Starting phenix.real_space_refine on Thu Jul 2 14:49:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vx8_32171/07_2026/7vx8_32171.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vx8_32171/07_2026/7vx8_32171.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vx8_32171/07_2026/7vx8_32171.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vx8_32171/07_2026/7vx8_32171.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vx8_32171/07_2026/7vx8_32171.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vx8_32171/07_2026/7vx8_32171.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7vx8_32171/07_2026/7vx8_32171.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vx8_32171/07_2026/7vx8_32171.cif" } resolution = 2.8 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= 0.005 sd= 0.094 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 42 5.16 5 C 5778 2.51 5 N 1590 2.21 5 O 1600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.01s 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: 9018 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4477 Classifications: {'peptide': 560} Link IDs: {'PTRANS': 19, 'TRANS': 540} Chain breaks: 2 Chain: "A" Number of atoms: 4477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4477 Classifications: {'peptide': 560} Link IDs: {'PTRANS': 19, 'TRANS': 540} Chain breaks: 2 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.71, per 1000 atoms: 0.19 Number of scatterers: 9018 At special positions: 0 Unit cell: (75.97, 84.53, 129.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 6 15.00 Mg 2 11.99 O 1600 8.00 N 1590 7.00 C 5778 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: 0.60 Conformation dependent library (CDL) restraints added in 220.3 milliseconds 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2088 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 6 sheets defined 66.4% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'B' and resid 68 through 83 removed outlier: 3.601A pdb=" N LEU B 81 " --> pdb=" O TRP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 112 removed outlier: 3.634A pdb=" N THR B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 120 Processing helix chain 'B' and resid 126 through 138 removed outlier: 3.887A pdb=" N PHE B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 135 " --> pdb=" O GLY B 131 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN B 136 " --> pdb=" O TRP B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 175 removed outlier: 5.125A pdb=" N VAL B 147 " --> pdb=" O PRO B 143 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASN B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE B 151 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG B 152 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY B 156 " --> pdb=" O ARG B 152 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 186 removed outlier: 4.034A pdb=" N SER B 184 " --> pdb=" O TYR B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 215 removed outlier: 4.962A pdb=" N VAL B 201 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 237 removed outlier: 3.648A pdb=" N LEU B 220 " --> pdb=" O THR B 216 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP B 221 " --> pdb=" O LYS B 217 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL B 222 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER B 226 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 230 " --> pdb=" O SER B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 254 removed outlier: 3.517A pdb=" N GLY B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 260 removed outlier: 3.647A pdb=" N ARG B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA B 260 " --> pdb=" O ASN B 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 255 through 260' Processing helix chain 'B' and resid 267 through 289 removed outlier: 3.507A pdb=" N GLU B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 297 Processing helix chain 'B' and resid 298 through 332 removed outlier: 3.597A pdb=" N LEU B 313 " --> pdb=" O SER B 309 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 325 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TRP B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 344 removed outlier: 3.872A pdb=" N LEU B 344 " --> pdb=" O SER B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 3.872A pdb=" N ALA B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 404 removed outlier: 3.670A pdb=" N ALA B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 430 removed outlier: 3.557A pdb=" N GLY B 414 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA B 417 " --> pdb=" O ALA B 413 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG B 418 " --> pdb=" O GLY B 414 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN B 430 " --> pdb=" O PHE B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 521 Processing helix chain 'B' and resid 535 through 537 No H-bonds generated for 'chain 'B' and resid 535 through 537' Processing helix chain 'B' and resid 552 through 558 removed outlier: 3.509A pdb=" N ILE B 558 " --> pdb=" O ARG B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 569 Processing helix chain 'B' and resid 574 through 583 Processing helix chain 'B' and resid 585 through 590 removed outlier: 4.116A pdb=" N LEU B 589 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN B 590 " --> pdb=" O HIS B 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 585 through 590' Processing helix chain 'B' and resid 593 through 597 removed outlier: 3.800A pdb=" N ALA B 597 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 605 Processing helix chain 'B' and resid 610 through 622 removed outlier: 3.671A pdb=" N GLY B 614 " --> pdb=" O LYS B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 650 removed outlier: 3.506A pdb=" N GLY B 641 " --> pdb=" O ILE B 637 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 646 " --> pdb=" O LYS B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 667 Processing helix chain 'A' and resid 68 through 83 removed outlier: 3.601A pdb=" N LEU A 81 " --> pdb=" O TRP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 112 removed outlier: 3.532A pdb=" N LEU A 94 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.887A pdb=" N PHE A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 135 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN A 136 " --> pdb=" O TRP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 175 removed outlier: 5.124A pdb=" N VAL A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASN A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE A 151 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 156 " --> pdb=" O ARG A 152 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 186 removed outlier: 4.033A pdb=" N SER A 184 " --> pdb=" O TYR A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 215 removed outlier: 4.962A pdb=" N VAL A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 237 removed outlier: 3.648A pdb=" N LEU A 220 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 254 removed outlier: 3.517A pdb=" N GLY A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 289 Processing helix chain 'A' and resid 289 through 297 Processing helix chain 'A' and resid 298 through 332 removed outlier: 3.598A pdb=" N LEU A 313 " --> pdb=" O SER A 309 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TRP A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 344 removed outlier: 3.871A pdb=" N LEU A 344 " --> pdb=" O SER A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.871A pdb=" N ALA A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 404 removed outlier: 3.670A pdb=" N ALA A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 430 removed outlier: 3.558A pdb=" N GLY A 414 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG A 418 " --> pdb=" O GLY A 414 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN A 430 " --> pdb=" O PHE A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 521 Processing helix chain 'A' and resid 535 through 537 No H-bonds generated for 'chain 'A' and resid 535 through 537' Processing helix chain 'A' and resid 552 through 558 removed outlier: 3.509A pdb=" N ILE A 558 " --> pdb=" O ARG A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 569 Processing helix chain 'A' and resid 574 through 583 Processing helix chain 'A' and resid 585 through 590 removed outlier: 4.117A pdb=" N LEU A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN A 590 " --> pdb=" O HIS A 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 585 through 590' Processing helix chain 'A' and resid 593 through 597 removed outlier: 3.800A pdb=" N ALA A 597 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'A' and resid 610 through 622 removed outlier: 3.671A pdb=" N GLY A 614 " --> pdb=" O LYS A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 650 removed outlier: 3.507A pdb=" N GLY A 641 " --> pdb=" O ILE A 637 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 646 " --> pdb=" O LYS A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 667 Processing sheet with id=AA1, first strand: chain 'B' and resid 466 through 469 Processing sheet with id=AA2, first strand: chain 'B' and resid 481 through 482 removed outlier: 6.877A pdb=" N ILE B 481 " --> pdb=" O VAL B 489 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 539 through 542 removed outlier: 6.546A pdb=" N PHE B 540 " --> pdb=" O LEU B 627 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ASP B 629 " --> pdb=" O PHE B 540 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE B 542 " --> pdb=" O ASP B 629 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ALA B 626 " --> pdb=" O LEU B 655 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ILE B 657 " --> pdb=" O ALA B 626 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU B 628 " --> pdb=" O ILE B 657 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU B 504 " --> pdb=" O LEU B 671 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N PHE B 673 " --> pdb=" O LEU B 504 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR B 506 " --> pdb=" O PHE B 673 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 466 through 469 Processing sheet with id=AA5, first strand: chain 'A' and resid 481 through 482 removed outlier: 6.877A pdb=" N ILE A 481 " --> pdb=" O VAL A 489 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 539 through 542 removed outlier: 6.547A pdb=" N PHE A 540 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ASP A 629 " --> pdb=" O PHE A 540 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE A 542 " --> pdb=" O ASP A 629 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ALA A 626 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ILE A 657 " --> pdb=" O ALA A 626 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU A 628 " --> pdb=" O ILE A 657 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU A 504 " --> pdb=" O LEU A 671 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N PHE A 673 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR A 506 " --> pdb=" O PHE A 673 " (cutoff:3.500A) 478 hydrogen bonds defined for protein. 1392 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: 0.99 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.24: 1162 1.24 - 1.38: 2549 1.38 - 1.52: 4208 1.52 - 1.67: 1231 1.67 - 1.81: 70 Bond restraints: 9220 Sorted by residual: bond pdb=" C SER B 515 " pdb=" O SER B 515 " ideal model delta sigma weight residual 1.237 1.101 0.136 1.17e-02 7.31e+03 1.35e+02 bond pdb=" C SER A 515 " pdb=" O SER A 515 " ideal model delta sigma weight residual 1.237 1.100 0.136 1.19e-02 7.06e+03 1.31e+02 bond pdb=" C SER A 514 " pdb=" O SER A 514 " ideal model delta sigma weight residual 1.236 1.096 0.141 1.32e-02 5.74e+03 1.14e+02 bond pdb=" O1G ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 1.491 1.289 0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C SER B 514 " pdb=" O SER B 514 " ideal model delta sigma weight residual 1.236 1.104 0.133 1.32e-02 5.74e+03 1.01e+02 ... (remaining 9215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.30: 12329 4.30 - 8.60: 140 8.60 - 12.90: 13 12.90 - 17.20: 10 17.20 - 21.50: 4 Bond angle restraints: 12496 Sorted by residual: angle pdb=" O2G ATP B 801 " pdb=" PG ATP B 801 " pdb=" O3B ATP B 801 " ideal model delta sigma weight residual 104.48 121.92 -17.44 1.14e+00 7.76e-01 2.36e+02 angle pdb=" PA ATP A 801 " pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 136.83 150.61 -13.78 1.00e+00 1.00e+00 1.90e+02 angle pdb=" PA ATP B 801 " pdb=" O3A ATP B 801 " pdb=" PB ATP B 801 " ideal model delta sigma weight residual 136.83 150.30 -13.47 1.00e+00 1.00e+00 1.81e+02 angle pdb=" O2G ATP A 801 " pdb=" PG ATP A 801 " pdb=" O3B ATP A 801 " ideal model delta sigma weight residual 104.48 118.99 -14.51 1.14e+00 7.76e-01 1.63e+02 angle pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " ideal model delta sigma weight residual 101.57 120.50 -18.93 1.54e+00 4.24e-01 1.52e+02 ... (remaining 12491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.53: 4873 16.53 - 33.06: 417 33.06 - 49.59: 110 49.59 - 66.11: 36 66.11 - 82.64: 16 Dihedral angle restraints: 5452 sinusoidal: 2202 harmonic: 3250 Sorted by residual: dihedral pdb=" CA ILE A 558 " pdb=" C ILE A 558 " pdb=" N TYR A 559 " pdb=" CA TYR A 559 " ideal model delta harmonic sigma weight residual -180.00 -152.11 -27.89 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA ILE B 558 " pdb=" C ILE B 558 " pdb=" N TYR B 559 " pdb=" CA TYR B 559 " ideal model delta harmonic sigma weight residual -180.00 -152.15 -27.85 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" C ARG A 259 " pdb=" N ARG A 259 " pdb=" CA ARG A 259 " pdb=" CB ARG A 259 " ideal model delta harmonic sigma weight residual -122.60 -108.86 -13.74 0 2.50e+00 1.60e-01 3.02e+01 ... (remaining 5449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1208 0.081 - 0.162: 148 0.162 - 0.243: 20 0.243 - 0.324: 5 0.324 - 0.405: 3 Chirality restraints: 1384 Sorted by residual: chirality pdb=" CA SER A 606 " pdb=" N SER A 606 " pdb=" C SER A 606 " pdb=" CB SER A 606 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CA GLU B 90 " pdb=" N GLU B 90 " pdb=" C GLU B 90 " pdb=" CB GLU B 90 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CA ARG A 259 " pdb=" N ARG A 259 " pdb=" C ARG A 259 " pdb=" CB ARG A 259 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 1381 not shown) Planarity restraints: 1572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 463 " 0.022 2.00e-02 2.50e+03 4.47e-02 2.00e+01 pdb=" C ILE A 463 " -0.077 2.00e-02 2.50e+03 pdb=" O ILE A 463 " 0.029 2.00e-02 2.50e+03 pdb=" N ARG A 464 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 463 " -0.021 2.00e-02 2.50e+03 4.28e-02 1.83e+01 pdb=" C ILE B 463 " 0.074 2.00e-02 2.50e+03 pdb=" O ILE B 463 " -0.028 2.00e-02 2.50e+03 pdb=" N ARG B 464 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ATP A 801 " 0.014 2.00e-02 2.50e+03 2.01e-02 1.11e+01 pdb=" C2 ATP A 801 " -0.023 2.00e-02 2.50e+03 pdb=" C4 ATP A 801 " -0.001 2.00e-02 2.50e+03 pdb=" C5 ATP A 801 " -0.025 2.00e-02 2.50e+03 pdb=" C6 ATP A 801 " -0.009 2.00e-02 2.50e+03 pdb=" C8 ATP A 801 " -0.004 2.00e-02 2.50e+03 pdb=" N1 ATP A 801 " -0.006 2.00e-02 2.50e+03 pdb=" N3 ATP A 801 " 0.020 2.00e-02 2.50e+03 pdb=" N6 ATP A 801 " 0.043 2.00e-02 2.50e+03 pdb=" N7 ATP A 801 " -0.022 2.00e-02 2.50e+03 pdb=" N9 ATP A 801 " 0.013 2.00e-02 2.50e+03 ... (remaining 1569 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 56 2.58 - 3.16: 7173 3.16 - 3.74: 13627 3.74 - 4.32: 20462 4.32 - 4.90: 33842 Nonbonded interactions: 75160 Sorted by model distance: nonbonded pdb=" OE1 GLN B 544 " pdb="MG MG B 802 " model vdw 1.995 2.170 nonbonded pdb=" OE1 GLN A 544 " pdb="MG MG A 802 " model vdw 2.026 2.170 nonbonded pdb=" OG SER B 514 " pdb="MG MG B 802 " model vdw 2.183 2.170 nonbonded pdb=" O MET B 548 " pdb=" NH2 ARG A 285 " model vdw 2.230 3.120 nonbonded pdb=" O VAL A 222 " pdb=" OG SER A 226 " model vdw 2.241 3.040 ... (remaining 75155 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.520 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 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 : 0.013 0.263 9220 Z= 0.680 Angle : 1.228 21.495 12496 Z= 0.745 Chirality : 0.061 0.405 1384 Planarity : 0.005 0.045 1572 Dihedral : 14.953 82.643 3364 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.06 % Allowed : 0.96 % Favored : 97.98 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 0.00 % 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: -3.11 (0.22), residues: 1108 helix: -1.96 (0.17), residues: 728 sheet: -2.07 (0.49), residues: 76 loop : -1.69 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 308 TYR 0.016 0.003 TYR A 310 PHE 0.027 0.003 PHE A 261 TRP 0.009 0.001 TRP B 601 HIS 0.004 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.01268 / 0.68 ( 9220) covalent geometry : angle 1.22833 / 0.75 (12496) hydrogen bonds : bond 0.22551 / 15.38 ( 478) hydrogen bonds : angle 8.20587 / 5.85 ( 1392) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.323 Fit side-chains REVERT: B 64 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7243 (mmtt) REVERT: B 227 TYR cc_start: 0.8190 (t80) cc_final: 0.7988 (t80) REVERT: B 400 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7271 (tp30) REVERT: B 624 LYS cc_start: 0.7813 (tptp) cc_final: 0.7357 (mmtt) REVERT: A 259 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7085 (mpt180) REVERT: A 400 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7352 (tp30) REVERT: A 464 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.6691 (mtp180) REVERT: A 565 ASP cc_start: 0.8564 (m-30) cc_final: 0.8346 (m-30) REVERT: A 624 LYS cc_start: 0.7741 (tptp) cc_final: 0.7338 (mmtt) outliers start: 10 outliers final: 3 residues processed: 146 average time/residue: 0.7223 time to fit residues: 110.3371 Evaluate side-chains 119 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 259 ARG Chi-restraints excluded: chain A residue 464 ARG Chi-restraints excluded: chain A residue 603 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.0980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.153389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.122212 restraints weight = 9591.157| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.44 r_work: 0.3351 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9220 Z= 0.141 Angle : 0.635 8.704 12496 Z= 0.325 Chirality : 0.042 0.156 1384 Planarity : 0.004 0.033 1572 Dihedral : 7.326 88.120 1276 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.97 % Allowed : 9.02 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.01 (0.23), residues: 1108 helix: -1.06 (0.18), residues: 748 sheet: -1.89 (0.54), residues: 72 loop : -1.39 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 259 TYR 0.012 0.002 TYR A 559 PHE 0.013 0.001 PHE B 130 TRP 0.011 0.001 TRP A 326 HIS 0.005 0.001 HIS B 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 9220) covalent geometry : angle 0.63528 / 0.33 (12496) hydrogen bonds : bond 0.04590 / 3.05 ( 478) hydrogen bonds : angle 4.99342 / 3.48 ( 1392) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.338 Fit side-chains REVERT: B 72 LEU cc_start: 0.8204 (tp) cc_final: 0.7984 (tp) REVERT: B 101 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8057 (tt) REVERT: B 227 TYR cc_start: 0.8204 (t80) cc_final: 0.7885 (t80) REVERT: B 400 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7083 (tp30) REVERT: B 427 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7281 (mp0) REVERT: B 564 GLU cc_start: 0.7162 (mp0) cc_final: 0.6950 (mp0) REVERT: B 624 LYS cc_start: 0.7523 (tptp) cc_final: 0.7081 (mmmt) REVERT: A 72 LEU cc_start: 0.7995 (tp) cc_final: 0.7746 (tp) REVERT: A 101 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8082 (tt) REVERT: A 259 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.6471 (mpt180) REVERT: A 400 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7127 (tp30) REVERT: A 427 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: A 565 ASP cc_start: 0.7795 (m-30) cc_final: 0.7532 (m-30) REVERT: A 624 LYS cc_start: 0.7542 (tptp) cc_final: 0.7073 (mmmt) outliers start: 28 outliers final: 4 residues processed: 137 average time/residue: 0.7008 time to fit residues: 100.9212 Evaluate side-chains 122 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 537 GLN Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 259 ARG Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 537 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 105 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 39 optimal weight: 0.0020 chunk 63 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 214 ASN A 214 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.159499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.128998 restraints weight = 9544.518| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.40 r_work: 0.3465 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9220 Z= 0.115 Angle : 0.549 8.133 12496 Z= 0.284 Chirality : 0.040 0.145 1384 Planarity : 0.003 0.029 1572 Dihedral : 6.033 77.798 1260 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.02 % Allowed : 13.69 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.19 (0.24), residues: 1108 helix: -0.32 (0.19), residues: 740 sheet: -1.60 (0.58), residues: 70 loop : -1.42 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 163 TYR 0.009 0.001 TYR A 559 PHE 0.014 0.001 PHE B 130 TRP 0.009 0.001 TRP A 326 HIS 0.006 0.001 HIS B 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 9220) covalent geometry : angle 0.54871 / 0.28 (12496) hydrogen bonds : bond 0.03912 / 2.60 ( 478) hydrogen bonds : angle 4.46224 / 3.10 ( 1392) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.222 Fit side-chains REVERT: B 72 LEU cc_start: 0.8364 (tp) cc_final: 0.8136 (tp) REVERT: B 227 TYR cc_start: 0.8257 (t80) cc_final: 0.8044 (t80) REVERT: B 400 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7243 (tp30) REVERT: B 427 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7489 (mp0) REVERT: B 563 VAL cc_start: 0.8386 (p) cc_final: 0.8097 (m) REVERT: B 582 VAL cc_start: 0.8350 (p) cc_final: 0.7970 (m) REVERT: B 615 MET cc_start: 0.9105 (mmm) cc_final: 0.8877 (mmp) REVERT: B 624 LYS cc_start: 0.7810 (tptp) cc_final: 0.7449 (mmmt) REVERT: A 400 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7294 (tp30) REVERT: A 427 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7453 (mp0) REVERT: A 565 ASP cc_start: 0.8172 (m-30) cc_final: 0.7728 (m-30) REVERT: A 582 VAL cc_start: 0.8348 (p) cc_final: 0.7977 (m) REVERT: A 615 MET cc_start: 0.9126 (mmm) cc_final: 0.8911 (mmp) REVERT: A 624 LYS cc_start: 0.7797 (tptp) cc_final: 0.7408 (mmmt) outliers start: 19 outliers final: 7 residues processed: 130 average time/residue: 0.6432 time to fit residues: 87.9293 Evaluate side-chains 123 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 422 MET Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 537 GLN Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 581 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 85 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 22 optimal weight: 0.0570 chunk 78 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 23 optimal weight: 0.0070 chunk 25 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 214 ASN A 214 ASN A 586 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.161350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.130813 restraints weight = 9645.089| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.42 r_work: 0.3490 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9220 Z= 0.101 Angle : 0.515 8.946 12496 Z= 0.267 Chirality : 0.039 0.142 1384 Planarity : 0.003 0.029 1572 Dihedral : 5.484 64.584 1256 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.70 % Allowed : 15.61 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.68 (0.25), residues: 1108 helix: 0.09 (0.19), residues: 740 sheet: -1.37 (0.59), residues: 70 loop : -1.29 (0.33), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 259 TYR 0.008 0.001 TYR A 310 PHE 0.010 0.001 PHE B 130 TRP 0.010 0.001 TRP B 326 HIS 0.005 0.001 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 ( 9220) covalent geometry : angle 0.51517 / 0.27 (12496) hydrogen bonds : bond 0.03514 / 2.34 ( 478) hydrogen bonds : angle 4.20236 / 2.90 ( 1392) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.258 Fit side-chains REVERT: B 72 LEU cc_start: 0.8387 (tp) cc_final: 0.8155 (tp) REVERT: B 427 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7542 (mp0) REVERT: B 429 VAL cc_start: 0.8687 (OUTLIER) cc_final: 0.8346 (m) REVERT: B 499 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7414 (mm-30) REVERT: B 615 MET cc_start: 0.9130 (mmm) cc_final: 0.8895 (mmp) REVERT: B 624 LYS cc_start: 0.7878 (tptp) cc_final: 0.7483 (mmmt) REVERT: A 292 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: A 427 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7511 (mp0) REVERT: A 429 VAL cc_start: 0.8712 (OUTLIER) cc_final: 0.8443 (m) REVERT: A 565 ASP cc_start: 0.8107 (m-30) cc_final: 0.7537 (m-30) REVERT: A 615 MET cc_start: 0.9135 (mmm) cc_final: 0.8913 (mmp) REVERT: A 624 LYS cc_start: 0.7812 (tptp) cc_final: 0.7453 (mmmt) outliers start: 16 outliers final: 6 residues processed: 125 average time/residue: 0.6585 time to fit residues: 86.4176 Evaluate side-chains 121 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 422 MET Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 537 GLN Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 581 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 8 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 2 optimal weight: 0.0980 chunk 12 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 214 ASN A 214 ASN A 586 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.155747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.124491 restraints weight = 9629.495| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.43 r_work: 0.3367 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 9220 Z= 0.194 Angle : 0.607 9.182 12496 Z= 0.307 Chirality : 0.044 0.148 1384 Planarity : 0.004 0.033 1572 Dihedral : 5.486 67.670 1256 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.08 % Allowed : 16.56 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.72 (0.24), residues: 1108 helix: -0.02 (0.19), residues: 748 sheet: -1.37 (0.58), residues: 70 loop : -1.11 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 259 TYR 0.016 0.002 TYR B 327 PHE 0.012 0.002 PHE A 130 TRP 0.006 0.001 TRP A 601 HIS 0.005 0.001 HIS B 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.19 ( 9220) covalent geometry : angle 0.60690 / 0.31 (12496) hydrogen bonds : bond 0.04364 / 2.87 ( 478) hydrogen bonds : angle 4.33492 / 3.01 ( 1392) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 332 GLN cc_start: 0.8240 (mt0) cc_final: 0.8008 (mt0) REVERT: B 624 LYS cc_start: 0.7937 (tptp) cc_final: 0.7497 (mmmt) REVERT: A 332 GLN cc_start: 0.8163 (mt0) cc_final: 0.7921 (mt0) REVERT: A 565 ASP cc_start: 0.8351 (m-30) cc_final: 0.7882 (m-30) REVERT: A 624 LYS cc_start: 0.7899 (tptp) cc_final: 0.7469 (mmmt) outliers start: 29 outliers final: 13 residues processed: 128 average time/residue: 0.6362 time to fit residues: 85.4752 Evaluate side-chains 126 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 537 GLN Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 581 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 60 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 75 optimal weight: 0.0370 chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 overall best weight: 1.4062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 214 ASN A 214 ASN A 586 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.156715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.125582 restraints weight = 9644.402| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.43 r_work: 0.3418 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 9220 Z= 0.154 Angle : 0.575 9.599 12496 Z= 0.291 Chirality : 0.042 0.146 1384 Planarity : 0.004 0.034 1572 Dihedral : 5.400 66.954 1256 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.44 % Allowed : 17.83 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.53 (0.24), residues: 1108 helix: 0.10 (0.19), residues: 750 sheet: -1.24 (0.59), residues: 70 loop : -0.97 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 259 TYR 0.012 0.002 TYR B 310 PHE 0.010 0.001 PHE A 130 TRP 0.009 0.001 TRP A 326 HIS 0.005 0.001 HIS B 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 ( 9220) covalent geometry : angle 0.57501 / 0.29 (12496) hydrogen bonds : bond 0.04043 / 2.66 ( 478) hydrogen bonds : angle 4.24291 / 2.95 ( 1392) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 332 GLN cc_start: 0.8184 (mt0) cc_final: 0.7951 (mt0) REVERT: B 499 GLU cc_start: 0.7777 (tp30) cc_final: 0.7493 (mm-30) REVERT: B 624 LYS cc_start: 0.7913 (tptp) cc_final: 0.7516 (mmmt) REVERT: A 332 GLN cc_start: 0.8129 (mt0) cc_final: 0.7893 (mt0) REVERT: A 499 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7473 (mm-30) REVERT: A 565 ASP cc_start: 0.8312 (m-30) cc_final: 0.7672 (m-30) REVERT: A 624 LYS cc_start: 0.7892 (tptp) cc_final: 0.7502 (mmmt) outliers start: 23 outliers final: 13 residues processed: 124 average time/residue: 0.6417 time to fit residues: 83.5248 Evaluate side-chains 131 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 422 MET Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 537 GLN Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 581 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 35 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 19 optimal weight: 0.0570 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 214 ASN A 214 ASN A 586 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.160091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.129714 restraints weight = 9628.034| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.53 r_work: 0.3460 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9220 Z= 0.107 Angle : 0.523 8.546 12496 Z= 0.270 Chirality : 0.040 0.145 1384 Planarity : 0.003 0.040 1572 Dihedral : 5.188 65.102 1256 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.02 % Allowed : 18.58 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.13 (0.25), residues: 1108 helix: 0.43 (0.19), residues: 750 sheet: -0.84 (0.62), residues: 66 loop : -0.99 (0.32), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 259 TYR 0.010 0.001 TYR A 227 PHE 0.008 0.001 PHE B 252 TRP 0.013 0.001 TRP A 326 HIS 0.005 0.001 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 9220) covalent geometry : angle 0.52344 / 0.27 (12496) hydrogen bonds : bond 0.03512 / 2.33 ( 478) hydrogen bonds : angle 4.04494 / 2.80 ( 1392) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: B 332 GLN cc_start: 0.8126 (mt0) cc_final: 0.7894 (mt0) REVERT: B 427 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7502 (mp0) REVERT: B 429 VAL cc_start: 0.8643 (OUTLIER) cc_final: 0.8280 (m) REVERT: B 499 GLU cc_start: 0.7702 (tp30) cc_final: 0.7442 (mm-30) REVERT: B 615 MET cc_start: 0.9064 (mmm) cc_final: 0.8841 (mmp) REVERT: B 624 LYS cc_start: 0.7875 (tptp) cc_final: 0.7497 (mmmt) REVERT: A 332 GLN cc_start: 0.8046 (mt0) cc_final: 0.7811 (mt0) REVERT: A 429 VAL cc_start: 0.8676 (OUTLIER) cc_final: 0.8339 (m) REVERT: A 499 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7409 (mm-30) REVERT: A 564 GLU cc_start: 0.7816 (mp0) cc_final: 0.7571 (mp0) REVERT: A 565 ASP cc_start: 0.8259 (m-30) cc_final: 0.7672 (m-30) REVERT: A 603 ASP cc_start: 0.8295 (p0) cc_final: 0.8079 (p0) REVERT: A 615 MET cc_start: 0.9161 (mmm) cc_final: 0.8920 (mmp) REVERT: A 624 LYS cc_start: 0.7844 (tptp) cc_final: 0.7468 (mmmt) outliers start: 19 outliers final: 10 residues processed: 123 average time/residue: 0.6199 time to fit residues: 80.0072 Evaluate side-chains 123 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 422 MET Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 537 GLN Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 581 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 chunk 100 optimal weight: 0.4980 chunk 75 optimal weight: 0.0370 chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 214 ASN A 214 ASN A 586 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.155751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.124904 restraints weight = 9515.814| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.45 r_work: 0.3386 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9220 Z= 0.103 Angle : 0.509 9.867 12496 Z= 0.260 Chirality : 0.040 0.151 1384 Planarity : 0.003 0.041 1572 Dihedral : 5.056 63.749 1256 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.23 % Allowed : 18.79 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.16 (0.25), residues: 1108 helix: 0.69 (0.19), residues: 748 sheet: -0.73 (0.62), residues: 66 loop : -0.98 (0.32), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 259 TYR 0.011 0.001 TYR A 227 PHE 0.007 0.001 PHE A 130 TRP 0.012 0.001 TRP B 326 HIS 0.005 0.001 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 9220) covalent geometry : angle 0.50872 / 0.26 (12496) hydrogen bonds : bond 0.03438 / 2.28 ( 478) hydrogen bonds : angle 3.93157 / 2.72 ( 1392) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 332 GLN cc_start: 0.7974 (mt0) cc_final: 0.7722 (mt0) REVERT: B 429 VAL cc_start: 0.8494 (OUTLIER) cc_final: 0.8134 (m) REVERT: B 464 ARG cc_start: 0.8003 (mtm180) cc_final: 0.7799 (mtt180) REVERT: B 624 LYS cc_start: 0.7622 (tptp) cc_final: 0.7230 (mmmt) REVERT: A 332 GLN cc_start: 0.7920 (mt0) cc_final: 0.7657 (mt0) REVERT: A 429 VAL cc_start: 0.8520 (OUTLIER) cc_final: 0.8171 (m) REVERT: A 564 GLU cc_start: 0.7537 (mp0) cc_final: 0.7305 (mp0) REVERT: A 565 ASP cc_start: 0.7976 (m-30) cc_final: 0.7352 (m-30) REVERT: A 603 ASP cc_start: 0.8183 (p0) cc_final: 0.7980 (p0) REVERT: A 615 MET cc_start: 0.8969 (mmm) cc_final: 0.8743 (mmp) REVERT: A 624 LYS cc_start: 0.7597 (tptp) cc_final: 0.7202 (mmmt) outliers start: 21 outliers final: 13 residues processed: 124 average time/residue: 0.6134 time to fit residues: 79.8429 Evaluate side-chains 127 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 582 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 7 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 61 optimal weight: 0.0470 chunk 96 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 chunk 105 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 214 ASN A 214 ASN A 586 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.159137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.128032 restraints weight = 9534.162| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.63 r_work: 0.3437 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9220 Z= 0.136 Angle : 0.547 9.168 12496 Z= 0.280 Chirality : 0.041 0.148 1384 Planarity : 0.004 0.040 1572 Dihedral : 5.142 64.868 1256 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.12 % Allowed : 18.90 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.09 (0.25), residues: 1108 helix: 0.67 (0.19), residues: 742 sheet: -0.97 (0.59), residues: 70 loop : -1.02 (0.32), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 259 TYR 0.011 0.001 TYR B 310 PHE 0.008 0.001 PHE A 130 TRP 0.007 0.001 TRP B 326 HIS 0.005 0.001 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 9220) covalent geometry : angle 0.54722 / 0.28 (12496) hydrogen bonds : bond 0.03704 / 2.45 ( 478) hydrogen bonds : angle 3.99266 / 2.77 ( 1392) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 332 GLN cc_start: 0.8126 (mt0) cc_final: 0.7881 (mt0) REVERT: B 429 VAL cc_start: 0.8618 (OUTLIER) cc_final: 0.8261 (m) REVERT: B 624 LYS cc_start: 0.7820 (tptp) cc_final: 0.7446 (mmmt) REVERT: A 332 GLN cc_start: 0.8065 (mt0) cc_final: 0.7831 (mt0) REVERT: A 429 VAL cc_start: 0.8660 (OUTLIER) cc_final: 0.8300 (m) REVERT: A 564 GLU cc_start: 0.7761 (mp0) cc_final: 0.7529 (mp0) REVERT: A 565 ASP cc_start: 0.8169 (m-30) cc_final: 0.7507 (m-30) REVERT: A 603 ASP cc_start: 0.8293 (p0) cc_final: 0.8068 (p0) REVERT: A 624 LYS cc_start: 0.7795 (tptp) cc_final: 0.7415 (mmmt) outliers start: 20 outliers final: 14 residues processed: 130 average time/residue: 0.5696 time to fit residues: 77.9383 Evaluate side-chains 132 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 582 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 90 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 84 optimal weight: 0.0270 chunk 49 optimal weight: 0.0020 chunk 78 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.4246 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 214 ASN B 537 GLN A 214 ASN A 586 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.143766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.110626 restraints weight = 9722.434| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.60 r_work: 0.2958 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9220 Z= 0.098 Angle : 0.520 9.344 12496 Z= 0.262 Chirality : 0.040 0.151 1384 Planarity : 0.003 0.041 1572 Dihedral : 5.056 63.822 1256 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.80 % Allowed : 19.00 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.31 (0.25), residues: 1108 helix: 0.86 (0.19), residues: 740 sheet: -0.67 (0.63), residues: 66 loop : -1.06 (0.32), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 259 TYR 0.009 0.001 TYR A 310 PHE 0.008 0.001 PHE B 252 TRP 0.012 0.001 TRP A 326 HIS 0.005 0.001 HIS B 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 ( 9220) covalent geometry : angle 0.51979 / 0.26 (12496) hydrogen bonds : bond 0.03416 / 2.26 ( 478) hydrogen bonds : angle 3.90493 / 2.70 ( 1392) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 332 GLN cc_start: 0.8059 (mt0) cc_final: 0.7835 (mt0) REVERT: B 429 VAL cc_start: 0.8459 (OUTLIER) cc_final: 0.8115 (m) REVERT: B 624 LYS cc_start: 0.7593 (tptp) cc_final: 0.7204 (mmmt) REVERT: A 332 GLN cc_start: 0.8058 (mt0) cc_final: 0.7823 (mt0) REVERT: A 429 VAL cc_start: 0.8491 (OUTLIER) cc_final: 0.8141 (m) REVERT: A 564 GLU cc_start: 0.7489 (mp0) cc_final: 0.7240 (mp0) REVERT: A 565 ASP cc_start: 0.7980 (m-30) cc_final: 0.7546 (m-30) REVERT: A 624 LYS cc_start: 0.7571 (tptp) cc_final: 0.7174 (mmmt) outliers start: 17 outliers final: 12 residues processed: 126 average time/residue: 0.6236 time to fit residues: 82.5259 Evaluate side-chains 125 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 537 GLN Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 582 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 8 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 108 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 214 ASN A 214 ASN A 586 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.156286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.124587 restraints weight = 9569.465| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.49 r_work: 0.3378 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9220 Z= 0.121 Angle : 0.550 9.897 12496 Z= 0.277 Chirality : 0.041 0.150 1384 Planarity : 0.003 0.042 1572 Dihedral : 5.087 64.209 1256 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.49 % Allowed : 19.53 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.33 (0.25), residues: 1108 helix: 0.83 (0.19), residues: 742 sheet: -0.66 (0.63), residues: 66 loop : -0.95 (0.32), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 259 TYR 0.010 0.001 TYR A 310 PHE 0.008 0.001 PHE B 252 TRP 0.010 0.001 TRP A 326 HIS 0.005 0.001 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 9220) covalent geometry : angle 0.54965 / 0.28 (12496) hydrogen bonds : bond 0.03531 / 2.33 ( 478) hydrogen bonds : angle 3.92123 / 2.71 ( 1392) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2622.64 seconds wall clock time: 45 minutes 19.58 seconds (2719.58 seconds total)