Starting phenix.real_space_refine on Fri Oct 30 09:21:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9syv_55355/10_2026/9syv_55355.cif Found real_map, /net/cci-nas-00/data/ceres_data/9syv_55355/10_2026/9syv_55355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9syv_55355/10_2026/9syv_55355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9syv_55355/10_2026/9syv_55355.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9syv_55355/10_2026/9syv_55355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9syv_55355/10_2026/9syv_55355.map" } resolution = 2.89 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= 0.001 sd= 0.043 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: 5 Type Number sf(0) Gaussians S 72 5.16 5 C 11136 2.51 5 N 2943 2.21 5 O 3039 1.98 5 H 17802 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34992 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 11090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 722, 11090 Classifications: {'peptide': 722} Link IDs: {'PTRANS': 30, 'TRANS': 691} Chain breaks: 1 Chain: "D" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 574 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 2, 'TRANS': 33} Restraints were copied for chains: B, C, E, F Time building chain proxies: 17.15, per 1000 atoms: 0.49 Number of scatterers: 34992 At special positions: 0 Unit cell: (124.8, 123.5, 119.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 O 3039 8.00 N 2943 7.00 C 11136 6.00 H 17802 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 434 " - pdb=" SG CYS E 39 " distance=2.03 Simple disulfide: pdb=" SG CYS B 434 " - pdb=" SG CYS F 39 " distance=2.04 Simple disulfide: pdb=" SG CYS C 434 " - pdb=" SG CYS D 39 " distance=2.03 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: 3.23 Conformation dependent library (CDL) restraints added in 961.7 milliseconds 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4140 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 9 sheets defined 72.8% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 18 through 27 Processing helix chain 'A' and resid 27 through 45 Processing helix chain 'A' and resid 48 through 56 Processing helix chain 'A' and resid 65 through 78 Processing helix chain 'A' and resid 97 through 115 removed outlier: 3.898A pdb=" N ALA A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 133 removed outlier: 4.658A pdb=" N ALA A 133 " --> pdb=" O PRO A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 136 No H-bonds generated for 'chain 'A' and resid 134 through 136' Processing helix chain 'A' and resid 155 through 172 Processing helix chain 'A' and resid 184 through 219 removed outlier: 4.074A pdb=" N ARG A 198 " --> pdb=" O HIS A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 249 Processing helix chain 'A' and resid 255 through 287 Processing helix chain 'A' and resid 290 through 319 removed outlier: 5.588A pdb=" N HIS A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N VAL A 305 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 323 Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 331 through 360 removed outlier: 3.613A pdb=" N SER A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) Proline residue: A 351 - end of helix removed outlier: 3.559A pdb=" N PHE A 360 " --> pdb=" O VAL A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 384 removed outlier: 3.759A pdb=" N GLY A 378 " --> pdb=" O TRP A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 401 removed outlier: 3.665A pdb=" N VAL A 388 " --> pdb=" O TRP A 384 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 433 removed outlier: 3.730A pdb=" N GLN A 424 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY A 425 " --> pdb=" O PRO A 421 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 469 removed outlier: 3.679A pdb=" N VAL A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 704 Processing helix chain 'A' and resid 723 through 741 removed outlier: 3.708A pdb=" N ILE A 730 " --> pdb=" O GLY A 726 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASP A 731 " --> pdb=" O ILE A 727 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 732 " --> pdb=" O LYS A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 749 removed outlier: 4.565A pdb=" N ASP A 748 " --> pdb=" O PRO A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 791 Processing helix chain 'A' and resid 792 through 820 removed outlier: 3.761A pdb=" N ALA A 796 " --> pdb=" O ALA A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 857 removed outlier: 4.202A pdb=" N ASP A 844 " --> pdb=" O ALA A 840 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR A 845 " --> pdb=" O VAL A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 889 removed outlier: 4.463A pdb=" N LYS A 874 " --> pdb=" O GLY A 870 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL A 875 " --> pdb=" O GLY A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 893 Processing helix chain 'A' and resid 895 through 915 Processing helix chain 'A' and resid 915 through 929 removed outlier: 4.726A pdb=" N THR A 921 " --> pdb=" O ARG A 917 " (cutoff:3.500A) Proline residue: A 922 - end of helix Processing helix chain 'A' and resid 930 through 934 removed outlier: 3.512A pdb=" N TRP A 934 " --> pdb=" O TRP A 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 27 Processing helix chain 'B' and resid 27 through 45 Processing helix chain 'B' and resid 48 through 56 Processing helix chain 'B' and resid 65 through 78 Processing helix chain 'B' and resid 97 through 115 removed outlier: 3.899A pdb=" N ALA B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 133 removed outlier: 4.657A pdb=" N ALA B 133 " --> pdb=" O PRO B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 155 through 172 Processing helix chain 'B' and resid 184 through 219 removed outlier: 4.074A pdb=" N ARG B 198 " --> pdb=" O HIS B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 249 Processing helix chain 'B' and resid 255 through 287 Processing helix chain 'B' and resid 290 through 319 removed outlier: 5.588A pdb=" N HIS B 304 " --> pdb=" O ARG B 300 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N VAL B 305 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 323 Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 331 through 360 removed outlier: 3.613A pdb=" N SER B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR B 348 " --> pdb=" O ALA B 344 " (cutoff:3.500A) Proline residue: B 351 - end of helix removed outlier: 3.559A pdb=" N PHE B 360 " --> pdb=" O VAL B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 384 removed outlier: 3.758A pdb=" N GLY B 378 " --> pdb=" O TRP B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 401 removed outlier: 3.665A pdb=" N VAL B 388 " --> pdb=" O TRP B 384 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY B 399 " --> pdb=" O ILE B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 433 removed outlier: 3.731A pdb=" N GLN B 424 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY B 425 " --> pdb=" O PRO B 421 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS B 432 " --> pdb=" O ALA B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 469 removed outlier: 3.680A pdb=" N VAL B 459 " --> pdb=" O ALA B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 704 Processing helix chain 'B' and resid 723 through 741 removed outlier: 3.708A pdb=" N ILE B 730 " --> pdb=" O GLY B 726 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ASP B 731 " --> pdb=" O ILE B 727 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA B 732 " --> pdb=" O LYS B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 removed outlier: 4.565A pdb=" N ASP B 748 " --> pdb=" O PRO B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 791 Processing helix chain 'B' and resid 792 through 820 removed outlier: 3.760A pdb=" N ALA B 796 " --> pdb=" O ALA B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 857 removed outlier: 4.202A pdb=" N ASP B 844 " --> pdb=" O ALA B 840 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR B 845 " --> pdb=" O VAL B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 889 removed outlier: 4.463A pdb=" N LYS B 874 " --> pdb=" O GLY B 870 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL B 875 " --> pdb=" O GLY B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 893 Processing helix chain 'B' and resid 895 through 915 Processing helix chain 'B' and resid 915 through 929 removed outlier: 4.726A pdb=" N THR B 921 " --> pdb=" O ARG B 917 " (cutoff:3.500A) Proline residue: B 922 - end of helix Processing helix chain 'B' and resid 930 through 934 removed outlier: 3.512A pdb=" N TRP B 934 " --> pdb=" O TRP B 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 27 Processing helix chain 'C' and resid 27 through 45 Processing helix chain 'C' and resid 48 through 56 Processing helix chain 'C' and resid 65 through 78 Processing helix chain 'C' and resid 97 through 115 removed outlier: 3.899A pdb=" N ALA C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 133 removed outlier: 4.657A pdb=" N ALA C 133 " --> pdb=" O PRO C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 136 No H-bonds generated for 'chain 'C' and resid 134 through 136' Processing helix chain 'C' and resid 155 through 172 Processing helix chain 'C' and resid 184 through 219 removed outlier: 4.074A pdb=" N ARG C 198 " --> pdb=" O HIS C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 249 Processing helix chain 'C' and resid 255 through 287 Processing helix chain 'C' and resid 290 through 319 removed outlier: 5.587A pdb=" N HIS C 304 " --> pdb=" O ARG C 300 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N VAL C 305 " --> pdb=" O GLY C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 323 Processing helix chain 'C' and resid 325 through 330 Processing helix chain 'C' and resid 331 through 360 removed outlier: 3.613A pdb=" N SER C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR C 348 " --> pdb=" O ALA C 344 " (cutoff:3.500A) Proline residue: C 351 - end of helix removed outlier: 3.559A pdb=" N PHE C 360 " --> pdb=" O VAL C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 384 removed outlier: 3.759A pdb=" N GLY C 378 " --> pdb=" O TRP C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 401 removed outlier: 3.665A pdb=" N VAL C 388 " --> pdb=" O TRP C 384 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY C 399 " --> pdb=" O ILE C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 433 removed outlier: 3.731A pdb=" N GLN C 424 " --> pdb=" O ILE C 420 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY C 425 " --> pdb=" O PRO C 421 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS C 432 " --> pdb=" O ALA C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 469 removed outlier: 3.680A pdb=" N VAL C 459 " --> pdb=" O ALA C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 704 Processing helix chain 'C' and resid 723 through 741 removed outlier: 3.709A pdb=" N ILE C 730 " --> pdb=" O GLY C 726 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ASP C 731 " --> pdb=" O ILE C 727 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA C 732 " --> pdb=" O LYS C 728 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 749 removed outlier: 4.565A pdb=" N ASP C 748 " --> pdb=" O PRO C 745 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 791 Processing helix chain 'C' and resid 792 through 820 removed outlier: 3.761A pdb=" N ALA C 796 " --> pdb=" O ALA C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 829 through 857 removed outlier: 4.201A pdb=" N ASP C 844 " --> pdb=" O ALA C 840 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR C 845 " --> pdb=" O VAL C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 860 through 889 removed outlier: 4.463A pdb=" N LYS C 874 " --> pdb=" O GLY C 870 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL C 875 " --> pdb=" O GLY C 871 " (cutoff:3.500A) Processing helix chain 'C' and resid 890 through 893 Processing helix chain 'C' and resid 895 through 915 Processing helix chain 'C' and resid 915 through 929 removed outlier: 4.726A pdb=" N THR C 921 " --> pdb=" O ARG C 917 " (cutoff:3.500A) Proline residue: C 922 - end of helix Processing helix chain 'C' and resid 930 through 934 removed outlier: 3.513A pdb=" N TRP C 934 " --> pdb=" O TRP C 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 28 removed outlier: 4.243A pdb=" N VAL D 13 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL D 14 " --> pdb=" O VAL D 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 28 removed outlier: 4.244A pdb=" N VAL E 13 " --> pdb=" O LEU E 9 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL E 14 " --> pdb=" O VAL E 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 28 removed outlier: 4.244A pdb=" N VAL F 13 " --> pdb=" O LEU F 9 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL F 14 " --> pdb=" O VAL F 10 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 123 removed outlier: 3.983A pdb=" N GLN A 146 " --> pdb=" O GLN A 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 408 through 409 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 477 removed outlier: 3.595A pdb=" N ARG A 475 " --> pdb=" O LEU A 716 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 119 through 123 removed outlier: 3.983A pdb=" N GLN B 146 " --> pdb=" O GLN B 123 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 408 through 409 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 477 removed outlier: 3.595A pdb=" N ARG B 475 " --> pdb=" O LEU B 716 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 119 through 123 removed outlier: 3.983A pdb=" N GLN C 146 " --> pdb=" O GLN C 123 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 408 through 409 Processing sheet with id=AA9, first strand: chain 'C' and resid 473 through 477 removed outlier: 3.595A pdb=" N ARG C 475 " --> pdb=" O LEU C 716 " (cutoff:3.500A) 1290 hydrogen bonds defined for protein. 3807 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: 8.25 Time building geometry restraints manager: 4.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 17802 1.03 - 1.23: 179 1.23 - 1.43: 6950 1.43 - 1.63: 10283 1.63 - 1.82: 138 Bond restraints: 35352 Sorted by residual: bond pdb=" C SER A 61 " pdb=" N PRO A 62 " ideal model delta sigma weight residual 1.335 1.355 -0.020 8.70e-03 1.32e+04 5.46e+00 bond pdb=" C SER B 61 " pdb=" N PRO B 62 " ideal model delta sigma weight residual 1.335 1.354 -0.019 8.70e-03 1.32e+04 4.91e+00 bond pdb=" C SER C 61 " pdb=" N PRO C 62 " ideal model delta sigma weight residual 1.335 1.354 -0.019 8.70e-03 1.32e+04 4.90e+00 bond pdb=" CB LYS B 63 " pdb=" CG LYS B 63 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.29e+00 bond pdb=" CB LYS C 63 " pdb=" CG LYS C 63 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.18e+00 ... (remaining 35347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 60858 1.36 - 2.73: 2872 2.73 - 4.09: 290 4.09 - 5.45: 84 5.45 - 6.82: 33 Bond angle restraints: 64137 Sorted by residual: angle pdb=" CB LYS A 63 " pdb=" CG LYS A 63 " pdb=" CD LYS A 63 " ideal model delta sigma weight residual 111.30 118.12 -6.82 2.30e+00 1.89e-01 8.78e+00 angle pdb=" CB LYS B 63 " pdb=" CG LYS B 63 " pdb=" CD LYS B 63 " ideal model delta sigma weight residual 111.30 118.11 -6.81 2.30e+00 1.89e-01 8.76e+00 angle pdb=" CB LYS C 63 " pdb=" CG LYS C 63 " pdb=" CD LYS C 63 " ideal model delta sigma weight residual 111.30 118.08 -6.78 2.30e+00 1.89e-01 8.68e+00 angle pdb=" CA TYR C 327 " pdb=" CB TYR C 327 " pdb=" CG TYR C 327 " ideal model delta sigma weight residual 113.90 119.15 -5.25 1.80e+00 3.09e-01 8.50e+00 angle pdb=" CA TYR A 327 " pdb=" CB TYR A 327 " pdb=" CG TYR A 327 " ideal model delta sigma weight residual 113.90 119.13 -5.23 1.80e+00 3.09e-01 8.43e+00 ... (remaining 64132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 14452 17.86 - 35.72: 1383 35.72 - 53.58: 511 53.58 - 71.44: 142 71.44 - 89.29: 36 Dihedral angle restraints: 16524 sinusoidal: 8973 harmonic: 7551 Sorted by residual: dihedral pdb=" CA HIS B 717 " pdb=" C HIS B 717 " pdb=" N ARG B 718 " pdb=" CA ARG B 718 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA HIS C 717 " pdb=" C HIS C 717 " pdb=" N ARG C 718 " pdb=" CA ARG C 718 " ideal model delta harmonic sigma weight residual 180.00 160.65 19.35 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA HIS A 717 " pdb=" C HIS A 717 " pdb=" N ARG A 718 " pdb=" CA ARG A 718 " ideal model delta harmonic sigma weight residual 180.00 160.65 19.35 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 16521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1805 0.032 - 0.064: 691 0.064 - 0.096: 262 0.096 - 0.129: 90 0.129 - 0.161: 5 Chirality restraints: 2853 Sorted by residual: chirality pdb=" CB VAL C 44 " pdb=" CA VAL C 44 " pdb=" CG1 VAL C 44 " pdb=" CG2 VAL C 44 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.45e-01 chirality pdb=" CB VAL B 44 " pdb=" CA VAL B 44 " pdb=" CG1 VAL B 44 " pdb=" CG2 VAL B 44 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.39e-01 chirality pdb=" CB VAL A 44 " pdb=" CA VAL A 44 " pdb=" CG1 VAL A 44 " pdb=" CG2 VAL A 44 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.26e-01 ... (remaining 2850 not shown) Planarity restraints: 5151 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 155 " 0.039 5.00e-02 4.00e+02 5.91e-02 5.59e+00 pdb=" N PRO B 156 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 156 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 156 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 155 " -0.039 5.00e-02 4.00e+02 5.91e-02 5.59e+00 pdb=" N PRO C 156 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 156 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 156 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 155 " -0.039 5.00e-02 4.00e+02 5.89e-02 5.55e+00 pdb=" N PRO A 156 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 156 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 156 " -0.033 5.00e-02 4.00e+02 ... (remaining 5148 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.30: 6316 2.30 - 2.87: 81076 2.87 - 3.45: 93205 3.45 - 4.02: 126112 4.02 - 4.60: 195661 Nonbonded interactions: 502370 Sorted by model distance: nonbonded pdb=" OE2 GLU B 739 " pdb=" HH TYR E 37 " model vdw 1.721 2.450 nonbonded pdb=" OE2 GLU C 739 " pdb=" HH TYR F 37 " model vdw 1.722 2.450 nonbonded pdb=" OE2 GLU A 739 " pdb=" HH TYR D 37 " model vdw 1.722 2.450 nonbonded pdb=" HZ2 LYS A 742 " pdb=" O PHE C 468 " model vdw 1.723 2.450 nonbonded pdb=" O PHE A 468 " pdb=" HZ2 LYS B 742 " model vdw 1.724 2.450 ... (remaining 502365 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.920 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: 0.080 Extract box with map and model: 0.570 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 43.750 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 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:5.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 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 : 0.004 0.045 17553 Z= 0.186 Angle : 0.697 6.816 23871 Z= 0.359 Chirality : 0.041 0.161 2853 Planarity : 0.006 0.059 2982 Dihedral : 14.324 89.294 6213 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.00 % Allowed : 9.58 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.17), residues: 2256 helix: 1.78 (0.13), residues: 1503 sheet: 0.55 (0.38), residues: 156 loop : 0.40 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 202 TYR 0.011 0.001 TYR B 105 PHE 0.017 0.002 PHE C 760 TRP 0.009 0.001 TRP D 6 HIS 0.006 0.001 HIS B 827 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (17550) covalent geometry : angle 0.69634 / 0.36 (23865) SS BOND : bond 0.00331 / 0.16 ( 3) SS BOND : angle 1.68879 / 0.93 ( 6) hydrogen bonds : bond 0.11832 / 8.37 ( 1290) hydrogen bonds : angle 5.53199 / 4.12 ( 3807) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 SER cc_start: 0.7989 (t) cc_final: 0.7704 (m) REVERT: A 45 PHE cc_start: 0.8312 (m-10) cc_final: 0.7686 (m-80) REVERT: A 63 LYS cc_start: 0.7863 (mmtm) cc_final: 0.7555 (mmmt) REVERT: A 160 GLU cc_start: 0.7857 (tt0) cc_final: 0.7574 (tp30) REVERT: A 430 ASP cc_start: 0.7613 (m-30) cc_final: 0.7323 (m-30) REVERT: A 833 MET cc_start: 0.8589 (mtp) cc_final: 0.8139 (mtp) REVERT: B 76 MET cc_start: 0.8268 (tmm) cc_final: 0.8027 (ptp) REVERT: B 696 PHE cc_start: 0.8015 (t80) cc_final: 0.7788 (t80) REVERT: C 76 MET cc_start: 0.8376 (tmm) cc_final: 0.8006 (ptp) REVERT: C 123 GLN cc_start: 0.8306 (tt0) cc_final: 0.8095 (tt0) REVERT: C 160 GLU cc_start: 0.7778 (tt0) cc_final: 0.7227 (tp30) REVERT: C 200 MET cc_start: 0.6795 (tpp) cc_final: 0.6539 (mmt) REVERT: C 202 ARG cc_start: 0.7145 (ttm-80) cc_final: 0.6920 (ttm110) REVERT: C 720 ASP cc_start: 0.8357 (t0) cc_final: 0.8112 (t70) REVERT: C 748 ASP cc_start: 0.8387 (p0) cc_final: 0.8003 (m-30) REVERT: C 791 ARG cc_start: 0.7805 (mmm-85) cc_final: 0.7561 (mmt90) REVERT: C 890 MET cc_start: 0.8802 (mtp) cc_final: 0.8546 (mtp) outliers start: 18 outliers final: 9 residues processed: 209 average time/residue: 1.1592 time to fit residues: 277.1438 Evaluate side-chains 188 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 179 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 695 ASP Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 695 ASP Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain E residue 16 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: [216, 98, 194, 107, 10, 66, 130, 124, 103, 200, 212] chunk 216 optimal weight: 0.0030 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.2980 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 0.8980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN A 123 GLN A 152 ASN B 94 ASN C 94 ASN ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.141402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.121933 restraints weight = 57480.226| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.53 r_work: 0.3160 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17553 Z= 0.121 Angle : 0.487 5.147 23871 Z= 0.259 Chirality : 0.039 0.143 2853 Planarity : 0.005 0.043 2982 Dihedral : 6.086 126.805 2460 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.38 % Allowed : 8.91 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.17), residues: 2256 helix: 2.26 (0.13), residues: 1503 sheet: 0.59 (0.39), residues: 156 loop : 0.57 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 867 TYR 0.011 0.001 TYR C 105 PHE 0.019 0.001 PHE B 696 TRP 0.007 0.001 TRP A 828 HIS 0.010 0.001 HIS C 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (17550) covalent geometry : angle 0.48648 / 0.26 (23865) SS BOND : bond 0.00114 / 0.06 ( 3) SS BOND : angle 1.03134 / 0.56 ( 6) hydrogen bonds : bond 0.04186 / 2.93 ( 1290) hydrogen bonds : angle 4.34311 / 3.21 ( 3807) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.8199 (m-10) cc_final: 0.7608 (m-80) REVERT: A 63 LYS cc_start: 0.7857 (mmtm) cc_final: 0.7595 (mmmt) REVERT: A 160 GLU cc_start: 0.8043 (tt0) cc_final: 0.7835 (tt0) REVERT: A 170 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6927 (mt-10) REVERT: A 200 MET cc_start: 0.6860 (tpp) cc_final: 0.6645 (mmt) REVERT: A 327 TYR cc_start: 0.8457 (m-80) cc_final: 0.8190 (m-80) REVERT: A 833 MET cc_start: 0.8484 (mtp) cc_final: 0.8053 (mtp) REVERT: C 76 MET cc_start: 0.8230 (tmm) cc_final: 0.7794 (ptp) REVERT: C 160 GLU cc_start: 0.7765 (tt0) cc_final: 0.7065 (tp30) REVERT: C 200 MET cc_start: 0.6668 (tpp) cc_final: 0.6393 (mmt) REVERT: C 202 ARG cc_start: 0.7032 (ttm-80) cc_final: 0.6829 (ttm110) REVERT: C 444 MET cc_start: 0.9054 (ttp) cc_final: 0.8645 (tmm) REVERT: C 791 ARG cc_start: 0.7877 (mmm-85) cc_final: 0.7640 (mpt-90) outliers start: 25 outliers final: 19 residues processed: 192 average time/residue: 1.0881 time to fit residues: 240.0894 Evaluate side-chains 191 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 786 MET Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 695 ASP Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 38 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: [220, 137, 49, 126, 45, 161, 152, 29, 19, 201, 198] chunk 220 optimal weight: 0.0670 chunk 137 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN A 123 GLN A 152 ASN B 94 ASN B 123 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.134911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.114766 restraints weight = 58904.227| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.57 r_work: 0.3016 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17553 Z= 0.191 Angle : 0.530 6.083 23871 Z= 0.283 Chirality : 0.040 0.157 2853 Planarity : 0.005 0.043 2982 Dihedral : 4.207 41.717 2454 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.50 % Allowed : 10.35 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.17), residues: 2256 helix: 2.07 (0.13), residues: 1515 sheet: 0.60 (0.38), residues: 156 loop : 0.82 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 852 TYR 0.016 0.002 TYR B 105 PHE 0.019 0.002 PHE C 760 TRP 0.008 0.001 TRP A 828 HIS 0.010 0.002 HIS C 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (17550) covalent geometry : angle 0.52966 / 0.28 (23865) SS BOND : bond 0.00052 / 0.03 ( 3) SS BOND : angle 1.25901 / 0.69 ( 6) hydrogen bonds : bond 0.04465 / 3.10 ( 1290) hydrogen bonds : angle 4.29804 / 3.18 ( 3807) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 191 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.7912 (m-10) cc_final: 0.7346 (m-80) REVERT: A 71 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7791 (mtp) REVERT: A 170 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6656 (mt-10) REVERT: A 200 MET cc_start: 0.7057 (tpp) cc_final: 0.6798 (mmt) REVERT: A 444 MET cc_start: 0.9101 (ttp) cc_final: 0.8901 (ttp) REVERT: A 725 GLU cc_start: 0.7622 (pm20) cc_final: 0.7342 (pt0) REVERT: A 771 LEU cc_start: 0.7945 (mm) cc_final: 0.7583 (tp) REVERT: A 833 MET cc_start: 0.8503 (mtp) cc_final: 0.8255 (mtp) REVERT: B 694 LYS cc_start: 0.8261 (ptmt) cc_final: 0.8035 (tptt) REVERT: B 896 ARG cc_start: 0.7262 (ttp-110) cc_final: 0.6976 (ttm170) REVERT: C 86 PHE cc_start: 0.8351 (m-80) cc_final: 0.8074 (m-80) REVERT: C 160 GLU cc_start: 0.7806 (tt0) cc_final: 0.7077 (tp30) REVERT: C 200 MET cc_start: 0.6929 (tpp) cc_final: 0.6454 (mmt) REVERT: C 202 ARG cc_start: 0.7061 (ttm-80) cc_final: 0.6858 (ttm110) REVERT: C 412 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7665 (m-30) REVERT: C 700 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8334 (mtp) REVERT: C 725 GLU cc_start: 0.7466 (pm20) cc_final: 0.7121 (pt0) REVERT: C 844 ASP cc_start: 0.8788 (m-30) cc_final: 0.8565 (m-30) outliers start: 27 outliers final: 21 residues processed: 204 average time/residue: 1.1044 time to fit residues: 259.2402 Evaluate side-chains 208 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 695 ASP Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain C residue 748 ASP Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain F residue 38 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: [99, 62, 156, 66, 70, 162, 119, 211, 13, 164, 24] chunk 99 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 162 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 211 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN A 123 GLN B 94 ASN B 123 GLN C 94 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.129421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.109008 restraints weight = 60073.355| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.59 r_work: 0.2972 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17553 Z= 0.180 Angle : 0.506 6.416 23871 Z= 0.270 Chirality : 0.039 0.138 2853 Planarity : 0.004 0.042 2982 Dihedral : 5.276 114.854 2454 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.88 % Allowed : 10.96 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.17), residues: 2256 helix: 2.04 (0.13), residues: 1512 sheet: 0.42 (0.37), residues: 156 loop : 0.81 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 852 TYR 0.013 0.002 TYR B 105 PHE 0.019 0.002 PHE C 760 TRP 0.008 0.001 TRP A 828 HIS 0.009 0.001 HIS C 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (17550) covalent geometry : angle 0.50600 / 0.27 (23865) SS BOND : bond 0.00130 / 0.06 ( 3) SS BOND : angle 1.42027 / 0.77 ( 6) hydrogen bonds : bond 0.04262 / 2.97 ( 1290) hydrogen bonds : angle 4.21939 / 3.12 ( 3807) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 187 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.7902 (m-10) cc_final: 0.7341 (m-80) REVERT: A 170 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6650 (mt-10) REVERT: A 200 MET cc_start: 0.7105 (tpp) cc_final: 0.6818 (mmt) REVERT: A 694 LYS cc_start: 0.8150 (ptmt) cc_final: 0.7870 (tptt) REVERT: A 771 LEU cc_start: 0.7929 (mm) cc_final: 0.7564 (tp) REVERT: B 424 GLN cc_start: 0.7570 (mt0) cc_final: 0.6678 (mp-120) REVERT: B 896 ARG cc_start: 0.7217 (ttp-110) cc_final: 0.6876 (ttm170) REVERT: C 86 PHE cc_start: 0.8261 (m-80) cc_final: 0.7943 (m-80) REVERT: C 160 GLU cc_start: 0.7818 (tt0) cc_final: 0.7040 (tp30) REVERT: C 202 ARG cc_start: 0.7078 (ttm-80) cc_final: 0.6876 (ttm110) REVERT: C 411 ASN cc_start: 0.8511 (OUTLIER) cc_final: 0.8294 (t0) REVERT: C 412 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7682 (m-30) REVERT: C 725 GLU cc_start: 0.7489 (pm20) cc_final: 0.7124 (pt0) REVERT: C 770 ASP cc_start: 0.7265 (m-30) cc_final: 0.6970 (m-30) REVERT: C 890 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8497 (mtt) outliers start: 34 outliers final: 27 residues processed: 201 average time/residue: 1.1302 time to fit residues: 259.8782 Evaluate side-chains 215 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 695 ASP Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 695 ASP Chi-restraints excluded: chain C residue 748 ASP Chi-restraints excluded: chain C residue 890 MET Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain F residue 38 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: [77, 175, 116, 62, 78, 8, 3, 165, 93, 220, 126] chunk 77 optimal weight: 0.0980 chunk 175 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 8 optimal weight: 0.0870 chunk 3 optimal weight: 0.9980 chunk 165 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 220 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN A 123 GLN B 94 ASN B 123 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.135790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.115639 restraints weight = 59228.855| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.58 r_work: 0.2921 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17553 Z= 0.114 Angle : 0.465 4.962 23871 Z= 0.245 Chirality : 0.038 0.133 2853 Planarity : 0.004 0.049 2982 Dihedral : 4.060 43.345 2452 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.61 % Allowed : 11.30 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.68 (0.17), residues: 2256 helix: 2.30 (0.13), residues: 1512 sheet: 0.39 (0.37), residues: 156 loop : 0.93 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 202 TYR 0.009 0.001 TYR B 105 PHE 0.015 0.001 PHE B 883 TRP 0.006 0.001 TRP C 931 HIS 0.008 0.001 HIS C 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (17550) covalent geometry : angle 0.46467 / 0.25 (23865) SS BOND : bond 0.00133 / 0.07 ( 3) SS BOND : angle 1.21328 / 0.65 ( 6) hydrogen bonds : bond 0.03918 / 2.73 ( 1290) hydrogen bonds : angle 4.09507 / 3.02 ( 3807) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.7879 (m-10) cc_final: 0.7333 (m-80) REVERT: A 170 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6856 (mt-10) REVERT: A 694 LYS cc_start: 0.8148 (ptmt) cc_final: 0.7862 (tptt) REVERT: A 725 GLU cc_start: 0.7647 (pm20) cc_final: 0.7265 (pt0) REVERT: A 771 LEU cc_start: 0.7940 (mm) cc_final: 0.7597 (tp) REVERT: B 86 PHE cc_start: 0.8146 (m-80) cc_final: 0.7914 (m-80) REVERT: B 424 GLN cc_start: 0.7619 (mt0) cc_final: 0.6747 (mp-120) REVERT: B 896 ARG cc_start: 0.7213 (ttp-110) cc_final: 0.6940 (ttm170) REVERT: C 86 PHE cc_start: 0.8213 (m-80) cc_final: 0.7912 (m-80) REVERT: C 160 GLU cc_start: 0.7843 (tt0) cc_final: 0.7066 (tp30) REVERT: C 202 ARG cc_start: 0.7029 (ttm-80) cc_final: 0.6823 (ttm110) REVERT: C 411 ASN cc_start: 0.8496 (OUTLIER) cc_final: 0.8282 (t0) REVERT: C 444 MET cc_start: 0.9179 (ttp) cc_final: 0.8922 (ttp) REVERT: C 725 GLU cc_start: 0.7438 (pm20) cc_final: 0.7099 (pt0) REVERT: C 890 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8496 (mtt) outliers start: 29 outliers final: 23 residues processed: 203 average time/residue: 1.0979 time to fit residues: 255.7011 Evaluate side-chains 209 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 695 ASP Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 748 ASP Chi-restraints excluded: chain C residue 890 MET Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain F residue 38 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: [37, 200, 163, 108, 66, 164, 147, 211, 110, 142, 165] chunk 37 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 211 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 165 optimal weight: 0.5980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN A 123 GLN B 94 ASN B 123 GLN C 94 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.125961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.104314 restraints weight = 59990.290| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.66 r_work: 0.2910 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17553 Z= 0.140 Angle : 0.477 5.805 23871 Z= 0.252 Chirality : 0.038 0.134 2853 Planarity : 0.004 0.056 2982 Dihedral : 4.567 109.585 2452 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.44 % Allowed : 12.35 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.67 (0.17), residues: 2256 helix: 2.29 (0.13), residues: 1515 sheet: 0.43 (0.37), residues: 156 loop : 0.93 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 202 TYR 0.011 0.001 TYR B 105 PHE 0.016 0.001 PHE C 760 TRP 0.007 0.001 TRP A 828 HIS 0.006 0.001 HIS B 761 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (17550) covalent geometry : angle 0.47630 / 0.25 (23865) SS BOND : bond 0.00107 / 0.05 ( 3) SS BOND : angle 1.19337 / 0.64 ( 6) hydrogen bonds : bond 0.03954 / 2.74 ( 1290) hydrogen bonds : angle 4.06412 / 3.00 ( 3807) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.7951 (m-10) cc_final: 0.7370 (m-80) REVERT: A 170 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6926 (mt-10) REVERT: A 198 ARG cc_start: 0.7524 (ttp-110) cc_final: 0.7264 (ptp-110) REVERT: A 694 LYS cc_start: 0.8189 (ptmt) cc_final: 0.7909 (tptt) REVERT: A 725 GLU cc_start: 0.7718 (pm20) cc_final: 0.7326 (pt0) REVERT: A 771 LEU cc_start: 0.8055 (mm) cc_final: 0.7713 (tp) REVERT: A 837 VAL cc_start: 0.8811 (t) cc_final: 0.8603 (t) REVERT: B 86 PHE cc_start: 0.8171 (m-80) cc_final: 0.7919 (m-80) REVERT: B 424 GLN cc_start: 0.7504 (mt0) cc_final: 0.6692 (mp-120) REVERT: B 896 ARG cc_start: 0.7343 (ttp-110) cc_final: 0.7050 (ttm170) REVERT: C 160 GLU cc_start: 0.7968 (tt0) cc_final: 0.7206 (tp30) REVERT: C 202 ARG cc_start: 0.7126 (ttm-80) cc_final: 0.6920 (ttm110) REVERT: C 411 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.8315 (t0) REVERT: C 725 GLU cc_start: 0.7476 (pm20) cc_final: 0.7148 (pt0) REVERT: C 770 ASP cc_start: 0.7313 (m-30) cc_final: 0.7036 (m-30) REVERT: C 890 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8565 (mtt) outliers start: 26 outliers final: 19 residues processed: 204 average time/residue: 1.1253 time to fit residues: 263.4204 Evaluate side-chains 207 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 748 ASP Chi-restraints excluded: chain C residue 890 MET Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain F residue 38 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: [35, 50, 204, 70, 19, 142, 109, 149, 49, 110, 94] chunk 35 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 149 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN A 123 GLN B 94 ASN B 123 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.130909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.110868 restraints weight = 60332.781| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.56 r_work: 0.2884 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 17553 Z= 0.197 Angle : 0.518 5.693 23871 Z= 0.276 Chirality : 0.040 0.143 2853 Planarity : 0.005 0.062 2982 Dihedral : 4.095 44.899 2448 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.77 % Allowed : 12.57 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.17), residues: 2256 helix: 2.06 (0.13), residues: 1515 sheet: 0.39 (0.37), residues: 156 loop : 0.79 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 202 TYR 0.014 0.002 TYR B 105 PHE 0.021 0.002 PHE C 760 TRP 0.008 0.001 TRP E 6 HIS 0.008 0.001 HIS C 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 (17550) covalent geometry : angle 0.51773 / 0.28 (23865) SS BOND : bond 0.00125 / 0.06 ( 3) SS BOND : angle 1.40963 / 0.76 ( 6) hydrogen bonds : bond 0.04299 / 2.98 ( 1290) hydrogen bonds : angle 4.18232 / 3.08 ( 3807) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.7925 (m-10) cc_final: 0.7350 (m-80) REVERT: A 170 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6676 (mt-10) REVERT: A 198 ARG cc_start: 0.7528 (ttp-110) cc_final: 0.7225 (ptp-110) REVERT: A 694 LYS cc_start: 0.8193 (ptmt) cc_final: 0.7899 (tptt) REVERT: A 725 GLU cc_start: 0.7649 (pm20) cc_final: 0.7274 (pt0) REVERT: A 771 LEU cc_start: 0.7974 (mm) cc_final: 0.7629 (tp) REVERT: A 837 VAL cc_start: 0.8824 (t) cc_final: 0.8606 (t) REVERT: B 67 SER cc_start: 0.8600 (t) cc_final: 0.8211 (p) REVERT: B 86 PHE cc_start: 0.8106 (m-80) cc_final: 0.7837 (m-80) REVERT: B 424 GLN cc_start: 0.7475 (mt0) cc_final: 0.6702 (mp-120) REVERT: B 748 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.8110 (m-30) REVERT: B 896 ARG cc_start: 0.7267 (ttp-110) cc_final: 0.6958 (ttm170) REVERT: C 160 GLU cc_start: 0.7888 (tt0) cc_final: 0.7127 (tp30) REVERT: C 202 ARG cc_start: 0.7074 (ttm-80) cc_final: 0.6866 (ttm110) REVERT: C 411 ASN cc_start: 0.8526 (OUTLIER) cc_final: 0.8318 (t0) REVERT: C 412 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7699 (m-30) REVERT: C 725 GLU cc_start: 0.7476 (pm20) cc_final: 0.7114 (pt0) REVERT: C 890 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8555 (mtt) outliers start: 32 outliers final: 24 residues processed: 201 average time/residue: 1.1565 time to fit residues: 265.3241 Evaluate side-chains 208 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 695 ASP Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 748 ASP Chi-restraints excluded: chain C residue 890 MET Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain F residue 38 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: [222, 141, 198, 112, 130, 52, 16, 202, 145, 142, 43] chunk 222 optimal weight: 0.6980 chunk 141 optimal weight: 0.9990 chunk 198 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 202 optimal weight: 0.9990 chunk 145 optimal weight: 0.8980 chunk 142 optimal weight: 0.1980 chunk 43 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 GLN B 94 ASN B 123 GLN C 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.133017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.113150 restraints weight = 59943.564| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.56 r_work: 0.2915 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17553 Z= 0.113 Angle : 0.467 5.232 23871 Z= 0.247 Chirality : 0.038 0.135 2853 Planarity : 0.004 0.060 2982 Dihedral : 3.950 44.954 2448 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.55 % Allowed : 12.79 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.69 (0.17), residues: 2256 helix: 2.31 (0.13), residues: 1515 sheet: 0.32 (0.37), residues: 156 loop : 0.91 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 202 TYR 0.009 0.001 TYR C 415 PHE 0.016 0.001 PHE B 883 TRP 0.007 0.001 TRP A 828 HIS 0.008 0.001 HIS C 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (17550) covalent geometry : angle 0.46657 / 0.25 (23865) SS BOND : bond 0.00164 / 0.08 ( 3) SS BOND : angle 1.24482 / 0.66 ( 6) hydrogen bonds : bond 0.03899 / 2.71 ( 1290) hydrogen bonds : angle 4.05889 / 2.99 ( 3807) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.7938 (m-10) cc_final: 0.7358 (m-80) REVERT: A 170 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6778 (mt-10) REVERT: A 418 ASP cc_start: 0.7993 (m-30) cc_final: 0.7762 (m-30) REVERT: A 694 LYS cc_start: 0.8187 (ptmt) cc_final: 0.7897 (tptt) REVERT: A 725 GLU cc_start: 0.7620 (pm20) cc_final: 0.7246 (pt0) REVERT: A 771 LEU cc_start: 0.7931 (mm) cc_final: 0.7598 (tp) REVERT: A 837 VAL cc_start: 0.8773 (t) cc_final: 0.8557 (t) REVERT: B 86 PHE cc_start: 0.8074 (m-80) cc_final: 0.7847 (m-80) REVERT: B 424 GLN cc_start: 0.7445 (mt0) cc_final: 0.6674 (mp-120) REVERT: B 748 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.8079 (m-30) REVERT: B 896 ARG cc_start: 0.7253 (ttp-110) cc_final: 0.6938 (ttm170) REVERT: C 160 GLU cc_start: 0.7914 (tt0) cc_final: 0.7159 (tp30) REVERT: C 202 ARG cc_start: 0.7026 (ttm-80) cc_final: 0.6816 (ttm110) REVERT: C 411 ASN cc_start: 0.8487 (OUTLIER) cc_final: 0.8276 (t0) REVERT: C 725 GLU cc_start: 0.7403 (pm20) cc_final: 0.7060 (pt0) outliers start: 28 outliers final: 23 residues processed: 201 average time/residue: 1.1127 time to fit residues: 257.1472 Evaluate side-chains 208 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 695 ASP Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 748 ASP Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain F residue 38 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: [50, 14, 207, 99, 8, 66, 199, 101, 2, 197, 115] chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 GLN B 94 ASN B 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.124397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.103486 restraints weight = 60259.167| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.57 r_work: 0.2895 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17553 Z= 0.186 Angle : 0.507 6.173 23871 Z= 0.269 Chirality : 0.040 0.244 2853 Planarity : 0.004 0.062 2982 Dihedral : 4.028 45.454 2448 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.55 % Allowed : 13.12 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.17), residues: 2256 helix: 2.16 (0.13), residues: 1515 sheet: 0.34 (0.37), residues: 156 loop : 0.81 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 202 TYR 0.012 0.002 TYR B 105 PHE 0.018 0.002 PHE B 883 TRP 0.008 0.001 TRP A 828 HIS 0.008 0.001 HIS C 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 (17550) covalent geometry : angle 0.50658 / 0.27 (23865) SS BOND : bond 0.00144 / 0.07 ( 3) SS BOND : angle 1.37015 / 0.74 ( 6) hydrogen bonds : bond 0.04178 / 2.90 ( 1290) hydrogen bonds : angle 4.12147 / 3.04 ( 3807) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.8012 (m-10) cc_final: 0.7414 (m-80) REVERT: A 170 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6628 (mt-10) REVERT: A 202 ARG cc_start: 0.6743 (ttm-80) cc_final: 0.6361 (ttp-110) REVERT: A 418 ASP cc_start: 0.7988 (m-30) cc_final: 0.7750 (m-30) REVERT: A 694 LYS cc_start: 0.8174 (ptmt) cc_final: 0.7892 (tppt) REVERT: A 725 GLU cc_start: 0.7773 (pm20) cc_final: 0.7412 (pt0) REVERT: A 771 LEU cc_start: 0.8111 (mm) cc_final: 0.7768 (tp) REVERT: A 837 VAL cc_start: 0.8872 (t) cc_final: 0.8660 (t) REVERT: B 67 SER cc_start: 0.8619 (t) cc_final: 0.8290 (p) REVERT: B 86 PHE cc_start: 0.8143 (m-80) cc_final: 0.7916 (m-80) REVERT: B 424 GLN cc_start: 0.7512 (mt0) cc_final: 0.6798 (mp-120) REVERT: B 748 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.8180 (m-30) REVERT: B 805 LEU cc_start: 0.8821 (tp) cc_final: 0.8520 (tt) REVERT: B 896 ARG cc_start: 0.7376 (ttp-110) cc_final: 0.7063 (ttm170) REVERT: C 160 GLU cc_start: 0.7925 (tt0) cc_final: 0.7202 (tp30) REVERT: C 202 ARG cc_start: 0.7190 (ttm-80) cc_final: 0.6528 (ttt180) REVERT: C 411 ASN cc_start: 0.8534 (OUTLIER) cc_final: 0.8328 (t0) REVERT: C 725 GLU cc_start: 0.7509 (pm20) cc_final: 0.7217 (pt0) REVERT: F 26 ARG cc_start: 0.7531 (tmm160) cc_final: 0.7075 (ttm170) outliers start: 28 outliers final: 25 residues processed: 199 average time/residue: 1.1629 time to fit residues: 264.4017 Evaluate side-chains 209 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 695 ASP Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 748 ASP Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain F residue 38 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: [168, 16, 133, 10, 193, 140, 149, 111, 124, 128, 219] chunk 168 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 chunk 140 optimal weight: 0.7980 chunk 149 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 219 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN A 123 GLN B 94 ASN B 123 GLN C 94 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.125069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.104140 restraints weight = 60347.848| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.58 r_work: 0.2912 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17553 Z= 0.138 Angle : 0.482 5.464 23871 Z= 0.255 Chirality : 0.039 0.135 2853 Planarity : 0.004 0.050 2982 Dihedral : 3.985 45.634 2448 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.50 % Allowed : 13.46 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.58 (0.17), residues: 2256 helix: 2.23 (0.13), residues: 1518 sheet: 0.32 (0.37), residues: 156 loop : 0.88 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 202 TYR 0.010 0.001 TYR C 415 PHE 0.021 0.001 PHE D 20 TRP 0.007 0.001 TRP A 828 HIS 0.008 0.001 HIS C 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (17550) covalent geometry : angle 0.48150 / 0.25 (23865) SS BOND : bond 0.00148 / 0.07 ( 3) SS BOND : angle 1.28127 / 0.69 ( 6) hydrogen bonds : bond 0.04000 / 2.78 ( 1290) hydrogen bonds : angle 4.07567 / 3.01 ( 3807) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.8014 (m-10) cc_final: 0.7415 (m-80) REVERT: A 170 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6838 (mt-10) REVERT: A 418 ASP cc_start: 0.7976 (m-30) cc_final: 0.7732 (m-30) REVERT: A 694 LYS cc_start: 0.8135 (ptmt) cc_final: 0.7827 (tppt) REVERT: A 725 GLU cc_start: 0.7747 (pm20) cc_final: 0.7407 (pt0) REVERT: A 771 LEU cc_start: 0.8091 (mm) cc_final: 0.7757 (tp) REVERT: A 837 VAL cc_start: 0.8840 (t) cc_final: 0.8630 (t) REVERT: B 86 PHE cc_start: 0.8130 (m-80) cc_final: 0.7915 (m-80) REVERT: B 424 GLN cc_start: 0.7503 (mt0) cc_final: 0.6795 (mp-120) REVERT: B 748 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.8148 (m-30) REVERT: B 890 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8595 (mtp) REVERT: B 896 ARG cc_start: 0.7363 (ttp-110) cc_final: 0.7047 (ttm170) REVERT: C 160 GLU cc_start: 0.8000 (tt0) cc_final: 0.7244 (tp30) REVERT: C 202 ARG cc_start: 0.7201 (ttm-80) cc_final: 0.6524 (ttt180) REVERT: C 411 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.8321 (t0) REVERT: C 430 ASP cc_start: 0.7735 (m-30) cc_final: 0.7128 (m-30) REVERT: C 725 GLU cc_start: 0.7503 (pm20) cc_final: 0.7204 (pt0) REVERT: F 26 ARG cc_start: 0.7523 (tmm160) cc_final: 0.7077 (ttm170) outliers start: 27 outliers final: 20 residues processed: 200 average time/residue: 1.1079 time to fit residues: 254.9206 Evaluate side-chains 207 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 890 MET Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 748 ASP Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain F residue 38 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: [214, 18, 48, 153, 11, 160, 80, 14, 10, 85, 199] chunk 214 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 160 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 199 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 GLN B 94 ASN B 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.125307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.104410 restraints weight = 60372.386| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.57 r_work: 0.2914 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17553 Z= 0.133 Angle : 0.475 6.630 23871 Z= 0.251 Chirality : 0.038 0.133 2853 Planarity : 0.004 0.041 2982 Dihedral : 3.962 45.785 2448 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.50 % Allowed : 13.40 % Favored : 85.11 % 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: 2.64 (0.17), residues: 2256 helix: 2.27 (0.13), residues: 1518 sheet: 0.32 (0.37), residues: 156 loop : 0.89 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 202 TYR 0.010 0.001 TYR B 105 PHE 0.018 0.001 PHE D 20 TRP 0.007 0.001 TRP A 828 HIS 0.008 0.001 HIS C 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (17550) covalent geometry : angle 0.47510 / 0.25 (23865) SS BOND : bond 0.00146 / 0.07 ( 3) SS BOND : angle 1.26572 / 0.68 ( 6) hydrogen bonds : bond 0.03947 / 2.74 ( 1290) hydrogen bonds : angle 4.05265 / 2.99 ( 3807) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8765.67 seconds wall clock time: 148 minutes 49.19 seconds (8929.19 seconds total)