Starting phenix.real_space_refine on Sat Jul 4 17:42:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zkq_60203/07_2026/8zkq_60203.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zkq_60203/07_2026/8zkq_60203.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zkq_60203/07_2026/8zkq_60203.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zkq_60203/07_2026/8zkq_60203.map" model { file = "/net/cci-nas-00/data/ceres_data/8zkq_60203/07_2026/8zkq_60203.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zkq_60203/07_2026/8zkq_60203.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1851 atoms to isotropic. 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 P 21 5.49 5 S 102 5.16 5 C 13740 2.51 5 N 3378 2.21 5 O 3846 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 166 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21087 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 5810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 5810 Classifications: {'peptide': 772} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 37, 'TRANS': 734} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 267 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "H" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 633 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "B" Number of atoms: 5810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 5810 Classifications: {'peptide': 772} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 37, 'TRANS': 734} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 267 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "D" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 633 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "E" Number of atoms: 5810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 5810 Classifications: {'peptide': 772} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 37, 'TRANS': 734} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 267 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "I" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 633 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "A" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 349 Unusual residues: {'CDL': 3, 'PEV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'PEV': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PN7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "B" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 298 Unusual residues: {'CDL': 2, 'PEV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PN7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "E" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 149 Unusual residues: {'CDL': 1, 'PEV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'PEV': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PN7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Time building chain proxies: 4.56, per 1000 atoms: 0.22 Number of scatterers: 21087 At special positions: 0 Unit cell: (150.592, 118.144, 121.472, 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 102 16.00 P 21 15.00 O 3846 8.00 N 3378 7.00 C 13740 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 991.8 milliseconds 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4884 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 9 sheets defined 70.1% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 22 through 31 Processing helix chain 'A' and resid 31 through 49 Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 69 through 82 Processing helix chain 'A' and resid 102 through 119 removed outlier: 3.559A pdb=" N ALA A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 removed outlier: 3.860A pdb=" N GLN A 140 " --> pdb=" O THR A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 175 removed outlier: 4.181A pdb=" N ASN A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 223 removed outlier: 4.167A pdb=" N VAL A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP A 201 " --> pdb=" O GLN A 197 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ARG A 202 " --> pdb=" O GLN A 198 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA A 209 " --> pdb=" O GLN A 205 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 217 " --> pdb=" O THR A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 253 Processing helix chain 'A' and resid 261 through 291 removed outlier: 3.844A pdb=" N VAL A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 323 removed outlier: 5.656A pdb=" N HIS A 308 " --> pdb=" O GLY A 304 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N VAL A 309 " --> pdb=" O GLY A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 327 Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 335 through 362 removed outlier: 3.515A pdb=" N LEU A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Proline residue: A 355 - end of helix Processing helix chain 'A' and resid 373 through 389 Processing helix chain 'A' and resid 389 through 406 removed outlier: 3.599A pdb=" N ILE A 393 " --> pdb=" O TRP A 389 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 416 through 420 removed outlier: 3.766A pdb=" N ASN A 419 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 Processing helix chain 'A' and resid 458 through 474 removed outlier: 3.903A pdb=" N LEU A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 removed outlier: 3.981A pdb=" N SER A 502 " --> pdb=" O PRO A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 680 Processing helix chain 'A' and resid 698 through 709 removed outlier: 4.072A pdb=" N ARG A 703 " --> pdb=" O PRO A 699 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY A 704 " --> pdb=" O ASP A 700 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN A 707 " --> pdb=" O ARG A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 746 removed outlier: 4.353A pdb=" N ILE A 735 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ALA A 736 " --> pdb=" O ILE A 732 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS A 737 " --> pdb=" O ALA A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 795 removed outlier: 3.873A pdb=" N MET A 764 " --> pdb=" O GLY A 760 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR A 773 " --> pdb=" O SER A 769 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR A 774 " --> pdb=" O ASP A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 825 Processing helix chain 'A' and resid 834 through 862 removed outlier: 3.660A pdb=" N ILE A 842 " --> pdb=" O MET A 838 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP A 849 " --> pdb=" O ALA A 845 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR A 850 " --> pdb=" O VAL A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 893 removed outlier: 4.670A pdb=" N SER A 879 " --> pdb=" O GLY A 875 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL A 880 " --> pdb=" O GLY A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 898 removed outlier: 3.945A pdb=" N VAL A 897 " --> pdb=" O SER A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 920 removed outlier: 3.609A pdb=" N ALA A 904 " --> pdb=" O LEU A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 933 removed outlier: 4.944A pdb=" N THR A 926 " --> pdb=" O ARG A 922 " (cutoff:3.500A) Proline residue: A 927 - end of helix Processing helix chain 'A' and resid 934 through 939 removed outlier: 3.872A pdb=" N PHE A 937 " --> pdb=" O GLY A 934 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TRP A 938 " --> pdb=" O LYS A 935 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP A 939 " --> pdb=" O TRP A 936 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 934 through 939' Processing helix chain 'F' and resid 8 through 29 Processing helix chain 'H' and resid 4 through 20 removed outlier: 3.738A pdb=" N GLU H 14 " --> pdb=" O ALA H 10 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE H 15 " --> pdb=" O GLY H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 56 removed outlier: 3.706A pdb=" N VAL H 45 " --> pdb=" O SER H 41 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU H 46 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 66 removed outlier: 3.965A pdb=" N ALA H 65 " --> pdb=" O ASP H 61 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY H 66 " --> pdb=" O GLU H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 83 removed outlier: 3.577A pdb=" N GLU H 83 " --> pdb=" O LYS H 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 31 Processing helix chain 'B' and resid 31 through 49 Processing helix chain 'B' and resid 52 through 60 Processing helix chain 'B' and resid 69 through 82 Processing helix chain 'B' and resid 102 through 119 removed outlier: 3.830A pdb=" N ASP B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 removed outlier: 3.999A pdb=" N GLN B 140 " --> pdb=" O THR B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 176 removed outlier: 4.016A pdb=" N ASN B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU B 176 " --> pdb=" O ILE B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 223 removed outlier: 3.930A pdb=" N ASP B 201 " --> pdb=" O GLN B 197 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG B 202 " --> pdb=" O GLN B 198 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL B 217 " --> pdb=" O THR B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 253 Processing helix chain 'B' and resid 261 through 291 removed outlier: 3.860A pdb=" N VAL B 268 " --> pdb=" O ASN B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 323 removed outlier: 5.682A pdb=" N HIS B 308 " --> pdb=" O GLY B 304 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N VAL B 309 " --> pdb=" O GLY B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 327 Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 335 through 362 removed outlier: 3.865A pdb=" N GLY B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Proline residue: B 355 - end of helix Processing helix chain 'B' and resid 373 through 389 removed outlier: 3.702A pdb=" N ARG B 377 " --> pdb=" O MET B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 406 removed outlier: 3.621A pdb=" N ILE B 393 " --> pdb=" O TRP B 389 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 403 " --> pdb=" O ALA B 399 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 411 Processing helix chain 'B' and resid 425 through 436 Processing helix chain 'B' and resid 458 through 474 removed outlier: 3.858A pdb=" N LEU B 463 " --> pdb=" O SER B 459 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL B 464 " --> pdb=" O ALA B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 501 Processing helix chain 'B' and resid 670 through 682 removed outlier: 3.852A pdb=" N ALA B 675 " --> pdb=" O GLU B 671 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY B 677 " --> pdb=" O SER B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 696 removed outlier: 3.909A pdb=" N PHE B 696 " --> pdb=" O PRO B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 709 removed outlier: 4.135A pdb=" N GLN B 707 " --> pdb=" O ARG B 703 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE B 708 " --> pdb=" O GLY B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 746 removed outlier: 4.342A pdb=" N ILE B 735 " --> pdb=" O GLY B 731 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ALA B 736 " --> pdb=" O ILE B 732 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE B 746 " --> pdb=" O ALA B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 795 removed outlier: 3.724A pdb=" N THR B 773 " --> pdb=" O SER B 769 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR B 774 " --> pdb=" O ASP B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 825 removed outlier: 3.607A pdb=" N ALA B 801 " --> pdb=" O SER B 797 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 862 removed outlier: 3.609A pdb=" N ILE B 842 " --> pdb=" O MET B 838 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP B 849 " --> pdb=" O ALA B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 893 removed outlier: 4.955A pdb=" N SER B 879 " --> pdb=" O GLY B 875 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL B 880 " --> pdb=" O GLY B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 898 removed outlier: 3.570A pdb=" N VAL B 897 " --> pdb=" O SER B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 920 Processing helix chain 'B' and resid 920 through 933 removed outlier: 5.049A pdb=" N THR B 926 " --> pdb=" O ARG B 922 " (cutoff:3.500A) Proline residue: B 927 - end of helix Processing helix chain 'B' and resid 935 through 939 removed outlier: 3.651A pdb=" N TRP B 939 " --> pdb=" O TRP B 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 8 through 29 Processing helix chain 'D' and resid 4 through 20 removed outlier: 3.626A pdb=" N GLU D 14 " --> pdb=" O ALA D 10 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE D 15 " --> pdb=" O GLY D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 56 removed outlier: 3.712A pdb=" N VAL D 45 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 82 Processing helix chain 'E' and resid 22 through 31 Processing helix chain 'E' and resid 31 through 50 removed outlier: 4.160A pdb=" N VAL E 50 " --> pdb=" O LEU E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 60 Processing helix chain 'E' and resid 69 through 82 Processing helix chain 'E' and resid 102 through 117 removed outlier: 3.784A pdb=" N HIS E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 140 removed outlier: 4.019A pdb=" N GLN E 140 " --> pdb=" O THR E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 176 removed outlier: 4.047A pdb=" N ASN E 163 " --> pdb=" O GLU E 159 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU E 176 " --> pdb=" O ILE E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 223 removed outlier: 3.688A pdb=" N VAL E 193 " --> pdb=" O SER E 189 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP E 201 " --> pdb=" O GLN E 197 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ARG E 202 " --> pdb=" O GLN E 198 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL E 206 " --> pdb=" O ARG E 202 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA E 209 " --> pdb=" O GLN E 205 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE E 212 " --> pdb=" O GLU E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 253 removed outlier: 3.708A pdb=" N SER E 229 " --> pdb=" O SER E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 291 removed outlier: 3.860A pdb=" N VAL E 268 " --> pdb=" O ASN E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 323 removed outlier: 5.625A pdb=" N HIS E 308 " --> pdb=" O GLY E 304 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N VAL E 309 " --> pdb=" O GLY E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 327 Processing helix chain 'E' and resid 329 through 334 Processing helix chain 'E' and resid 335 through 362 removed outlier: 4.105A pdb=" N GLY E 354 " --> pdb=" O ALA E 350 " (cutoff:3.500A) Proline residue: E 355 - end of helix Processing helix chain 'E' and resid 373 through 389 removed outlier: 3.692A pdb=" N ARG E 377 " --> pdb=" O MET E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 406 removed outlier: 3.504A pdb=" N ILE E 393 " --> pdb=" O TRP E 389 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL E 403 " --> pdb=" O ALA E 399 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY E 404 " --> pdb=" O LEU E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 411 removed outlier: 3.568A pdb=" N GLY E 410 " --> pdb=" O THR E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 421 removed outlier: 3.933A pdb=" N LEU E 421 " --> pdb=" O ARG E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 436 Processing helix chain 'E' and resid 460 through 474 removed outlier: 4.183A pdb=" N VAL E 464 " --> pdb=" O ALA E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 683 removed outlier: 3.521A pdb=" N SER E 683 " --> pdb=" O ALA E 679 " (cutoff:3.500A) Processing helix chain 'E' and resid 692 through 696 removed outlier: 3.932A pdb=" N PHE E 696 " --> pdb=" O PRO E 693 " (cutoff:3.500A) Processing helix chain 'E' and resid 698 through 709 removed outlier: 3.685A pdb=" N GLN E 702 " --> pdb=" O ASN E 698 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ARG E 703 " --> pdb=" O PRO E 699 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N GLY E 704 " --> pdb=" O ASP E 700 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN E 707 " --> pdb=" O ARG E 703 " (cutoff:3.500A) Processing helix chain 'E' and resid 728 through 746 removed outlier: 4.215A pdb=" N ILE E 735 " --> pdb=" O GLY E 731 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA E 736 " --> pdb=" O ILE E 732 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS E 737 " --> pdb=" O ALA E 733 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE E 746 " --> pdb=" O ALA E 742 " (cutoff:3.500A) Processing helix chain 'E' and resid 760 through 795 removed outlier: 3.510A pdb=" N MET E 764 " --> pdb=" O GLY E 760 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR E 773 " --> pdb=" O SER E 769 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR E 774 " --> pdb=" O ASP E 770 " (cutoff:3.500A) Processing helix chain 'E' and resid 797 through 825 removed outlier: 3.516A pdb=" N ALA E 801 " --> pdb=" O SER E 797 " (cutoff:3.500A) Processing helix chain 'E' and resid 834 through 862 removed outlier: 3.705A pdb=" N ILE E 842 " --> pdb=" O MET E 838 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU E 852 " --> pdb=" O ALA E 848 " (cutoff:3.500A) Processing helix chain 'E' and resid 865 through 893 removed outlier: 4.874A pdb=" N SER E 879 " --> pdb=" O GLY E 875 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL E 880 " --> pdb=" O GLY E 876 " (cutoff:3.500A) Processing helix chain 'E' and resid 894 through 898 removed outlier: 3.731A pdb=" N VAL E 897 " --> pdb=" O SER E 894 " (cutoff:3.500A) Processing helix chain 'E' and resid 900 through 920 Processing helix chain 'E' and resid 920 through 933 removed outlier: 4.939A pdb=" N THR E 926 " --> pdb=" O ARG E 922 " (cutoff:3.500A) Proline residue: E 927 - end of helix Processing helix chain 'E' and resid 935 through 939 removed outlier: 3.698A pdb=" N TRP E 938 " --> pdb=" O LYS E 935 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 7 Processing helix chain 'G' and resid 8 through 29 removed outlier: 3.526A pdb=" N LEU G 12 " --> pdb=" O ALA G 8 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 20 removed outlier: 3.562A pdb=" N GLU I 14 " --> pdb=" O ALA I 10 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE I 15 " --> pdb=" O GLY I 11 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 56 removed outlier: 3.787A pdb=" N VAL I 45 " --> pdb=" O SER I 41 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU I 46 " --> pdb=" O LEU I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 65 removed outlier: 3.955A pdb=" N ALA I 65 " --> pdb=" O ASP I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 83 removed outlier: 3.717A pdb=" N GLU I 83 " --> pdb=" O LYS I 79 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 123 through 127 removed outlier: 6.721A pdb=" N LYS A 152 " --> pdb=" O GLN A 124 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU A 126 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLN A 150 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 413 through 414 removed outlier: 3.670A pdb=" N ASN A 414 " --> pdb=" O LEU A 831 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 478 through 482 removed outlier: 4.844A pdb=" N ARG A 480 " --> pdb=" O SER A 721 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 123 through 127 removed outlier: 6.575A pdb=" N LYS B 152 " --> pdb=" O GLN B 124 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU B 126 " --> pdb=" O GLN B 150 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLN B 150 " --> pdb=" O LEU B 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 413 through 414 removed outlier: 3.602A pdb=" N ASN B 414 " --> pdb=" O LEU B 831 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 478 through 482 removed outlier: 4.783A pdb=" N ARG B 480 " --> pdb=" O SER B 721 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 123 through 127 removed outlier: 3.897A pdb=" N SER E 125 " --> pdb=" O LYS E 152 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN E 150 " --> pdb=" O GLN E 127 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 413 through 414 removed outlier: 3.588A pdb=" N ASN E 414 " --> pdb=" O LEU E 831 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 478 through 482 removed outlier: 4.766A pdb=" N ARG E 480 " --> pdb=" O SER E 721 " (cutoff:3.500A) 1354 hydrogen bonds defined for protein. 3969 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.62 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 3355 1.25 - 1.39: 4681 1.39 - 1.53: 12580 1.53 - 1.67: 648 1.67 - 1.81: 195 Bond restraints: 21459 Sorted by residual: bond pdb=" C4 PN7 D 101 " pdb=" N5 PN7 D 101 " ideal model delta sigma weight residual 1.337 1.455 -0.118 2.00e-02 2.50e+03 3.50e+01 bond pdb=" C8 PN7 H 101 " pdb=" O8 PN7 H 101 " ideal model delta sigma weight residual 1.223 1.110 0.113 2.00e-02 2.50e+03 3.19e+01 bond pdb=" C4 PN7 I 101 " pdb=" N5 PN7 I 101 " ideal model delta sigma weight residual 1.337 1.436 -0.099 2.00e-02 2.50e+03 2.43e+01 bond pdb=" C8 PN7 D 101 " pdb=" O8 PN7 D 101 " ideal model delta sigma weight residual 1.223 1.128 0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C8 PN7 I 101 " pdb=" O8 PN7 I 101 " ideal model delta sigma weight residual 1.223 1.132 0.091 2.00e-02 2.50e+03 2.06e+01 ... (remaining 21454 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.51: 28495 4.51 - 9.01: 410 9.01 - 13.52: 63 13.52 - 18.02: 10 18.02 - 22.53: 2 Bond angle restraints: 28980 Sorted by residual: angle pdb=" C7 PN7 H 101 " pdb=" C8 PN7 H 101 " pdb=" N9 PN7 H 101 " ideal model delta sigma weight residual 114.76 137.29 -22.53 3.00e+00 1.11e-01 5.64e+01 angle pdb=" CE1 PN7 I 101 " pdb=" C2 PN7 I 101 " pdb=" C1 PN7 I 101 " ideal model delta sigma weight residual 110.19 91.18 19.01 3.00e+00 1.11e-01 4.02e+01 angle pdb=" O3P PEV B1003 " pdb=" P PEV B1003 " pdb=" O4P PEV B1003 " ideal model delta sigma weight residual 93.57 110.70 -17.13 3.00e+00 1.11e-01 3.26e+01 angle pdb=" O3P PEV G 201 " pdb=" P PEV G 201 " pdb=" O4P PEV G 201 " ideal model delta sigma weight residual 93.57 110.42 -16.85 3.00e+00 1.11e-01 3.15e+01 angle pdb=" O3P PEV B1004 " pdb=" P PEV B1004 " pdb=" O4P PEV B1004 " ideal model delta sigma weight residual 93.57 110.00 -16.43 3.00e+00 1.11e-01 3.00e+01 ... (remaining 28975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.06: 12474 30.06 - 60.11: 673 60.11 - 90.17: 24 90.17 - 120.23: 1 120.23 - 150.28: 1 Dihedral angle restraints: 13173 sinusoidal: 5577 harmonic: 7596 Sorted by residual: dihedral pdb=" CA TRP A 938 " pdb=" C TRP A 938 " pdb=" N TRP A 939 " pdb=" CA TRP A 939 " ideal model delta harmonic sigma weight residual -180.00 -150.30 -29.70 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA TRP B 938 " pdb=" C TRP B 938 " pdb=" N TRP B 939 " pdb=" CA TRP B 939 " ideal model delta harmonic sigma weight residual -180.00 -150.81 -29.19 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA TRP E 938 " pdb=" C TRP E 938 " pdb=" N TRP E 939 " pdb=" CA TRP E 939 " ideal model delta harmonic sigma weight residual -180.00 -154.37 -25.63 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 13170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1889 0.038 - 0.076: 1095 0.076 - 0.114: 299 0.114 - 0.152: 81 0.152 - 0.189: 8 Chirality restraints: 3372 Sorted by residual: chirality pdb=" C2 PEV B1004 " pdb=" C1 PEV B1004 " pdb=" C3 PEV B1004 " pdb=" O2 PEV B1004 " both_signs ideal model delta sigma weight residual False 2.36 2.55 -0.19 2.00e-01 2.50e+01 8.97e-01 chirality pdb=" C2 PEV A1004 " pdb=" C1 PEV A1004 " pdb=" C3 PEV A1004 " pdb=" O2 PEV A1004 " both_signs ideal model delta sigma weight residual False 2.36 2.54 -0.18 2.00e-01 2.50e+01 8.48e-01 chirality pdb=" C2 PEV B1003 " pdb=" C1 PEV B1003 " pdb=" C3 PEV B1003 " pdb=" O2 PEV B1003 " both_signs ideal model delta sigma weight residual False 2.36 2.53 -0.17 2.00e-01 2.50e+01 7.42e-01 ... (remaining 3369 not shown) Planarity restraints: 3582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 PN7 H 101 " 0.018 2.00e-02 2.50e+03 2.36e-02 6.94e+00 pdb=" C4 PN7 H 101 " -0.003 2.00e-02 2.50e+03 pdb=" C6 PN7 H 101 " 0.027 2.00e-02 2.50e+03 pdb=" N5 PN7 H 101 " -0.041 2.00e-02 2.50e+03 pdb=" O4 PN7 H 101 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 462 " 0.013 2.00e-02 2.50e+03 1.60e-02 4.50e+00 pdb=" CG PHE B 462 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE B 462 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE B 462 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE B 462 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 462 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 462 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 438 " 0.017 2.00e-02 2.50e+03 1.31e-02 3.00e+00 pdb=" CG PHE A 438 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE A 438 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 438 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 438 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 438 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 438 " 0.005 2.00e-02 2.50e+03 ... (remaining 3579 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3017 2.74 - 3.28: 20544 3.28 - 3.82: 34480 3.82 - 4.36: 43024 4.36 - 4.90: 75987 Nonbonded interactions: 177052 Sorted by model distance: nonbonded pdb=" O PRO A 70 " pdb=" OG SER A 74 " model vdw 2.203 3.040 nonbonded pdb=" OH TYR E 109 " pdb=" OD1 ASP E 128 " model vdw 2.206 3.040 nonbonded pdb=" NE2 GLN B 60 " pdb=" O GLY B 251 " model vdw 2.209 3.120 nonbonded pdb=" OE2 GLU B 287 " pdb=" NH2 ARG B 857 " model vdw 2.216 3.120 nonbonded pdb=" OG1 THR B 137 " pdb=" OD2 ASP B 488 " model vdw 2.219 3.040 ... (remaining 177047 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 19 through 1001) selection = (chain 'B' and resid 19 through 1001) selection = (chain 'E' and resid 19 through 1001) } ncs_group { reference = chain 'C' selection = (chain 'F' and resid 1 through 34) selection = (chain 'G' and resid 1 through 34) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' } 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: 3.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.110 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.030 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:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 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 : 0.010 0.294 21462 Z= 0.516 Angle : 1.231 22.530 28980 Z= 0.523 Chirality : 0.049 0.189 3372 Planarity : 0.004 0.039 3582 Dihedral : 16.322 150.284 8289 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.19 % Allowed : 3.45 % Favored : 96.36 % 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: -2.25 (0.15), residues: 2643 helix: -1.22 (0.11), residues: 1770 sheet: -1.49 (0.44), residues: 156 loop : -1.72 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 480 TYR 0.015 0.002 TYR E 223 PHE 0.037 0.002 PHE B 462 TRP 0.013 0.002 TRP B 379 HIS 0.004 0.001 HIS E 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00958 / 0.42 (21459) covalent geometry : angle 1.23072 / 0.52 (28980) hydrogen bonds : bond 0.13083 / 8.93 ( 1354) hydrogen bonds : angle 5.54445 / 4.09 ( 3969) Misc. bond : bond 0.25675 / 11.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 339 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.8459 (mmt) cc_final: 0.8184 (mmt) REVERT: A 202 ARG cc_start: 0.7884 (mtm180) cc_final: 0.7630 (mtm110) REVERT: A 205 GLN cc_start: 0.7115 (tt0) cc_final: 0.6583 (pt0) REVERT: F 6 LYS cc_start: 0.7416 (pttt) cc_final: 0.6397 (mmtt) REVERT: F 23 PHE cc_start: 0.8015 (m-80) cc_final: 0.6765 (t80) REVERT: H 23 GLU cc_start: 0.8097 (mp0) cc_final: 0.7821 (mp0) REVERT: H 31 LYS cc_start: 0.8242 (mttm) cc_final: 0.7871 (mtpt) REVERT: H 63 ASP cc_start: 0.8549 (m-30) cc_final: 0.8113 (m-30) REVERT: B 197 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7980 (tm-30) REVERT: B 205 GLN cc_start: 0.8018 (pt0) cc_final: 0.7693 (pt0) REVERT: B 446 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7660 (mm-30) REVERT: B 892 MET cc_start: 0.8850 (mmm) cc_final: 0.8605 (mmp) REVERT: C 6 LYS cc_start: 0.7615 (pttt) cc_final: 0.6962 (ptpt) REVERT: D 4 THR cc_start: 0.8743 (t) cc_final: 0.8446 (p) REVERT: D 32 SER cc_start: 0.8669 (t) cc_final: 0.8466 (p) REVERT: E 196 GLN cc_start: 0.8580 (tt0) cc_final: 0.8362 (tt0) REVERT: E 198 GLN cc_start: 0.7899 (pt0) cc_final: 0.7427 (tm-30) REVERT: G 12 LEU cc_start: 0.8885 (mt) cc_final: 0.8664 (mt) REVERT: I 58 LYS cc_start: 0.9175 (ttmt) cc_final: 0.8790 (tttm) outliers start: 4 outliers final: 1 residues processed: 343 average time/residue: 0.6567 time to fit residues: 253.7886 Evaluate side-chains 265 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 264 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 417 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.2980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.0570 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 GLN A 419 ASN A 482 GLN A 494 HIS A 685 ASN A 707 GLN A 722 HIS A 824 GLN A 941 GLN H 50 GLN B 77 HIS B 253 HIS B 286 GLN B 482 GLN B 707 GLN B 722 HIS B 824 GLN B 941 GLN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 GLN E 60 GLN E 77 HIS E 111 GLN E 286 GLN E 440 GLN E 454 HIS E 466 ASN E 482 GLN E 714 HIS E 722 HIS E 824 GLN E 825 HIS E 941 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.129750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.102113 restraints weight = 28502.218| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.39 r_work: 0.3107 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21462 Z= 0.115 Angle : 0.553 10.061 28980 Z= 0.278 Chirality : 0.041 0.172 3372 Planarity : 0.004 0.037 3582 Dihedral : 15.272 148.457 3788 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.89 % Allowed : 10.59 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.16), residues: 2643 helix: 0.38 (0.12), residues: 1779 sheet: -0.95 (0.44), residues: 147 loop : -0.99 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 99 TYR 0.008 0.001 TYR E 420 PHE 0.023 0.001 PHE E 438 TRP 0.012 0.001 TRP A 379 HIS 0.003 0.001 HIS B 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (21459) covalent geometry : angle 0.55266 / 0.28 (28980) hydrogen bonds : bond 0.03917 / 2.66 ( 1354) hydrogen bonds : angle 4.17800 / 3.05 ( 3969) Misc. bond : bond 0.00084 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 301 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ILE cc_start: 0.8098 (pt) cc_final: 0.7847 (pp) REVERT: A 167 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7836 (tm-30) REVERT: A 205 GLN cc_start: 0.7046 (tt0) cc_final: 0.6468 (pt0) REVERT: A 254 ARG cc_start: 0.7903 (mmt180) cc_final: 0.7058 (mpp-170) REVERT: F 6 LYS cc_start: 0.6814 (pttt) cc_final: 0.6564 (ptmt) REVERT: F 7 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7717 (mtp85) REVERT: F 23 PHE cc_start: 0.7861 (m-80) cc_final: 0.6500 (t80) REVERT: H 1 MET cc_start: 0.0082 (OUTLIER) cc_final: -0.0277 (pmt) REVERT: H 23 GLU cc_start: 0.8255 (mp0) cc_final: 0.7851 (mp0) REVERT: H 31 LYS cc_start: 0.8265 (mttm) cc_final: 0.7910 (mtpt) REVERT: H 44 MET cc_start: 0.8699 (mmm) cc_final: 0.8486 (mmm) REVERT: H 63 ASP cc_start: 0.8543 (m-30) cc_final: 0.8140 (m-30) REVERT: B 176 LEU cc_start: 0.8306 (mm) cc_final: 0.7933 (tp) REVERT: B 197 GLN cc_start: 0.8167 (tm-30) cc_final: 0.7889 (tm-30) REVERT: B 369 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7652 (mm-30) REVERT: B 903 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7749 (ttm) REVERT: C 6 LYS cc_start: 0.7045 (pttt) cc_final: 0.6353 (ptpp) REVERT: D 72 ASP cc_start: 0.8657 (m-30) cc_final: 0.8410 (m-30) REVERT: E 72 MET cc_start: 0.8379 (tmm) cc_final: 0.7899 (tpt) REVERT: E 99 ARG cc_start: 0.7816 (mtm110) cc_final: 0.7470 (mpp80) REVERT: E 183 LYS cc_start: 0.8034 (mmtm) cc_final: 0.7682 (mtpt) REVERT: E 196 GLN cc_start: 0.8456 (tt0) cc_final: 0.8202 (tt0) REVERT: E 198 GLN cc_start: 0.7919 (pt0) cc_final: 0.7355 (tm-30) REVERT: E 456 MET cc_start: 0.9359 (mtm) cc_final: 0.9104 (mtm) REVERT: E 903 MET cc_start: 0.7246 (OUTLIER) cc_final: 0.6660 (ttm) REVERT: I 31 LYS cc_start: 0.8487 (mttm) cc_final: 0.8140 (mmtp) REVERT: I 58 LYS cc_start: 0.9235 (ttmt) cc_final: 0.8732 (tttp) REVERT: I 72 ASP cc_start: 0.8723 (m-30) cc_final: 0.8496 (m-30) outliers start: 40 outliers final: 8 residues processed: 315 average time/residue: 0.5683 time to fit residues: 202.6158 Evaluate side-chains 267 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 254 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 7 ARG Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 196 GLN Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 903 MET Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 903 MET Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 53 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 34 optimal weight: 5.9990 chunk 213 optimal weight: 0.9980 chunk 50 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 224 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 419 ASN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 GLN E 60 GLN E 729 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.125552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.097731 restraints weight = 28855.347| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.39 r_work: 0.3035 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 21462 Z= 0.255 Angle : 0.623 10.952 28980 Z= 0.312 Chirality : 0.045 0.165 3372 Planarity : 0.004 0.040 3582 Dihedral : 14.911 140.980 3786 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.70 % Allowed : 12.48 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.16), residues: 2643 helix: 0.64 (0.12), residues: 1773 sheet: -0.60 (0.43), residues: 147 loop : -0.66 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 175 TYR 0.012 0.002 TYR E 415 PHE 0.029 0.002 PHE E 438 TRP 0.014 0.002 TRP B 936 HIS 0.004 0.001 HIS E 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00620 / 0.25 (21459) covalent geometry : angle 0.62327 / 0.31 (28980) hydrogen bonds : bond 0.04528 / 3.08 ( 1354) hydrogen bonds : angle 4.22461 / 3.09 ( 3969) Misc. bond : bond 0.00192 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 257 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 SER cc_start: 0.9069 (t) cc_final: 0.8848 (p) REVERT: A 205 GLN cc_start: 0.7032 (tt0) cc_final: 0.6437 (pt0) REVERT: A 686 ASP cc_start: 0.7290 (p0) cc_final: 0.6977 (p0) REVERT: A 849 ASP cc_start: 0.8896 (m-30) cc_final: 0.8666 (m-30) REVERT: A 858 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8357 (tt) REVERT: F 6 LYS cc_start: 0.6808 (pttt) cc_final: 0.6558 (ptmt) REVERT: F 23 PHE cc_start: 0.8014 (m-80) cc_final: 0.6600 (t80) REVERT: H 23 GLU cc_start: 0.8289 (mp0) cc_final: 0.8043 (mt-10) REVERT: H 31 LYS cc_start: 0.8232 (mttm) cc_final: 0.7857 (mtpt) REVERT: H 63 ASP cc_start: 0.8651 (m-30) cc_final: 0.8237 (m-30) REVERT: B 176 LEU cc_start: 0.8307 (mm) cc_final: 0.7943 (tp) REVERT: B 197 GLN cc_start: 0.8185 (tm-30) cc_final: 0.7911 (tm-30) REVERT: B 369 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7753 (mm-30) REVERT: B 669 MET cc_start: 0.3363 (OUTLIER) cc_final: 0.3111 (mtp) REVERT: B 732 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8564 (mp) REVERT: B 838 MET cc_start: 0.8738 (mtm) cc_final: 0.8490 (ttt) REVERT: C 6 LYS cc_start: 0.7121 (pttt) cc_final: 0.6440 (ptpp) REVERT: D 4 THR cc_start: 0.8336 (t) cc_final: 0.7958 (p) REVERT: E 111 GLN cc_start: 0.8695 (mt0) cc_final: 0.8495 (tp-100) REVERT: E 183 LYS cc_start: 0.8089 (mmtm) cc_final: 0.7693 (mtpt) REVERT: E 196 GLN cc_start: 0.8503 (tt0) cc_final: 0.8261 (tt0) REVERT: E 198 GLN cc_start: 0.7977 (pt0) cc_final: 0.7393 (tm-30) REVERT: E 232 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7499 (tmt) REVERT: E 476 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: E 903 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.6772 (ttm) REVERT: I 31 LYS cc_start: 0.8501 (mttm) cc_final: 0.8203 (mmtp) REVERT: I 58 LYS cc_start: 0.9298 (ttmt) cc_final: 0.8789 (tttp) outliers start: 57 outliers final: 20 residues processed: 286 average time/residue: 0.5730 time to fit residues: 185.3720 Evaluate side-chains 279 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 252 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain B residue 196 GLN Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 669 MET Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 917 ASP Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 232 MET Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 476 GLU Chi-restraints excluded: chain E residue 804 ILE Chi-restraints excluded: chain E residue 812 LEU Chi-restraints excluded: chain E residue 902 VAL Chi-restraints excluded: chain E residue 903 MET Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 34 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 139 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 231 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 209 optimal weight: 0.9980 chunk 223 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 GLN B 419 ASN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 GLN E 156 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.128229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.100425 restraints weight = 28784.083| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.39 r_work: 0.3078 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21462 Z= 0.146 Angle : 0.541 8.884 28980 Z= 0.272 Chirality : 0.042 0.175 3372 Planarity : 0.004 0.040 3582 Dihedral : 14.333 133.868 3786 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.84 % Allowed : 13.48 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.17), residues: 2643 helix: 1.06 (0.12), residues: 1785 sheet: -0.50 (0.43), residues: 147 loop : -0.37 (0.24), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 99 TYR 0.008 0.001 TYR E 415 PHE 0.024 0.001 PHE E 438 TRP 0.012 0.001 TRP A 379 HIS 0.004 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (21459) covalent geometry : angle 0.54076 / 0.27 (28980) hydrogen bonds : bond 0.03823 / 2.59 ( 1354) hydrogen bonds : angle 4.02146 / 2.95 ( 3969) Misc. bond : bond 0.00086 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 255 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8252 (pp) REVERT: A 113 ILE cc_start: 0.8167 (pp) cc_final: 0.7915 (pp) REVERT: A 167 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8192 (tm-30) REVERT: A 202 ARG cc_start: 0.7702 (ttp-110) cc_final: 0.7301 (tpt90) REVERT: A 205 GLN cc_start: 0.7026 (tt0) cc_final: 0.6432 (pt0) REVERT: A 686 ASP cc_start: 0.7327 (p0) cc_final: 0.6991 (p0) REVERT: A 849 ASP cc_start: 0.8685 (m-30) cc_final: 0.8457 (m-30) REVERT: F 6 LYS cc_start: 0.6787 (pttt) cc_final: 0.6538 (ptmt) REVERT: F 23 PHE cc_start: 0.7866 (m-80) cc_final: 0.6547 (t80) REVERT: H 31 LYS cc_start: 0.8195 (mttm) cc_final: 0.7826 (mtpt) REVERT: H 44 MET cc_start: 0.8710 (mmm) cc_final: 0.8508 (mmm) REVERT: H 63 ASP cc_start: 0.8554 (m-30) cc_final: 0.8206 (m-30) REVERT: B 175 ARG cc_start: 0.8170 (ttm-80) cc_final: 0.7768 (ttm170) REVERT: B 176 LEU cc_start: 0.8198 (mm) cc_final: 0.7851 (tp) REVERT: B 197 GLN cc_start: 0.8124 (tm-30) cc_final: 0.7848 (tm-30) REVERT: B 369 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7663 (mm-30) REVERT: B 732 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8494 (mp) REVERT: B 838 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8207 (ttt) REVERT: C 1 MET cc_start: 0.5340 (tmt) cc_final: 0.4934 (ppp) REVERT: C 6 LYS cc_start: 0.6971 (pttt) cc_final: 0.6347 (ptpp) REVERT: D 4 THR cc_start: 0.8289 (t) cc_final: 0.7916 (p) REVERT: E 99 ARG cc_start: 0.7786 (mtm110) cc_final: 0.7447 (mpp80) REVERT: E 183 LYS cc_start: 0.7976 (mmtm) cc_final: 0.7607 (mttt) REVERT: E 196 GLN cc_start: 0.8443 (tt0) cc_final: 0.8217 (tt0) REVERT: E 198 GLN cc_start: 0.7846 (pt0) cc_final: 0.7113 (tm-30) REVERT: E 201 ASP cc_start: 0.6924 (m-30) cc_final: 0.6497 (p0) REVERT: E 232 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7249 (tmt) REVERT: E 456 MET cc_start: 0.9361 (mtm) cc_final: 0.9140 (mtm) REVERT: E 903 MET cc_start: 0.7200 (OUTLIER) cc_final: 0.6635 (ttm) REVERT: I 31 LYS cc_start: 0.8589 (mttm) cc_final: 0.8291 (mmtp) REVERT: I 58 LYS cc_start: 0.9238 (ttmt) cc_final: 0.8735 (tttp) outliers start: 60 outliers final: 23 residues processed: 287 average time/residue: 0.5707 time to fit residues: 185.4117 Evaluate side-chains 276 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 247 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 681 ASP Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 770 ASP Chi-restraints excluded: chain B residue 838 MET Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 232 MET Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 804 ILE Chi-restraints excluded: chain E residue 812 LEU Chi-restraints excluded: chain E residue 902 VAL Chi-restraints excluded: chain E residue 903 MET Chi-restraints excluded: chain E residue 925 MET Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 53 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 68 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 167 optimal weight: 0.0570 chunk 185 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 146 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 825 HIS B 308 HIS D 50 GLN E 58 GLN E 156 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.125915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.098791 restraints weight = 28562.520| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.32 r_work: 0.3065 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21462 Z= 0.109 Angle : 0.505 7.149 28980 Z= 0.253 Chirality : 0.040 0.188 3372 Planarity : 0.004 0.042 3582 Dihedral : 13.584 128.269 3786 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.32 % Allowed : 14.52 % Favored : 83.17 % 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: 1.31 (0.17), residues: 2643 helix: 1.43 (0.12), residues: 1797 sheet: -0.32 (0.43), residues: 147 loop : -0.18 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 99 TYR 0.007 0.001 TYR A 109 PHE 0.020 0.001 PHE E 438 TRP 0.010 0.001 TRP A 379 HIS 0.004 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (21459) covalent geometry : angle 0.50460 / 0.25 (28980) hydrogen bonds : bond 0.03395 / 2.29 ( 1354) hydrogen bonds : angle 3.86647 / 2.83 ( 3969) Misc. bond : bond 0.00040 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 275 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8066 (pp) REVERT: A 113 ILE cc_start: 0.7930 (pp) cc_final: 0.7700 (pp) REVERT: A 202 ARG cc_start: 0.7683 (ttp-110) cc_final: 0.7160 (tpt90) REVERT: A 205 GLN cc_start: 0.6795 (tt0) cc_final: 0.6251 (pt0) REVERT: A 686 ASP cc_start: 0.7339 (p0) cc_final: 0.6963 (p0) REVERT: A 743 LYS cc_start: 0.8683 (tttt) cc_final: 0.8389 (tttm) REVERT: A 849 ASP cc_start: 0.8564 (m-30) cc_final: 0.8347 (m-30) REVERT: F 6 LYS cc_start: 0.6253 (pttt) cc_final: 0.6034 (ptmt) REVERT: F 23 PHE cc_start: 0.7557 (m-80) cc_final: 0.6207 (t80) REVERT: H 31 LYS cc_start: 0.7992 (mttm) cc_final: 0.7651 (mtpt) REVERT: H 44 MET cc_start: 0.8631 (mmm) cc_final: 0.8429 (mmm) REVERT: H 63 ASP cc_start: 0.8368 (m-30) cc_final: 0.7998 (m-30) REVERT: B 175 ARG cc_start: 0.8165 (ttm-80) cc_final: 0.7638 (ttm170) REVERT: B 176 LEU cc_start: 0.8172 (mm) cc_final: 0.7843 (tp) REVERT: B 197 GLN cc_start: 0.7825 (tm-30) cc_final: 0.7558 (tm-30) REVERT: B 369 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7565 (mm-30) REVERT: B 429 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8392 (mm-30) REVERT: B 838 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8137 (ttt) REVERT: B 903 MET cc_start: 0.7992 (mtm) cc_final: 0.7628 (ttm) REVERT: C 6 LYS cc_start: 0.6330 (pttt) cc_final: 0.6125 (ptpt) REVERT: D 4 THR cc_start: 0.8026 (t) cc_final: 0.7647 (p) REVERT: D 61 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.8138 (m-30) REVERT: E 99 ARG cc_start: 0.7841 (mtm110) cc_final: 0.7411 (mpp80) REVERT: E 183 LYS cc_start: 0.7717 (mmtm) cc_final: 0.7390 (mtpt) REVERT: E 196 GLN cc_start: 0.8263 (tt0) cc_final: 0.8017 (tt0) REVERT: E 198 GLN cc_start: 0.7781 (pt0) cc_final: 0.7019 (tm-30) REVERT: E 201 ASP cc_start: 0.6678 (m-30) cc_final: 0.6255 (p0) REVERT: E 232 MET cc_start: 0.7573 (OUTLIER) cc_final: 0.7145 (tmt) REVERT: E 903 MET cc_start: 0.7240 (OUTLIER) cc_final: 0.6517 (ttp) REVERT: G 1 MET cc_start: 0.4495 (OUTLIER) cc_final: 0.3824 (ttp) REVERT: I 17 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7374 (tp30) REVERT: I 31 LYS cc_start: 0.8203 (mttm) cc_final: 0.7932 (mmtp) REVERT: I 58 LYS cc_start: 0.9131 (ttmt) cc_final: 0.8587 (tttp) outliers start: 49 outliers final: 18 residues processed: 299 average time/residue: 0.5682 time to fit residues: 192.0740 Evaluate side-chains 282 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 257 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 681 ASP Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 838 MET Chi-restraints excluded: chain B residue 917 ASP Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 232 MET Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 804 ILE Chi-restraints excluded: chain E residue 812 LEU Chi-restraints excluded: chain E residue 902 VAL Chi-restraints excluded: chain E residue 903 MET Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 53 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 215 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 254 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 128 optimal weight: 0.0870 chunk 221 optimal weight: 1.9990 chunk 248 optimal weight: 0.6980 chunk 244 optimal weight: 0.6980 chunk 6 optimal weight: 0.0870 chunk 181 optimal weight: 0.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 205 GLN E 58 GLN E 264 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.131632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.105069 restraints weight = 28686.033| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.33 r_work: 0.3148 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 21462 Z= 0.100 Angle : 0.494 7.309 28980 Z= 0.247 Chirality : 0.040 0.194 3372 Planarity : 0.004 0.041 3582 Dihedral : 13.052 125.356 3786 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.32 % Allowed : 15.46 % Favored : 82.22 % 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: 1.70 (0.17), residues: 2643 helix: 1.69 (0.12), residues: 1797 sheet: -0.10 (0.44), residues: 147 loop : 0.06 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 99 TYR 0.010 0.001 TYR A 331 PHE 0.018 0.001 PHE E 438 TRP 0.009 0.001 TRP A 379 HIS 0.004 0.000 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (21459) covalent geometry : angle 0.49365 / 0.25 (28980) hydrogen bonds : bond 0.03192 / 2.15 ( 1354) hydrogen bonds : angle 3.77643 / 2.77 ( 3969) Misc. bond : bond 0.00026 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 272 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8240 (pp) REVERT: A 113 ILE cc_start: 0.8241 (pp) cc_final: 0.8003 (pp) REVERT: A 170 LYS cc_start: 0.8155 (ttmm) cc_final: 0.7494 (mttm) REVERT: A 202 ARG cc_start: 0.7673 (ttp-110) cc_final: 0.7450 (mtp85) REVERT: A 205 GLN cc_start: 0.6986 (tt0) cc_final: 0.6455 (pt0) REVERT: A 676 MET cc_start: 0.6166 (OUTLIER) cc_final: 0.5818 (ttt) REVERT: A 686 ASP cc_start: 0.7330 (p0) cc_final: 0.6944 (p0) REVERT: A 743 LYS cc_start: 0.8933 (tttt) cc_final: 0.8687 (tttm) REVERT: F 23 PHE cc_start: 0.7792 (m-80) cc_final: 0.6533 (t80) REVERT: H 31 LYS cc_start: 0.8313 (mttm) cc_final: 0.8034 (mtpt) REVERT: H 44 MET cc_start: 0.8676 (mmm) cc_final: 0.8441 (mmm) REVERT: H 63 ASP cc_start: 0.8460 (m-30) cc_final: 0.8173 (m-30) REVERT: B 67 ASP cc_start: 0.8313 (m-30) cc_final: 0.7753 (m-30) REVERT: B 176 LEU cc_start: 0.8420 (mm) cc_final: 0.8024 (tp) REVERT: B 197 GLN cc_start: 0.7954 (tm-30) cc_final: 0.7718 (tm-30) REVERT: B 261 PHE cc_start: 0.8257 (t80) cc_final: 0.7966 (t80) REVERT: B 369 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7686 (tp30) REVERT: B 429 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8411 (mm-30) REVERT: B 903 MET cc_start: 0.8110 (mtm) cc_final: 0.7835 (ttm) REVERT: D 4 THR cc_start: 0.8411 (t) cc_final: 0.8043 (p) REVERT: D 30 GLU cc_start: 0.8061 (pm20) cc_final: 0.7671 (pm20) REVERT: E 99 ARG cc_start: 0.7879 (mtm110) cc_final: 0.7558 (mpp80) REVERT: E 183 LYS cc_start: 0.7875 (mmtm) cc_final: 0.7572 (mtpt) REVERT: E 196 GLN cc_start: 0.8492 (tt0) cc_final: 0.8245 (tt0) REVERT: E 198 GLN cc_start: 0.7889 (pt0) cc_final: 0.7159 (tm-30) REVERT: E 201 ASP cc_start: 0.6979 (m-30) cc_final: 0.6461 (p0) REVERT: E 232 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7205 (tmt) REVERT: E 892 MET cc_start: 0.8916 (mmm) cc_final: 0.8697 (mmp) REVERT: E 903 MET cc_start: 0.7280 (OUTLIER) cc_final: 0.6761 (ttm) REVERT: G 23 PHE cc_start: 0.7356 (m-10) cc_final: 0.6206 (t80) REVERT: I 31 LYS cc_start: 0.8653 (mttm) cc_final: 0.8251 (mmmm) REVERT: I 58 LYS cc_start: 0.9218 (ttmt) cc_final: 0.8780 (tttp) outliers start: 49 outliers final: 23 residues processed: 299 average time/residue: 0.5540 time to fit residues: 188.3225 Evaluate side-chains 275 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 247 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain A residue 681 ASP Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 196 GLN Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 917 ASP Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 232 MET Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 709 LEU Chi-restraints excluded: chain E residue 804 ILE Chi-restraints excluded: chain E residue 812 LEU Chi-restraints excluded: chain E residue 840 VAL Chi-restraints excluded: chain E residue 860 GLU Chi-restraints excluded: chain E residue 902 VAL Chi-restraints excluded: chain E residue 903 MET Chi-restraints excluded: chain I residue 28 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 236 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 246 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 222 optimal weight: 1.9990 chunk 199 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 205 GLN E 58 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.131614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.104817 restraints weight = 28632.031| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.34 r_work: 0.3123 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21462 Z= 0.122 Angle : 0.516 7.972 28980 Z= 0.257 Chirality : 0.041 0.192 3372 Planarity : 0.004 0.043 3582 Dihedral : 12.924 123.655 3786 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.41 % Allowed : 16.22 % Favored : 81.37 % 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: 1.80 (0.17), residues: 2643 helix: 1.73 (0.12), residues: 1797 sheet: -0.04 (0.43), residues: 156 loop : 0.21 (0.26), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 175 TYR 0.007 0.001 TYR E 431 PHE 0.019 0.001 PHE E 438 TRP 0.009 0.001 TRP A 379 HIS 0.004 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (21459) covalent geometry : angle 0.51598 / 0.26 (28980) hydrogen bonds : bond 0.03382 / 2.28 ( 1354) hydrogen bonds : angle 3.80094 / 2.78 ( 3969) Misc. bond : bond 0.00056 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 259 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8578 (tpp) cc_final: 0.8355 (tpt) REVERT: A 95 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8309 (pp) REVERT: A 686 ASP cc_start: 0.7314 (p0) cc_final: 0.6951 (p0) REVERT: A 743 LYS cc_start: 0.8948 (tttt) cc_final: 0.8700 (tttm) REVERT: F 23 PHE cc_start: 0.7808 (m-80) cc_final: 0.6532 (t80) REVERT: H 31 LYS cc_start: 0.8301 (mttm) cc_final: 0.8041 (mtpt) REVERT: H 44 MET cc_start: 0.8683 (mmm) cc_final: 0.8443 (mmm) REVERT: H 63 ASP cc_start: 0.8498 (m-30) cc_final: 0.8207 (m-30) REVERT: B 67 ASP cc_start: 0.8326 (m-30) cc_final: 0.7764 (m-30) REVERT: B 176 LEU cc_start: 0.8345 (mm) cc_final: 0.7970 (tp) REVERT: B 197 GLN cc_start: 0.7933 (tm-30) cc_final: 0.7680 (tm-30) REVERT: B 369 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7700 (tp30) REVERT: B 429 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8424 (mm-30) REVERT: B 903 MET cc_start: 0.8132 (mtm) cc_final: 0.7794 (ttm) REVERT: C 1 MET cc_start: 0.5561 (ppp) cc_final: 0.5236 (ppp) REVERT: D 4 THR cc_start: 0.8410 (t) cc_final: 0.8035 (p) REVERT: D 30 GLU cc_start: 0.8123 (pm20) cc_final: 0.7784 (pm20) REVERT: E 99 ARG cc_start: 0.7888 (mtm110) cc_final: 0.7569 (mpp80) REVERT: E 183 LYS cc_start: 0.7853 (mmtm) cc_final: 0.7607 (mtpt) REVERT: E 196 GLN cc_start: 0.8500 (tt0) cc_final: 0.8252 (tt0) REVERT: E 198 GLN cc_start: 0.7834 (pt0) cc_final: 0.7133 (tm-30) REVERT: E 201 ASP cc_start: 0.6951 (m-30) cc_final: 0.6492 (p0) REVERT: E 232 MET cc_start: 0.7453 (OUTLIER) cc_final: 0.7094 (tmt) REVERT: E 892 MET cc_start: 0.8924 (mmm) cc_final: 0.8710 (mmp) REVERT: E 903 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.6817 (ttp) REVERT: G 23 PHE cc_start: 0.7426 (m-10) cc_final: 0.6241 (t80) REVERT: I 1 MET cc_start: 0.2750 (OUTLIER) cc_final: 0.1481 (mmt) REVERT: I 17 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7479 (tp30) REVERT: I 31 LYS cc_start: 0.8625 (mttm) cc_final: 0.8163 (mmmm) REVERT: I 58 LYS cc_start: 0.9244 (ttmt) cc_final: 0.8798 (tttp) outliers start: 51 outliers final: 28 residues processed: 290 average time/residue: 0.6108 time to fit residues: 201.1475 Evaluate side-chains 281 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 248 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 681 ASP Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 196 GLN Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 770 ASP Chi-restraints excluded: chain B residue 917 ASP Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 232 MET Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 709 LEU Chi-restraints excluded: chain E residue 812 LEU Chi-restraints excluded: chain E residue 840 VAL Chi-restraints excluded: chain E residue 860 GLU Chi-restraints excluded: chain E residue 902 VAL Chi-restraints excluded: chain E residue 903 MET Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 70 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 99 optimal weight: 0.0270 chunk 15 optimal weight: 1.9990 chunk 241 optimal weight: 0.5980 chunk 236 optimal weight: 0.8980 chunk 180 optimal weight: 0.0770 chunk 118 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 225 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 253 HIS E 58 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.133273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.106551 restraints weight = 28453.289| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.35 r_work: 0.3149 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 21462 Z= 0.100 Angle : 0.498 7.453 28980 Z= 0.248 Chirality : 0.040 0.207 3372 Planarity : 0.004 0.042 3582 Dihedral : 12.620 121.321 3786 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.17 % Allowed : 16.78 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.17), residues: 2643 helix: 1.86 (0.12), residues: 1800 sheet: 0.14 (0.44), residues: 147 loop : 0.26 (0.26), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 175 TYR 0.007 0.001 TYR A 109 PHE 0.018 0.001 PHE A 438 TRP 0.009 0.001 TRP A 379 HIS 0.004 0.000 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (21459) covalent geometry : angle 0.49758 / 0.25 (28980) hydrogen bonds : bond 0.03133 / 2.11 ( 1354) hydrogen bonds : angle 3.73400 / 2.73 ( 3969) Misc. bond : bond 0.00022 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 257 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8568 (tpp) cc_final: 0.8333 (tpt) REVERT: A 95 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8214 (pp) REVERT: A 113 ILE cc_start: 0.8291 (pp) cc_final: 0.7998 (pp) REVERT: A 686 ASP cc_start: 0.7293 (p0) cc_final: 0.6930 (p0) REVERT: A 743 LYS cc_start: 0.8918 (tttt) cc_final: 0.8685 (tttm) REVERT: F 23 PHE cc_start: 0.7777 (m-80) cc_final: 0.6513 (t80) REVERT: H 31 LYS cc_start: 0.8299 (mttm) cc_final: 0.8058 (mtpt) REVERT: H 63 ASP cc_start: 0.8458 (m-30) cc_final: 0.8193 (m-30) REVERT: B 67 ASP cc_start: 0.8273 (m-30) cc_final: 0.7718 (m-30) REVERT: B 176 LEU cc_start: 0.8355 (mm) cc_final: 0.7978 (tp) REVERT: B 197 GLN cc_start: 0.7930 (tm-30) cc_final: 0.7687 (tm-30) REVERT: B 369 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7713 (tp30) REVERT: B 429 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8400 (mm-30) REVERT: B 903 MET cc_start: 0.8104 (mtm) cc_final: 0.7830 (ttm) REVERT: C 1 MET cc_start: 0.5438 (ppp) cc_final: 0.5121 (ppp) REVERT: D 4 THR cc_start: 0.8405 (t) cc_final: 0.8021 (p) REVERT: D 30 GLU cc_start: 0.8122 (pm20) cc_final: 0.7804 (pm20) REVERT: E 27 MET cc_start: 0.8790 (mmt) cc_final: 0.8332 (mmt) REVERT: E 99 ARG cc_start: 0.7931 (mtm110) cc_final: 0.7609 (mpp80) REVERT: E 183 LYS cc_start: 0.7790 (mmtm) cc_final: 0.7588 (mtpt) REVERT: E 196 GLN cc_start: 0.8467 (tt0) cc_final: 0.8248 (tt0) REVERT: E 198 GLN cc_start: 0.7815 (pt0) cc_final: 0.7138 (tm130) REVERT: E 201 ASP cc_start: 0.6911 (m-30) cc_final: 0.6490 (p0) REVERT: E 232 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7169 (tmt) REVERT: E 892 MET cc_start: 0.8890 (mmm) cc_final: 0.8681 (mmp) REVERT: E 903 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.6789 (ttp) REVERT: G 23 PHE cc_start: 0.7335 (m-10) cc_final: 0.6177 (t80) REVERT: I 17 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7537 (tp30) REVERT: I 31 LYS cc_start: 0.8624 (mttm) cc_final: 0.8266 (mmmm) REVERT: I 58 LYS cc_start: 0.9240 (ttmt) cc_final: 0.8712 (tttp) outliers start: 46 outliers final: 23 residues processed: 288 average time/residue: 0.5857 time to fit residues: 191.6669 Evaluate side-chains 275 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 248 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 770 ASP Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 232 MET Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 709 LEU Chi-restraints excluded: chain E residue 840 VAL Chi-restraints excluded: chain E residue 860 GLU Chi-restraints excluded: chain E residue 902 VAL Chi-restraints excluded: chain E residue 903 MET Chi-restraints excluded: chain I residue 28 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 147 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 142 optimal weight: 0.2980 chunk 127 optimal weight: 0.6980 chunk 259 optimal weight: 6.9990 chunk 245 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 197 optimal weight: 5.9990 chunk 50 optimal weight: 0.0770 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.133603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.106892 restraints weight = 28520.637| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.36 r_work: 0.3150 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 21462 Z= 0.102 Angle : 0.500 7.829 28980 Z= 0.249 Chirality : 0.040 0.205 3372 Planarity : 0.004 0.042 3582 Dihedral : 12.403 119.693 3786 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.89 % Allowed : 17.16 % Favored : 80.95 % 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: 2643 helix: 1.89 (0.12), residues: 1809 sheet: 0.12 (0.43), residues: 156 loop : 0.45 (0.26), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 175 TYR 0.008 0.001 TYR A 331 PHE 0.017 0.001 PHE A 438 TRP 0.009 0.001 TRP A 379 HIS 0.002 0.000 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (21459) covalent geometry : angle 0.49997 / 0.25 (28980) hydrogen bonds : bond 0.03146 / 2.12 ( 1354) hydrogen bonds : angle 3.71470 / 2.72 ( 3969) Misc. bond : bond 0.00027 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 259 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8587 (tpp) cc_final: 0.8342 (tpt) REVERT: A 95 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8116 (pp) REVERT: A 113 ILE cc_start: 0.8298 (pp) cc_final: 0.8005 (pp) REVERT: A 202 ARG cc_start: 0.7707 (ttt-90) cc_final: 0.7302 (ttp-110) REVERT: A 686 ASP cc_start: 0.7288 (p0) cc_final: 0.6899 (p0) REVERT: A 743 LYS cc_start: 0.8920 (tttt) cc_final: 0.8689 (tttm) REVERT: F 23 PHE cc_start: 0.7771 (m-10) cc_final: 0.6514 (t80) REVERT: H 31 LYS cc_start: 0.8283 (mttm) cc_final: 0.8038 (mtpt) REVERT: H 63 ASP cc_start: 0.8451 (m-30) cc_final: 0.8183 (m-30) REVERT: B 67 ASP cc_start: 0.8282 (m-30) cc_final: 0.7752 (m-30) REVERT: B 176 LEU cc_start: 0.8354 (mm) cc_final: 0.7966 (tp) REVERT: B 197 GLN cc_start: 0.7910 (tm-30) cc_final: 0.7661 (tm-30) REVERT: B 417 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8188 (t0) REVERT: B 429 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8414 (mm-30) REVERT: B 903 MET cc_start: 0.8107 (mtm) cc_final: 0.7818 (ttm) REVERT: C 1 MET cc_start: 0.5455 (ppp) cc_final: 0.5236 (ppp) REVERT: D 4 THR cc_start: 0.8424 (t) cc_final: 0.8035 (p) REVERT: D 30 GLU cc_start: 0.8144 (pm20) cc_final: 0.7818 (pm20) REVERT: E 99 ARG cc_start: 0.7936 (mtm110) cc_final: 0.7617 (mpp80) REVERT: E 183 LYS cc_start: 0.7775 (mmtm) cc_final: 0.7509 (mttt) REVERT: E 196 GLN cc_start: 0.8446 (tt0) cc_final: 0.8225 (tt0) REVERT: E 198 GLN cc_start: 0.7808 (pt0) cc_final: 0.7155 (tm130) REVERT: E 201 ASP cc_start: 0.6924 (m-30) cc_final: 0.6500 (p0) REVERT: E 232 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.7161 (tmt) REVERT: E 903 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.6774 (ttp) REVERT: G 23 PHE cc_start: 0.7317 (m-10) cc_final: 0.6157 (t80) REVERT: I 17 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7562 (tp30) REVERT: I 31 LYS cc_start: 0.8580 (mttm) cc_final: 0.8244 (mmmm) REVERT: I 58 LYS cc_start: 0.9243 (ttmt) cc_final: 0.8715 (tttp) outliers start: 40 outliers final: 23 residues processed: 286 average time/residue: 0.5472 time to fit residues: 178.2520 Evaluate side-chains 278 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 251 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 770 ASP Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 917 ASP Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 232 MET Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 709 LEU Chi-restraints excluded: chain E residue 840 VAL Chi-restraints excluded: chain E residue 902 VAL Chi-restraints excluded: chain E residue 903 MET Chi-restraints excluded: chain I residue 28 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 112 optimal weight: 0.6980 chunk 119 optimal weight: 4.9990 chunk 251 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 257 optimal weight: 4.9990 chunk 177 optimal weight: 0.7980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 157 GLN B 205 GLN B 419 ASN E 60 GLN E 150 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.126353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.100545 restraints weight = 28969.145| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.21 r_work: 0.3110 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21462 Z= 0.171 Angle : 0.566 9.146 28980 Z= 0.281 Chirality : 0.042 0.192 3372 Planarity : 0.004 0.042 3582 Dihedral : 12.726 119.758 3786 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.80 % Allowed : 17.59 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.17), residues: 2643 helix: 1.68 (0.12), residues: 1803 sheet: 0.17 (0.43), residues: 156 loop : 0.38 (0.26), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 175 TYR 0.009 0.001 TYR B 690 PHE 0.022 0.002 PHE E 438 TRP 0.010 0.001 TRP B 936 HIS 0.003 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 (21459) covalent geometry : angle 0.56562 / 0.28 (28980) hydrogen bonds : bond 0.03795 / 2.57 ( 1354) hydrogen bonds : angle 3.91057 / 2.86 ( 3969) Misc. bond : bond 0.00094 / 0.04 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 254 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8507 (pp) REVERT: A 113 ILE cc_start: 0.8480 (pp) cc_final: 0.8221 (pp) REVERT: A 202 ARG cc_start: 0.7884 (ttt-90) cc_final: 0.7260 (mtp85) REVERT: A 686 ASP cc_start: 0.7289 (p0) cc_final: 0.6905 (p0) REVERT: A 743 LYS cc_start: 0.9118 (tttt) cc_final: 0.8887 (tttm) REVERT: F 23 PHE cc_start: 0.8027 (m-10) cc_final: 0.6722 (t80) REVERT: H 31 LYS cc_start: 0.8371 (mttm) cc_final: 0.8157 (mtpt) REVERT: H 63 ASP cc_start: 0.8654 (m-30) cc_final: 0.8377 (m-30) REVERT: B 67 ASP cc_start: 0.8433 (m-30) cc_final: 0.7905 (m-30) REVERT: B 176 LEU cc_start: 0.8398 (mm) cc_final: 0.8016 (tp) REVERT: B 197 GLN cc_start: 0.7983 (tm-30) cc_final: 0.7754 (tm-30) REVERT: B 417 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8310 (t0) REVERT: B 429 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8539 (mm-30) REVERT: C 6 LYS cc_start: 0.6853 (pttt) cc_final: 0.6531 (ptpt) REVERT: D 4 THR cc_start: 0.8563 (t) cc_final: 0.8175 (p) REVERT: E 99 ARG cc_start: 0.8019 (mtm110) cc_final: 0.7690 (mpp80) REVERT: E 183 LYS cc_start: 0.7999 (mmtm) cc_final: 0.7722 (mtpt) REVERT: E 196 GLN cc_start: 0.8546 (tt0) cc_final: 0.8340 (tt0) REVERT: E 198 GLN cc_start: 0.7897 (pt0) cc_final: 0.7270 (tm-30) REVERT: E 201 ASP cc_start: 0.7024 (m-30) cc_final: 0.6566 (p0) REVERT: E 232 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7486 (tmt) REVERT: E 373 MET cc_start: 0.7081 (mmp) cc_final: 0.6855 (tpt) REVERT: E 903 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.6981 (ttp) REVERT: G 23 PHE cc_start: 0.7673 (m-10) cc_final: 0.6464 (t80) REVERT: I 1 MET cc_start: 0.2436 (OUTLIER) cc_final: 0.1227 (mmt) REVERT: I 17 GLU cc_start: 0.8395 (tm-30) cc_final: 0.7559 (tp30) REVERT: I 31 LYS cc_start: 0.8706 (mttm) cc_final: 0.8354 (mmmm) REVERT: I 58 LYS cc_start: 0.9316 (ttmt) cc_final: 0.8878 (tttp) outliers start: 38 outliers final: 21 residues processed: 279 average time/residue: 0.5984 time to fit residues: 190.0103 Evaluate side-chains 275 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 249 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 917 ASP Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 232 MET Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 709 LEU Chi-restraints excluded: chain E residue 840 VAL Chi-restraints excluded: chain E residue 902 VAL Chi-restraints excluded: chain E residue 903 MET Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 34 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 33 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 255 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 137 optimal weight: 0.0770 chunk 15 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 216 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 157 GLN B 205 GLN B 419 ASN E 58 GLN E 150 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.131324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.104889 restraints weight = 28746.962| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.33 r_work: 0.3161 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 21462 Z= 0.108 Angle : 0.515 9.141 28980 Z= 0.256 Chirality : 0.040 0.212 3372 Planarity : 0.004 0.043 3582 Dihedral : 12.387 117.982 3786 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.65 % Allowed : 17.68 % Favored : 80.66 % 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: 2.08 (0.17), residues: 2643 helix: 1.92 (0.12), residues: 1791 sheet: 0.16 (0.43), residues: 156 loop : 0.40 (0.26), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 175 TYR 0.008 0.001 TYR A 331 PHE 0.020 0.001 PHE A 438 TRP 0.010 0.001 TRP A 379 HIS 0.002 0.000 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (21459) covalent geometry : angle 0.51482 / 0.26 (28980) hydrogen bonds : bond 0.03262 / 2.20 ( 1354) hydrogen bonds : angle 3.76792 / 2.76 ( 3969) Misc. bond : bond 0.00024 / 0.01 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5837.81 seconds wall clock time: 100 minutes 11.95 seconds (6011.95 seconds total)