Starting phenix.real_space_refine on Wed Feb 4 05:20:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vx8_32171/02_2026/7vx8_32171.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vx8_32171/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7vx8_32171/02_2026/7vx8_32171.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vx8_32171/02_2026/7vx8_32171.map" model { file = "/net/cci-nas-00/data/ceres_data/7vx8_32171/02_2026/7vx8_32171.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vx8_32171/02_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-2.0-5952/lib/python3.9/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: 2.54, per 1000 atoms: 0.28 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: 0.68 Conformation dependent library (CDL) restraints added in 356.0 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: 0.27 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: 1.13 Time building geometry restraints manager: 0.94 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 - 17.64: 4935 17.64 - 35.27: 418 35.27 - 52.91: 114 52.91 - 70.54: 32 70.54 - 88.18: 15 Dihedral angle restraints: 5514 sinusoidal: 2264 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 5511 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: 0.01 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: 0.760 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.420 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 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 : 15.856 88.180 3426 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 covalent geometry : bond 0.01268 ( 9220) covalent geometry : angle 1.22833 (12496) hydrogen bonds : bond 0.22551 ( 478) hydrogen bonds : angle 8.20587 ( 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 : 0.224 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: 0.7392 time to fit residues: 112.7565 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 : 0.335 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.153264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.121884 restraints weight = 9584.696| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.45 r_work: 0.3354 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9220 Z= 0.145 Angle : 0.639 8.772 12496 Z= 0.328 Chirality : 0.043 0.159 1384 Planarity : 0.004 0.033 1572 Dihedral : 9.873 80.817 1338 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.08 % Allowed : 8.92 % 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: -2.03 (0.23), residues: 1108 helix: -1.07 (0.18), residues: 748 sheet: -1.90 (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 0.006 0.001 HIS B 210 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9220) covalent geometry : angle 0.63899 (12496) hydrogen bonds : bond 0.04609 ( 478) hydrogen bonds : angle 5.00134 ( 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 156 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.329 Fit side-chains REVERT: B 72 LEU cc_start: 0.8179 (tp) cc_final: 0.7953 (tp) REVERT: B 101 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.8021 (tt) REVERT: B 227 TYR cc_start: 0.8177 (t80) cc_final: 0.7851 (t80) REVERT: B 292 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: B 400 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7046 (tp30) REVERT: B 427 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: B 564 GLU cc_start: 0.7108 (mp0) cc_final: 0.6893 (mp0) REVERT: B 624 LYS cc_start: 0.7472 (tptp) cc_final: 0.7025 (mmmt) REVERT: B 676 GLU cc_start: 0.7560 (mp0) cc_final: 0.7343 (mp0) REVERT: A 72 LEU cc_start: 0.7954 (tp) cc_final: 0.7706 (tp) REVERT: A 101 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8045 (tt) REVERT: A 259 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.6412 (mpt180) REVERT: A 400 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7093 (tp30) REVERT: A 427 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7212 (mp0) REVERT: A 565 ASP cc_start: 0.7731 (m-30) cc_final: 0.7468 (m-30) REVERT: A 571 TYR cc_start: 0.7420 (m-80) cc_final: 0.7209 (m-80) REVERT: A 624 LYS cc_start: 0.7498 (tptp) cc_final: 0.7026 (mmmt) outliers start: 29 outliers final: 4 residues processed: 138 average time/residue: 0.7583 time to fit residues: 109.6286 Evaluate side-chains 123 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 292 GLU 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: 3.9990 chunk 69 optimal weight: 3.9990 chunk 39 optimal weight: 0.0970 chunk 63 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 72 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3881 r_free = 0.3881 target = 0.159522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.129060 restraints weight = 9553.843| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.61 r_work: 0.3463 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1633 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= 0.114 Angle : 0.549 8.023 12496 Z= 0.285 Chirality : 0.040 0.144 1384 Planarity : 0.003 0.029 1572 Dihedral : 8.655 86.361 1322 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.91 % Allowed : 13.80 % 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: -1.24 (0.24), residues: 1108 helix: -0.36 (0.19), residues: 740 sheet: -1.62 (0.58), residues: 70 loop : -1.43 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 163 TYR 0.009 0.001 TYR A 559 PHE 0.012 0.001 PHE B 130 TRP 0.009 0.001 TRP A 326 HIS 0.005 0.001 HIS B 210 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 9220) covalent geometry : angle 0.54947 (12496) hydrogen bonds : bond 0.03931 ( 478) hydrogen bonds : angle 4.50740 ( 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 141 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.337 Fit side-chains REVERT: B 72 LEU cc_start: 0.8364 (tp) cc_final: 0.8141 (tp) REVERT: B 227 TYR cc_start: 0.8256 (t80) cc_final: 0.8036 (t80) REVERT: B 400 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7283 (tp30) REVERT: B 427 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7519 (mp0) REVERT: B 582 VAL cc_start: 0.8357 (p) cc_final: 0.7990 (m) REVERT: B 615 MET cc_start: 0.9097 (mmm) cc_final: 0.8891 (mmp) REVERT: B 624 LYS cc_start: 0.7793 (tptp) cc_final: 0.7426 (mmmt) REVERT: A 400 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7289 (tp30) REVERT: A 427 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7478 (mp0) REVERT: A 565 ASP cc_start: 0.8173 (m-30) cc_final: 0.7535 (m-30) REVERT: A 582 VAL cc_start: 0.8359 (p) cc_final: 0.7998 (m) REVERT: A 624 LYS cc_start: 0.7787 (tptp) cc_final: 0.7400 (mmmt) outliers start: 18 outliers final: 7 residues processed: 127 average time/residue: 0.7850 time to fit residues: 104.4955 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 : 0.370 ------------------------------------------------------------------------------- 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: 0.9980 chunk 63 optimal weight: 0.8980 chunk 73 optimal weight: 20.0000 chunk 22 optimal weight: 0.0020 chunk 78 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 23 optimal weight: 0.0050 chunk 25 optimal weight: 0.7980 chunk 2 optimal weight: 0.4980 overall best weight: 0.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3910 r_free = 0.3910 target = 0.162170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.131986 restraints weight = 9609.583| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.58 r_work: 0.3352 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1961 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 : 0.512 9.204 12496 Z= 0.267 Chirality : 0.039 0.139 1384 Planarity : 0.003 0.029 1572 Dihedral : 7.921 81.747 1318 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.12 % Allowed : 15.07 % Favored : 82.80 % 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: 0.10 (0.19), residues: 740 sheet: -1.36 (0.59), residues: 70 loop : -1.33 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 259 TYR 0.015 0.001 TYR A 227 PHE 0.011 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 covalent geometry : bond 0.00199 ( 9220) covalent geometry : angle 0.51228 (12496) hydrogen bonds : bond 0.03457 ( 478) hydrogen bonds : angle 4.19018 ( 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 140 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.330 Fit side-chains REVERT: B 72 LEU cc_start: 0.8245 (tp) cc_final: 0.8009 (tp) REVERT: B 227 TYR cc_start: 0.8121 (t80) cc_final: 0.7901 (t80) REVERT: B 400 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7214 (tp30) REVERT: B 427 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7339 (mp0) REVERT: B 429 VAL cc_start: 0.8541 (OUTLIER) cc_final: 0.8185 (m) REVERT: B 582 VAL cc_start: 0.7971 (p) cc_final: 0.7524 (m) REVERT: B 615 MET cc_start: 0.8982 (mmm) cc_final: 0.8780 (mmp) REVERT: B 624 LYS cc_start: 0.7634 (tptp) cc_final: 0.7186 (mmmt) REVERT: A 292 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7140 (mp0) REVERT: A 400 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7161 (tp30) REVERT: A 427 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7302 (mp0) REVERT: A 429 VAL cc_start: 0.8594 (OUTLIER) cc_final: 0.8291 (m) REVERT: A 565 ASP cc_start: 0.7931 (m-30) cc_final: 0.7482 (m-30) REVERT: A 624 LYS cc_start: 0.7571 (tptp) cc_final: 0.7164 (mmmt) outliers start: 20 outliers final: 5 residues processed: 127 average time/residue: 0.7002 time to fit residues: 93.3961 Evaluate side-chains 115 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 429 VAL 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 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: 5.9990 chunk 95 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3844 r_free = 0.3844 target = 0.156416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.125393 restraints weight = 9657.011| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.43 r_work: 0.3402 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9220 Z= 0.185 Angle : 0.591 8.316 12496 Z= 0.301 Chirality : 0.043 0.140 1384 Planarity : 0.004 0.030 1572 Dihedral : 8.432 89.244 1318 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.87 % Allowed : 16.14 % Favored : 81.00 % 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: -0.67 (0.24), residues: 1108 helix: 0.06 (0.19), residues: 742 sheet: -1.39 (0.58), residues: 70 loop : -1.17 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 259 TYR 0.014 0.002 TYR B 327 PHE 0.011 0.001 PHE A 130 TRP 0.005 0.001 TRP A 601 HIS 0.005 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 9220) covalent geometry : angle 0.59116 (12496) hydrogen bonds : bond 0.04214 ( 478) hydrogen bonds : angle 4.27958 ( 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 141 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.219 Fit side-chains REVERT: B 227 TYR cc_start: 0.8225 (t80) cc_final: 0.8008 (t80) REVERT: B 332 GLN cc_start: 0.8167 (mt0) cc_final: 0.7927 (mt0) REVERT: B 400 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7329 (tp30) REVERT: B 427 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7453 (mp0) REVERT: B 624 LYS cc_start: 0.7868 (tptp) cc_final: 0.7442 (mmmt) REVERT: A 332 GLN cc_start: 0.8130 (mt0) cc_final: 0.7892 (mt0) REVERT: A 400 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7350 (tp30) REVERT: A 427 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7484 (mp0) REVERT: A 565 ASP cc_start: 0.8249 (m-30) cc_final: 0.7652 (m-30) REVERT: A 624 LYS cc_start: 0.7829 (tptp) cc_final: 0.7409 (mmmt) outliers start: 27 outliers final: 10 residues processed: 122 average time/residue: 0.7883 time to fit residues: 100.7151 Evaluate side-chains 122 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 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 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: 7.9990 chunk 33 optimal weight: 0.0970 chunk 84 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 75 optimal weight: 0.3980 chunk 22 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3882 r_free = 0.3882 target = 0.159805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.129119 restraints weight = 9633.680| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.42 r_work: 0.3462 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2072 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= 0.107 Angle : 0.533 9.434 12496 Z= 0.271 Chirality : 0.040 0.144 1384 Planarity : 0.003 0.037 1572 Dihedral : 8.053 85.697 1318 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.02 % Allowed : 17.83 % Favored : 80.15 % 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: -0.29 (0.25), residues: 1108 helix: 0.35 (0.19), residues: 742 sheet: -1.19 (0.60), residues: 70 loop : -1.07 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 259 TYR 0.015 0.001 TYR A 227 PHE 0.008 0.001 PHE B 130 TRP 0.011 0.001 TRP B 326 HIS 0.005 0.001 HIS B 210 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 9220) covalent geometry : angle 0.53258 (12496) hydrogen bonds : bond 0.03581 ( 478) hydrogen bonds : angle 4.06731 ( 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 133 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.270 Fit side-chains REVERT: B 332 GLN cc_start: 0.8123 (mt0) cc_final: 0.7908 (mt0) REVERT: B 427 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7533 (mp0) REVERT: B 429 VAL cc_start: 0.8666 (OUTLIER) cc_final: 0.8309 (m) REVERT: B 615 MET cc_start: 0.9142 (mmm) cc_final: 0.8934 (mmp) REVERT: B 624 LYS cc_start: 0.7915 (tptp) cc_final: 0.7536 (mmmt) REVERT: A 332 GLN cc_start: 0.8082 (mt0) cc_final: 0.7860 (mt0) REVERT: A 427 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7556 (mp0) REVERT: A 429 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8376 (m) REVERT: A 499 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7414 (mm-30) REVERT: A 565 ASP cc_start: 0.8219 (m-30) cc_final: 0.7630 (m-30) REVERT: A 603 ASP cc_start: 0.8402 (p0) cc_final: 0.8133 (p0) REVERT: A 624 LYS cc_start: 0.7851 (tptp) cc_final: 0.7510 (mmmt) outliers start: 19 outliers final: 5 residues processed: 117 average time/residue: 0.8150 time to fit residues: 99.7974 Evaluate side-chains 119 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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: 5.9990 chunk 26 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 19 optimal weight: 0.0770 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3875 r_free = 0.3875 target = 0.158958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.128175 restraints weight = 9672.137| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.41 r_work: 0.3447 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9220 Z= 0.127 Angle : 0.541 7.987 12496 Z= 0.276 Chirality : 0.041 0.143 1384 Planarity : 0.003 0.038 1572 Dihedral : 8.053 89.480 1318 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.91 % Allowed : 18.79 % Favored : 79.30 % 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: -0.15 (0.25), residues: 1108 helix: 0.47 (0.19), residues: 742 sheet: -1.18 (0.58), residues: 70 loop : -1.02 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 259 TYR 0.020 0.002 TYR B 227 PHE 0.009 0.001 PHE A 130 TRP 0.009 0.001 TRP B 326 HIS 0.005 0.001 HIS B 210 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9220) covalent geometry : angle 0.54062 (12496) hydrogen bonds : bond 0.03703 ( 478) hydrogen bonds : angle 4.02628 ( 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: 18 poor density : 118 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 332 GLN cc_start: 0.8132 (mt0) cc_final: 0.7911 (mt0) REVERT: B 429 VAL cc_start: 0.8662 (OUTLIER) cc_final: 0.8303 (m) REVERT: B 538 ARG cc_start: 0.7895 (mmp-170) cc_final: 0.7679 (mmm160) REVERT: B 624 LYS cc_start: 0.7910 (tptp) cc_final: 0.7543 (mmmt) REVERT: A 332 GLN cc_start: 0.8085 (mt0) cc_final: 0.7844 (mt0) REVERT: A 400 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7951 (tm-30) REVERT: A 429 VAL cc_start: 0.8694 (OUTLIER) cc_final: 0.8363 (m) REVERT: A 499 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7462 (mm-30) REVERT: A 565 ASP cc_start: 0.8271 (m-30) cc_final: 0.7852 (m-30) REVERT: A 603 ASP cc_start: 0.8418 (p0) cc_final: 0.8137 (p0) REVERT: A 624 LYS cc_start: 0.7901 (tptp) cc_final: 0.7543 (mmmt) outliers start: 18 outliers final: 10 residues processed: 122 average time/residue: 0.8141 time to fit residues: 104.0332 Evaluate side-chains 125 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 499 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 58 optimal weight: 0.0870 chunk 90 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 75 optimal weight: 0.1980 chunk 38 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3830 r_free = 0.3830 target = 0.157051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.125513 restraints weight = 9666.993| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.49 r_work: 0.3391 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9220 Z= 0.103 Angle : 0.536 10.592 12496 Z= 0.271 Chirality : 0.040 0.144 1384 Planarity : 0.003 0.040 1572 Dihedral : 7.751 85.920 1318 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.70 % Allowed : 19.32 % 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: 0.13 (0.25), residues: 1108 helix: 0.71 (0.19), residues: 740 sheet: -0.84 (0.62), 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 0.007 0.001 PHE B 252 TRP 0.012 0.001 TRP B 326 HIS 0.005 0.001 HIS B 210 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 9220) covalent geometry : angle 0.53579 (12496) hydrogen bonds : bond 0.03401 ( 478) hydrogen bonds : angle 3.90754 ( 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 137 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: B 332 GLN cc_start: 0.7983 (mt0) cc_final: 0.7737 (mt0) REVERT: B 429 VAL cc_start: 0.8519 (OUTLIER) cc_final: 0.8164 (m) REVERT: B 464 ARG cc_start: 0.7962 (mtm180) cc_final: 0.7744 (mtt180) REVERT: B 471 GLU cc_start: 0.6866 (pm20) cc_final: 0.6644 (mm-30) REVERT: B 538 ARG cc_start: 0.7575 (mmp-170) cc_final: 0.7357 (mmm160) REVERT: B 624 LYS cc_start: 0.7634 (tptp) cc_final: 0.7218 (mmmt) REVERT: A 264 LYS cc_start: 0.8479 (mttp) cc_final: 0.8202 (mttp) REVERT: A 332 GLN cc_start: 0.8006 (mt0) cc_final: 0.7767 (mt0) REVERT: A 400 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7811 (tm-30) REVERT: A 427 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7238 (mp0) REVERT: A 429 VAL cc_start: 0.8555 (OUTLIER) cc_final: 0.8221 (m) REVERT: A 471 GLU cc_start: 0.6971 (pm20) cc_final: 0.6766 (mm-30) REVERT: A 565 ASP cc_start: 0.7857 (m-30) cc_final: 0.7210 (m-30) REVERT: A 603 ASP cc_start: 0.8228 (p0) cc_final: 0.7985 (p0) REVERT: A 624 LYS cc_start: 0.7608 (tptp) cc_final: 0.7219 (mmmt) outliers start: 16 outliers final: 9 residues processed: 125 average time/residue: 0.8439 time to fit residues: 110.3854 Evaluate side-chains 124 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 429 VAL 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 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: 0.9990 chunk 3 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 105 optimal weight: 0.0370 chunk 11 optimal weight: 0.7980 chunk 63 optimal weight: 0.3980 chunk 70 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.161617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.130769 restraints weight = 9516.460| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.42 r_work: 0.3481 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9220 Z= 0.106 Angle : 0.526 9.156 12496 Z= 0.268 Chirality : 0.040 0.145 1384 Planarity : 0.003 0.039 1572 Dihedral : 7.570 83.907 1318 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.91 % Allowed : 19.43 % Favored : 78.66 % 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: 0.26 (0.25), residues: 1108 helix: 0.80 (0.19), residues: 740 sheet: -0.79 (0.62), residues: 66 loop : -0.99 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 259 TYR 0.009 0.001 TYR B 310 PHE 0.007 0.001 PHE B 252 TRP 0.010 0.001 TRP B 326 HIS 0.005 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 9220) covalent geometry : angle 0.52583 (12496) hydrogen bonds : bond 0.03384 ( 478) hydrogen bonds : angle 3.87419 ( 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 138 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: B 85 ARG cc_start: 0.7871 (ptt-90) cc_final: 0.7652 (ptp90) REVERT: B 332 GLN cc_start: 0.8115 (mt0) cc_final: 0.7885 (mt0) REVERT: B 429 VAL cc_start: 0.8618 (OUTLIER) cc_final: 0.8294 (m) REVERT: B 538 ARG cc_start: 0.7926 (mmp-170) cc_final: 0.7701 (mmm160) REVERT: B 624 LYS cc_start: 0.7865 (tptp) cc_final: 0.7511 (mmmt) REVERT: A 264 LYS cc_start: 0.8511 (mttp) cc_final: 0.8286 (mttp) REVERT: A 332 GLN cc_start: 0.8052 (mt0) cc_final: 0.7824 (mt0) REVERT: A 400 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7905 (tm-30) REVERT: A 427 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: A 429 VAL cc_start: 0.8669 (OUTLIER) cc_final: 0.8361 (m) REVERT: A 565 ASP cc_start: 0.8214 (m-30) cc_final: 0.7597 (m-30) REVERT: A 603 ASP cc_start: 0.8326 (p0) cc_final: 0.8067 (p0) REVERT: A 624 LYS cc_start: 0.7871 (tptp) cc_final: 0.7527 (mmmt) outliers start: 18 outliers final: 11 residues processed: 126 average time/residue: 0.8261 time to fit residues: 109.0368 Evaluate side-chains 129 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 167 VAL 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 482 VAL Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 582 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 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: 0.4980 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 49 optimal weight: 0.0970 chunk 78 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3826 r_free = 0.3826 target = 0.156401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.125720 restraints weight = 9536.562| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.47 r_work: 0.3395 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2389 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= 0.108 Angle : 0.527 10.008 12496 Z= 0.266 Chirality : 0.040 0.145 1384 Planarity : 0.003 0.042 1572 Dihedral : 7.505 82.014 1318 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.70 % Allowed : 19.64 % Favored : 78.66 % 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: 0.83 (0.19), residues: 742 sheet: -0.69 (0.63), residues: 66 loop : -0.97 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 259 TYR 0.010 0.001 TYR B 310 PHE 0.007 0.001 PHE B 252 TRP 0.010 0.001 TRP B 326 HIS 0.005 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9220) covalent geometry : angle 0.52704 (12496) hydrogen bonds : bond 0.03429 ( 478) hydrogen bonds : angle 3.85875 ( 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: 16 poor density : 119 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: B 85 ARG cc_start: 0.7731 (ptt-90) cc_final: 0.7519 (ptp90) REVERT: B 332 GLN cc_start: 0.7916 (mt0) cc_final: 0.7674 (mt0) REVERT: B 429 VAL cc_start: 0.8407 (OUTLIER) cc_final: 0.8047 (m) REVERT: B 538 ARG cc_start: 0.7384 (mmp-170) cc_final: 0.7162 (mmm160) REVERT: B 624 LYS cc_start: 0.7484 (tptp) cc_final: 0.7101 (mmmt) REVERT: A 264 LYS cc_start: 0.8474 (mttp) cc_final: 0.8188 (mttp) REVERT: A 332 GLN cc_start: 0.7924 (mt0) cc_final: 0.7678 (mt0) REVERT: A 400 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7762 (tm-30) REVERT: A 427 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: A 429 VAL cc_start: 0.8446 (OUTLIER) cc_final: 0.8085 (m) REVERT: A 565 ASP cc_start: 0.7854 (m-30) cc_final: 0.7172 (m-30) REVERT: A 603 ASP cc_start: 0.8217 (p0) cc_final: 0.7973 (p0) REVERT: A 624 LYS cc_start: 0.7532 (tptp) cc_final: 0.7147 (mmmt) outliers start: 16 outliers final: 12 residues processed: 125 average time/residue: 0.8698 time to fit residues: 113.7283 Evaluate side-chains 130 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 VAL 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 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 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 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: 0.9980 chunk 111 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN A 586 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.160678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.129813 restraints weight = 9433.437| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.42 r_work: 0.3468 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9220 Z= 0.125 Angle : 0.547 9.855 12496 Z= 0.277 Chirality : 0.041 0.146 1384 Planarity : 0.004 0.042 1572 Dihedral : 7.533 81.045 1318 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.02 % Allowed : 19.53 % Favored : 78.45 % 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: 0.82 (0.19), residues: 744 sheet: -0.67 (0.63), residues: 66 loop : -0.89 (0.33), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 259 TYR 0.019 0.001 TYR A 281 PHE 0.008 0.001 PHE A 130 TRP 0.008 0.001 TRP A 326 HIS 0.005 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9220) covalent geometry : angle 0.54668 (12496) hydrogen bonds : bond 0.03534 ( 478) hydrogen bonds : angle 3.88210 ( 1392) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3109.57 seconds wall clock time: 53 minutes 44.28 seconds (3224.28 seconds total)