Starting phenix.real_space_refine on Sun Feb 8 00:21:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9syj_55350/02_2026/9syj_55350_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9syj_55350/02_2026/9syj_55350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9syj_55350/02_2026/9syj_55350_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9syj_55350/02_2026/9syj_55350_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9syj_55350/02_2026/9syj_55350.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9syj_55350/02_2026/9syj_55350.map" } resolution = 3.09 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= 0.033 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 87 5.16 5 C 11924 2.51 5 N 3137 2.21 5 O 3305 1.98 5 H 18917 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37370 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 12179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 793, 12179 Classifications: {'peptide': 793} Link IDs: {'PTRANS': 33, 'TRANS': 759} Chain breaks: 1 Chain: "B" Number of atoms: 12273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 799, 12273 Classifications: {'peptide': 799} Link IDs: {'PTRANS': 33, 'TRANS': 765} Chain breaks: 2 Chain: "C" Number of atoms: 11091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 722, 11091 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} Chain: "E" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 574 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 2, 'TRANS': 33} Chain: "F" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 574 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 2, 'TRANS': 33} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.62, per 1000 atoms: 0.18 Number of scatterers: 37370 At special positions: 0 Unit cell: (145.6, 120.9, 126.1, 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 87 16.00 O 3305 8.00 N 3137 7.00 C 11924 6.00 H 18917 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=2.03 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: 3.46 Conformation dependent library (CDL) restraints added in 1.0 seconds 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4424 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 8 sheets defined 73.8% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 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: 3.737A pdb=" N ALA A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 136 removed outlier: 4.622A pdb=" N ALA A 133 " --> pdb=" O PRO A 129 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N GLY A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL A 135 " --> pdb=" O THR A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 172 Processing helix chain 'A' and resid 184 through 219 removed outlier: 3.677A pdb=" N HIS A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG A 202 " --> pdb=" O ARG A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 249 removed outlier: 3.516A pdb=" N VAL A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 287 Processing helix chain 'A' and resid 290 through 319 removed outlier: 5.743A pdb=" N HIS A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 4.886A 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 332 through 360 removed outlier: 3.634A pdb=" N THR A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) Proline residue: A 351 - end of helix removed outlier: 3.583A pdb=" N PHE A 360 " --> pdb=" O VAL A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 384 Processing helix chain 'A' and resid 384 through 401 removed outlier: 3.685A pdb=" N VAL A 388 " --> pdb=" O TRP A 384 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 406 Processing helix chain 'A' and resid 420 through 433 removed outlier: 4.035A pdb=" N HIS A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 469 removed outlier: 3.592A pdb=" N VAL A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 507 Processing helix chain 'A' and resid 507 through 512 Processing helix chain 'A' and resid 513 through 515 No H-bonds generated for 'chain 'A' and resid 513 through 515' Processing helix chain 'A' and resid 648 through 679 removed outlier: 3.951A pdb=" N GLN A 660 " --> pdb=" O GLY A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 692 removed outlier: 4.182A pdb=" N PHE A 691 " --> pdb=" O PRO A 687 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS A 692 " --> pdb=" O PRO A 688 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 687 through 692' Processing helix chain 'A' and resid 695 through 704 removed outlier: 4.465A pdb=" N ALA A 699 " --> pdb=" O ASP A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 741 removed outlier: 3.516A pdb=" N ILE A 730 " --> pdb=" O GLY A 726 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASP A 731 " --> pdb=" O ILE A 727 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA A 732 " --> pdb=" O LYS A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 749 removed outlier: 4.365A pdb=" N ASP A 748 " --> pdb=" O PRO A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 791 removed outlier: 3.622A pdb=" N ASP A 762 " --> pdb=" O ALA A 758 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TRP A 769 " --> pdb=" O GLU A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 820 Processing helix chain 'A' and resid 829 through 857 removed outlier: 3.879A pdb=" N VAL A 837 " --> pdb=" O MET A 833 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP A 844 " --> pdb=" O ALA A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 871 Processing helix chain 'A' and resid 871 through 889 Processing helix chain 'A' and resid 890 through 893 Processing helix chain 'A' and resid 895 through 920 removed outlier: 3.575A pdb=" N VAL A 916 " --> pdb=" O ASP A 912 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG A 917 " --> pdb=" O THR A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 929 Processing helix chain 'A' and resid 930 through 934 removed outlier: 3.554A pdb=" N TRP A 933 " --> pdb=" O ARG A 930 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TRP A 934 " --> pdb=" O TRP A 931 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 930 through 934' 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: 3.695A pdb=" N ALA B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 136 removed outlier: 4.081A pdb=" N VAL B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 172 removed outlier: 3.504A pdb=" N ASN B 159 " --> pdb=" O THR B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 219 removed outlier: 4.243A pdb=" N ARG B 198 " --> pdb=" O HIS B 194 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ALA B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG B 202 " --> pdb=" O ARG B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 249 Processing helix chain 'B' and resid 255 through 287 removed outlier: 3.885A pdb=" N VAL B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 260 " --> pdb=" O THR B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 319 removed outlier: 5.544A pdb=" N HIS B 304 " --> pdb=" O ARG B 300 " (cutoff:3.500A) removed outlier: 4.977A 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 332 through 360 Proline residue: B 351 - end of helix removed outlier: 3.699A pdb=" N PHE B 360 " --> pdb=" O VAL B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 384 Processing helix chain 'B' and resid 384 through 401 removed outlier: 3.543A pdb=" N VAL B 388 " --> pdb=" O TRP B 384 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY B 399 " --> pdb=" O ILE B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 406 Processing helix chain 'B' and resid 420 through 433 removed outlier: 3.665A pdb=" N HIS B 432 " --> pdb=" O ALA B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 469 removed outlier: 3.601A pdb=" N VAL B 459 " --> pdb=" O ALA B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 526 Processing helix chain 'B' and resid 646 through 677 removed outlier: 3.854A pdb=" N MET B 650 " --> pdb=" O MET B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 704 Processing helix chain 'B' and resid 723 through 741 removed outlier: 3.687A pdb=" N ILE B 730 " --> pdb=" O GLY B 726 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASP B 731 " --> pdb=" O ILE B 727 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA B 732 " --> pdb=" O LYS B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 removed outlier: 4.512A pdb=" N ASP B 748 " --> pdb=" O PRO B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 791 Processing helix chain 'B' and resid 792 through 820 removed outlier: 3.762A pdb=" N ALA B 796 " --> pdb=" O ALA B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 856 removed outlier: 3.612A pdb=" N SER B 843 " --> pdb=" O LEU B 839 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP B 844 " --> pdb=" O ALA B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 859 No H-bonds generated for 'chain 'B' and resid 857 through 859' Processing helix chain 'B' and resid 862 through 889 removed outlier: 4.178A pdb=" N LYS B 874 " --> pdb=" O GLY B 870 " (cutoff:3.500A) removed outlier: 3.943A 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 919 through 929 Processing helix chain 'B' and resid 930 through 933 removed outlier: 3.543A pdb=" N TRP B 933 " --> pdb=" O ARG B 930 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 930 through 933' 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 79 Processing helix chain 'C' and resid 97 through 115 removed outlier: 3.840A pdb=" N ALA C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 136 removed outlier: 3.707A pdb=" N GLN C 136 " --> pdb=" O ALA C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 172 Processing helix chain 'C' and resid 184 through 219 removed outlier: 3.922A pdb=" N ARG C 202 " --> pdb=" O ARG C 198 " (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: 5.495A pdb=" N HIS C 304 " --> pdb=" O ARG C 300 " (cutoff:3.500A) removed outlier: 5.156A 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 Proline residue: C 351 - end of helix removed outlier: 3.964A pdb=" N PHE C 360 " --> pdb=" O VAL C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 384 Processing helix chain 'C' and resid 384 through 401 removed outlier: 3.505A pdb=" N VAL C 388 " --> pdb=" O TRP C 384 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY C 399 " --> pdb=" O ILE C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 420 through 433 removed outlier: 3.740A pdb=" N HIS C 432 " --> pdb=" O ALA C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 469 removed outlier: 3.686A pdb=" N VAL C 459 " --> pdb=" O ALA C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 704 removed outlier: 3.873A pdb=" N ARG C 698 " --> pdb=" O LYS C 694 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ALA C 699 " --> pdb=" O ASP C 695 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER C 702 " --> pdb=" O ARG C 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 741 removed outlier: 3.616A pdb=" N ILE C 730 " --> pdb=" O GLY C 726 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASP C 731 " --> pdb=" O ILE C 727 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA C 732 " --> pdb=" O LYS C 728 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 749 removed outlier: 4.587A pdb=" N ASP C 748 " --> pdb=" O PRO C 745 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 791 removed outlier: 3.807A pdb=" N GLU C 765 " --> pdb=" O HIS C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 820 Processing helix chain 'C' and resid 829 through 856 removed outlier: 3.508A pdb=" N MET C 833 " --> pdb=" O LEU C 829 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP C 844 " --> pdb=" O ALA C 840 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU C 847 " --> pdb=" O SER C 843 " (cutoff:3.500A) Processing helix chain 'C' and resid 860 through 889 removed outlier: 3.671A pdb=" N ILE C 865 " --> pdb=" O LEU C 861 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS C 874 " --> pdb=" O GLY C 870 " (cutoff:3.500A) removed outlier: 3.830A 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 919 through 929 Processing helix chain 'C' and resid 930 through 934 Processing helix chain 'D' and resid 6 through 27 removed outlier: 3.934A pdb=" N VAL D 13 " --> pdb=" O LEU D 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 28 removed outlier: 3.716A pdb=" N ILE E 11 " --> pdb=" O ILE E 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 27 removed outlier: 3.956A pdb=" N VAL F 13 " --> pdb=" O LEU F 9 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 123 removed outlier: 6.621A pdb=" N SER A 148 " --> pdb=" O GLN A 120 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N VAL A 122 " --> pdb=" O GLN A 146 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLN A 146 " --> pdb=" O VAL A 122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 473 through 477 removed outlier: 6.848A pdb=" N LEU A 716 " --> pdb=" O SER A 474 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL A 476 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ILE A 714 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 119 through 123 removed outlier: 3.825A pdb=" N SER B 121 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN B 146 " --> pdb=" O GLN B 123 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 408 through 409 Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 477 Processing sheet with id=AA6, first strand: chain 'C' and resid 119 through 123 removed outlier: 3.881A pdb=" N GLN C 146 " --> pdb=" O GLN C 123 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 408 through 409 Processing sheet with id=AA8, first strand: chain 'C' and resid 473 through 477 1394 hydrogen bonds defined for protein. 4095 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: 8.93 Time building geometry restraints manager: 4.63 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: 18917 1.03 - 1.23: 37 1.23 - 1.43: 7616 1.43 - 1.62: 11015 1.62 - 1.82: 168 Bond restraints: 37753 Sorted by residual: bond pdb=" C3' LMT A1001 " pdb=" O3' LMT A1001 " ideal model delta sigma weight residual 1.404 1.359 0.045 2.00e-02 2.50e+03 4.97e+00 bond pdb=" C3' LMT B1001 " pdb=" O3' LMT B1001 " ideal model delta sigma weight residual 1.404 1.362 0.042 2.00e-02 2.50e+03 4.47e+00 bond pdb=" C7 LMT A1001 " pdb=" C8 LMT A1001 " ideal model delta sigma weight residual 1.529 1.488 0.041 2.00e-02 2.50e+03 4.28e+00 bond pdb=" C3' LMT C1001 " pdb=" O3' LMT C1001 " ideal model delta sigma weight residual 1.404 1.363 0.041 2.00e-02 2.50e+03 4.18e+00 bond pdb=" C7 LMT C1001 " pdb=" C8 LMT C1001 " ideal model delta sigma weight residual 1.529 1.489 0.040 2.00e-02 2.50e+03 4.08e+00 ... (remaining 37748 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 67510 2.01 - 4.03: 770 4.03 - 6.04: 100 6.04 - 8.06: 17 8.06 - 10.07: 8 Bond angle restraints: 68405 Sorted by residual: angle pdb=" O GLY A 332 " pdb=" C GLY A 332 " pdb=" N ILE A 333 " ideal model delta sigma weight residual 121.85 123.88 -2.03 5.60e-01 3.19e+00 1.32e+01 angle pdb=" C2 LMT A1001 " pdb=" C3 LMT A1001 " pdb=" C4 LMT A1001 " ideal model delta sigma weight residual 117.09 107.02 10.07 3.00e+00 1.11e-01 1.13e+01 angle pdb=" CA LYS C 103 " pdb=" CB LYS C 103 " pdb=" CG LYS C 103 " ideal model delta sigma weight residual 114.10 120.81 -6.71 2.00e+00 2.50e-01 1.13e+01 angle pdb=" N ILE A 492 " pdb=" CA ILE A 492 " pdb=" C ILE A 492 " ideal model delta sigma weight residual 108.88 115.56 -6.68 2.16e+00 2.14e-01 9.55e+00 angle pdb=" CA MET A 88 " pdb=" CB MET A 88 " pdb=" CG MET A 88 " ideal model delta sigma weight residual 114.10 119.76 -5.66 2.00e+00 2.50e-01 8.00e+00 ... (remaining 68400 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.37: 16483 25.37 - 50.74: 970 50.74 - 76.11: 298 76.11 - 101.48: 39 101.48 - 126.85: 18 Dihedral angle restraints: 17808 sinusoidal: 9755 harmonic: 8053 Sorted by residual: dihedral pdb=" CB CYS C 434 " pdb=" SG CYS C 434 " pdb=" SG CYS D 39 " pdb=" CB CYS D 39 " ideal model delta sinusoidal sigma weight residual -86.00 -50.66 -35.34 1 1.00e+01 1.00e-02 1.77e+01 dihedral pdb=" C1' LMT B1001 " pdb=" C5' LMT B1001 " pdb=" O5' LMT B1001 " pdb=" C4' LMT B1001 " ideal model delta sinusoidal sigma weight residual -62.78 64.07 -126.85 1 3.00e+01 1.11e-03 1.71e+01 dihedral pdb=" C1' LMT C1001 " pdb=" C5' LMT C1001 " pdb=" O5' LMT C1001 " pdb=" C4' LMT C1001 " ideal model delta sinusoidal sigma weight residual -62.78 63.91 -126.69 1 3.00e+01 1.11e-03 1.70e+01 ... (remaining 17805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 2859 0.076 - 0.153: 190 0.153 - 0.229: 5 0.229 - 0.306: 2 0.306 - 0.382: 2 Chirality restraints: 3058 Sorted by residual: chirality pdb=" C5' LMT A1001 " pdb=" C4' LMT A1001 " pdb=" C6' LMT A1001 " pdb=" O5' LMT A1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.13 -0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" C5' LMT C1001 " pdb=" C4' LMT C1001 " pdb=" C6' LMT C1001 " pdb=" O5' LMT C1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.15 -0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" C5' LMT B1001 " pdb=" C4' LMT B1001 " pdb=" C6' LMT B1001 " pdb=" O5' LMT B1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.21 -0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 3055 not shown) Planarity restraints: 5503 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 914 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.71e+00 pdb=" C LEU A 914 " 0.045 2.00e-02 2.50e+03 pdb=" O LEU A 914 " -0.017 2.00e-02 2.50e+03 pdb=" N ILE A 915 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN C 95 " -0.039 5.00e-02 4.00e+02 5.90e-02 5.58e+00 pdb=" N PRO C 96 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 96 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 96 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 420 " -0.036 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO C 421 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 421 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 421 " -0.030 5.00e-02 4.00e+02 ... (remaining 5500 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.30: 6366 2.30 - 2.87: 86382 2.87 - 3.45: 99420 3.45 - 4.02: 132598 4.02 - 4.60: 204693 Nonbonded interactions: 529459 Sorted by model distance: nonbonded pdb=" OD1 ASP A 461 " pdb="HH21 ARG A 481 " model vdw 1.720 2.450 nonbonded pdb=" HH TYR A 105 " pdb=" OD1 ASP A 124 " model vdw 1.722 2.450 nonbonded pdb=" O MET A 786 " pdb=" HG1 THR A 790 " model vdw 1.727 2.450 nonbonded pdb=" OE2 GLU B 739 " pdb=" HH TYR E 37 " model vdw 1.731 2.450 nonbonded pdb=" OE2 GLU C 739 " pdb=" HH TYR F 37 " model vdw 1.732 2.450 ... (remaining 529454 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 16 through 24 or (resid 25 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name H \ E2)) or resid 26 through 448 or (resid 449 and (name N or name CA or name C or n \ ame O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or n \ ame H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1)) o \ r resid 450 through 487 or resid 690 through 1001)) selection = (chain 'B' and (resid 16 through 192 or (resid 193 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 194 through 487 or resid 690 through 1001)) selection = (chain 'C' and (resid 16 through 303 or (resid 304 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 305 through 1001)) } 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: 1.860 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: 0.240 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 33.980 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 18839 Z= 0.181 Angle : 0.662 10.074 25600 Z= 0.324 Chirality : 0.042 0.382 3058 Planarity : 0.005 0.071 3193 Dihedral : 17.025 126.847 6841 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.17), residues: 2402 helix: 1.99 (0.13), residues: 1624 sheet: 0.25 (0.42), residues: 151 loop : 0.13 (0.27), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 930 TYR 0.023 0.001 TYR A 845 PHE 0.022 0.001 PHE B 883 TRP 0.014 0.001 TRP B 933 HIS 0.007 0.001 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00404 (18836) covalent geometry : angle 0.66210 (25594) SS BOND : bond 0.00124 ( 3) SS BOND : angle 1.43651 ( 6) hydrogen bonds : bond 0.12371 ( 1394) hydrogen bonds : angle 5.61252 ( 4095) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.7872 (mmt) cc_final: 0.7595 (ttt) REVERT: B 235 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7681 (mt-10) REVERT: B 912 ASP cc_start: 0.7709 (t70) cc_final: 0.7308 (t70) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.3097 time to fit residues: 92.5514 Evaluate side-chains 189 residues out of total 1933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.135807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.110205 restraints weight = 73895.062| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.09 r_work: 0.3225 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.0576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18839 Z= 0.162 Angle : 0.527 8.843 25600 Z= 0.272 Chirality : 0.039 0.175 3058 Planarity : 0.004 0.045 3193 Dihedral : 10.442 107.365 2780 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.62 % Allowed : 10.71 % Favored : 88.67 % 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: 2.34 (0.17), residues: 2402 helix: 2.19 (0.13), residues: 1631 sheet: 0.18 (0.40), residues: 156 loop : 0.27 (0.27), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 930 TYR 0.012 0.001 TYR B 415 PHE 0.017 0.001 PHE A 883 TRP 0.007 0.001 TRP B 933 HIS 0.005 0.001 HIS B 489 Details of bonding type rmsd covalent geometry : bond 0.00350 (18836) covalent geometry : angle 0.52658 (25594) SS BOND : bond 0.00101 ( 3) SS BOND : angle 1.16898 ( 6) hydrogen bonds : bond 0.04465 ( 1394) hydrogen bonds : angle 4.52680 ( 4095) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 195 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8206 (mt) REVERT: A 676 ASP cc_start: 0.6196 (t0) cc_final: 0.5808 (t0) REVERT: B 235 GLU cc_start: 0.8251 (mt-10) cc_final: 0.8001 (mt-10) REVERT: C 317 THR cc_start: 0.8168 (p) cc_final: 0.7965 (p) REVERT: C 325 MET cc_start: 0.7872 (mtp) cc_final: 0.7647 (mtp) outliers start: 12 outliers final: 8 residues processed: 200 average time/residue: 0.3412 time to fit residues: 103.5771 Evaluate side-chains 198 residues out of total 1933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 189 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain D residue 12 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 49 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 230 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.132834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.106783 restraints weight = 74576.295| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.11 r_work: 0.3185 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 18839 Z= 0.211 Angle : 0.542 10.362 25600 Z= 0.282 Chirality : 0.040 0.176 3058 Planarity : 0.004 0.049 3193 Dihedral : 7.000 70.099 2780 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.09 % Allowed : 10.86 % Favored : 88.05 % 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: 2.22 (0.17), residues: 2402 helix: 2.11 (0.12), residues: 1638 sheet: 0.15 (0.39), residues: 156 loop : 0.17 (0.27), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 917 TYR 0.013 0.002 TYR B 105 PHE 0.019 0.002 PHE C 433 TRP 0.008 0.001 TRP A 828 HIS 0.006 0.001 HIS B 761 Details of bonding type rmsd covalent geometry : bond 0.00477 (18836) covalent geometry : angle 0.54168 (25594) SS BOND : bond 0.00109 ( 3) SS BOND : angle 1.53964 ( 6) hydrogen bonds : bond 0.04274 ( 1394) hydrogen bonds : angle 4.38752 ( 4095) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 200 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 166 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7826 (mtm-85) REVERT: B 836 ILE cc_start: 0.8141 (mt) cc_final: 0.7850 (mm) REVERT: C 317 THR cc_start: 0.8217 (p) cc_final: 0.7977 (p) REVERT: C 325 MET cc_start: 0.8150 (mtp) cc_final: 0.7930 (mtm) REVERT: C 696 PHE cc_start: 0.7302 (OUTLIER) cc_final: 0.6425 (t80) REVERT: C 748 ASP cc_start: 0.8563 (m-30) cc_final: 0.8355 (p0) outliers start: 21 outliers final: 15 residues processed: 214 average time/residue: 0.3431 time to fit residues: 112.5473 Evaluate side-chains 205 residues out of total 1933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 786 MET Chi-restraints excluded: chain B residue 806 SER Chi-restraints excluded: chain B residue 912 ASP Chi-restraints excluded: chain C residue 696 PHE Chi-restraints excluded: chain C residue 727 ILE Chi-restraints excluded: chain C residue 907 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 46 optimal weight: 0.9980 chunk 182 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 220 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.131696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.105837 restraints weight = 74021.836| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.08 r_work: 0.3204 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18839 Z= 0.170 Angle : 0.497 7.928 25600 Z= 0.262 Chirality : 0.038 0.150 3058 Planarity : 0.004 0.051 3193 Dihedral : 5.992 54.255 2780 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.93 % Allowed : 11.59 % Favored : 87.48 % 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: 2.33 (0.17), residues: 2402 helix: 2.22 (0.13), residues: 1630 sheet: 0.30 (0.39), residues: 150 loop : 0.11 (0.27), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 930 TYR 0.011 0.001 TYR B 415 PHE 0.017 0.001 PHE A 883 TRP 0.005 0.001 TRP A 828 HIS 0.006 0.001 HIS B 761 Details of bonding type rmsd covalent geometry : bond 0.00380 (18836) covalent geometry : angle 0.49398 (25594) SS BOND : bond 0.00752 ( 3) SS BOND : angle 3.59297 ( 6) hydrogen bonds : bond 0.04014 ( 1394) hydrogen bonds : angle 4.27674 ( 4095) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 676 ASP cc_start: 0.6278 (t0) cc_final: 0.5987 (t0) REVERT: B 166 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7858 (mtm-85) REVERT: C 748 ASP cc_start: 0.8545 (m-30) cc_final: 0.8332 (p0) outliers start: 18 outliers final: 14 residues processed: 203 average time/residue: 0.3486 time to fit residues: 107.9397 Evaluate side-chains 201 residues out of total 1933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 186 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 786 MET Chi-restraints excluded: chain B residue 912 ASP Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 907 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 180 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 81 optimal weight: 0.0870 chunk 204 optimal weight: 0.9990 chunk 172 optimal weight: 3.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.133321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.105947 restraints weight = 74176.354| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.20 r_work: 0.3199 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18839 Z= 0.156 Angle : 0.477 6.561 25600 Z= 0.252 Chirality : 0.038 0.211 3058 Planarity : 0.004 0.051 3193 Dihedral : 5.422 53.154 2780 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.24 % Allowed : 12.36 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.17), residues: 2402 helix: 2.31 (0.13), residues: 1628 sheet: 0.23 (0.39), residues: 150 loop : 0.12 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 917 TYR 0.011 0.001 TYR B 415 PHE 0.016 0.001 PHE A 883 TRP 0.005 0.001 TRP B 35 HIS 0.005 0.001 HIS B 761 Details of bonding type rmsd covalent geometry : bond 0.00347 (18836) covalent geometry : angle 0.47568 (25594) SS BOND : bond 0.00343 ( 3) SS BOND : angle 2.41299 ( 6) hydrogen bonds : bond 0.03880 ( 1394) hydrogen bonds : angle 4.21875 ( 4095) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 195 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 676 ASP cc_start: 0.6252 (t0) cc_final: 0.5937 (t0) REVERT: B 166 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7854 (mtm-85) REVERT: B 324 ARG cc_start: 0.6940 (ttp-170) cc_final: 0.6668 (ttp-170) REVERT: B 836 ILE cc_start: 0.8221 (mt) cc_final: 0.7908 (mm) REVERT: C 696 PHE cc_start: 0.7267 (OUTLIER) cc_final: 0.6411 (t80) outliers start: 24 outliers final: 19 residues processed: 212 average time/residue: 0.3549 time to fit residues: 114.0270 Evaluate side-chains 214 residues out of total 1933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 786 MET Chi-restraints excluded: chain B residue 912 ASP Chi-restraints excluded: chain B residue 933 TRP Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 696 PHE Chi-restraints excluded: chain C residue 727 ILE Chi-restraints excluded: chain C residue 907 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 15 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 232 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 31 optimal weight: 0.0000 chunk 129 optimal weight: 9.9990 chunk 152 optimal weight: 1.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.133178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.105881 restraints weight = 74099.402| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.19 r_work: 0.3198 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18839 Z= 0.158 Angle : 0.473 5.596 25600 Z= 0.251 Chirality : 0.038 0.145 3058 Planarity : 0.004 0.052 3193 Dihedral : 5.214 55.124 2780 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.29 % Allowed : 12.36 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.46 (0.17), residues: 2402 helix: 2.35 (0.13), residues: 1628 sheet: 0.20 (0.39), residues: 150 loop : 0.12 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 917 TYR 0.009 0.001 TYR B 144 PHE 0.015 0.001 PHE A 883 TRP 0.006 0.001 TRP B 933 HIS 0.005 0.001 HIS B 761 Details of bonding type rmsd covalent geometry : bond 0.00353 (18836) covalent geometry : angle 0.47235 (25594) SS BOND : bond 0.00229 ( 3) SS BOND : angle 1.62879 ( 6) hydrogen bonds : bond 0.03839 ( 1394) hydrogen bonds : angle 4.17876 ( 4095) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 201 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 676 ASP cc_start: 0.6331 (t0) cc_final: 0.5999 (t0) REVERT: B 166 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7865 (mtm-85) REVERT: B 324 ARG cc_start: 0.6971 (ttp-170) cc_final: 0.6650 (ttp-170) REVERT: C 325 MET cc_start: 0.8128 (mtm) cc_final: 0.7925 (mtm) REVERT: C 696 PHE cc_start: 0.7288 (OUTLIER) cc_final: 0.6440 (t80) REVERT: C 748 ASP cc_start: 0.8544 (m-30) cc_final: 0.8289 (p0) outliers start: 25 outliers final: 19 residues processed: 219 average time/residue: 0.3410 time to fit residues: 113.9085 Evaluate side-chains 211 residues out of total 1933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 190 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 786 MET Chi-restraints excluded: chain B residue 912 ASP Chi-restraints excluded: chain B residue 933 TRP Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 457 PHE Chi-restraints excluded: chain C residue 696 PHE Chi-restraints excluded: chain C residue 907 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 160 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 233 optimal weight: 0.0570 chunk 219 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 182 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.133748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.107728 restraints weight = 73910.845| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.11 r_work: 0.3204 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18839 Z= 0.151 Angle : 0.468 5.228 25600 Z= 0.248 Chirality : 0.038 0.194 3058 Planarity : 0.004 0.052 3193 Dihedral : 5.165 58.643 2780 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.45 % Allowed : 12.36 % Favored : 86.19 % 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: 2.51 (0.17), residues: 2402 helix: 2.38 (0.13), residues: 1628 sheet: 0.22 (0.39), residues: 150 loop : 0.14 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 917 TYR 0.009 0.001 TYR B 144 PHE 0.015 0.001 PHE A 883 TRP 0.006 0.001 TRP B 933 HIS 0.005 0.001 HIS B 761 Details of bonding type rmsd covalent geometry : bond 0.00336 (18836) covalent geometry : angle 0.46700 (25594) SS BOND : bond 0.00187 ( 3) SS BOND : angle 1.57087 ( 6) hydrogen bonds : bond 0.03787 ( 1394) hydrogen bonds : angle 4.15706 ( 4095) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 197 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 676 ASP cc_start: 0.6289 (t0) cc_final: 0.5965 (t0) REVERT: B 166 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7791 (mtm-85) REVERT: B 324 ARG cc_start: 0.6882 (ttp-170) cc_final: 0.6610 (ttp-170) REVERT: C 696 PHE cc_start: 0.7257 (OUTLIER) cc_final: 0.6422 (t80) REVERT: E 23 HIS cc_start: 0.7017 (OUTLIER) cc_final: 0.6621 (t70) outliers start: 28 outliers final: 22 residues processed: 217 average time/residue: 0.3343 time to fit residues: 111.6184 Evaluate side-chains 217 residues out of total 1933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 192 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 786 MET Chi-restraints excluded: chain B residue 912 ASP Chi-restraints excluded: chain B residue 933 TRP Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 457 PHE Chi-restraints excluded: chain C residue 696 PHE Chi-restraints excluded: chain C residue 727 ILE Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain E residue 23 HIS Chi-restraints excluded: chain E residue 39 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 11 optimal weight: 2.9990 chunk 176 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.133227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.107209 restraints weight = 73622.060| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.10 r_work: 0.3194 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18839 Z= 0.173 Angle : 0.480 5.261 25600 Z= 0.255 Chirality : 0.038 0.145 3058 Planarity : 0.004 0.053 3193 Dihedral : 5.235 59.622 2780 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.40 % Allowed : 12.57 % Favored : 86.03 % 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: 2.44 (0.17), residues: 2402 helix: 2.33 (0.13), residues: 1628 sheet: 0.22 (0.39), residues: 150 loop : 0.11 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 917 TYR 0.010 0.001 TYR B 144 PHE 0.016 0.001 PHE B 883 TRP 0.006 0.001 TRP B 933 HIS 0.005 0.001 HIS B 761 Details of bonding type rmsd covalent geometry : bond 0.00391 (18836) covalent geometry : angle 0.47890 (25594) SS BOND : bond 0.00172 ( 3) SS BOND : angle 1.67324 ( 6) hydrogen bonds : bond 0.03854 ( 1394) hydrogen bonds : angle 4.16944 ( 4095) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 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: B 166 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7809 (mtm-85) REVERT: B 324 ARG cc_start: 0.7016 (ttp-170) cc_final: 0.6730 (ttp-170) REVERT: C 696 PHE cc_start: 0.7267 (OUTLIER) cc_final: 0.6418 (t80) REVERT: C 748 ASP cc_start: 0.8580 (m-30) cc_final: 0.8353 (p0) REVERT: E 23 HIS cc_start: 0.7029 (OUTLIER) cc_final: 0.6607 (t70) outliers start: 27 outliers final: 23 residues processed: 217 average time/residue: 0.3239 time to fit residues: 108.3877 Evaluate side-chains 217 residues out of total 1933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 786 MET Chi-restraints excluded: chain B residue 912 ASP Chi-restraints excluded: chain B residue 933 TRP Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 457 PHE Chi-restraints excluded: chain C residue 696 PHE Chi-restraints excluded: chain C residue 727 ILE Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain D residue 23 HIS Chi-restraints excluded: chain E residue 23 HIS Chi-restraints excluded: chain E residue 39 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 155 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 chunk 198 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.133301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.105761 restraints weight = 73647.559| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.21 r_work: 0.3197 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18839 Z= 0.123 Angle : 0.452 5.096 25600 Z= 0.240 Chirality : 0.038 0.141 3058 Planarity : 0.004 0.061 3193 Dihedral : 5.066 59.894 2780 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.29 % Allowed : 12.67 % Favored : 86.03 % 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: 2.62 (0.17), residues: 2402 helix: 2.45 (0.13), residues: 1630 sheet: 0.24 (0.39), residues: 150 loop : 0.22 (0.27), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 930 TYR 0.008 0.001 TYR A 105 PHE 0.014 0.001 PHE B 883 TRP 0.006 0.001 TRP B 933 HIS 0.005 0.001 HIS B 761 Details of bonding type rmsd covalent geometry : bond 0.00265 (18836) covalent geometry : angle 0.45151 (25594) SS BOND : bond 0.00214 ( 3) SS BOND : angle 1.49862 ( 6) hydrogen bonds : bond 0.03664 ( 1394) hydrogen bonds : angle 4.10502 ( 4095) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.8219 (mtt) cc_final: 0.7992 (mmm) REVERT: B 166 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7709 (mtm-85) REVERT: B 324 ARG cc_start: 0.7054 (ttp-170) cc_final: 0.6748 (ttp-170) REVERT: B 739 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8259 (mm-30) REVERT: C 696 PHE cc_start: 0.7293 (OUTLIER) cc_final: 0.6455 (t80) REVERT: C 912 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.8421 (m-30) REVERT: E 23 HIS cc_start: 0.7008 (OUTLIER) cc_final: 0.6582 (t70) outliers start: 25 outliers final: 18 residues processed: 217 average time/residue: 0.3314 time to fit residues: 110.5503 Evaluate side-chains 215 residues out of total 1933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 193 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 786 MET Chi-restraints excluded: chain B residue 912 ASP Chi-restraints excluded: chain B residue 933 TRP Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 457 PHE Chi-restraints excluded: chain C residue 696 PHE Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 912 ASP Chi-restraints excluded: chain D residue 23 HIS Chi-restraints excluded: chain E residue 23 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 207 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 229 optimal weight: 0.9980 chunk 198 optimal weight: 0.3980 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.131363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.104962 restraints weight = 73514.429| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.12 r_work: 0.3190 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18839 Z= 0.162 Angle : 0.480 8.607 25600 Z= 0.255 Chirality : 0.038 0.143 3058 Planarity : 0.004 0.053 3193 Dihedral : 5.130 59.695 2780 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.29 % Allowed : 13.04 % Favored : 85.67 % 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: 2.55 (0.17), residues: 2402 helix: 2.41 (0.13), residues: 1629 sheet: 0.28 (0.39), residues: 150 loop : 0.16 (0.27), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 930 TYR 0.009 0.001 TYR B 415 PHE 0.015 0.001 PHE B 883 TRP 0.007 0.001 TRP A 933 HIS 0.005 0.001 HIS B 761 Details of bonding type rmsd covalent geometry : bond 0.00365 (18836) covalent geometry : angle 0.47703 (25594) SS BOND : bond 0.00475 ( 3) SS BOND : angle 3.77283 ( 6) hydrogen bonds : bond 0.03761 ( 1394) hydrogen bonds : angle 4.12487 ( 4095) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.8239 (mtt) cc_final: 0.8000 (mmm) REVERT: B 166 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7727 (mtm-85) REVERT: B 324 ARG cc_start: 0.7054 (ttp-170) cc_final: 0.6729 (ttp-170) REVERT: C 214 MET cc_start: 0.8337 (mmm) cc_final: 0.7979 (mmm) REVERT: C 696 PHE cc_start: 0.7299 (OUTLIER) cc_final: 0.6470 (t80) REVERT: E 23 HIS cc_start: 0.7008 (OUTLIER) cc_final: 0.6582 (t70) outliers start: 25 outliers final: 20 residues processed: 213 average time/residue: 0.3203 time to fit residues: 104.8077 Evaluate side-chains 214 residues out of total 1933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 191 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 481 ARG Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 786 MET Chi-restraints excluded: chain B residue 912 ASP Chi-restraints excluded: chain B residue 933 TRP Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 457 PHE Chi-restraints excluded: chain C residue 696 PHE Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain D residue 23 HIS Chi-restraints excluded: chain E residue 23 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 85 optimal weight: 0.8980 chunk 180 optimal weight: 2.9990 chunk 114 optimal weight: 0.0670 chunk 237 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.131264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.104902 restraints weight = 73424.530| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.13 r_work: 0.3201 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18839 Z= 0.133 Angle : 0.462 7.586 25600 Z= 0.244 Chirality : 0.038 0.140 3058 Planarity : 0.004 0.053 3193 Dihedral : 5.028 59.154 2780 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.24 % Allowed : 12.98 % Favored : 85.77 % 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: 2.63 (0.17), residues: 2402 helix: 2.46 (0.13), residues: 1631 sheet: 0.29 (0.39), residues: 150 loop : 0.21 (0.27), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 930 TYR 0.009 0.001 TYR A 845 PHE 0.014 0.001 PHE A 883 TRP 0.007 0.001 TRP A 933 HIS 0.004 0.001 HIS B 761 Details of bonding type rmsd covalent geometry : bond 0.00293 (18836) covalent geometry : angle 0.45872 (25594) SS BOND : bond 0.00217 ( 3) SS BOND : angle 3.43186 ( 6) hydrogen bonds : bond 0.03660 ( 1394) hydrogen bonds : angle 4.08636 ( 4095) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8534.01 seconds wall clock time: 145 minutes 24.47 seconds (8724.47 seconds total)