Starting phenix.real_space_refine on Thu Aug 6 02:32:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10es_75117/08_2026/10es_75117.cif Found real_map, /net/cci-nas-00/data/ceres_data/10es_75117/08_2026/10es_75117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10es_75117/08_2026/10es_75117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10es_75117/08_2026/10es_75117.map" model { file = "/net/cci-nas-00/data/ceres_data/10es_75117/08_2026/10es_75117.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10es_75117/08_2026/10es_75117.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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 8006 2.51 5 N 2150 2.21 5 O 2388 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s 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: 12586 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 797, 6293 Classifications: {'peptide': 797} Link IDs: {'PTRANS': 57, 'TRANS': 739} Chain breaks: 1 Chain: "B" Number of atoms: 6293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 797, 6293 Classifications: {'peptide': 797} Link IDs: {'PTRANS': 57, 'TRANS': 739} Chain breaks: 1 Time building chain proxies: 2.40, per 1000 atoms: 0.19 Number of scatterers: 12586 At special positions: 0 Unit cell: (97.27, 168.51, 98.64, 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 2388 8.00 N 2150 7.00 C 8006 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 522.5 milliseconds 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2968 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 24 sheets defined 15.4% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 114 through 122 Processing helix chain 'A' and resid 315 through 327 removed outlier: 3.529A pdb=" N ALA A 319 " --> pdb=" O ASP A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 719 through 726 removed outlier: 3.599A pdb=" N TRP A 722 " --> pdb=" O ALA A 719 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA A 724 " --> pdb=" O LEU A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 747 No H-bonds generated for 'chain 'A' and resid 745 through 747' Processing helix chain 'A' and resid 748 through 768 removed outlier: 3.955A pdb=" N ALA A 755 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA A 760 " --> pdb=" O SER A 756 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 765 " --> pdb=" O VAL A 761 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG A 766 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 794 Processing helix chain 'A' and resid 827 through 834 removed outlier: 4.110A pdb=" N TYR A 831 " --> pdb=" O ALA A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 843 removed outlier: 5.094A pdb=" N ASN A 841 " --> pdb=" O MET A 838 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 843 " --> pdb=" O ALA A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 875 removed outlier: 3.709A pdb=" N SER A 865 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 912 Processing helix chain 'B' and resid 114 through 122 Processing helix chain 'B' and resid 315 through 327 removed outlier: 3.529A pdb=" N ALA B 319 " --> pdb=" O ASP B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 378 Processing helix chain 'B' and resid 719 through 726 removed outlier: 3.599A pdb=" N TRP B 722 " --> pdb=" O ALA B 719 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA B 724 " --> pdb=" O LEU B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 747 No H-bonds generated for 'chain 'B' and resid 745 through 747' Processing helix chain 'B' and resid 748 through 768 removed outlier: 3.955A pdb=" N ALA B 755 " --> pdb=" O GLU B 751 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA B 759 " --> pdb=" O ALA B 755 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL B 765 " --> pdb=" O VAL B 761 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG B 766 " --> pdb=" O GLU B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 794 Processing helix chain 'B' and resid 827 through 834 removed outlier: 4.110A pdb=" N TYR B 831 " --> pdb=" O ALA B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 843 removed outlier: 5.095A pdb=" N ASN B 841 " --> pdb=" O MET B 838 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE B 843 " --> pdb=" O ALA B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 875 removed outlier: 3.709A pdb=" N SER B 865 " --> pdb=" O LEU B 861 " (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: 3.833A pdb=" N ILE A 182 " --> pdb=" O LYS A 195 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 159 removed outlier: 3.529A pdb=" N THR A 170 " --> pdb=" O ASP A 165 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 206 through 210 removed outlier: 4.649A pdb=" N VAL A 209 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ALA A 219 " --> pdb=" O VAL A 209 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 264 through 265 removed outlier: 3.543A pdb=" N VAL A 264 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 272 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 294 through 297 removed outlier: 6.858A pdb=" N GLY B 801 " --> pdb=" O LEU B 848 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ILE B 850 " --> pdb=" O GLY B 801 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ALA B 803 " --> pdb=" O ILE B 850 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N GLY B 852 " --> pdb=" O ALA B 803 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N ILE B 802 " --> pdb=" O ILE B 775 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL B 777 " --> pdb=" O ILE B 802 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ARG B 804 " --> pdb=" O VAL B 777 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLY B 779 " --> pdb=" O ARG B 804 " (cutoff:3.500A) removed outlier: 10.957A pdb=" N LEU B 684 " --> pdb=" O ARG B 772 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LYS B 774 " --> pdb=" O LEU B 684 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU B 730 " --> pdb=" O PRO B 685 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU B 687 " --> pdb=" O LEU B 730 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR B 669 " --> pdb=" O SER B 731 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 353 removed outlier: 7.163A pdb=" N SER A 363 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU A 351 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU A 361 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N TYR A 359 " --> pdb=" O PRO A 353 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL A 384 " --> pdb=" O GLN A 394 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N GLN A 394 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N THR A 386 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N VAL A 392 " --> pdb=" O THR A 386 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 427 through 433 removed outlier: 3.806A pdb=" N TRP A 430 " --> pdb=" O TYR A 450 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU A 465 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 475 through 479 removed outlier: 3.648A pdb=" N SER A 476 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS A 478 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU A 482 " --> pdb=" O CYS A 478 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 526 through 527 removed outlier: 5.388A pdb=" N GLU A 583 " --> pdb=" O PRO A 566 " (cutoff:3.500A) removed outlier: 6.573A 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 590 through 596 removed outlier: 3.858A pdb=" N SER A 615 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU A 613 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LEU A 596 " --> pdb=" O LYS A 611 " (cutoff:3.500A) removed outlier: 7.093A 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: 3.764A pdb=" N THR A 669 " --> pdb=" O SER A 731 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU A 730 " --> pdb=" O PRO A 685 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU A 687 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 10.957A pdb=" N LEU A 684 " --> pdb=" O ARG A 772 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LYS A 774 " --> pdb=" O LEU A 684 " (cutoff:3.500A) removed outlier: 9.102A pdb=" N ILE A 802 " --> pdb=" O ILE A 775 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL A 777 " --> pdb=" O ILE A 802 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ARG A 804 " --> pdb=" O VAL A 777 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLY A 779 " --> pdb=" O ARG A 804 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLY A 801 " --> pdb=" O LEU A 848 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ILE A 850 " --> pdb=" O GLY A 801 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA A 803 " --> pdb=" O ILE A 850 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N GLY A 852 " --> pdb=" O ALA A 803 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 128 through 131 removed outlier: 3.833A pdb=" N ILE B 182 " --> pdb=" O LYS B 195 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 156 through 159 removed outlier: 3.528A pdb=" N THR B 170 " --> pdb=" O ASP B 165 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 206 through 210 removed outlier: 4.648A pdb=" N VAL B 209 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ALA B 219 " --> pdb=" O VAL B 209 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 264 through 265 removed outlier: 3.542A pdb=" N VAL B 264 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU B 272 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 348 through 353 removed outlier: 7.163A pdb=" N SER B 363 " --> pdb=" O THR B 349 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU B 351 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU B 361 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N TYR B 359 " --> pdb=" O PRO B 353 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL B 384 " --> pdb=" O GLN B 394 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N GLN B 394 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N THR B 386 " --> pdb=" O VAL B 392 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N VAL B 392 " --> pdb=" O THR B 386 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 427 through 433 removed outlier: 3.806A pdb=" N TRP B 430 " --> pdb=" O TYR B 450 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU B 465 " --> pdb=" O VAL B 449 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 475 through 479 removed outlier: 3.648A pdb=" N SER B 476 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS B 478 " --> pdb=" O LEU B 482 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU B 482 " --> pdb=" O CYS B 478 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 526 through 527 removed outlier: 5.387A pdb=" N GLU B 583 " --> pdb=" O PRO B 566 " (cutoff:3.500A) removed outlier: 6.573A 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 590 through 596 removed outlier: 3.859A pdb=" N SER B 615 " --> pdb=" O THR B 592 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU B 613 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LEU B 596 " --> pdb=" O LYS B 611 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LYS B 611 " --> pdb=" O LEU B 596 " (cutoff:3.500A) 368 hydrogen bonds defined for protein. 978 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.79 Time building geometry restraints manager: 1.38 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: 4136 1.34 - 1.46: 2859 1.46 - 1.58: 5847 1.58 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 12910 Sorted by residual: bond pdb=" CA ILE B 200 " pdb=" CB ILE B 200 " ideal model delta sigma weight residual 1.537 1.524 0.013 1.29e-02 6.01e+03 9.92e-01 bond pdb=" CA ILE A 200 " pdb=" CB ILE A 200 " ideal model delta sigma weight residual 1.537 1.525 0.012 1.29e-02 6.01e+03 9.34e-01 bond pdb=" C TRP A 630 " pdb=" N PRO A 631 " ideal model delta sigma weight residual 1.335 1.347 -0.011 1.36e-02 5.41e+03 6.68e-01 bond pdb=" CB LYS A 285 " pdb=" CG LYS A 285 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.51e-01 bond pdb=" CB LYS B 285 " pdb=" CG LYS B 285 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 5.94e-01 ... (remaining 12905 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 17109 1.13 - 2.27: 288 2.27 - 3.40: 129 3.40 - 4.53: 26 4.53 - 5.66: 10 Bond angle restraints: 17562 Sorted by residual: angle pdb=" CA ARG A 515 " pdb=" CB ARG A 515 " pdb=" CG ARG A 515 " ideal model delta sigma weight residual 114.10 119.76 -5.66 2.00e+00 2.50e-01 8.02e+00 angle pdb=" CA ARG B 515 " pdb=" CB ARG B 515 " pdb=" CG ARG B 515 " ideal model delta sigma weight residual 114.10 119.75 -5.65 2.00e+00 2.50e-01 7.98e+00 angle pdb=" CB LYS A 285 " pdb=" CG LYS A 285 " pdb=" CD LYS A 285 " ideal model delta sigma weight residual 111.30 116.59 -5.29 2.30e+00 1.89e-01 5.29e+00 angle pdb=" CB LYS B 285 " pdb=" CG LYS B 285 " pdb=" CD LYS B 285 " ideal model delta sigma weight residual 111.30 116.57 -5.27 2.30e+00 1.89e-01 5.25e+00 angle pdb=" CA MET A 441 " pdb=" CB MET A 441 " pdb=" CG MET A 441 " ideal model delta sigma weight residual 114.10 118.22 -4.12 2.00e+00 2.50e-01 4.25e+00 ... (remaining 17557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.12: 6877 16.12 - 32.24: 663 32.24 - 48.35: 174 48.35 - 64.47: 44 64.47 - 80.59: 12 Dihedral angle restraints: 7770 sinusoidal: 3152 harmonic: 4618 Sorted by residual: dihedral pdb=" CA ASP A 214 " pdb=" CB ASP A 214 " pdb=" CG ASP A 214 " pdb=" OD1 ASP A 214 " ideal model delta sinusoidal sigma weight residual -30.00 -89.03 59.03 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA ASP B 214 " pdb=" CB ASP B 214 " pdb=" CG ASP B 214 " pdb=" OD1 ASP B 214 " ideal model delta sinusoidal sigma weight residual -30.00 -88.98 58.98 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CG ARG B 118 " pdb=" CD ARG B 118 " pdb=" NE ARG B 118 " pdb=" CZ ARG B 118 " ideal model delta sinusoidal sigma weight residual 180.00 136.93 43.07 2 1.50e+01 4.44e-03 9.95e+00 ... (remaining 7767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1152 0.027 - 0.054: 492 0.054 - 0.080: 112 0.080 - 0.107: 105 0.107 - 0.134: 55 Chirality restraints: 1916 Sorted by residual: 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 4.49e-01 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 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA VAL A 443 " pdb=" N VAL A 443 " pdb=" C VAL A 443 " pdb=" CB VAL A 443 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 1913 not shown) Planarity restraints: 2288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 560 " -0.025 5.00e-02 4.00e+02 3.80e-02 2.30e+00 pdb=" N PRO A 561 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 561 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 561 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 560 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO B 561 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 561 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 561 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 113 " 0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO B 114 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 114 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 114 " 0.020 5.00e-02 4.00e+02 ... (remaining 2285 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3668 2.83 - 3.35: 10174 3.35 - 3.86: 19120 3.86 - 4.38: 20818 4.38 - 4.90: 38579 Nonbonded interactions: 92359 Sorted by model distance: nonbonded pdb=" OE1 GLU A 299 " pdb=" OH TYR B 911 " model vdw 2.308 3.040 nonbonded pdb=" NH1 ARG B 510 " pdb=" O ILE B 511 " model vdw 2.333 3.120 nonbonded pdb=" NH1 ARG A 510 " pdb=" O ILE A 511 " model vdw 2.334 3.120 nonbonded pdb=" OD1 ASP B 151 " pdb=" NH2 ARG B 154 " model vdw 2.341 3.120 nonbonded pdb=" OD1 ASP A 151 " pdb=" NH2 ARG A 154 " model vdw 2.341 3.120 ... (remaining 92354 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 0.020 Set scattering table: 0.030 Process input model: 10.650 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 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 0.025 12910 Z= 0.081 Angle : 0.457 5.664 17562 Z= 0.225 Chirality : 0.040 0.134 1916 Planarity : 0.004 0.038 2288 Dihedral : 14.131 80.588 4802 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % 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: 0.32 (0.21), residues: 1586 helix: 1.86 (0.39), residues: 182 sheet: 1.21 (0.27), residues: 408 loop : -0.54 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 493 TYR 0.012 0.001 TYR A 645 PHE 0.016 0.001 PHE A 567 TRP 0.015 0.001 TRP A 477 HIS 0.002 0.000 HIS B 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00176 / 0.08 (12910) covalent geometry : angle 0.45657 / 0.22 (17562) hydrogen bonds : bond 0.15638 / 11.29 ( 368) hydrogen bonds : angle 5.97465 / 4.08 ( 978) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 236 TRP cc_start: 0.4546 (m100) cc_final: 0.4263 (m100) REVERT: B 415 MET cc_start: 0.6099 (mtm) cc_final: 0.5385 (mtm) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.3968 time to fit residues: 96.8773 Evaluate side-chains 115 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.0060 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 268 ASN A 366 HIS A 419 ASN A 577 ASN A 628 GLN A 780 HIS B 207 ASN B 268 ASN B 419 ASN B 434 GLN B 577 ASN B 628 GLN B 780 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.170030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.114841 restraints weight = 16947.595| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 3.06 r_work: 0.3247 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12910 Z= 0.132 Angle : 0.584 12.575 17562 Z= 0.290 Chirality : 0.043 0.154 1916 Planarity : 0.005 0.053 2288 Dihedral : 3.225 14.718 1742 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.95 % Allowed : 9.33 % Favored : 88.71 % 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: 0.12 (0.21), residues: 1586 helix: 1.64 (0.39), residues: 194 sheet: 1.07 (0.26), residues: 406 loop : -0.69 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 657 TYR 0.015 0.002 TYR B 486 PHE 0.017 0.002 PHE A 837 TRP 0.016 0.001 TRP B 477 HIS 0.006 0.001 HIS A 875 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (12910) covalent geometry : angle 0.58429 / 0.29 (17562) hydrogen bonds : bond 0.04215 / 2.84 ( 368) hydrogen bonds : angle 4.45841 / 3.01 ( 978) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.330 Fit side-chains REVERT: A 131 PHE cc_start: 0.8938 (m-80) cc_final: 0.8466 (m-80) REVERT: A 684 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8029 (mt) REVERT: B 129 LEU cc_start: 0.6984 (pt) cc_final: 0.6685 (mp) REVERT: B 139 LEU cc_start: 0.7822 (tp) cc_final: 0.7307 (tm) REVERT: B 236 TRP cc_start: 0.6427 (m100) cc_final: 0.6226 (m100) REVERT: B 415 MET cc_start: 0.6617 (mtm) cc_final: 0.6086 (mtm) REVERT: B 528 MET cc_start: 0.7464 (OUTLIER) cc_final: 0.7172 (mtp) outliers start: 27 outliers final: 12 residues processed: 158 average time/residue: 0.2925 time to fit residues: 52.8346 Evaluate side-chains 131 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 866 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 156 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 127 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 298 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.147363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.090967 restraints weight = 16900.292| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 3.58 r_work: 0.2857 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 12910 Z= 0.246 Angle : 0.727 15.349 17562 Z= 0.373 Chirality : 0.049 0.177 1916 Planarity : 0.006 0.084 2288 Dihedral : 4.455 21.400 1742 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.04 % Allowed : 10.85 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.54 (0.20), residues: 1586 helix: 0.39 (0.36), residues: 210 sheet: 0.80 (0.26), residues: 402 loop : -1.08 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 493 TYR 0.020 0.002 TYR A 691 PHE 0.021 0.003 PHE A 688 TRP 0.016 0.002 TRP A 477 HIS 0.008 0.002 HIS B 851 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.25 (12910) covalent geometry : angle 0.72703 / 0.37 (17562) hydrogen bonds : bond 0.07304 / 5.00 ( 368) hydrogen bonds : angle 5.12771 / 3.51 ( 978) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 127 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: A 441 MET cc_start: 0.6976 (ppp) cc_final: 0.6701 (ppp) REVERT: B 126 VAL cc_start: 0.8698 (OUTLIER) cc_final: 0.8164 (p) REVERT: B 129 LEU cc_start: 0.8205 (pt) cc_final: 0.7629 (mp) REVERT: B 192 SER cc_start: 0.6364 (t) cc_final: 0.5733 (p) REVERT: B 196 GLU cc_start: 0.8061 (tt0) cc_final: 0.7782 (pm20) REVERT: B 198 THR cc_start: 0.7855 (OUTLIER) cc_final: 0.7613 (p) REVERT: B 329 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7809 (tp40) REVERT: B 341 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7609 (mp0) REVERT: B 373 VAL cc_start: 0.6394 (t) cc_final: 0.6093 (p) REVERT: B 415 MET cc_start: 0.6547 (mtm) cc_final: 0.5688 (mtm) REVERT: B 461 GLU cc_start: 0.7801 (mp0) cc_final: 0.7347 (mp0) REVERT: B 601 LYS cc_start: 0.7140 (tppp) cc_final: 0.6571 (tmtt) REVERT: B 730 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8797 (tp) REVERT: B 851 HIS cc_start: 0.8843 (OUTLIER) cc_final: 0.8580 (t-90) outliers start: 42 outliers final: 19 residues processed: 158 average time/residue: 0.3588 time to fit residues: 63.7480 Evaluate side-chains 126 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 329 GLN Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 851 HIS Chi-restraints excluded: chain B residue 866 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 139 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 120 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 ASN ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.145952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.093809 restraints weight = 16486.435| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.98 r_work: 0.2934 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.5398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12910 Z= 0.197 Angle : 0.630 11.306 17562 Z= 0.322 Chirality : 0.046 0.170 1916 Planarity : 0.005 0.059 2288 Dihedral : 4.268 19.018 1742 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.97 % Allowed : 13.10 % Favored : 83.94 % 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: -0.73 (0.20), residues: 1586 helix: 0.37 (0.36), residues: 210 sheet: 0.61 (0.26), residues: 414 loop : -1.23 (0.18), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 493 TYR 0.024 0.002 TYR A 521 PHE 0.020 0.002 PHE A 131 TRP 0.017 0.002 TRP A 477 HIS 0.006 0.002 HIS B 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.20 (12910) covalent geometry : angle 0.63036 / 0.32 (17562) hydrogen bonds : bond 0.05713 / 3.86 ( 368) hydrogen bonds : angle 4.86404 / 3.31 ( 978) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 115 time to evaluate : 0.463 Fit side-chains REVERT: A 329 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.7400 (tt0) REVERT: A 441 MET cc_start: 0.6964 (ppp) cc_final: 0.6657 (ppp) REVERT: A 521 TYR cc_start: 0.8131 (p90) cc_final: 0.7888 (p90) REVERT: A 523 ASP cc_start: 0.8089 (t0) cc_final: 0.7884 (t0) REVERT: B 126 VAL cc_start: 0.8880 (OUTLIER) cc_final: 0.8566 (p) REVERT: B 192 SER cc_start: 0.7495 (t) cc_final: 0.6861 (p) REVERT: B 352 ASP cc_start: 0.8629 (t0) cc_final: 0.8152 (t0) REVERT: B 514 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.7184 (t0) REVERT: B 601 LYS cc_start: 0.7830 (tppp) cc_final: 0.7241 (tmtt) outliers start: 41 outliers final: 17 residues processed: 147 average time/residue: 0.3634 time to fit residues: 59.6688 Evaluate side-chains 124 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 514 ASP Chi-restraints excluded: chain B residue 866 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 56 optimal weight: 0.4980 chunk 120 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 155 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN B 466 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.147387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.090913 restraints weight = 16862.937| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.39 r_work: 0.2875 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.5410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12910 Z= 0.106 Angle : 0.540 8.696 17562 Z= 0.272 Chirality : 0.043 0.142 1916 Planarity : 0.005 0.050 2288 Dihedral : 3.916 17.078 1742 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.75 % Allowed : 14.54 % Favored : 82.71 % 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: -0.43 (0.21), residues: 1586 helix: 1.28 (0.38), residues: 192 sheet: 0.62 (0.26), residues: 430 loop : -1.09 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 493 TYR 0.013 0.001 TYR A 521 PHE 0.010 0.001 PHE A 131 TRP 0.020 0.001 TRP A 477 HIS 0.003 0.001 HIS B 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (12910) covalent geometry : angle 0.54018 / 0.27 (17562) hydrogen bonds : bond 0.04445 / 2.97 ( 368) hydrogen bonds : angle 4.69844 / 3.20 ( 978) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 112 time to evaluate : 0.392 Fit side-chains REVERT: A 136 ASP cc_start: 0.8773 (t0) cc_final: 0.8013 (t0) REVERT: A 441 MET cc_start: 0.6961 (OUTLIER) cc_final: 0.6596 (ppp) REVERT: A 521 TYR cc_start: 0.7915 (p90) cc_final: 0.7619 (p90) REVERT: B 126 VAL cc_start: 0.8629 (OUTLIER) cc_final: 0.8261 (p) REVERT: B 192 SER cc_start: 0.7175 (t) cc_final: 0.6449 (p) REVERT: B 352 ASP cc_start: 0.8207 (t0) cc_final: 0.7569 (t0) REVERT: B 371 PHE cc_start: 0.7908 (m-80) cc_final: 0.7659 (m-80) REVERT: B 415 MET cc_start: 0.7379 (mtp) cc_final: 0.6937 (ptp) REVERT: B 551 TYR cc_start: 0.7906 (m-80) cc_final: 0.7685 (m-80) REVERT: B 601 LYS cc_start: 0.7916 (tppp) cc_final: 0.7253 (tmtt) outliers start: 38 outliers final: 17 residues processed: 138 average time/residue: 0.3544 time to fit residues: 54.9136 Evaluate side-chains 124 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 329 GLN Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 866 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 154 optimal weight: 3.9990 chunk 39 optimal weight: 0.2980 chunk 100 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 ASN ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.143963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.089657 restraints weight = 16521.233| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.05 r_work: 0.2924 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.5661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12910 Z= 0.152 Angle : 0.579 10.515 17562 Z= 0.293 Chirality : 0.044 0.156 1916 Planarity : 0.005 0.066 2288 Dihedral : 4.039 18.081 1742 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.82 % Allowed : 14.98 % Favored : 82.20 % 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: -0.62 (0.21), residues: 1586 helix: 0.67 (0.37), residues: 210 sheet: 0.70 (0.26), residues: 438 loop : -1.28 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 493 TYR 0.014 0.001 TYR A 521 PHE 0.015 0.002 PHE A 837 TRP 0.018 0.002 TRP A 477 HIS 0.005 0.001 HIS B 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.15 (12910) covalent geometry : angle 0.57873 / 0.29 (17562) hydrogen bonds : bond 0.05315 / 3.58 ( 368) hydrogen bonds : angle 4.71266 / 3.21 ( 978) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 105 time to evaluate : 0.323 Fit side-chains REVERT: A 173 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.6656 (mpt180) REVERT: A 329 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.7353 (tt0) REVERT: A 441 MET cc_start: 0.6994 (OUTLIER) cc_final: 0.6570 (ppp) REVERT: A 521 TYR cc_start: 0.8117 (p90) cc_final: 0.7821 (p90) REVERT: B 126 VAL cc_start: 0.8995 (OUTLIER) cc_final: 0.8693 (p) REVERT: B 192 SER cc_start: 0.7801 (t) cc_final: 0.7112 (p) REVERT: B 202 ASP cc_start: 0.9204 (OUTLIER) cc_final: 0.8989 (t70) REVERT: B 352 ASP cc_start: 0.8507 (t0) cc_final: 0.8088 (t0) REVERT: B 415 MET cc_start: 0.7828 (mtp) cc_final: 0.7448 (ptp) REVERT: B 601 LYS cc_start: 0.8161 (tppp) cc_final: 0.7570 (tmtt) REVERT: B 863 MET cc_start: 0.7781 (ppp) cc_final: 0.7055 (mtm) outliers start: 39 outliers final: 23 residues processed: 137 average time/residue: 0.3925 time to fit residues: 60.1175 Evaluate side-chains 128 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 329 GLN Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 866 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.145638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.091842 restraints weight = 16446.143| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.03 r_work: 0.2957 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.5658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12910 Z= 0.101 Angle : 0.527 8.499 17562 Z= 0.265 Chirality : 0.043 0.144 1916 Planarity : 0.004 0.049 2288 Dihedral : 3.806 16.663 1742 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.46 % Allowed : 15.70 % Favored : 81.84 % 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: -0.42 (0.21), residues: 1586 helix: 1.46 (0.38), residues: 192 sheet: 0.56 (0.25), residues: 464 loop : -1.15 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 515 TYR 0.012 0.001 TYR A 521 PHE 0.008 0.001 PHE A 131 TRP 0.023 0.001 TRP A 477 HIS 0.003 0.001 HIS B 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (12910) covalent geometry : angle 0.52668 / 0.26 (17562) hydrogen bonds : bond 0.04194 / 2.80 ( 368) hydrogen bonds : angle 4.56921 / 3.11 ( 978) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 106 time to evaluate : 0.302 Fit side-chains REVERT: A 136 ASP cc_start: 0.8858 (t0) cc_final: 0.8105 (t0) REVERT: A 329 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7239 (tt0) REVERT: A 441 MET cc_start: 0.6965 (OUTLIER) cc_final: 0.6731 (ppp) REVERT: A 521 TYR cc_start: 0.8024 (p90) cc_final: 0.7689 (p90) REVERT: B 126 VAL cc_start: 0.8981 (OUTLIER) cc_final: 0.8675 (p) REVERT: B 252 GLN cc_start: 0.8840 (mm110) cc_final: 0.8605 (mp10) REVERT: B 352 ASP cc_start: 0.8424 (t0) cc_final: 0.8042 (t0) REVERT: B 415 MET cc_start: 0.7798 (mtp) cc_final: 0.7432 (ptp) REVERT: B 601 LYS cc_start: 0.8192 (tppp) cc_final: 0.7625 (tmtt) REVERT: B 863 MET cc_start: 0.7598 (ppp) cc_final: 0.6927 (mtm) REVERT: B 898 MET cc_start: 0.8766 (mmt) cc_final: 0.8292 (mmm) outliers start: 34 outliers final: 17 residues processed: 132 average time/residue: 0.3828 time to fit residues: 56.6315 Evaluate side-chains 122 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 329 GLN Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 866 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 113 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 99 optimal weight: 0.0870 chunk 16 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 ASN A 366 HIS ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 851 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.145660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.092872 restraints weight = 16273.557| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.94 r_work: 0.2949 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.5825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12910 Z= 0.134 Angle : 0.564 9.962 17562 Z= 0.285 Chirality : 0.044 0.153 1916 Planarity : 0.005 0.050 2288 Dihedral : 3.921 16.981 1742 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.39 % Allowed : 16.21 % Favored : 81.40 % 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: -0.59 (0.21), residues: 1586 helix: 0.82 (0.37), residues: 210 sheet: 0.74 (0.26), residues: 438 loop : -1.29 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 515 TYR 0.012 0.001 TYR A 521 PHE 0.013 0.001 PHE A 837 TRP 0.023 0.001 TRP A 477 HIS 0.005 0.001 HIS B 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.13 (12910) covalent geometry : angle 0.56443 / 0.28 (17562) hydrogen bonds : bond 0.04964 / 3.34 ( 368) hydrogen bonds : angle 4.60601 / 3.13 ( 978) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 0.293 Fit side-chains REVERT: A 136 ASP cc_start: 0.8858 (t0) cc_final: 0.8121 (t0) REVERT: A 173 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.6634 (mpt180) REVERT: A 285 LYS cc_start: 0.8153 (mmmt) cc_final: 0.7763 (mtpp) REVERT: A 329 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.7373 (tt0) REVERT: A 441 MET cc_start: 0.7042 (OUTLIER) cc_final: 0.6820 (ppp) REVERT: A 493 ARG cc_start: 0.8117 (mmm-85) cc_final: 0.7740 (mmm-85) REVERT: A 521 TYR cc_start: 0.8082 (p90) cc_final: 0.7824 (p90) REVERT: B 126 VAL cc_start: 0.9088 (OUTLIER) cc_final: 0.8819 (p) REVERT: B 252 GLN cc_start: 0.8858 (mm110) cc_final: 0.8609 (mp10) REVERT: B 352 ASP cc_start: 0.8470 (t0) cc_final: 0.8116 (OUTLIER) REVERT: B 415 MET cc_start: 0.7852 (mtp) cc_final: 0.7488 (ptp) REVERT: B 464 VAL cc_start: 0.6830 (t) cc_final: 0.6346 (t) REVERT: B 524 PRO cc_start: 0.7077 (Cg_exo) cc_final: 0.6726 (Cg_endo) REVERT: B 601 LYS cc_start: 0.8276 (tppp) cc_final: 0.7675 (tmtt) REVERT: B 632 ASP cc_start: 0.5428 (OUTLIER) cc_final: 0.5130 (p0) REVERT: B 863 MET cc_start: 0.7594 (ppp) cc_final: 0.6996 (mtm) outliers start: 33 outliers final: 16 residues processed: 130 average time/residue: 0.4105 time to fit residues: 59.4086 Evaluate side-chains 120 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 329 GLN Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 866 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 144 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.144290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.087704 restraints weight = 16637.343| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.78 r_work: 0.2883 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.6200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 12910 Z= 0.232 Angle : 0.663 11.508 17562 Z= 0.339 Chirality : 0.048 0.183 1916 Planarity : 0.006 0.055 2288 Dihedral : 4.452 20.907 1742 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.32 % Allowed : 16.06 % Favored : 81.62 % 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: -0.99 (0.20), residues: 1586 helix: 0.40 (0.37), residues: 208 sheet: 0.23 (0.25), residues: 448 loop : -1.41 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 515 TYR 0.020 0.002 TYR A 691 PHE 0.019 0.002 PHE A 837 TRP 0.018 0.002 TRP A 477 HIS 0.006 0.001 HIS B 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.23 (12910) covalent geometry : angle 0.66265 / 0.34 (17562) hydrogen bonds : bond 0.06567 / 4.42 ( 368) hydrogen bonds : angle 4.86808 / 3.31 ( 978) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 107 time to evaluate : 0.475 Fit side-chains REVERT: A 173 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.6972 (mpt180) REVERT: A 329 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.7469 (tt0) REVERT: A 399 PRO cc_start: 0.8290 (Cg_endo) cc_final: 0.8024 (Cg_exo) REVERT: A 415 MET cc_start: 0.7683 (ptp) cc_final: 0.6998 (ptt) REVERT: A 498 TRP cc_start: 0.6902 (m100) cc_final: 0.6486 (m100) REVERT: A 521 TYR cc_start: 0.8138 (p90) cc_final: 0.7702 (p90) REVERT: A 629 LEU cc_start: 0.7229 (tt) cc_final: 0.6998 (tm) REVERT: B 126 VAL cc_start: 0.9118 (OUTLIER) cc_final: 0.8884 (p) REVERT: B 252 GLN cc_start: 0.8943 (mm110) cc_final: 0.8674 (mp10) REVERT: B 352 ASP cc_start: 0.8558 (t0) cc_final: 0.8213 (OUTLIER) REVERT: B 415 MET cc_start: 0.8127 (mtp) cc_final: 0.7778 (ptp) REVERT: B 524 PRO cc_start: 0.7392 (Cg_exo) cc_final: 0.7110 (Cg_endo) REVERT: B 632 ASP cc_start: 0.4848 (OUTLIER) cc_final: 0.4604 (p0) REVERT: B 636 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7378 (tm-30) REVERT: B 856 ASN cc_start: 0.8690 (p0) cc_final: 0.8470 (m110) REVERT: B 863 MET cc_start: 0.7763 (ppp) cc_final: 0.7078 (mtm) outliers start: 32 outliers final: 19 residues processed: 133 average time/residue: 0.3885 time to fit residues: 57.7244 Evaluate side-chains 123 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 329 GLN Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 636 GLN Chi-restraints excluded: chain B residue 866 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 151 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 41 optimal weight: 0.4980 chunk 109 optimal weight: 1.9990 chunk 99 optimal weight: 0.0470 chunk 135 optimal weight: 0.8980 chunk 61 optimal weight: 0.3980 chunk 29 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.146892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.094854 restraints weight = 16409.967| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.93 r_work: 0.2951 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.6083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12910 Z= 0.098 Angle : 0.541 9.557 17562 Z= 0.273 Chirality : 0.043 0.163 1916 Planarity : 0.005 0.049 2288 Dihedral : 3.953 17.647 1742 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.16 % Allowed : 17.15 % Favored : 81.69 % 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: -0.55 (0.21), residues: 1586 helix: 1.42 (0.39), residues: 192 sheet: 0.59 (0.26), residues: 448 loop : -1.29 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 416 TYR 0.010 0.001 TYR B 486 PHE 0.007 0.001 PHE B 785 TRP 0.031 0.001 TRP A 477 HIS 0.002 0.001 HIS B 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (12910) covalent geometry : angle 0.54091 / 0.27 (17562) hydrogen bonds : bond 0.04078 / 2.71 ( 368) hydrogen bonds : angle 4.59360 / 3.12 ( 978) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.305 Fit side-chains REVERT: A 136 ASP cc_start: 0.8844 (t0) cc_final: 0.8123 (t0) REVERT: A 329 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.7297 (tt0) REVERT: A 415 MET cc_start: 0.7434 (ptp) cc_final: 0.6948 (ptt) REVERT: A 498 TRP cc_start: 0.6707 (m100) cc_final: 0.6332 (m100) REVERT: B 352 ASP cc_start: 0.8506 (t0) cc_final: 0.8147 (t0) REVERT: B 415 MET cc_start: 0.8003 (mtp) cc_final: 0.7621 (ptp) REVERT: B 510 ARG cc_start: 0.7623 (mmm160) cc_final: 0.7193 (mmm160) REVERT: B 524 PRO cc_start: 0.7424 (Cg_exo) cc_final: 0.7147 (Cg_endo) REVERT: B 863 MET cc_start: 0.7500 (ppp) cc_final: 0.6942 (mtm) REVERT: B 898 MET cc_start: 0.8758 (mmt) cc_final: 0.8289 (mmm) outliers start: 16 outliers final: 12 residues processed: 116 average time/residue: 0.3913 time to fit residues: 51.1572 Evaluate side-chains 112 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 329 GLN Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 866 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 20 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.143303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.089664 restraints weight = 16427.802| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.04 r_work: 0.2927 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.6145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12910 Z= 0.129 Angle : 0.574 11.058 17562 Z= 0.287 Chirality : 0.044 0.162 1916 Planarity : 0.005 0.056 2288 Dihedral : 3.990 17.919 1742 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.45 % Allowed : 17.15 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.21), residues: 1586 helix: 0.89 (0.38), residues: 208 sheet: 0.59 (0.26), residues: 446 loop : -1.35 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 416 TYR 0.011 0.001 TYR A 645 PHE 0.012 0.001 PHE A 837 TRP 0.029 0.002 TRP A 477 HIS 0.005 0.001 HIS B 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (12910) covalent geometry : angle 0.57433 / 0.29 (17562) hydrogen bonds : bond 0.04761 / 3.19 ( 368) hydrogen bonds : angle 4.56197 / 3.10 ( 978) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3577.37 seconds wall clock time: 61 minutes 22.87 seconds (3682.87 seconds total)