpt) cc_final: 0.7384 (tpp) REVERT: A 468 MET cc_start: 0.6701 (ppp) cc_final: 0.6247 (tmm) REVERT: A 640 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8187 (ttp) REVERT: A 708 GLU cc_start: 0.8652 (tt0) cc_final: 0.8379 (mt-10) REVERT: B 189 ASP cc_start: 0.7712 (t0) cc_final: 0.7285 (t0) REVERT: B 191 HIS cc_start: 0.8287 (m170) cc_final: 0.7938 (m-70) REVERT: B 371 ARG cc_start: 0.8013 (mmt90) cc_final: 0.7134 (mmp-170) REVERT: B 388 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7956 (ttt180) REVERT: B 433 MET cc_start: 0.7699 (tpt) cc_final: 0.7387 (tpp) REVERT: B 520 GLN cc_start: 0.6729 (pm20) cc_final: 0.6441 (pm20) REVERT: B 528 MET cc_start: 0.5819 (OUTLIER) cc_final: 0.5220 (mpt) REVERT: B 539 ARG cc_start: 0.6973 (OUTLIER) cc_final: 0.6311 (ptt90) REVERT: B 640 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.8120 (ttp) REVERT: B 708 GLU cc_start: 0.8683 (tt0) cc_final: 0.8408 (mt-10) REVERT: C 189 ASP cc_start: 0.7757 (t0) cc_final: 0.7323 (t0) REVERT: C 191 HIS cc_start: 0.8286 (m170) cc_final: 0.7902 (m-70) REVERT: C 371 ARG cc_start: 0.8014 (mmt90) cc_final: 0.7138 (mmp-170) REVERT: C 388 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7951 (ttt180) REVERT: C 433 MET cc_start: 0.7693 (tpt) cc_final: 0.7381 (tpp) REVERT: C 520 GLN cc_start: 0.6724 (pm20) cc_final: 0.6429 (pm20) REVERT: C 528 MET cc_start: 0.5829 (OUTLIER) cc_final: 0.5214 (mpt) REVERT: C 640 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.8178 (ttp) REVERT: C 708 GLU cc_start: 0.8667 (tt0) cc_final: 0.8394 (mt-10) REVERT: D 173 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7692 (tm-30) REVERT: D 189 ASP cc_start: 0.7728 (t0) cc_final: 0.7304 (t0) REVERT: D 191 HIS cc_start: 0.8286 (m170) cc_final: 0.7946 (m-70) REVERT: D 371 ARG cc_start: 0.8013 (mmt90) cc_final: 0.7136 (mmp-170) REVERT: D 388 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7952 (ttt180) REVERT: D 469 ASP cc_start: 0.7574 (m-30) cc_final: 0.7356 (m-30) REVERT: D 520 GLN cc_start: 0.6736 (pm20) cc_final: 0.6440 (pm20) REVERT: D 528 MET cc_start: 0.5855 (OUTLIER) cc_final: 0.5232 (mpt) REVERT: D 640 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.8163 (ttp) REVERT: D 708 GLU cc_start: 0.8641 (tt0) cc_final: 0.8346 (mt-10) outliers start: 69 outliers final: 44 residues processed: 365 average time/residue: 0.5045 time to fit residues: 214.7165 Evaluate side-chains 368 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 312 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 539 ARG Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 539 ARG Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 539 ARG Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 640 MET Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 34 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 191 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 209 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 178 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 413 HIS B 413 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.150874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.119101 restraints weight = 23503.899| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.85 r_work: 0.3214 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20192 Z= 0.121 Angle : 0.511 8.295 27396 Z= 0.255 Chirality : 0.037 0.207 3132 Planarity : 0.004 0.037 3352 Dihedral : 4.611 40.158 2748 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.12 % Allowed : 17.43 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.17), residues: 2412 helix: 2.01 (0.13), residues: 1452 sheet: 0.93 (0.56), residues: 88 loop : -1.08 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 539 TYR 0.015 0.001 TYR D 162 PHE 0.017 0.001 PHE B 161 TRP 0.011 0.001 TRP A 223 HIS 0.004 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (20192) covalent geometry : angle 0.51072 / 0.26 (27396) hydrogen bonds : bond 0.03473 / 2.43 ( 1056) hydrogen bonds : angle 3.31878 / 2.28 ( 3012) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 336 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7690 (tm-30) REVERT: A 189 ASP cc_start: 0.7777 (t0) cc_final: 0.7337 (t0) REVERT: A 191 HIS cc_start: 0.8321 (m170) cc_final: 0.8045 (m-70) REVERT: A 221 LYS cc_start: 0.8271 (ttpt) cc_final: 0.7845 (tttm) REVERT: A 371 ARG cc_start: 0.7993 (mmt90) cc_final: 0.7173 (mmp-170) REVERT: A 388 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7983 (ttt180) REVERT: A 433 MET cc_start: 0.7712 (tpt) cc_final: 0.7397 (tpp) REVERT: A 528 MET cc_start: 0.5908 (OUTLIER) cc_final: 0.5178 (mpp) REVERT: A 624 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8618 (mp) REVERT: A 708 GLU cc_start: 0.8641 (tt0) cc_final: 0.8395 (mt-10) REVERT: B 173 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7710 (tm-30) REVERT: B 189 ASP cc_start: 0.7781 (t0) cc_final: 0.7343 (t0) REVERT: B 371 ARG cc_start: 0.7992 (mmt90) cc_final: 0.7177 (mmp-170) REVERT: B 388 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7925 (ttt180) REVERT: B 433 MET cc_start: 0.7727 (tpt) cc_final: 0.7409 (tpp) REVERT: B 520 GLN cc_start: 0.6863 (pm20) cc_final: 0.6621 (pm20) REVERT: B 528 MET cc_start: 0.5862 (OUTLIER) cc_final: 0.5227 (mpt) REVERT: B 624 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8625 (mp) REVERT: B 640 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.8191 (ttp) REVERT: B 708 GLU cc_start: 0.8654 (tt0) cc_final: 0.8404 (mt-10) REVERT: C 173 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7701 (tm-30) REVERT: C 189 ASP cc_start: 0.7743 (t0) cc_final: 0.7304 (t0) REVERT: C 221 LYS cc_start: 0.8281 (ttpt) cc_final: 0.7837 (tttm) REVERT: C 371 ARG cc_start: 0.7996 (mmt90) cc_final: 0.7171 (mmp-170) REVERT: C 388 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7970 (ttt180) REVERT: C 520 GLN cc_start: 0.6826 (pm20) cc_final: 0.6562 (mp10) REVERT: C 640 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8192 (ttp) REVERT: C 708 GLU cc_start: 0.8643 (tt0) cc_final: 0.8392 (mt-10) REVERT: D 173 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7687 (tm-30) REVERT: D 189 ASP cc_start: 0.7766 (t0) cc_final: 0.7309 (t0) REVERT: D 371 ARG cc_start: 0.7997 (mmt90) cc_final: 0.7181 (mmp-170) REVERT: D 388 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7923 (ttt180) REVERT: D 520 GLN cc_start: 0.6864 (pm20) cc_final: 0.6615 (pm20) REVERT: D 539 ARG cc_start: 0.7090 (OUTLIER) cc_final: 0.6434 (ptt90) REVERT: D 624 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8633 (mp) REVERT: D 640 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.8188 (ttp) REVERT: D 708 GLU cc_start: 0.8623 (tt0) cc_final: 0.8371 (mt-10) outliers start: 86 outliers final: 46 residues processed: 372 average time/residue: 0.4763 time to fit residues: 204.1885 Evaluate side-chains 377 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 318 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 727 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 539 ARG Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 640 MET Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain D residue 727 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 168 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 241 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 195 optimal weight: 0.0670 chunk 149 optimal weight: 4.9990 chunk 150 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.152364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.120801 restraints weight = 23534.671| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.85 r_work: 0.3201 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20192 Z= 0.107 Angle : 0.504 8.194 27396 Z= 0.250 Chirality : 0.037 0.218 3132 Planarity : 0.004 0.038 3352 Dihedral : 4.507 38.631 2748 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.93 % Allowed : 18.92 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.17), residues: 2412 helix: 2.08 (0.13), residues: 1452 sheet: 0.84 (0.56), residues: 88 loop : -1.02 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 539 TYR 0.010 0.001 TYR A 525 PHE 0.015 0.001 PHE C 161 TRP 0.011 0.001 TRP D 223 HIS 0.006 0.001 HIS A 521 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (20192) covalent geometry : angle 0.50374 / 0.25 (27396) hydrogen bonds : bond 0.03338 / 2.35 ( 1056) hydrogen bonds : angle 3.26674 / 2.25 ( 3012) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 349 time to evaluate : 0.927 Fit side-chains REVERT: A 162 TYR cc_start: 0.8467 (OUTLIER) cc_final: 0.7930 (t80) REVERT: A 173 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7721 (tm-30) REVERT: A 189 ASP cc_start: 0.7760 (t0) cc_final: 0.7280 (t0) REVERT: A 191 HIS cc_start: 0.8306 (m170) cc_final: 0.8004 (m-70) REVERT: A 221 LYS cc_start: 0.8304 (ttpt) cc_final: 0.7866 (tttm) REVERT: A 234 HIS cc_start: 0.7413 (m90) cc_final: 0.7199 (m-70) REVERT: A 371 ARG cc_start: 0.7996 (mmt90) cc_final: 0.7157 (mmp-170) REVERT: A 388 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7999 (ttt180) REVERT: A 433 MET cc_start: 0.7670 (tpt) cc_final: 0.7363 (tpp) REVERT: A 528 MET cc_start: 0.5829 (OUTLIER) cc_final: 0.5138 (mpp) REVERT: A 640 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.8172 (ttp) REVERT: A 708 GLU cc_start: 0.8644 (tt0) cc_final: 0.8337 (mt-10) REVERT: B 173 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7704 (tm-30) REVERT: B 189 ASP cc_start: 0.7739 (t0) cc_final: 0.7255 (t0) REVERT: B 371 ARG cc_start: 0.7999 (mmt90) cc_final: 0.7149 (mmp-170) REVERT: B 388 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7962 (ttt180) REVERT: B 433 MET cc_start: 0.7694 (tpt) cc_final: 0.7382 (tpp) REVERT: B 520 GLN cc_start: 0.6746 (pm20) cc_final: 0.6518 (pm20) REVERT: B 528 MET cc_start: 0.5832 (OUTLIER) cc_final: 0.5135 (mpp) REVERT: B 640 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8158 (ttp) REVERT: B 708 GLU cc_start: 0.8647 (tt0) cc_final: 0.8377 (mt-10) REVERT: C 189 ASP cc_start: 0.7754 (t0) cc_final: 0.7269 (t0) REVERT: C 221 LYS cc_start: 0.8295 (ttpt) cc_final: 0.7848 (tttm) REVERT: C 371 ARG cc_start: 0.7994 (mmt90) cc_final: 0.7148 (mmp-170) REVERT: C 388 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7983 (ttt180) REVERT: C 406 ILE cc_start: 0.8742 (mm) cc_final: 0.8512 (mt) REVERT: C 520 GLN cc_start: 0.6785 (pm20) cc_final: 0.6543 (mp10) REVERT: C 640 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.8189 (ttp) REVERT: C 708 GLU cc_start: 0.8633 (tt0) cc_final: 0.8366 (mt-10) REVERT: D 189 ASP cc_start: 0.7744 (t0) cc_final: 0.7247 (t0) REVERT: D 371 ARG cc_start: 0.8006 (mmt90) cc_final: 0.7169 (mmp-170) REVERT: D 388 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7971 (ttt180) REVERT: D 520 GLN cc_start: 0.6817 (pm20) cc_final: 0.6604 (pm20) REVERT: D 528 MET cc_start: 0.5827 (mpt) cc_final: 0.5467 (mmm) REVERT: D 640 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8193 (ttp) REVERT: D 708 GLU cc_start: 0.8634 (tt0) cc_final: 0.8326 (mt-10) outliers start: 82 outliers final: 38 residues processed: 388 average time/residue: 0.4943 time to fit residues: 223.0214 Evaluate side-chains 383 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 334 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 727 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 640 MET Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 217 optimal weight: 0.0670 chunk 54 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 193 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 168 optimal weight: 0.5980 chunk 170 optimal weight: 0.8980 chunk 179 optimal weight: 2.9990 chunk 195 optimal weight: 0.0170 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 413 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.153708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.121831 restraints weight = 23423.290| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.86 r_work: 0.3252 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20192 Z= 0.097 Angle : 0.505 8.840 27396 Z= 0.250 Chirality : 0.036 0.225 3132 Planarity : 0.003 0.033 3352 Dihedral : 4.342 35.162 2748 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.87 % Allowed : 20.50 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.17), residues: 2412 helix: 2.15 (0.13), residues: 1464 sheet: 0.83 (0.56), residues: 88 loop : -1.07 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 312 TYR 0.008 0.001 TYR C 271 PHE 0.014 0.001 PHE B 161 TRP 0.015 0.001 TRP C 223 HIS 0.006 0.001 HIS C 521 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (20192) covalent geometry : angle 0.50515 / 0.25 (27396) hydrogen bonds : bond 0.03176 / 2.24 ( 1056) hydrogen bonds : angle 3.19693 / 2.19 ( 3012) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 352 time to evaluate : 0.761 Fit side-chains REVERT: A 162 TYR cc_start: 0.8490 (OUTLIER) cc_final: 0.7963 (t80) REVERT: A 173 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7721 (tm-30) REVERT: A 189 ASP cc_start: 0.7737 (t0) cc_final: 0.7235 (t0) REVERT: A 191 HIS cc_start: 0.8257 (m170) cc_final: 0.7846 (m-70) REVERT: A 371 ARG cc_start: 0.7976 (mmt90) cc_final: 0.7139 (mmp-170) REVERT: A 388 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7963 (ttt180) REVERT: A 433 MET cc_start: 0.7698 (tpt) cc_final: 0.7398 (tpp) REVERT: A 528 MET cc_start: 0.5801 (OUTLIER) cc_final: 0.5116 (mpp) REVERT: A 538 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7897 (mp) REVERT: B 173 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7700 (tm-30) REVERT: B 189 ASP cc_start: 0.7731 (t0) cc_final: 0.7228 (t0) REVERT: B 191 HIS cc_start: 0.8242 (m170) cc_final: 0.7845 (m-70) REVERT: B 371 ARG cc_start: 0.7965 (mmt90) cc_final: 0.7117 (mmp-170) REVERT: B 388 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7942 (ttt180) REVERT: B 433 MET cc_start: 0.7728 (tpt) cc_final: 0.7420 (tpp) REVERT: B 528 MET cc_start: 0.5841 (OUTLIER) cc_final: 0.5144 (mpp) REVERT: B 645 MET cc_start: 0.7314 (tpp) cc_final: 0.7023 (ttp) REVERT: B 708 GLU cc_start: 0.8604 (tt0) cc_final: 0.8291 (mt-10) REVERT: C 189 ASP cc_start: 0.7713 (t0) cc_final: 0.7220 (t0) REVERT: C 191 HIS cc_start: 0.8233 (m170) cc_final: 0.7833 (m-70) REVERT: C 371 ARG cc_start: 0.7964 (mmt90) cc_final: 0.7120 (mmp-170) REVERT: C 388 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7934 (ttt180) REVERT: C 520 GLN cc_start: 0.6707 (pm20) cc_final: 0.6482 (pm20) REVERT: C 528 MET cc_start: 0.5809 (mpt) cc_final: 0.5096 (mpp) REVERT: C 708 GLU cc_start: 0.8591 (tt0) cc_final: 0.8282 (mt-10) REVERT: D 189 ASP cc_start: 0.7754 (t0) cc_final: 0.7249 (t0) REVERT: D 191 HIS cc_start: 0.8259 (m170) cc_final: 0.7877 (m-70) REVERT: D 371 ARG cc_start: 0.7992 (mmt90) cc_final: 0.7156 (mmp-170) REVERT: D 388 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7833 (mtp180) REVERT: D 528 MET cc_start: 0.5820 (mpt) cc_final: 0.5106 (mpp) outliers start: 60 outliers final: 37 residues processed: 378 average time/residue: 0.4576 time to fit residues: 202.3575 Evaluate side-chains 384 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 339 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 35 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 225 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 201 optimal weight: 0.0060 chunk 4 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 165 optimal weight: 5.9990 overall best weight: 1.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.150595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.118923 restraints weight = 23315.234| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.76 r_work: 0.3114 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20192 Z= 0.172 Angle : 0.575 9.885 27396 Z= 0.286 Chirality : 0.040 0.236 3132 Planarity : 0.004 0.036 3352 Dihedral : 4.874 46.248 2748 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.35 % Allowed : 19.92 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.17), residues: 2412 helix: 1.95 (0.13), residues: 1456 sheet: 0.40 (0.55), residues: 88 loop : -1.00 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 560 TYR 0.012 0.001 TYR C 525 PHE 0.016 0.001 PHE B 161 TRP 0.012 0.001 TRP C 223 HIS 0.005 0.001 HIS B 521 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (20192) covalent geometry : angle 0.57466 / 0.29 (27396) hydrogen bonds : bond 0.03903 / 2.73 ( 1056) hydrogen bonds : angle 3.42393 / 2.35 ( 3012) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 339 time to evaluate : 0.772 Fit side-chains REVERT: A 160 GLU cc_start: 0.8027 (tp30) cc_final: 0.7123 (pt0) REVERT: A 173 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7653 (tm-30) REVERT: A 189 ASP cc_start: 0.7644 (t0) cc_final: 0.7138 (t0) REVERT: A 191 HIS cc_start: 0.8287 (m170) cc_final: 0.7987 (m-70) REVERT: A 221 LYS cc_start: 0.8343 (ttpt) cc_final: 0.8009 (ttmm) REVERT: A 371 ARG cc_start: 0.7993 (mmt90) cc_final: 0.7157 (mmp-170) REVERT: A 388 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7987 (ttt180) REVERT: A 406 ILE cc_start: 0.8745 (mm) cc_final: 0.8531 (mt) REVERT: A 433 MET cc_start: 0.7645 (tpt) cc_final: 0.7344 (tpp) REVERT: A 528 MET cc_start: 0.5927 (OUTLIER) cc_final: 0.5177 (mpp) REVERT: A 538 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7959 (mp) REVERT: A 645 MET cc_start: 0.7141 (OUTLIER) cc_final: 0.6935 (tpp) REVERT: B 173 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7659 (tm-30) REVERT: B 189 ASP cc_start: 0.7675 (t0) cc_final: 0.7162 (t0) REVERT: B 191 HIS cc_start: 0.8283 (m170) cc_final: 0.7860 (m-70) REVERT: B 221 LYS cc_start: 0.8349 (ttpt) cc_final: 0.8015 (ttmm) REVERT: B 371 ARG cc_start: 0.7988 (mmt90) cc_final: 0.7151 (mmp-170) REVERT: B 388 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7927 (ttt180) REVERT: B 406 ILE cc_start: 0.8759 (mm) cc_final: 0.8547 (mt) REVERT: B 433 MET cc_start: 0.7678 (tpt) cc_final: 0.7369 (tpp) REVERT: B 520 GLN cc_start: 0.6816 (pm20) cc_final: 0.6476 (pm20) REVERT: C 189 ASP cc_start: 0.7624 (t0) cc_final: 0.7119 (t0) REVERT: C 221 LYS cc_start: 0.8340 (ttpt) cc_final: 0.8003 (ttmm) REVERT: C 371 ARG cc_start: 0.7987 (mmt90) cc_final: 0.7148 (mmp-170) REVERT: C 388 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7972 (ttt180) REVERT: C 406 ILE cc_start: 0.8751 (mm) cc_final: 0.8545 (mt) REVERT: C 433 MET cc_start: 0.7686 (tpt) cc_final: 0.7385 (tpp) REVERT: C 520 GLN cc_start: 0.6721 (pm20) cc_final: 0.6506 (pm20) REVERT: C 528 MET cc_start: 0.5924 (OUTLIER) cc_final: 0.5605 (mmm) REVERT: C 708 GLU cc_start: 0.8679 (tt0) cc_final: 0.8435 (mt-10) REVERT: D 173 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7678 (tm-30) REVERT: D 189 ASP cc_start: 0.7615 (t0) cc_final: 0.7108 (t0) REVERT: D 221 LYS cc_start: 0.8346 (ttpt) cc_final: 0.8002 (ttmm) REVERT: D 371 ARG cc_start: 0.7988 (mmt90) cc_final: 0.7164 (mmp-170) REVERT: D 388 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7935 (ttt180) REVERT: D 406 ILE cc_start: 0.8748 (mm) cc_final: 0.8539 (mt) REVERT: D 520 GLN cc_start: 0.6829 (pm20) cc_final: 0.6523 (pm20) outliers start: 70 outliers final: 44 residues processed: 367 average time/residue: 0.4825 time to fit residues: 205.1767 Evaluate side-chains 376 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 324 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 727 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain D residue 727 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 198 optimal weight: 0.4980 chunk 129 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 137 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 220 optimal weight: 0.8980 chunk 151 optimal weight: 0.3980 chunk 188 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.151299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.119975 restraints weight = 23537.929| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.74 r_work: 0.3150 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20192 Z= 0.112 Angle : 0.534 10.364 27396 Z= 0.265 Chirality : 0.037 0.241 3132 Planarity : 0.004 0.034 3352 Dihedral : 4.592 40.975 2748 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.54 % Allowed : 21.41 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.17), residues: 2412 helix: 2.04 (0.13), residues: 1472 sheet: 0.42 (0.56), residues: 88 loop : -0.98 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 560 TYR 0.009 0.001 TYR B 271 PHE 0.015 0.001 PHE B 161 TRP 0.014 0.001 TRP A 223 HIS 0.005 0.001 HIS A 521 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (20192) covalent geometry : angle 0.53425 / 0.26 (27396) hydrogen bonds : bond 0.03408 / 2.40 ( 1056) hydrogen bonds : angle 3.29235 / 2.26 ( 3012) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 335 time to evaluate : 0.819 Fit side-chains REVERT: A 160 GLU cc_start: 0.8016 (tp30) cc_final: 0.7204 (pt0) REVERT: A 173 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7692 (tm-30) REVERT: A 189 ASP cc_start: 0.7666 (t0) cc_final: 0.7138 (t0) REVERT: A 191 HIS cc_start: 0.8269 (m170) cc_final: 0.7859 (m-70) REVERT: A 371 ARG cc_start: 0.7968 (mmt90) cc_final: 0.7137 (mmp-170) REVERT: A 388 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7971 (ttt180) REVERT: A 406 ILE cc_start: 0.8776 (mm) cc_final: 0.8549 (mt) REVERT: A 433 MET cc_start: 0.7702 (tpt) cc_final: 0.7406 (tpp) REVERT: A 528 MET cc_start: 0.5835 (OUTLIER) cc_final: 0.5141 (mpp) REVERT: A 538 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7895 (mp) REVERT: B 173 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7718 (tm-30) REVERT: B 189 ASP cc_start: 0.7642 (t0) cc_final: 0.7115 (t0) REVERT: B 191 HIS cc_start: 0.8271 (m170) cc_final: 0.7905 (m-70) REVERT: B 371 ARG cc_start: 0.7957 (mmt90) cc_final: 0.7138 (mmp-170) REVERT: B 388 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7907 (ttt180) REVERT: B 406 ILE cc_start: 0.8788 (mm) cc_final: 0.8563 (mt) REVERT: B 433 MET cc_start: 0.7724 (tpt) cc_final: 0.7422 (tpp) REVERT: B 520 GLN cc_start: 0.6746 (pm20) cc_final: 0.6542 (pm20) REVERT: B 528 MET cc_start: 0.5816 (mpt) cc_final: 0.5080 (mpp) REVERT: C 189 ASP cc_start: 0.7636 (t0) cc_final: 0.7126 (t0) REVERT: C 191 HIS cc_start: 0.8282 (m170) cc_final: 0.7882 (m-70) REVERT: C 371 ARG cc_start: 0.7937 (mmt90) cc_final: 0.7121 (mmp-170) REVERT: C 388 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7945 (ttt180) REVERT: C 406 ILE cc_start: 0.8803 (mm) cc_final: 0.8582 (mt) REVERT: C 528 MET cc_start: 0.5814 (OUTLIER) cc_final: 0.5547 (mmm) REVERT: C 708 GLU cc_start: 0.8610 (tt0) cc_final: 0.8357 (mt-10) REVERT: D 173 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7697 (tm-30) REVERT: D 189 ASP cc_start: 0.7640 (t0) cc_final: 0.7098 (t0) REVERT: D 191 HIS cc_start: 0.8284 (m170) cc_final: 0.7864 (m-70) REVERT: D 371 ARG cc_start: 0.7964 (mmt90) cc_final: 0.7140 (mmp-170) REVERT: D 388 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7914 (ttt180) REVERT: D 406 ILE cc_start: 0.8777 (mm) cc_final: 0.8572 (mt) REVERT: D 520 GLN cc_start: 0.6730 (pm20) cc_final: 0.6501 (pm20) REVERT: D 645 MET cc_start: 0.7541 (tmm) cc_final: 0.7210 (mtp) outliers start: 53 outliers final: 37 residues processed: 356 average time/residue: 0.4564 time to fit residues: 190.3409 Evaluate side-chains 377 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 333 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 204 optimal weight: 0.0970 chunk 96 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 233 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 117 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.150543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.118187 restraints weight = 23525.329| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.88 r_work: 0.3140 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20192 Z= 0.116 Angle : 0.536 10.417 27396 Z= 0.266 Chirality : 0.038 0.239 3132 Planarity : 0.004 0.034 3352 Dihedral : 4.557 40.389 2748 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.83 % Allowed : 21.41 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.17), residues: 2412 helix: 2.08 (0.13), residues: 1472 sheet: 0.41 (0.56), residues: 88 loop : -0.98 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 560 TYR 0.009 0.001 TYR D 403 PHE 0.014 0.001 PHE D 161 TRP 0.017 0.001 TRP D 223 HIS 0.005 0.001 HIS A 521 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (20192) covalent geometry : angle 0.53612 / 0.27 (27396) hydrogen bonds : bond 0.03399 / 2.39 ( 1056) hydrogen bonds : angle 3.28417 / 2.25 ( 3012) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6858.56 seconds wall clock time: 117 minutes 41.24 seconds (7061.24 seconds total)