Starting phenix.real_space_refine on Thu Mar 13 16:48:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vx8_32171/03_2025/7vx8_32171.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vx8_32171/03_2025/7vx8_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_32171/03_2025/7vx8_32171.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vx8_32171/03_2025/7vx8_32171.map" model { file = "/net/cci-nas-00/data/ceres_data/7vx8_32171/03_2025/7vx8_32171.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vx8_32171/03_2025/7vx8_32171.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.38, per 1000 atoms: 0.60 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: 2.20 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.94 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: 2.60 Time building geometry restraints manager: 2.62 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: 0.04 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: 0.600 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.570 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.980 ------------------------------------------------------------------------------- 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= 0.834 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (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 TRP 0.009 0.001 TRP B 601 HIS 0.004 0.001 HIS A 502 PHE 0.027 0.003 PHE A 261 TYR 0.016 0.003 TYR A 310 ARG 0.010 0.001 ARG B 308 *********************** 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 : 0.962 Fit side-chains REVERT: B 64 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7242 (mmtt) REVERT: B 227 TYR cc_start: 0.8191 (t80) cc_final: 0.7988 (t80) REVERT: B 400 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7269 (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: 0.6692 (mtp180) REVERT: A 565 ASP cc_start: 0.8563 (m-30) cc_final: 0.8344 (m-30) outliers start: 10 outliers final: 3 residues processed: 146 average time/residue: 1.8498 time to fit residues: 283.3095 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 : 1.428 ------------------------------------------------------------------------------- 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 94 optimal weight: 0.9980 chunk 84 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.153672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.122642 restraints weight = 9552.590| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.45 r_work: 0.3361 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1301 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= 0.192 Angle : 0.629 8.663 12496 Z= 0.324 Chirality : 0.042 0.158 1384 Planarity : 0.004 0.033 1572 Dihedral : 9.849 81.350 1338 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.29 % Allowed : 8.60 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.23), residues: 1108 helix: -1.03 (0.18), residues: 746 sheet: -1.88 (0.54), residues: 72 loop : -1.38 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 326 HIS 0.006 0.001 HIS B 210 PHE 0.013 0.001 PHE B 130 TYR 0.012 0.002 TYR A 559 ARG 0.005 0.000 ARG B 259 *********************** 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 160 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 0.956 Fit side-chains REVERT: B 72 LEU cc_start: 0.8217 (tp) cc_final: 0.7997 (tp) REVERT: B 101 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8082 (tt) REVERT: B 227 TYR cc_start: 0.8224 (t80) cc_final: 0.7915 (t80) REVERT: B 292 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7362 (mp0) REVERT: B 400 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7117 (tp30) REVERT: B 427 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7330 (mp0) REVERT: B 624 LYS cc_start: 0.7565 (tptp) cc_final: 0.7130 (mmmt) REVERT: B 676 GLU cc_start: 0.7616 (mp0) cc_final: 0.7401 (mp0) REVERT: A 72 LEU cc_start: 0.8024 (tp) cc_final: 0.7786 (tp) REVERT: A 101 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8106 (tt) REVERT: A 259 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.6526 (mpt180) REVERT: A 400 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7147 (tp30) REVERT: A 427 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7317 (mp0) REVERT: A 565 ASP cc_start: 0.7752 (m-30) cc_final: 0.7477 (m-30) REVERT: A 624 LYS cc_start: 0.7641 (tptp) cc_final: 0.7353 (mmmt) outliers start: 31 outliers final: 4 residues processed: 140 average time/residue: 1.8028 time to fit residues: 264.9518 Evaluate side-chains 125 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 32 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 75 optimal weight: 0.0010 chunk 98 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 94 optimal weight: 0.1980 chunk 41 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 overall best weight: 0.5588 ------------------------------------------------------------------------------- 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 = 0.3890 r_free = 0.3890 target = 0.160340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.129950 restraints weight = 9602.722| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.41 r_work: 0.3476 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1718 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= 0.151 Angle : 0.542 8.083 12496 Z= 0.282 Chirality : 0.040 0.144 1384 Planarity : 0.003 0.029 1572 Dihedral : 8.447 82.017 1322 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.02 % Allowed : 13.59 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.24), residues: 1108 helix: -0.27 (0.19), residues: 740 sheet: -1.52 (0.58), residues: 70 loop : -1.43 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 326 HIS 0.005 0.001 HIS B 210 PHE 0.013 0.001 PHE B 130 TYR 0.008 0.001 TYR A 559 ARG 0.003 0.000 ARG A 163 *********************** 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 143 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 1.386 Fit side-chains REVERT: B 72 LEU cc_start: 0.8360 (tp) cc_final: 0.8136 (tp) REVERT: B 427 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: B 582 VAL cc_start: 0.8263 (p) cc_final: 0.7904 (m) REVERT: B 624 LYS cc_start: 0.7794 (tptp) cc_final: 0.7432 (mmmt) REVERT: A 427 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7472 (mp0) REVERT: A 565 ASP cc_start: 0.8140 (m-30) cc_final: 0.7522 (m-30) REVERT: A 582 VAL cc_start: 0.8256 (p) cc_final: 0.7899 (m) REVERT: A 624 LYS cc_start: 0.7891 (tptp) cc_final: 0.7577 (mmmt) outliers start: 19 outliers final: 7 residues processed: 129 average time/residue: 1.9001 time to fit residues: 257.5631 Evaluate side-chains 128 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 34 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 82 optimal weight: 0.0980 chunk 43 optimal weight: 0.9990 chunk 73 optimal weight: 20.0000 overall best weight: 1.8188 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.156122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.125091 restraints weight = 9517.138| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.42 r_work: 0.3404 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 9220 Z= 0.298 Angle : 0.606 8.733 12496 Z= 0.309 Chirality : 0.044 0.146 1384 Planarity : 0.004 0.030 1572 Dihedral : 8.559 86.112 1318 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.23 % Allowed : 16.03 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.24), residues: 1108 helix: -0.17 (0.19), residues: 742 sheet: -1.53 (0.57), residues: 70 loop : -1.28 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 326 HIS 0.005 0.001 HIS A 210 PHE 0.013 0.001 PHE A 130 TYR 0.013 0.002 TYR A 327 ARG 0.004 0.000 ARG A 163 *********************** 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 141 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.987 Fit side-chains REVERT: B 332 GLN cc_start: 0.8220 (mt0) cc_final: 0.7986 (mt0) REVERT: B 427 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7419 (mp0) REVERT: B 624 LYS cc_start: 0.7846 (tptp) cc_final: 0.7392 (mmmt) REVERT: A 332 GLN cc_start: 0.8173 (mt0) cc_final: 0.7935 (mt0) REVERT: A 427 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7441 (mp0) REVERT: A 538 ARG cc_start: 0.7776 (mmp-170) cc_final: 0.7564 (mmm160) REVERT: A 565 ASP cc_start: 0.8248 (m-30) cc_final: 0.7847 (m-30) REVERT: A 600 ASP cc_start: 0.7021 (OUTLIER) cc_final: 0.6549 (t0) REVERT: A 624 LYS cc_start: 0.7893 (tptp) cc_final: 0.7563 (mmmt) outliers start: 21 outliers final: 10 residues processed: 128 average time/residue: 1.6709 time to fit residues: 224.6156 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 : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Chi-restraints excluded: chain A residue 600 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 53 optimal weight: 0.0670 chunk 65 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 100 optimal weight: 0.2980 chunk 35 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.3885 r_free = 0.3885 target = 0.160142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.129887 restraints weight = 9515.420| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.53 r_work: 0.3476 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1976 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= 0.141 Angle : 0.515 9.253 12496 Z= 0.269 Chirality : 0.040 0.143 1384 Planarity : 0.003 0.029 1572 Dihedral : 8.091 88.602 1318 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.55 % Allowed : 16.77 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.25), residues: 1108 helix: 0.18 (0.19), residues: 742 sheet: -0.99 (0.62), residues: 66 loop : -1.25 (0.32), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 326 HIS 0.005 0.001 HIS B 210 PHE 0.009 0.001 PHE B 252 TYR 0.009 0.001 TYR B 559 ARG 0.006 0.000 ARG B 259 *********************** 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 143 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: B 281 TYR cc_start: 0.8920 (t80) cc_final: 0.8672 (t80) REVERT: B 332 GLN cc_start: 0.8110 (mt0) cc_final: 0.7879 (mt0) REVERT: B 429 VAL cc_start: 0.8651 (OUTLIER) cc_final: 0.8291 (m) REVERT: B 499 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7375 (mm-30) REVERT: B 624 LYS cc_start: 0.7773 (tptp) cc_final: 0.7375 (mmmt) REVERT: A 332 GLN cc_start: 0.8071 (mt0) cc_final: 0.7830 (mt0) REVERT: A 427 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7400 (mp0) REVERT: A 429 VAL cc_start: 0.8647 (OUTLIER) cc_final: 0.8285 (m) REVERT: A 499 GLU cc_start: 0.7657 (tp30) cc_final: 0.7414 (mm-30) REVERT: A 538 ARG cc_start: 0.7715 (mmp-170) cc_final: 0.7457 (mmm160) REVERT: A 564 GLU cc_start: 0.7662 (mp0) cc_final: 0.7454 (mp0) REVERT: A 565 ASP cc_start: 0.8129 (m-30) cc_final: 0.7542 (m-30) REVERT: A 624 LYS cc_start: 0.7810 (tptp) cc_final: 0.7533 (mmmt) outliers start: 24 outliers final: 6 residues processed: 126 average time/residue: 1.6779 time to fit residues: 222.1479 Evaluate side-chains 121 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 499 GLU 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 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 2 optimal weight: 0.2980 chunk 68 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 33 optimal weight: 0.0670 chunk 97 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 76 optimal weight: 0.0670 chunk 81 optimal weight: 1.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.161115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.130909 restraints weight = 9462.514| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.57 r_work: 0.3478 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2150 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= 0.135 Angle : 0.514 10.383 12496 Z= 0.264 Chirality : 0.040 0.147 1384 Planarity : 0.003 0.042 1572 Dihedral : 7.888 86.039 1318 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.91 % Allowed : 18.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.25), residues: 1108 helix: 0.43 (0.19), residues: 748 sheet: -0.87 (0.62), residues: 66 loop : -1.07 (0.32), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 326 HIS 0.005 0.001 HIS B 210 PHE 0.008 0.001 PHE B 252 TYR 0.016 0.001 TYR A 227 ARG 0.009 0.000 ARG B 259 *********************** 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 135 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: B 281 TYR cc_start: 0.8921 (t80) cc_final: 0.8626 (t80) REVERT: B 332 GLN cc_start: 0.8122 (mt0) cc_final: 0.7898 (mt0) REVERT: B 427 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7438 (mp0) REVERT: B 429 VAL cc_start: 0.8617 (OUTLIER) cc_final: 0.8281 (m) REVERT: B 615 MET cc_start: 0.9005 (mmm) cc_final: 0.8805 (mmp) REVERT: B 624 LYS cc_start: 0.7777 (tptp) cc_final: 0.7384 (mmmt) REVERT: A 332 GLN cc_start: 0.8060 (mt0) cc_final: 0.7831 (mt0) REVERT: A 429 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8379 (m) REVERT: A 499 GLU cc_start: 0.7609 (tp30) cc_final: 0.7385 (mm-30) REVERT: A 538 ARG cc_start: 0.7757 (mmp-170) cc_final: 0.7486 (mmm160) REVERT: A 564 GLU cc_start: 0.7659 (mp0) cc_final: 0.7417 (mp0) REVERT: A 565 ASP cc_start: 0.8061 (m-30) cc_final: 0.7480 (m-30) REVERT: A 624 LYS cc_start: 0.7819 (tptp) cc_final: 0.7560 (mmmt) outliers start: 18 outliers final: 9 residues processed: 120 average time/residue: 1.7244 time to fit residues: 217.0502 Evaluate side-chains 122 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 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 537 GLN Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 582 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 43 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 92 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.159835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.129251 restraints weight = 9591.275| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.39 r_work: 0.3455 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2202 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= 0.180 Angle : 0.530 8.582 12496 Z= 0.272 Chirality : 0.041 0.146 1384 Planarity : 0.003 0.037 1572 Dihedral : 7.939 89.986 1318 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.12 % Allowed : 18.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.25), residues: 1108 helix: 0.50 (0.19), residues: 750 sheet: -1.09 (0.59), residues: 70 loop : -0.90 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 326 HIS 0.005 0.001 HIS B 210 PHE 0.008 0.001 PHE A 130 TYR 0.010 0.001 TYR A 310 ARG 0.009 0.000 ARG B 259 *********************** 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 137 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 332 GLN cc_start: 0.8127 (mt0) cc_final: 0.7899 (mt0) REVERT: B 429 VAL cc_start: 0.8627 (OUTLIER) cc_final: 0.8275 (m) REVERT: B 624 LYS cc_start: 0.7821 (tptp) cc_final: 0.7448 (mmmt) REVERT: A 332 GLN cc_start: 0.8085 (mt0) cc_final: 0.7862 (mt0) REVERT: A 429 VAL cc_start: 0.8670 (OUTLIER) cc_final: 0.8363 (m) REVERT: A 499 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7478 (mm-30) REVERT: A 538 ARG cc_start: 0.7807 (mmp-170) cc_final: 0.7505 (mmm160) REVERT: A 565 ASP cc_start: 0.8180 (m-30) cc_final: 0.7620 (m-30) REVERT: A 624 LYS cc_start: 0.7876 (tptp) cc_final: 0.7615 (mmmt) outliers start: 20 outliers final: 9 residues processed: 119 average time/residue: 1.7206 time to fit residues: 214.9664 Evaluate side-chains 123 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 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 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 72 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 13 optimal weight: 0.3980 chunk 75 optimal weight: 0.0270 chunk 51 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 33 optimal weight: 0.0670 chunk 4 optimal weight: 0.8980 chunk 104 optimal weight: 0.0980 chunk 61 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 overall best weight: 0.2576 ------------------------------------------------------------------------------- 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 = 0.3872 r_free = 0.3872 target = 0.159689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.129018 restraints weight = 9584.654| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.62 r_work: 0.3438 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9220 Z= 0.126 Angle : 0.508 9.258 12496 Z= 0.261 Chirality : 0.039 0.145 1384 Planarity : 0.003 0.039 1572 Dihedral : 7.618 86.602 1318 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.12 % Allowed : 18.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.25), residues: 1108 helix: 0.73 (0.19), residues: 748 sheet: -0.73 (0.62), residues: 66 loop : -0.92 (0.32), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 326 HIS 0.005 0.001 HIS A 210 PHE 0.008 0.001 PHE B 252 TYR 0.008 0.001 TYR B 559 ARG 0.009 0.000 ARG B 259 *********************** 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 142 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.919 Fit side-chains REVERT: B 332 GLN cc_start: 0.7995 (mt0) cc_final: 0.7768 (mt0) REVERT: B 427 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7322 (mp0) REVERT: B 429 VAL cc_start: 0.8519 (OUTLIER) cc_final: 0.8169 (m) REVERT: B 471 GLU cc_start: 0.6818 (pm20) cc_final: 0.6578 (mm-30) REVERT: B 624 LYS cc_start: 0.7612 (tptp) cc_final: 0.7240 (mmmt) REVERT: A 264 LYS cc_start: 0.8525 (mttt) cc_final: 0.8206 (mttp) REVERT: A 332 GLN cc_start: 0.7979 (mt0) cc_final: 0.7740 (mt0) REVERT: A 427 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7265 (mp0) REVERT: A 429 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8277 (m) REVERT: A 538 ARG cc_start: 0.7618 (mmp-170) cc_final: 0.7298 (mmm160) REVERT: A 565 ASP cc_start: 0.7937 (m-30) cc_final: 0.7484 (m-30) REVERT: A 622 ARG cc_start: 0.7632 (mtt-85) cc_final: 0.7431 (mtp85) REVERT: A 624 LYS cc_start: 0.7645 (tptp) cc_final: 0.7410 (mmmt) outliers start: 20 outliers final: 9 residues processed: 128 average time/residue: 1.8151 time to fit residues: 245.2005 Evaluate side-chains 130 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 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 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 103 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 62 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3877 r_free = 0.3877 target = 0.159440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.128545 restraints weight = 9520.858| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.42 r_work: 0.3456 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2302 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= 0.211 Angle : 0.565 10.306 12496 Z= 0.285 Chirality : 0.041 0.148 1384 Planarity : 0.004 0.040 1572 Dihedral : 7.755 85.181 1318 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.59 % Allowed : 19.32 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1108 helix: 0.67 (0.19), residues: 748 sheet: -0.94 (0.59), residues: 70 loop : -0.82 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 326 HIS 0.005 0.001 HIS B 210 PHE 0.008 0.001 PHE A 130 TYR 0.021 0.002 TYR B 227 ARG 0.009 0.000 ARG B 259 *********************** 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 135 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 332 GLN cc_start: 0.8124 (mt0) cc_final: 0.7895 (mt0) REVERT: B 429 VAL cc_start: 0.8655 (OUTLIER) cc_final: 0.8309 (m) REVERT: B 624 LYS cc_start: 0.7919 (tptp) cc_final: 0.7561 (mmmt) REVERT: A 264 LYS cc_start: 0.8508 (mttt) cc_final: 0.8232 (mttp) REVERT: A 332 GLN cc_start: 0.8065 (mt0) cc_final: 0.7833 (mt0) REVERT: A 429 VAL cc_start: 0.8706 (OUTLIER) cc_final: 0.8397 (m) REVERT: A 565 ASP cc_start: 0.8279 (m-30) cc_final: 0.7867 (m-30) REVERT: A 603 ASP cc_start: 0.8429 (p0) cc_final: 0.8143 (p0) REVERT: A 624 LYS cc_start: 0.7942 (tptp) cc_final: 0.7712 (mmmt) outliers start: 15 outliers final: 10 residues processed: 126 average time/residue: 1.6663 time to fit residues: 221.0830 Evaluate side-chains 129 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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 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 82 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 22 optimal weight: 0.0170 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- 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 537 GLN A 586 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.159660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.129705 restraints weight = 9875.863| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.44 r_work: 0.3434 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2341 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= 0.158 Angle : 0.539 9.746 12496 Z= 0.272 Chirality : 0.040 0.147 1384 Planarity : 0.003 0.042 1572 Dihedral : 7.632 83.144 1318 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.59 % Allowed : 19.53 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.25), residues: 1108 helix: 0.76 (0.19), residues: 748 sheet: -0.67 (0.63), residues: 66 loop : -0.81 (0.32), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 326 HIS 0.005 0.001 HIS A 210 PHE 0.008 0.001 PHE A 252 TYR 0.010 0.001 TYR B 559 ARG 0.009 0.000 ARG B 259 ********************** 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 132 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 332 GLN cc_start: 0.8042 (mt0) cc_final: 0.7822 (mt0) REVERT: B 429 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8208 (m) REVERT: B 624 LYS cc_start: 0.7757 (tptp) cc_final: 0.7381 (mmmt) REVERT: A 264 LYS cc_start: 0.8569 (mttt) cc_final: 0.8290 (mttp) REVERT: A 429 VAL cc_start: 0.8602 (OUTLIER) cc_final: 0.8276 (m) REVERT: A 565 ASP cc_start: 0.8135 (m-30) cc_final: 0.7490 (m-30) REVERT: A 603 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8202 (p0) REVERT: A 624 LYS cc_start: 0.7832 (tptp) cc_final: 0.7597 (mmmt) outliers start: 15 outliers final: 11 residues processed: 124 average time/residue: 1.6597 time to fit residues: 216.6419 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 : 1.037 ------------------------------------------------------------------------------- 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 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 537 GLN Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 603 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 75 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 105 optimal weight: 0.0000 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.156505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.125627 restraints weight = 9864.879| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.48 r_work: 0.3372 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9220 Z= 0.176 Angle : 0.555 9.864 12496 Z= 0.280 Chirality : 0.040 0.146 1384 Planarity : 0.003 0.042 1572 Dihedral : 7.574 82.113 1318 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.70 % Allowed : 19.75 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.25), residues: 1108 helix: 0.80 (0.19), residues: 748 sheet: -0.70 (0.62), residues: 66 loop : -0.79 (0.32), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 326 HIS 0.006 0.001 HIS B 586 PHE 0.008 0.001 PHE B 252 TYR 0.010 0.001 TYR A 310 ARG 0.009 0.000 ARG B 259 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6635.46 seconds wall clock time: 115 minutes 42.46 seconds (6942.46 seconds total)