Starting phenix.real_space_refine on Thu Aug 6 03:05:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10eo_75113/08_2026/10eo_75113.cif Found real_map, /net/cci-nas-00/data/ceres_data/10eo_75113/08_2026/10eo_75113.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10eo_75113/08_2026/10eo_75113.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10eo_75113/08_2026/10eo_75113.map" model { file = "/net/cci-nas-00/data/ceres_data/10eo_75113/08_2026/10eo_75113.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10eo_75113/08_2026/10eo_75113.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 8098 2.51 5 N 2188 2.21 5 O 2414 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12742 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 807, 6371 Classifications: {'peptide': 807} Link IDs: {'PTRANS': 57, 'TRANS': 749} Restraints were copied for chains: B Time building chain proxies: 6.20, per 1000 atoms: 0.49 Number of scatterers: 12742 At special positions: 0 Unit cell: (108.23, 160.29, 89.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 2414 8.00 N 2188 7.00 C 8098 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 566.6 milliseconds 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3004 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 24 sheets defined 17.2% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 114 through 122 removed outlier: 3.987A pdb=" N ILE A 120 " --> pdb=" O GLU A 116 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 121 " --> pdb=" O ILE A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 153 removed outlier: 4.087A pdb=" N LEU A 152 " --> pdb=" O PRO A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 327 removed outlier: 3.503A pdb=" N ALA A 319 " --> pdb=" O ASP A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 378 removed outlier: 3.598A pdb=" N ARG A 377 " --> pdb=" O PRO A 374 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE A 378 " --> pdb=" O CYS A 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 374 through 378' Processing helix chain 'A' and resid 645 through 649 removed outlier: 3.569A pdb=" N LEU A 648 " --> pdb=" O TYR A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 702 removed outlier: 3.691A pdb=" N ALA A 701 " --> pdb=" O SER A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 726 removed outlier: 3.947A pdb=" N ARG A 726 " --> pdb=" O LEU A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 747 removed outlier: 3.522A pdb=" N ASP A 747 " --> pdb=" O GLU A 744 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 744 through 747' Processing helix chain 'A' and resid 748 through 756 Processing helix chain 'A' and resid 757 through 767 Processing helix chain 'A' and resid 781 through 794 removed outlier: 3.939A pdb=" N PHE A 785 " --> pdb=" O ARG A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 834 Processing helix chain 'A' and resid 839 through 843 removed outlier: 3.672A pdb=" N ILE A 843 " --> pdb=" O ALA A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 875 removed outlier: 3.741A pdb=" N SER A 865 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 912 Processing helix chain 'B' and resid 114 through 122 removed outlier: 3.987A pdb=" N ILE B 120 " --> pdb=" O GLU B 116 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 153 removed outlier: 4.087A pdb=" N LEU B 152 " --> pdb=" O PRO B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 327 removed outlier: 3.503A pdb=" N ALA B 319 " --> pdb=" O ASP B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.598A pdb=" N ARG B 377 " --> pdb=" O PRO B 374 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE B 378 " --> pdb=" O CYS B 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 374 through 378' Processing helix chain 'B' and resid 645 through 649 removed outlier: 3.569A pdb=" N LEU B 648 " --> pdb=" O TYR B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 702 removed outlier: 3.691A pdb=" N ALA B 701 " --> pdb=" O SER B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 726 removed outlier: 3.947A pdb=" N ARG B 726 " --> pdb=" O LEU B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 747 removed outlier: 3.522A pdb=" N ASP B 747 " --> pdb=" O GLU B 744 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 744 through 747' Processing helix chain 'B' and resid 748 through 756 Processing helix chain 'B' and resid 757 through 767 Processing helix chain 'B' and resid 781 through 794 removed outlier: 3.939A pdb=" N PHE B 785 " --> pdb=" O ARG B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 834 Processing helix chain 'B' and resid 839 through 843 removed outlier: 3.672A pdb=" N ILE B 843 " --> pdb=" O ALA B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 875 removed outlier: 3.741A pdb=" N SER B 865 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS B 875 " --> pdb=" O ALA B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 912 Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 131 removed outlier: 4.205A pdb=" N GLY A 179 " --> pdb=" O LYS A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 157 through 159 removed outlier: 3.706A pdb=" N THR A 170 " --> pdb=" O ASP A 165 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 205 through 211 removed outlier: 4.370A pdb=" N VAL A 209 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ALA A 219 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N TRP A 211 " --> pdb=" O HIS A 217 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N HIS A 217 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 263 through 265 removed outlier: 6.872A pdb=" N SER A 328 " --> pdb=" O VAL A 344 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL A 344 " --> pdb=" O SER A 328 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU A 330 " --> pdb=" O VAL A 342 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 294 through 297 removed outlier: 7.600A pdb=" N CYS B 800 " --> pdb=" O SER B 773 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ILE B 775 " --> pdb=" O CYS B 800 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N ILE B 802 " --> pdb=" O ILE B 775 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL B 777 " --> pdb=" O ILE B 802 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N ARG B 804 " --> pdb=" O VAL B 777 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N GLY B 779 " --> pdb=" O ARG B 804 " (cutoff:3.500A) removed outlier: 10.350A pdb=" N LEU B 684 " --> pdb=" O ARG B 772 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LYS B 774 " --> pdb=" O LEU B 684 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LEU B 730 " --> pdb=" O PRO B 685 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU B 687 " --> pdb=" O LEU B 730 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR B 669 " --> pdb=" O SER B 731 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN B 652 " --> pdb=" O LEU B 672 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 353 removed outlier: 6.723A pdb=" N SER A 363 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU A 351 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU A 361 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR A 359 " --> pdb=" O PRO A 353 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL A 384 " --> pdb=" O GLN A 394 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLN A 394 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N THR A 386 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N VAL A 392 " --> pdb=" O THR A 386 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 415 through 420 removed outlier: 7.817A pdb=" N MET A 415 " --> pdb=" O THR A 433 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N THR A 433 " --> pdb=" O MET A 415 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N SER A 417 " --> pdb=" O ALA A 431 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ALA A 431 " --> pdb=" O SER A 417 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASP A 447 " --> pdb=" O LYS A 467 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS A 467 " --> pdb=" O ASP A 447 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL A 449 " --> pdb=" O LEU A 465 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 471 through 479 removed outlier: 6.690A pdb=" N TYR A 486 " --> pdb=" O GLY A 473 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE A 475 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU A 484 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N TRP A 477 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N LEU A 482 " --> pdb=" O TRP A 477 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 513 " --> pdb=" O THR A 497 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N VAL A 499 " --> pdb=" O ILE A 511 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ILE A 511 " --> pdb=" O VAL A 499 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.606A pdb=" N GLY A 556 " --> pdb=" O PHE A 567 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N GLU A 583 " --> pdb=" O PRO A 566 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU A 568 " --> pdb=" O ILE A 581 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 529 through 531 Processing sheet with id=AB2, first strand: chain 'A' and resid 542 through 543 Processing sheet with id=AB3, first strand: chain 'A' and resid 592 through 596 removed outlier: 6.810A pdb=" N LEU A 613 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LEU A 596 " --> pdb=" O LYS A 611 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LYS A 611 " --> pdb=" O LEU A 596 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 652 through 659 removed outlier: 3.670A pdb=" N GLN A 652 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 669 " --> pdb=" O SER A 731 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LEU A 730 " --> pdb=" O PRO A 685 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU A 687 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 10.350A pdb=" N LEU A 684 " --> pdb=" O ARG A 772 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LYS A 774 " --> pdb=" O LEU A 684 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N CYS A 800 " --> pdb=" O SER A 773 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ILE A 775 " --> pdb=" O CYS A 800 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N ILE A 802 " --> pdb=" O ILE A 775 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL A 777 " --> pdb=" O ILE A 802 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N ARG A 804 " --> pdb=" O VAL A 777 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N GLY A 779 " --> pdb=" O ARG A 804 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 128 through 131 removed outlier: 4.205A pdb=" N GLY B 179 " --> pdb=" O LYS B 142 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 157 through 159 removed outlier: 3.706A pdb=" N THR B 170 " --> pdb=" O ASP B 165 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 205 through 211 removed outlier: 4.370A pdb=" N VAL B 209 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ALA B 219 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N TRP B 211 " --> pdb=" O HIS B 217 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N HIS B 217 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 263 through 265 removed outlier: 6.872A pdb=" N SER B 328 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL B 344 " --> pdb=" O SER B 328 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU B 330 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 348 through 353 removed outlier: 6.723A pdb=" N SER B 363 " --> pdb=" O THR B 349 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU B 351 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU B 361 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR B 359 " --> pdb=" O PRO B 353 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL B 384 " --> pdb=" O GLN B 394 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLN B 394 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N THR B 386 " --> pdb=" O VAL B 392 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N VAL B 392 " --> pdb=" O THR B 386 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 415 through 420 removed outlier: 7.817A pdb=" N MET B 415 " --> pdb=" O THR B 433 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N THR B 433 " --> pdb=" O MET B 415 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N SER B 417 " --> pdb=" O ALA B 431 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ALA B 431 " --> pdb=" O SER B 417 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASP B 447 " --> pdb=" O LYS B 467 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS B 467 " --> pdb=" O ASP B 447 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL B 449 " --> pdb=" O LEU B 465 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 471 through 479 removed outlier: 6.690A pdb=" N TYR B 486 " --> pdb=" O GLY B 473 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE B 475 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU B 484 " --> pdb=" O ILE B 475 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N TRP B 477 " --> pdb=" O LEU B 482 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N LEU B 482 " --> pdb=" O TRP B 477 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE B 513 " --> pdb=" O THR B 497 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N VAL B 499 " --> pdb=" O ILE B 511 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ILE B 511 " --> pdb=" O VAL B 499 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 526 through 527 removed outlier: 3.606A pdb=" N GLY B 556 " --> pdb=" O PHE B 567 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N GLU B 583 " --> pdb=" O PRO B 566 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU B 568 " --> pdb=" O ILE B 581 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 529 through 531 Processing sheet with id=AC5, first strand: chain 'B' and resid 542 through 543 Processing sheet with id=AC6, first strand: chain 'B' and resid 592 through 596 removed outlier: 6.810A pdb=" N LEU B 613 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LEU B 596 " --> pdb=" O LYS B 611 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LYS B 611 " --> pdb=" O LEU B 596 " (cutoff:3.500A) 400 hydrogen bonds defined for protein. 1068 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.12 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4196 1.34 - 1.46: 2812 1.46 - 1.58: 5992 1.58 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 13068 Sorted by residual: bond pdb=" C VAL B 913 " pdb=" N PRO B 914 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.50e+00 bond pdb=" C VAL A 913 " pdb=" N PRO A 914 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.50e+00 bond pdb=" C ASP A 352 " pdb=" O ASP A 352 " ideal model delta sigma weight residual 1.249 1.238 0.011 8.50e-03 1.38e+04 1.70e+00 bond pdb=" C ASP B 352 " pdb=" O ASP B 352 " ideal model delta sigma weight residual 1.249 1.238 0.011 8.50e-03 1.38e+04 1.70e+00 bond pdb=" N PRO A 283 " pdb=" CA PRO A 283 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.31e-02 5.83e+03 7.31e-01 ... (remaining 13063 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 17626 2.17 - 4.33: 134 4.33 - 6.50: 10 6.50 - 8.67: 0 8.67 - 10.84: 2 Bond angle restraints: 17772 Sorted by residual: angle pdb=" CA LEU A 648 " pdb=" CB LEU A 648 " pdb=" CG LEU A 648 " ideal model delta sigma weight residual 116.30 127.14 -10.84 3.50e+00 8.16e-02 9.58e+00 angle pdb=" CA LEU B 648 " pdb=" CB LEU B 648 " pdb=" CG LEU B 648 " ideal model delta sigma weight residual 116.30 127.14 -10.84 3.50e+00 8.16e-02 9.58e+00 angle pdb=" N TRP B 630 " pdb=" CA TRP B 630 " pdb=" C TRP B 630 " ideal model delta sigma weight residual 109.81 115.91 -6.10 2.21e+00 2.05e-01 7.63e+00 angle pdb=" N TRP A 630 " pdb=" CA TRP A 630 " pdb=" C TRP A 630 " ideal model delta sigma weight residual 109.81 115.91 -6.10 2.21e+00 2.05e-01 7.63e+00 angle pdb=" CA VAL A 392 " pdb=" C VAL A 392 " pdb=" N ARG A 393 " ideal model delta sigma weight residual 116.60 120.29 -3.69 1.45e+00 4.76e-01 6.48e+00 ... (remaining 17767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.23: 7044 16.23 - 32.45: 674 32.45 - 48.68: 122 48.68 - 64.90: 20 64.90 - 81.13: 16 Dihedral angle restraints: 7876 sinusoidal: 3200 harmonic: 4676 Sorted by residual: dihedral pdb=" CA ASP A 165 " pdb=" CB ASP A 165 " pdb=" CG ASP A 165 " pdb=" OD1 ASP A 165 " ideal model delta sinusoidal sigma weight residual -30.00 -87.27 57.27 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CA ASP B 165 " pdb=" CB ASP B 165 " pdb=" CG ASP B 165 " pdb=" OD1 ASP B 165 " ideal model delta sinusoidal sigma weight residual -30.00 -87.27 57.27 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CA ASP B 506 " pdb=" CB ASP B 506 " pdb=" CG ASP B 506 " pdb=" OD1 ASP B 506 " ideal model delta sinusoidal sigma weight residual -30.00 -86.25 56.25 1 2.00e+01 2.50e-03 1.07e+01 ... (remaining 7873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1162 0.026 - 0.053: 486 0.053 - 0.079: 120 0.079 - 0.105: 100 0.105 - 0.132: 68 Chirality restraints: 1936 Sorted by residual: chirality pdb=" CA ILE B 276 " pdb=" N ILE B 276 " pdb=" C ILE B 276 " pdb=" CB ILE B 276 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA ILE A 276 " pdb=" N ILE A 276 " pdb=" C ILE A 276 " pdb=" CB ILE A 276 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA ILE B 850 " pdb=" N ILE B 850 " pdb=" C ILE B 850 " pdb=" CB ILE B 850 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 ... (remaining 1933 not shown) Planarity restraints: 2318 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 113 " 0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO B 114 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 114 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 114 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 113 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO A 114 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 114 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 114 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 192 " 0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO A 193 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 193 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 193 " 0.015 5.00e-02 4.00e+02 ... (remaining 2315 not shown) Histogram of nonbonded interaction distances: 2.62 - 3.08: 7718 3.08 - 3.53: 11320 3.53 - 3.99: 17660 3.99 - 4.44: 20580 4.44 - 4.90: 35423 Nonbonded interactions: 92701 Sorted by model distance: nonbonded pdb=" O HIS B 780 " pdb=" O ARG B 804 " model vdw 2.624 3.040 nonbonded pdb=" O HIS A 780 " pdb=" O ARG A 804 " model vdw 2.624 3.040 nonbonded pdb=" N ALA A 346 " pdb=" O ALA A 346 " model vdw 2.629 2.496 nonbonded pdb=" N ALA B 346 " pdb=" O ALA B 346 " model vdw 2.629 2.496 nonbonded pdb=" N GLU B 740 " pdb=" O GLU B 740 " model vdw 2.631 2.496 ... (remaining 92696 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: 0.03 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.310 Find NCS groups from input model: 0.130 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 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 : 0.002 0.044 13068 Z= 0.095 Angle : 0.465 10.835 17772 Z= 0.248 Chirality : 0.040 0.132 1936 Planarity : 0.003 0.037 2318 Dihedral : 13.391 81.126 4872 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % 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: 0.23 (0.22), residues: 1610 helix: 0.69 (0.40), residues: 198 sheet: 1.15 (0.26), residues: 458 loop : -0.45 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 531 TYR 0.013 0.001 TYR B 645 PHE 0.007 0.001 PHE B 785 TRP 0.004 0.000 TRP A 722 HIS 0.001 0.000 HIS B 851 Details of bonding type rmsd/Z covalent geometry : bond 0.00177 / 0.09 (13068) covalent geometry : angle 0.46460 / 0.25 (17772) hydrogen bonds : bond 0.18894 / 12.34 ( 400) hydrogen bonds : angle 6.90697 / 4.90 ( 1068) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 441 MET cc_start: 0.7618 (ttt) cc_final: 0.7202 (ttm) REVERT: A 786 MET cc_start: 0.7952 (ptp) cc_final: 0.7665 (ptp) REVERT: A 898 MET cc_start: 0.8730 (mmt) cc_final: 0.8480 (mmt) REVERT: B 648 LEU cc_start: 0.8784 (tp) cc_final: 0.8572 (tt) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1047 time to fit residues: 13.0711 Evaluate side-chains 53 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 257 ASN A 659 GLN A 780 HIS B 257 ASN B 659 GLN B 780 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.102359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.077583 restraints weight = 20683.328| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.78 r_work: 0.2784 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 13068 Z= 0.151 Angle : 0.526 6.870 17772 Z= 0.268 Chirality : 0.043 0.138 1936 Planarity : 0.004 0.042 2318 Dihedral : 3.478 13.962 1768 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.57 % Allowed : 3.58 % Favored : 95.85 % 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: 0.18 (0.22), residues: 1610 helix: 0.96 (0.37), residues: 222 sheet: 1.08 (0.25), residues: 488 loop : -0.65 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 393 TYR 0.011 0.001 TYR B 472 PHE 0.016 0.002 PHE A 817 TRP 0.010 0.001 TRP B 722 HIS 0.005 0.001 HIS B 851 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 (13068) covalent geometry : angle 0.52597 / 0.27 (17772) hydrogen bonds : bond 0.04950 / 3.29 ( 400) hydrogen bonds : angle 4.80220 / 3.39 ( 1068) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 550 THR cc_start: 0.8342 (m) cc_final: 0.8093 (p) REVERT: B 528 MET cc_start: 0.9039 (mtt) cc_final: 0.8550 (mtt) outliers start: 8 outliers final: 4 residues processed: 57 average time/residue: 0.0904 time to fit residues: 8.6453 Evaluate side-chains 49 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 786 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 152 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 819 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.097877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.073229 restraints weight = 21009.547| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 2.72 r_work: 0.2702 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13068 Z= 0.188 Angle : 0.586 9.158 17772 Z= 0.301 Chirality : 0.045 0.165 1936 Planarity : 0.005 0.050 2318 Dihedral : 3.976 16.160 1768 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.72 % Allowed : 6.95 % Favored : 92.34 % 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: -0.11 (0.21), residues: 1610 helix: 1.07 (0.38), residues: 208 sheet: 0.82 (0.24), residues: 496 loop : -0.88 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 810 TYR 0.012 0.002 TYR B 472 PHE 0.021 0.002 PHE A 817 TRP 0.012 0.002 TRP B 722 HIS 0.009 0.001 HIS B 851 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.19 (13068) covalent geometry : angle 0.58636 / 0.30 (17772) hydrogen bonds : bond 0.05820 / 3.86 ( 400) hydrogen bonds : angle 4.88353 / 3.46 ( 1068) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: A 550 THR cc_start: 0.8393 (m) cc_final: 0.8130 (p) REVERT: A 821 ASP cc_start: 0.7987 (m-30) cc_final: 0.7740 (t0) REVERT: B 747 ASP cc_start: 0.8313 (t70) cc_final: 0.7930 (t0) REVERT: B 821 ASP cc_start: 0.8020 (m-30) cc_final: 0.7435 (p0) outliers start: 10 outliers final: 8 residues processed: 56 average time/residue: 0.0880 time to fit residues: 8.3593 Evaluate side-chains 52 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 786 MET Chi-restraints excluded: chain B residue 854 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 158 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 0.0970 chunk 10 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 819 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.097732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.073155 restraints weight = 20832.006| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.75 r_work: 0.2701 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13068 Z= 0.161 Angle : 0.548 8.009 17772 Z= 0.281 Chirality : 0.044 0.159 1936 Planarity : 0.005 0.051 2318 Dihedral : 3.968 16.081 1768 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.72 % Allowed : 9.31 % Favored : 89.97 % 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 (0.21), residues: 1610 helix: 0.72 (0.36), residues: 230 sheet: 0.74 (0.24), residues: 488 loop : -1.06 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 810 TYR 0.012 0.001 TYR B 472 PHE 0.019 0.002 PHE B 817 TRP 0.012 0.001 TRP B 722 HIS 0.006 0.001 HIS B 851 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.16 (13068) covalent geometry : angle 0.54774 / 0.28 (17772) hydrogen bonds : bond 0.04978 / 3.32 ( 400) hydrogen bonds : angle 4.74952 / 3.37 ( 1068) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.488 Fit side-chains REVERT: A 550 THR cc_start: 0.8319 (m) cc_final: 0.8039 (p) REVERT: A 821 ASP cc_start: 0.8008 (m-30) cc_final: 0.7800 (t0) REVERT: B 172 SER cc_start: 0.8755 (p) cc_final: 0.8374 (m) REVERT: B 528 MET cc_start: 0.9200 (mtt) cc_final: 0.8647 (mtt) REVERT: B 747 ASP cc_start: 0.8318 (t70) cc_final: 0.7973 (t0) outliers start: 10 outliers final: 8 residues processed: 54 average time/residue: 0.0892 time to fit residues: 8.0968 Evaluate side-chains 52 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 786 MET Chi-restraints excluded: chain B residue 854 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 138 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 31 optimal weight: 0.2980 chunk 36 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 111 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.100070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.075675 restraints weight = 20912.179| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.72 r_work: 0.2749 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13068 Z= 0.090 Angle : 0.474 6.946 17772 Z= 0.243 Chirality : 0.041 0.139 1936 Planarity : 0.004 0.049 2318 Dihedral : 3.684 14.524 1768 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.64 % Allowed : 10.17 % Favored : 89.18 % 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: -0.25 (0.21), residues: 1610 helix: 0.72 (0.36), residues: 238 sheet: 0.82 (0.24), residues: 488 loop : -1.01 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 781 TYR 0.011 0.001 TYR A 472 PHE 0.010 0.001 PHE B 785 TRP 0.009 0.001 TRP B 722 HIS 0.004 0.000 HIS B 851 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.09 (13068) covalent geometry : angle 0.47444 / 0.24 (17772) hydrogen bonds : bond 0.03563 / 2.38 ( 400) hydrogen bonds : angle 4.49438 / 3.17 ( 1068) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.419 Fit side-chains REVERT: A 441 MET cc_start: 0.7113 (ttt) cc_final: 0.6673 (ttm) REVERT: A 550 THR cc_start: 0.8375 (m) cc_final: 0.8087 (p) REVERT: B 202 ASP cc_start: 0.8949 (p0) cc_final: 0.8727 (p0) REVERT: B 546 ASN cc_start: 0.8681 (t0) cc_final: 0.8477 (t0) REVERT: B 747 ASP cc_start: 0.8278 (t70) cc_final: 0.7965 (t0) outliers start: 9 outliers final: 8 residues processed: 53 average time/residue: 0.0915 time to fit residues: 8.2635 Evaluate side-chains 51 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 786 MET Chi-restraints excluded: chain B residue 819 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 72 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 146 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 819 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.096904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.072382 restraints weight = 20959.724| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 2.71 r_work: 0.2685 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13068 Z= 0.183 Angle : 0.564 8.725 17772 Z= 0.289 Chirality : 0.044 0.165 1936 Planarity : 0.005 0.053 2318 Dihedral : 4.005 16.330 1768 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.22 % Allowed : 10.32 % Favored : 88.47 % 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: -0.39 (0.21), residues: 1610 helix: 0.86 (0.36), residues: 228 sheet: 0.66 (0.24), residues: 488 loop : -1.12 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 173 TYR 0.011 0.001 TYR B 472 PHE 0.018 0.002 PHE A 817 TRP 0.013 0.002 TRP B 722 HIS 0.005 0.001 HIS B 851 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.18 (13068) covalent geometry : angle 0.56384 / 0.29 (17772) hydrogen bonds : bond 0.05434 / 3.61 ( 400) hydrogen bonds : angle 4.72914 / 3.36 ( 1068) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.371 Fit side-chains REVERT: A 550 THR cc_start: 0.8320 (m) cc_final: 0.8048 (p) REVERT: B 202 ASP cc_start: 0.8899 (p0) cc_final: 0.8681 (p0) REVERT: B 546 ASN cc_start: 0.8606 (t0) cc_final: 0.8272 (t0) outliers start: 17 outliers final: 16 residues processed: 60 average time/residue: 0.0806 time to fit residues: 8.2603 Evaluate side-chains 59 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 786 MET Chi-restraints excluded: chain B residue 819 ASN Chi-restraints excluded: chain B residue 853 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 139 optimal weight: 4.9990 chunk 140 optimal weight: 0.0270 chunk 142 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 14 optimal weight: 0.5980 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 819 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.098353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.073993 restraints weight = 20902.893| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.69 r_work: 0.2719 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 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 : 0.003 0.024 13068 Z= 0.113 Angle : 0.503 7.400 17772 Z= 0.258 Chirality : 0.042 0.151 1936 Planarity : 0.004 0.051 2318 Dihedral : 3.856 15.630 1768 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.07 % Allowed : 10.89 % Favored : 88.04 % 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: -0.35 (0.21), residues: 1610 helix: 0.96 (0.36), residues: 228 sheet: 0.69 (0.24), residues: 488 loop : -1.11 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 894 TYR 0.011 0.001 TYR B 472 PHE 0.012 0.001 PHE A 817 TRP 0.011 0.001 TRP B 722 HIS 0.003 0.001 HIS A 851 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.11 (13068) covalent geometry : angle 0.50317 / 0.26 (17772) hydrogen bonds : bond 0.04278 / 2.84 ( 400) hydrogen bonds : angle 4.58707 / 3.24 ( 1068) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.344 Fit side-chains REVERT: A 550 THR cc_start: 0.8326 (m) cc_final: 0.8022 (p) REVERT: B 546 ASN cc_start: 0.8602 (t0) cc_final: 0.8272 (t0) outliers start: 15 outliers final: 14 residues processed: 56 average time/residue: 0.0830 time to fit residues: 7.8845 Evaluate side-chains 58 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 786 MET Chi-restraints excluded: chain B residue 819 ASN Chi-restraints excluded: chain B residue 853 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 41 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 819 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.096838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.071986 restraints weight = 20852.603| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 2.77 r_work: 0.2681 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2535 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13068 Z= 0.186 Angle : 0.563 8.403 17772 Z= 0.289 Chirality : 0.044 0.165 1936 Planarity : 0.005 0.053 2318 Dihedral : 4.023 16.462 1768 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.36 % Allowed : 10.96 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.50 (0.21), residues: 1610 helix: 0.83 (0.36), residues: 228 sheet: 0.58 (0.24), residues: 488 loop : -1.21 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 515 TYR 0.011 0.001 TYR B 472 PHE 0.018 0.002 PHE A 817 TRP 0.012 0.002 TRP B 722 HIS 0.004 0.001 HIS B 851 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.19 (13068) covalent geometry : angle 0.56281 / 0.29 (17772) hydrogen bonds : bond 0.05327 / 3.55 ( 400) hydrogen bonds : angle 4.69395 / 3.33 ( 1068) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 0.479 Fit side-chains REVERT: A 550 THR cc_start: 0.8320 (m) cc_final: 0.8049 (p) REVERT: B 546 ASN cc_start: 0.8625 (t0) cc_final: 0.8297 (t0) outliers start: 19 outliers final: 17 residues processed: 61 average time/residue: 0.0806 time to fit residues: 8.5044 Evaluate side-chains 59 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 786 MET Chi-restraints excluded: chain B residue 819 ASN Chi-restraints excluded: chain B residue 853 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 45 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 153 optimal weight: 0.0870 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 819 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.099027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.074643 restraints weight = 20690.695| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.70 r_work: 0.2732 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13068 Z= 0.092 Angle : 0.486 7.094 17772 Z= 0.250 Chirality : 0.041 0.144 1936 Planarity : 0.004 0.050 2318 Dihedral : 3.790 15.334 1768 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.07 % Allowed : 11.32 % Favored : 87.61 % 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: -0.38 (0.21), residues: 1610 helix: 1.02 (0.36), residues: 228 sheet: 0.85 (0.26), residues: 432 loop : -1.16 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 171 TYR 0.012 0.001 TYR A 472 PHE 0.011 0.001 PHE B 785 TRP 0.010 0.001 TRP B 722 HIS 0.003 0.000 HIS B 851 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.09 (13068) covalent geometry : angle 0.48640 / 0.25 (17772) hydrogen bonds : bond 0.03754 / 2.49 ( 400) hydrogen bonds : angle 4.50741 / 3.18 ( 1068) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.474 Fit side-chains REVERT: A 550 THR cc_start: 0.8305 (m) cc_final: 0.7997 (p) REVERT: B 546 ASN cc_start: 0.8647 (t0) cc_final: 0.8328 (t0) outliers start: 15 outliers final: 15 residues processed: 57 average time/residue: 0.0901 time to fit residues: 8.6902 Evaluate side-chains 58 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 786 MET Chi-restraints excluded: chain B residue 819 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 25 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 93 optimal weight: 0.2980 chunk 62 optimal weight: 0.0870 chunk 68 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 118 optimal weight: 0.5980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 819 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.100069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.075581 restraints weight = 20889.991| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.72 r_work: 0.2747 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13068 Z= 0.085 Angle : 0.472 6.857 17772 Z= 0.242 Chirality : 0.041 0.138 1936 Planarity : 0.004 0.049 2318 Dihedral : 3.659 14.570 1768 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.86 % Allowed : 11.68 % Favored : 87.46 % 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: -0.28 (0.21), residues: 1610 helix: 1.13 (0.36), residues: 228 sheet: 0.91 (0.26), residues: 432 loop : -1.10 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 173 TYR 0.011 0.001 TYR A 472 PHE 0.010 0.001 PHE B 785 TRP 0.010 0.001 TRP B 722 HIS 0.003 0.000 HIS B 851 Details of bonding type rmsd/Z covalent geometry : bond 0.00194 / 0.08 (13068) covalent geometry : angle 0.47204 / 0.24 (17772) hydrogen bonds : bond 0.03376 / 2.25 ( 400) hydrogen bonds : angle 4.40037 / 3.10 ( 1068) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.536 Fit side-chains REVERT: A 550 THR cc_start: 0.8382 (m) cc_final: 0.8091 (p) REVERT: B 546 ASN cc_start: 0.8655 (t0) cc_final: 0.8337 (t0) REVERT: B 747 ASP cc_start: 0.8129 (t0) cc_final: 0.7894 (t0) outliers start: 12 outliers final: 12 residues processed: 54 average time/residue: 0.0893 time to fit residues: 8.0653 Evaluate side-chains 56 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 786 MET Chi-restraints excluded: chain B residue 819 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 18 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 134 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 156 optimal weight: 0.0770 chunk 48 optimal weight: 5.9990 chunk 2 optimal weight: 0.3980 chunk 73 optimal weight: 0.0970 chunk 95 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.100786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.076323 restraints weight = 20743.112| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.72 r_work: 0.2762 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13068 Z= 0.080 Angle : 0.462 6.720 17772 Z= 0.236 Chirality : 0.041 0.138 1936 Planarity : 0.004 0.048 2318 Dihedral : 3.570 14.275 1768 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.79 % Allowed : 11.82 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.27 (0.21), residues: 1610 helix: 0.97 (0.36), residues: 236 sheet: 0.95 (0.26), residues: 430 loop : -1.07 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 307 TYR 0.011 0.001 TYR A 472 PHE 0.009 0.001 PHE B 785 TRP 0.010 0.001 TRP B 722 HIS 0.004 0.000 HIS B 851 Details of bonding type rmsd/Z covalent geometry : bond 0.00183 / 0.08 (13068) covalent geometry : angle 0.46179 / 0.24 (17772) hydrogen bonds : bond 0.03160 / 2.10 ( 400) hydrogen bonds : angle 4.31751 / 3.04 ( 1068) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2727.60 seconds wall clock time: 47 minutes 29.84 seconds (2849.84 seconds total)