Starting phenix.real_space_refine on Mon May 4 15:48:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zkq_60203/05_2026/8zkq_60203.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zkq_60203/05_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 { model { file = "/net/cci-nas-00/data/ceres_data/8zkq_60203/05_2026/8zkq_60203.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zkq_60203/05_2026/8zkq_60203.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zkq_60203/05_2026/8zkq_60203.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zkq_60203/05_2026/8zkq_60203.map" } 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-2.1rc2-6044/lib/python3.9/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: 4.61, 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: 1.59 Conformation dependent library (CDL) restraints added in 999.6 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: 0.75 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: 3.82 Time building geometry restraints manager: 2.08 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=" CA7 CDL B1001 " pdb=" OA8 CDL B1001 " ideal model delta sigma weight residual 1.334 1.402 -0.068 1.10e-02 8.26e+03 3.87e+01 bond pdb=" CA7 CDL A1001 " pdb=" OA8 CDL A1001 " ideal model delta sigma weight residual 1.334 1.400 -0.066 1.10e-02 8.26e+03 3.61e+01 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=" CA7 CDL A1003 " pdb=" OA8 CDL A1003 " ideal model delta sigma weight residual 1.334 1.399 -0.065 1.10e-02 8.26e+03 3.49e+01 bond pdb=" CA7 CDL E1001 " pdb=" OA8 CDL E1001 " ideal model delta sigma weight residual 1.334 1.397 -0.063 1.10e-02 8.26e+03 3.30e+01 ... (remaining 21454 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.51: 28533 4.51 - 9.01: 398 9.01 - 13.52: 40 13.52 - 18.02: 7 18.02 - 22.53: 2 Bond angle restraints: 28980 Sorted by residual: angle pdb=" C51 CDL A1003 " pdb=" CB5 CDL A1003 " pdb=" OB6 CDL A1003 " ideal model delta sigma weight residual 111.33 121.62 -10.29 1.32e+00 5.72e-01 6.06e+01 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=" C51 CDL A1001 " pdb=" CB5 CDL A1001 " pdb=" OB6 CDL A1001 " ideal model delta sigma weight residual 111.33 120.94 -9.61 1.32e+00 5.72e-01 5.29e+01 angle pdb=" C11 CDL E1001 " pdb=" CA5 CDL E1001 " pdb=" OA6 CDL E1001 " ideal model delta sigma weight residual 111.33 120.86 -9.53 1.32e+00 5.72e-01 5.20e+01 angle pdb=" C51 CDL A1002 " pdb=" CB5 CDL A1002 " pdb=" OB6 CDL A1002 " ideal model delta sigma weight residual 111.33 120.59 -9.26 1.32e+00 5.72e-01 4.90e+01 ... (remaining 28975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.06: 12344 30.06 - 60.11: 707 60.11 - 90.17: 23 90.17 - 120.23: 2 120.23 - 150.28: 1 Dihedral angle restraints: 13077 sinusoidal: 5481 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 13074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1887 0.038 - 0.076: 1096 0.076 - 0.114: 300 0.114 - 0.152: 82 0.152 - 0.189: 7 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: 3.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 19.040 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 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 : 0.011 0.294 21462 Z= 0.575 Angle : 1.164 22.530 28980 Z= 0.559 Chirality : 0.049 0.189 3372 Planarity : 0.004 0.039 3582 Dihedral : 16.685 150.284 8193 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 covalent geometry : bond 0.01018 (21459) covalent geometry : angle 1.16394 (28980) hydrogen bonds : bond 0.13083 ( 1354) hydrogen bonds : angle 5.54445 ( 3969) Misc. bond : bond 0.25675 ( 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 : 0.866 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: 0.6593 time to fit residues: 253.4297 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 : 0.588 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 HIS B 253 HIS B 286 GLN B 419 ASN B 482 GLN B 707 GLN B 722 HIS B 824 GLN ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.129214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.101568 restraints weight = 28499.439| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.39 r_work: 0.3098 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1346 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= 0.120 Angle : 0.551 10.740 28980 Z= 0.279 Chirality : 0.041 0.173 3372 Planarity : 0.004 0.038 3582 Dihedral : 15.978 149.751 3692 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.89 % Allowed : 10.64 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.16), residues: 2643 helix: 0.32 (0.12), residues: 1785 sheet: -0.97 (0.43), residues: 147 loop : -1.05 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 175 TYR 0.008 0.001 TYR E 420 PHE 0.024 0.001 PHE E 438 TRP 0.013 0.001 TRP A 379 HIS 0.003 0.001 HIS B 437 Details of bonding type rmsd covalent geometry : bond 0.00259 (21459) covalent geometry : angle 0.55078 (28980) hydrogen bonds : bond 0.04077 ( 1354) hydrogen bonds : angle 4.21895 ( 3969) Misc. bond : bond 0.00104 ( 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 338 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 298 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ILE cc_start: 0.8145 (pt) cc_final: 0.7886 (pp) REVERT: A 205 GLN cc_start: 0.7085 (tt0) cc_final: 0.6757 (mm-40) REVERT: A 254 ARG cc_start: 0.7903 (mmt180) cc_final: 0.7079 (mpp-170) REVERT: F 6 LYS cc_start: 0.6854 (pttt) cc_final: 0.6600 (ptmt) REVERT: F 7 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7728 (mtp85) REVERT: F 23 PHE cc_start: 0.7894 (m-80) cc_final: 0.6531 (t80) REVERT: H 23 GLU cc_start: 0.8254 (mp0) cc_final: 0.7862 (mp0) REVERT: H 31 LYS cc_start: 0.8281 (mttm) cc_final: 0.7914 (mtpt) REVERT: H 63 ASP cc_start: 0.8563 (m-30) cc_final: 0.8159 (m-30) REVERT: B 176 LEU cc_start: 0.8309 (mm) cc_final: 0.7939 (tp) REVERT: B 197 GLN cc_start: 0.8189 (tm-30) cc_final: 0.7912 (tm-30) REVERT: B 369 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7679 (mm-30) REVERT: B 446 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8053 (mm-30) REVERT: B 903 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7805 (ttm) REVERT: C 6 LYS cc_start: 0.7024 (pttt) cc_final: 0.6400 (ptpp) REVERT: D 4 THR cc_start: 0.8277 (t) cc_final: 0.7922 (p) REVERT: E 99 ARG cc_start: 0.7841 (mtm110) cc_final: 0.7475 (mpp80) REVERT: E 183 LYS cc_start: 0.8054 (mmtm) cc_final: 0.7711 (mtpt) REVERT: E 196 GLN cc_start: 0.8455 (tt0) cc_final: 0.8207 (tt0) REVERT: E 198 GLN cc_start: 0.7933 (pt0) cc_final: 0.7361 (tm-30) REVERT: E 456 MET cc_start: 0.9346 (mtm) cc_final: 0.9094 (mtm) REVERT: E 903 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.6696 (ttm) REVERT: I 31 LYS cc_start: 0.8518 (mttm) cc_final: 0.8190 (mmtp) REVERT: I 58 LYS cc_start: 0.9249 (ttmt) cc_final: 0.8753 (tttp) outliers start: 40 outliers final: 10 residues processed: 311 average time/residue: 0.6751 time to fit residues: 236.1216 Evaluate side-chains 268 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 255 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 7 ARG Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 196 GLN 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 804 ILE 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: 2.9990 chunk 213 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 227 optimal weight: 0.4980 chunk 224 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 253 HIS A 825 HIS ** H 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 ASN B 941 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.128612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.100786 restraints weight = 28570.041| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.40 r_work: 0.3086 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21462 Z= 0.141 Angle : 0.539 8.738 28980 Z= 0.272 Chirality : 0.041 0.167 3372 Planarity : 0.004 0.038 3582 Dihedral : 14.819 140.921 3690 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.22 % Allowed : 12.91 % Favored : 84.87 % 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: 0.58 (0.16), residues: 2643 helix: 0.92 (0.12), residues: 1788 sheet: -0.56 (0.42), residues: 147 loop : -0.55 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 175 TYR 0.009 0.001 TYR E 415 PHE 0.024 0.001 PHE E 438 TRP 0.011 0.001 TRP A 379 HIS 0.004 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00334 (21459) covalent geometry : angle 0.53868 (28980) hydrogen bonds : bond 0.03846 ( 1354) hydrogen bonds : angle 4.03183 ( 3969) Misc. bond : bond 0.00082 ( 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 317 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 270 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ILE cc_start: 0.8105 (pt) cc_final: 0.7892 (pp) REVERT: A 205 GLN cc_start: 0.6999 (tt0) cc_final: 0.6431 (pt0) REVERT: A 254 ARG cc_start: 0.7975 (mmt180) cc_final: 0.7058 (mpp-170) REVERT: A 686 ASP cc_start: 0.7316 (p0) cc_final: 0.6985 (p0) REVERT: A 743 LYS cc_start: 0.8931 (tttt) cc_final: 0.8668 (tttm) REVERT: A 849 ASP cc_start: 0.8685 (m-30) cc_final: 0.8422 (m-30) REVERT: F 6 LYS cc_start: 0.6772 (pttt) cc_final: 0.6549 (ptmt) REVERT: F 23 PHE cc_start: 0.7864 (m-80) cc_final: 0.6543 (t80) REVERT: H 23 GLU cc_start: 0.8265 (mp0) cc_final: 0.8048 (mt-10) REVERT: H 31 LYS cc_start: 0.8252 (mttm) cc_final: 0.7899 (mtpt) REVERT: H 63 ASP cc_start: 0.8542 (m-30) cc_final: 0.8170 (m-30) REVERT: B 175 ARG cc_start: 0.8116 (ttm-80) cc_final: 0.7750 (ttm170) REVERT: B 176 LEU cc_start: 0.8262 (mm) cc_final: 0.7909 (tp) REVERT: B 197 GLN cc_start: 0.8150 (tm-30) cc_final: 0.7853 (tm-30) REVERT: B 369 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7682 (mm-30) REVERT: B 412 ARG cc_start: 0.7894 (mtm-85) cc_final: 0.7627 (mtp-110) REVERT: B 732 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8555 (mp) REVERT: B 838 MET cc_start: 0.8600 (ttm) cc_final: 0.8360 (ttt) REVERT: B 903 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7804 (ttm) REVERT: C 6 LYS cc_start: 0.6958 (pttt) cc_final: 0.6324 (ptpp) REVERT: D 4 THR cc_start: 0.8298 (t) cc_final: 0.7937 (p) REVERT: E 183 LYS cc_start: 0.7948 (mmtm) cc_final: 0.7586 (mttt) REVERT: E 196 GLN cc_start: 0.8472 (tt0) cc_final: 0.8228 (tt0) REVERT: E 198 GLN cc_start: 0.7868 (pt0) cc_final: 0.7337 (tm-30) REVERT: E 232 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7261 (tmt) REVERT: E 903 MET cc_start: 0.7287 (OUTLIER) cc_final: 0.6736 (ttp) REVERT: I 58 LYS cc_start: 0.9258 (ttmt) cc_final: 0.8761 (tttp) outliers start: 47 outliers final: 13 residues processed: 290 average time/residue: 0.6249 time to fit residues: 204.5302 Evaluate side-chains 273 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 255 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain B residue 62 VAL 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 840 VAL Chi-restraints excluded: chain B residue 903 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 232 MET Chi-restraints excluded: chain E residue 403 VAL 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 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: 0.2980 chunk 30 optimal weight: 0.6980 chunk 231 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 209 optimal weight: 0.0870 chunk 223 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 153 optimal weight: 0.0770 chunk 83 optimal weight: 4.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 50 GLN B 308 HIS D 50 GLN E 58 GLN E 264 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.127218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.100026 restraints weight = 28733.556| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.35 r_work: 0.3087 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 21462 Z= 0.098 Angle : 0.494 7.872 28980 Z= 0.248 Chirality : 0.040 0.181 3372 Planarity : 0.004 0.042 3582 Dihedral : 13.779 132.436 3690 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.41 % Allowed : 13.43 % Favored : 84.16 % 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: 1.24 (0.17), residues: 2643 helix: 1.40 (0.12), residues: 1794 sheet: -0.39 (0.43), residues: 147 loop : -0.24 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 99 TYR 0.007 0.001 TYR A 109 PHE 0.019 0.001 PHE A 438 TRP 0.009 0.001 TRP A 379 HIS 0.002 0.000 HIS B 437 Details of bonding type rmsd covalent geometry : bond 0.00213 (21459) covalent geometry : angle 0.49390 (28980) hydrogen bonds : bond 0.03250 ( 1354) hydrogen bonds : angle 3.84296 ( 3969) Misc. bond : bond 0.00020 ( 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 334 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 283 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7890 (pp) REVERT: A 113 ILE cc_start: 0.7812 (pt) cc_final: 0.7610 (pp) REVERT: A 167 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8288 (mm-30) REVERT: A 202 ARG cc_start: 0.7601 (ttp-110) cc_final: 0.7129 (tpt90) REVERT: A 205 GLN cc_start: 0.6836 (tt0) cc_final: 0.6282 (pt0) REVERT: A 686 ASP cc_start: 0.7339 (p0) cc_final: 0.6967 (p0) REVERT: A 743 LYS cc_start: 0.8603 (tttt) cc_final: 0.8302 (tttm) REVERT: A 849 ASP cc_start: 0.8397 (m-30) cc_final: 0.8163 (m-30) REVERT: F 6 LYS cc_start: 0.6319 (pttt) cc_final: 0.6080 (ptmt) REVERT: F 23 PHE cc_start: 0.7505 (m-80) cc_final: 0.6210 (t80) REVERT: H 23 GLU cc_start: 0.8143 (mp0) cc_final: 0.7915 (mt-10) REVERT: H 31 LYS cc_start: 0.7994 (mttm) cc_final: 0.7695 (mtpt) REVERT: H 63 ASP cc_start: 0.8291 (m-30) cc_final: 0.7907 (m-30) REVERT: B 92 MET cc_start: 0.8070 (mmt) cc_final: 0.7856 (mmt) REVERT: B 176 LEU cc_start: 0.8123 (mm) cc_final: 0.7794 (tp) REVERT: B 197 GLN cc_start: 0.7860 (tm-30) cc_final: 0.7569 (tm-30) REVERT: B 369 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7448 (tp30) REVERT: B 424 ASP cc_start: 0.8175 (t0) cc_final: 0.7787 (m-30) REVERT: B 429 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8323 (mm-30) REVERT: B 732 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8157 (mp) REVERT: B 903 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7483 (ttm) REVERT: C 1 MET cc_start: 0.5205 (OUTLIER) cc_final: 0.4885 (ppp) REVERT: D 4 THR cc_start: 0.7984 (t) cc_final: 0.7604 (p) REVERT: E 99 ARG cc_start: 0.7635 (mtm110) cc_final: 0.7269 (mpp80) REVERT: E 183 LYS cc_start: 0.7673 (mmtm) cc_final: 0.7306 (mtpt) REVERT: E 196 GLN cc_start: 0.8253 (tt0) cc_final: 0.7992 (tt0) REVERT: E 198 GLN cc_start: 0.7757 (pt0) cc_final: 0.7236 (tm-30) REVERT: E 232 MET cc_start: 0.7275 (OUTLIER) cc_final: 0.6863 (tmt) REVERT: E 903 MET cc_start: 0.6992 (OUTLIER) cc_final: 0.6412 (ttp) REVERT: G 23 PHE cc_start: 0.6985 (m-10) cc_final: 0.5797 (t80) REVERT: I 17 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7299 (tp30) REVERT: I 31 LYS cc_start: 0.8191 (mttm) cc_final: 0.7916 (mmtp) REVERT: I 58 LYS cc_start: 0.9108 (ttmt) cc_final: 0.8565 (tttp) outliers start: 51 outliers final: 14 residues processed: 306 average time/residue: 0.6427 time to fit residues: 222.0424 Evaluate side-chains 280 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 259 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 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 732 ILE Chi-restraints excluded: chain B residue 770 ASP Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 903 MET Chi-restraints excluded: chain B residue 917 ASP Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain E residue 232 MET Chi-restraints excluded: chain E residue 403 VAL 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 68 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 185 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 GLN B 419 ASN E 58 GLN E 698 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.125537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.099548 restraints weight = 28816.740| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.21 r_work: 0.3120 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 21462 Z= 0.192 Angle : 0.556 7.621 28980 Z= 0.279 Chirality : 0.043 0.173 3372 Planarity : 0.004 0.046 3582 Dihedral : 13.681 130.133 3690 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.74 % Allowed : 14.75 % Favored : 82.51 % 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: 1.24 (0.17), residues: 2643 helix: 1.32 (0.12), residues: 1803 sheet: -0.21 (0.44), residues: 147 loop : -0.08 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 175 TYR 0.009 0.001 TYR A 300 PHE 0.024 0.002 PHE E 438 TRP 0.011 0.001 TRP B 936 HIS 0.003 0.001 HIS E 253 Details of bonding type rmsd covalent geometry : bond 0.00462 (21459) covalent geometry : angle 0.55630 (28980) hydrogen bonds : bond 0.03933 ( 1354) hydrogen bonds : angle 3.99049 ( 3969) Misc. bond : bond 0.00135 ( 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 317 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 259 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8507 (pp) REVERT: A 167 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8361 (mm-30) REVERT: A 170 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8141 (mtmt) REVERT: A 202 ARG cc_start: 0.7899 (ttp-110) cc_final: 0.7430 (tpt90) REVERT: A 205 GLN cc_start: 0.7031 (tt0) cc_final: 0.6483 (pt0) REVERT: A 686 ASP cc_start: 0.7341 (p0) cc_final: 0.6988 (p0) REVERT: A 743 LYS cc_start: 0.9110 (tttt) cc_final: 0.8870 (tttm) REVERT: A 849 ASP cc_start: 0.8831 (m-30) cc_final: 0.8620 (m-30) REVERT: F 6 LYS cc_start: 0.6737 (pttt) cc_final: 0.6491 (ptmt) REVERT: F 23 PHE cc_start: 0.7986 (m-80) cc_final: 0.6655 (t80) REVERT: H 12 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8824 (mp) REVERT: H 23 GLU cc_start: 0.8304 (mp0) cc_final: 0.8077 (mt-10) REVERT: H 31 LYS cc_start: 0.8351 (mttm) cc_final: 0.8030 (mtpt) REVERT: H 63 ASP cc_start: 0.8651 (m-30) cc_final: 0.8326 (m-30) REVERT: B 175 ARG cc_start: 0.8152 (ttm-80) cc_final: 0.7551 (ttm170) REVERT: B 176 LEU cc_start: 0.8273 (mm) cc_final: 0.7936 (tp) REVERT: B 197 GLN cc_start: 0.8018 (tm-30) cc_final: 0.7779 (tm-30) REVERT: B 369 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7800 (mm-30) REVERT: B 429 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8519 (mm-30) REVERT: B 732 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8616 (mp) REVERT: B 903 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8066 (ttm) REVERT: C 1 MET cc_start: 0.5237 (OUTLIER) cc_final: 0.4936 (ppp) REVERT: D 4 THR cc_start: 0.8471 (t) cc_final: 0.8089 (p) REVERT: E 99 ARG cc_start: 0.7986 (mtm110) cc_final: 0.7584 (mpp80) REVERT: E 183 LYS cc_start: 0.8070 (mmtm) cc_final: 0.7733 (mtpt) REVERT: E 196 GLN cc_start: 0.8557 (tt0) cc_final: 0.8304 (tt0) REVERT: E 198 GLN cc_start: 0.7922 (pt0) cc_final: 0.7391 (tm-30) REVERT: E 232 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7453 (tmt) REVERT: E 903 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.6936 (ttp) REVERT: I 1 MET cc_start: 0.2712 (mmt) cc_final: 0.1850 (mmt) REVERT: I 31 LYS cc_start: 0.8623 (mttm) cc_final: 0.8361 (mmtp) REVERT: I 58 LYS cc_start: 0.9308 (ttmt) cc_final: 0.8853 (tttp) outliers start: 58 outliers final: 29 residues processed: 289 average time/residue: 0.6485 time to fit residues: 210.9035 Evaluate side-chains 294 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 256 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 170 LYS Chi-restraints excluded: chain A residue 221 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 12 LEU Chi-restraints excluded: chain H residue 34 VAL 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 207 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 903 MET Chi-restraints excluded: chain B residue 917 ASP Chi-restraints excluded: chain C residue 1 MET 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 237 VAL 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 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 Chi-restraints excluded: chain I residue 70 VAL 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: 1.9990 chunk 93 optimal weight: 0.6980 chunk 254 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 chunk 221 optimal weight: 0.9980 chunk 248 optimal weight: 0.7980 chunk 244 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 181 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 GLN B 419 ASN E 58 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.131591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.104731 restraints weight = 28701.735| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.34 r_work: 0.3143 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2093 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= 0.110 Angle : 0.502 7.249 28980 Z= 0.252 Chirality : 0.040 0.197 3372 Planarity : 0.004 0.046 3582 Dihedral : 13.053 126.601 3690 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.22 % Allowed : 15.32 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.17), residues: 2643 helix: 1.61 (0.12), residues: 1803 sheet: -0.09 (0.44), residues: 147 loop : 0.07 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 99 TYR 0.009 0.001 TYR E 850 PHE 0.019 0.001 PHE E 438 TRP 0.011 0.001 TRP A 379 HIS 0.003 0.001 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00255 (21459) covalent geometry : angle 0.50207 (28980) hydrogen bonds : bond 0.03382 ( 1354) hydrogen bonds : angle 3.85105 ( 3969) Misc. bond : bond 0.00039 ( 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 308 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 261 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8279 (pp) REVERT: A 113 ILE cc_start: 0.8251 (pp) cc_final: 0.7979 (pp) REVERT: A 167 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8283 (mm-30) REVERT: A 170 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8042 (mttt) REVERT: A 205 GLN cc_start: 0.7004 (tt0) cc_final: 0.6471 (pt0) REVERT: A 686 ASP cc_start: 0.7336 (p0) cc_final: 0.7006 (p0) REVERT: A 743 LYS cc_start: 0.8987 (tttt) cc_final: 0.8743 (tttm) REVERT: F 6 LYS cc_start: 0.6663 (pttt) cc_final: 0.6462 (ptmt) REVERT: F 23 PHE cc_start: 0.7838 (m-80) cc_final: 0.6560 (t80) REVERT: H 31 LYS cc_start: 0.8358 (mttm) cc_final: 0.8075 (mtpt) REVERT: H 63 ASP cc_start: 0.8479 (m-30) cc_final: 0.8184 (m-30) REVERT: B 67 ASP cc_start: 0.8315 (m-30) cc_final: 0.7733 (m-30) REVERT: B 176 LEU cc_start: 0.8364 (mm) cc_final: 0.7969 (tp) REVERT: B 197 GLN cc_start: 0.7983 (tm-30) cc_final: 0.7755 (tm-30) REVERT: B 369 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7683 (tp30) REVERT: B 429 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8374 (mm-30) REVERT: B 903 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7918 (ttm) REVERT: C 1 MET cc_start: 0.5298 (OUTLIER) cc_final: 0.5046 (ppp) REVERT: D 4 THR cc_start: 0.8431 (t) cc_final: 0.8058 (p) REVERT: E 99 ARG cc_start: 0.7900 (mtm110) cc_final: 0.7573 (mpp80) REVERT: E 183 LYS cc_start: 0.7978 (mmtm) cc_final: 0.7652 (mtpt) REVERT: E 196 GLN cc_start: 0.8525 (tt0) cc_final: 0.8284 (tt0) REVERT: E 198 GLN cc_start: 0.7896 (pt0) cc_final: 0.7172 (tm-30) REVERT: E 201 ASP cc_start: 0.6981 (m-30) cc_final: 0.6525 (p0) REVERT: E 232 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.7160 (tmt) REVERT: E 903 MET cc_start: 0.7331 (OUTLIER) cc_final: 0.6832 (ttp) REVERT: G 1 MET cc_start: 0.4721 (OUTLIER) cc_final: 0.4115 (ttp) REVERT: G 23 PHE cc_start: 0.7435 (m-10) cc_final: 0.6272 (t80) REVERT: I 1 MET cc_start: 0.2872 (mmt) cc_final: 0.1879 (mmt) REVERT: I 17 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7516 (tp30) REVERT: I 31 LYS cc_start: 0.8679 (mttm) cc_final: 0.8389 (mmtp) REVERT: I 58 LYS cc_start: 0.9262 (ttmt) cc_final: 0.8817 (tttp) outliers start: 47 outliers final: 19 residues processed: 286 average time/residue: 0.6474 time to fit residues: 208.0016 Evaluate side-chains 280 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 253 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 170 LYS 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 34 VAL Chi-restraints excluded: chain H residue 72 ASP 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 812 LEU Chi-restraints excluded: chain B residue 903 MET Chi-restraints excluded: chain B residue 917 ASP Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain E residue 232 MET 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 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 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: 0.9980 chunk 246 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 244 optimal weight: 0.6980 chunk 158 optimal weight: 0.6980 chunk 133 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 222 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.128418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.102688 restraints weight = 28662.661| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.22 r_work: 0.3143 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2200 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= 0.112 Angle : 0.502 7.292 28980 Z= 0.251 Chirality : 0.040 0.198 3372 Planarity : 0.004 0.046 3582 Dihedral : 12.619 124.189 3690 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.60 % Allowed : 15.65 % Favored : 81.75 % 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: 1.74 (0.12), residues: 1797 sheet: 0.05 (0.44), residues: 147 loop : 0.18 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 175 TYR 0.006 0.001 TYR A 331 PHE 0.018 0.001 PHE E 438 TRP 0.009 0.001 TRP A 379 HIS 0.002 0.000 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00260 (21459) covalent geometry : angle 0.50192 (28980) hydrogen bonds : bond 0.03332 ( 1354) hydrogen bonds : angle 3.80954 ( 3969) Misc. bond : bond 0.00040 ( 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 309 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 254 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8453 (pp) REVERT: A 113 ILE cc_start: 0.8439 (pp) cc_final: 0.8178 (pp) REVERT: A 167 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8355 (mm-30) REVERT: A 205 GLN cc_start: 0.7090 (tt0) cc_final: 0.6534 (pt0) REVERT: A 686 ASP cc_start: 0.7358 (p0) cc_final: 0.6970 (p0) REVERT: A 743 LYS cc_start: 0.9102 (tttt) cc_final: 0.8876 (tttm) REVERT: F 23 PHE cc_start: 0.7987 (m-10) cc_final: 0.6711 (t80) REVERT: H 31 LYS cc_start: 0.8404 (mttm) cc_final: 0.8138 (mtpt) REVERT: H 63 ASP cc_start: 0.8545 (m-30) cc_final: 0.8267 (m-30) REVERT: B 67 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.7850 (m-30) REVERT: B 72 MET cc_start: 0.8884 (tpp) cc_final: 0.8591 (tpt) REVERT: B 175 ARG cc_start: 0.8120 (ttm-80) cc_final: 0.7892 (ttm-80) REVERT: B 176 LEU cc_start: 0.8343 (mm) cc_final: 0.7941 (tp) REVERT: B 197 GLN cc_start: 0.8003 (tm-30) cc_final: 0.7749 (tm-30) REVERT: B 369 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7799 (tp30) REVERT: B 429 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8455 (mm-30) REVERT: B 903 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8116 (ttm) REVERT: C 1 MET cc_start: 0.5143 (OUTLIER) cc_final: 0.4887 (ppp) REVERT: D 4 THR cc_start: 0.8529 (t) cc_final: 0.8157 (p) REVERT: E 99 ARG cc_start: 0.7995 (mtm110) cc_final: 0.7646 (mpp80) REVERT: E 183 LYS cc_start: 0.8005 (mmtm) cc_final: 0.7701 (mtpt) REVERT: E 196 GLN cc_start: 0.8587 (tt0) cc_final: 0.8344 (tt0) REVERT: E 198 GLN cc_start: 0.7911 (pt0) cc_final: 0.7185 (tm130) REVERT: E 201 ASP cc_start: 0.6951 (m-30) cc_final: 0.6504 (p0) REVERT: E 206 VAL cc_start: 0.8058 (t) cc_final: 0.7822 (m) REVERT: E 232 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7467 (tmt) REVERT: E 903 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.7044 (ttp) REVERT: G 1 MET cc_start: 0.4800 (OUTLIER) cc_final: 0.4115 (ttm) REVERT: G 23 PHE cc_start: 0.7643 (m-10) cc_final: 0.6442 (t80) REVERT: I 1 MET cc_start: 0.2565 (mmt) cc_final: 0.1670 (mmt) REVERT: I 17 GLU cc_start: 0.8379 (tm-30) cc_final: 0.7711 (tp30) REVERT: I 31 LYS cc_start: 0.8692 (mttm) cc_final: 0.8281 (mmmm) REVERT: I 58 LYS cc_start: 0.9289 (ttmt) cc_final: 0.8873 (tttp) REVERT: I 79 LYS cc_start: 0.8907 (tmmt) cc_final: 0.8576 (ttmm) outliers start: 55 outliers final: 24 residues processed: 287 average time/residue: 0.6437 time to fit residues: 208.3593 Evaluate side-chains 280 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 248 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 72 ASP Chi-restraints excluded: chain B residue 67 ASP 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 812 LEU Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 903 MET Chi-restraints excluded: chain B residue 917 ASP Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 6 LYS 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 265 LEU 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 840 VAL 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 70 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 99 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 241 optimal weight: 4.9990 chunk 236 optimal weight: 0.7980 chunk 180 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 192 optimal weight: 2.9990 chunk 225 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 GLN B 419 ASN E 58 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.127111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.101383 restraints weight = 28669.029| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.21 r_work: 0.3144 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21462 Z= 0.144 Angle : 0.527 8.759 28980 Z= 0.264 Chirality : 0.041 0.197 3372 Planarity : 0.004 0.045 3582 Dihedral : 12.551 123.005 3690 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.88 % Allowed : 15.46 % Favored : 81.65 % 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: 1.79 (0.17), residues: 2643 helix: 1.68 (0.12), residues: 1803 sheet: 0.13 (0.44), residues: 147 loop : 0.26 (0.26), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 202 TYR 0.007 0.001 TYR A 331 PHE 0.021 0.001 PHE E 438 TRP 0.009 0.001 TRP B 936 HIS 0.003 0.001 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00346 (21459) covalent geometry : angle 0.52691 (28980) hydrogen bonds : bond 0.03585 ( 1354) hydrogen bonds : angle 3.87152 ( 3969) Misc. bond : bond 0.00077 ( 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 314 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 253 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8479 (pp) REVERT: A 113 ILE cc_start: 0.8411 (pp) cc_final: 0.8171 (pp) REVERT: A 205 GLN cc_start: 0.7057 (tt0) cc_final: 0.6740 (tp40) REVERT: A 686 ASP cc_start: 0.7357 (p0) cc_final: 0.6963 (p0) REVERT: A 743 LYS cc_start: 0.9088 (tttt) cc_final: 0.8848 (tttm) REVERT: F 23 PHE cc_start: 0.7944 (m-10) cc_final: 0.6628 (t80) REVERT: H 31 LYS cc_start: 0.8365 (mttm) cc_final: 0.8104 (mtpt) REVERT: H 63 ASP cc_start: 0.8587 (m-30) cc_final: 0.8288 (m-30) REVERT: B 67 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.7875 (m-30) REVERT: B 72 MET cc_start: 0.8883 (tpp) cc_final: 0.8602 (mmt) REVERT: B 176 LEU cc_start: 0.8356 (mm) cc_final: 0.7962 (tp) REVERT: B 197 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7751 (tm-30) REVERT: B 369 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7802 (tp30) REVERT: B 429 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8462 (mm-30) REVERT: B 903 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8069 (ttm) REVERT: D 4 THR cc_start: 0.8517 (t) cc_final: 0.8135 (p) REVERT: E 99 ARG cc_start: 0.8003 (mtm110) cc_final: 0.7648 (mpp80) REVERT: E 183 LYS cc_start: 0.7976 (mmtm) cc_final: 0.7706 (mtpt) REVERT: E 196 GLN cc_start: 0.8555 (tt0) cc_final: 0.8315 (tt0) REVERT: E 198 GLN cc_start: 0.7880 (pt0) cc_final: 0.7207 (tm130) REVERT: E 201 ASP cc_start: 0.6958 (m-30) cc_final: 0.6486 (p0) REVERT: E 232 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7435 (tmt) REVERT: E 903 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.6929 (ttp) REVERT: G 1 MET cc_start: 0.4786 (OUTLIER) cc_final: 0.4163 (ttp) REVERT: G 23 PHE cc_start: 0.7606 (m-10) cc_final: 0.6366 (t80) REVERT: I 1 MET cc_start: 0.2571 (mmt) cc_final: 0.1742 (mmt) REVERT: I 17 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7650 (tp30) REVERT: I 31 LYS cc_start: 0.8753 (mttm) cc_final: 0.8308 (mmmm) REVERT: I 58 LYS cc_start: 0.9307 (ttmt) cc_final: 0.8856 (tttp) outliers start: 61 outliers final: 30 residues processed: 286 average time/residue: 0.6644 time to fit residues: 214.0504 Evaluate side-chains 286 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 249 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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 72 ASP Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 67 ASP 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 413 THR 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 903 MET Chi-restraints excluded: chain B residue 917 ASP Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain D residue 53 ASP 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 232 MET Chi-restraints excluded: chain E residue 237 VAL 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 812 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 G residue 1 MET Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 70 VAL 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: 2.9990 chunk 142 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 259 optimal weight: 0.6980 chunk 245 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 GLN B 205 GLN B 419 ASN E 58 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.130531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.103935 restraints weight = 28630.459| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.32 r_work: 0.3129 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21462 Z= 0.117 Angle : 0.510 8.968 28980 Z= 0.255 Chirality : 0.040 0.207 3372 Planarity : 0.004 0.045 3582 Dihedral : 12.293 121.248 3690 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.17 % Allowed : 16.26 % Favored : 81.56 % 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: 1.91 (0.17), residues: 2643 helix: 1.78 (0.12), residues: 1803 sheet: 0.07 (0.43), residues: 156 loop : 0.33 (0.26), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 175 TYR 0.006 0.001 TYR A 415 PHE 0.019 0.001 PHE E 438 TRP 0.010 0.001 TRP A 379 HIS 0.003 0.001 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00275 (21459) covalent geometry : angle 0.50974 (28980) hydrogen bonds : bond 0.03381 ( 1354) hydrogen bonds : angle 3.81927 ( 3969) Misc. bond : bond 0.00046 ( 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 294 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 248 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8297 (pp) REVERT: A 113 ILE cc_start: 0.8285 (pp) cc_final: 0.8032 (pp) REVERT: A 676 MET cc_start: 0.6464 (ttp) cc_final: 0.6082 (ttt) REVERT: A 686 ASP cc_start: 0.7328 (p0) cc_final: 0.6940 (p0) REVERT: A 743 LYS cc_start: 0.8956 (tttt) cc_final: 0.8702 (tttm) REVERT: F 23 PHE cc_start: 0.7814 (m-10) cc_final: 0.6528 (t80) REVERT: H 31 LYS cc_start: 0.8286 (mttm) cc_final: 0.8050 (mtpt) REVERT: H 63 ASP cc_start: 0.8475 (m-30) cc_final: 0.8180 (m-30) REVERT: B 67 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7684 (m-30) REVERT: B 72 MET cc_start: 0.8728 (tpp) cc_final: 0.8454 (mmt) REVERT: B 176 LEU cc_start: 0.8370 (mm) cc_final: 0.7954 (tp) REVERT: B 197 GLN cc_start: 0.7942 (tm-30) cc_final: 0.7687 (tm-30) REVERT: B 369 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7699 (mm-30) REVERT: B 429 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8420 (mm-30) REVERT: B 903 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7836 (ttm) REVERT: C 1 MET cc_start: 0.5483 (ppp) cc_final: 0.5197 (ppp) REVERT: D 4 THR cc_start: 0.8438 (t) cc_final: 0.8051 (p) REVERT: E 99 ARG cc_start: 0.7928 (mtm110) cc_final: 0.7615 (mpp80) REVERT: E 183 LYS cc_start: 0.7856 (mmtm) cc_final: 0.7580 (mtpt) REVERT: E 196 GLN cc_start: 0.8506 (tt0) cc_final: 0.8261 (tt0) REVERT: E 198 GLN cc_start: 0.7808 (pt0) cc_final: 0.7165 (tm130) REVERT: E 201 ASP cc_start: 0.6956 (m-30) cc_final: 0.6522 (p0) REVERT: E 232 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.7174 (tmt) REVERT: E 903 MET cc_start: 0.7324 (OUTLIER) cc_final: 0.6768 (ttp) REVERT: G 1 MET cc_start: 0.4784 (OUTLIER) cc_final: 0.4176 (ttm) REVERT: G 23 PHE cc_start: 0.7392 (m-10) cc_final: 0.6215 (t80) REVERT: I 1 MET cc_start: 0.2781 (mmt) cc_final: 0.1943 (mmt) REVERT: I 17 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7534 (tp30) REVERT: I 31 LYS cc_start: 0.8730 (mttm) cc_final: 0.8285 (mmmm) REVERT: I 58 LYS cc_start: 0.9259 (ttmt) cc_final: 0.8797 (tttp) REVERT: I 79 LYS cc_start: 0.8859 (tmmt) cc_final: 0.8518 (ttmm) outliers start: 46 outliers final: 28 residues processed: 274 average time/residue: 0.6291 time to fit residues: 194.1640 Evaluate side-chains 281 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 246 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 67 ASP 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 413 THR 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 B residue 903 MET Chi-restraints excluded: chain B residue 917 ASP Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 232 MET 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 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 G residue 1 MET Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 112 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 251 optimal weight: 0.9990 chunk 130 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 257 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 GLN B 419 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.129442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.102765 restraints weight = 28903.372| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.33 r_work: 0.3111 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21462 Z= 0.148 Angle : 0.537 10.401 28980 Z= 0.268 Chirality : 0.041 0.202 3372 Planarity : 0.004 0.049 3582 Dihedral : 12.301 120.784 3690 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.94 % Allowed : 16.74 % Favored : 81.32 % 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: 1.86 (0.17), residues: 2643 helix: 1.74 (0.12), residues: 1797 sheet: 0.12 (0.43), residues: 156 loop : 0.32 (0.26), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 68 TYR 0.007 0.001 TYR A 300 PHE 0.021 0.001 PHE E 438 TRP 0.009 0.001 TRP B 936 HIS 0.003 0.001 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00357 (21459) covalent geometry : angle 0.53743 (28980) hydrogen bonds : bond 0.03604 ( 1354) hydrogen bonds : angle 3.87009 ( 3969) Misc. bond : bond 0.00075 ( 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: 41 poor density : 251 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8314 (pp) REVERT: A 113 ILE cc_start: 0.8295 (pp) cc_final: 0.8063 (pp) REVERT: A 676 MET cc_start: 0.6449 (ttp) cc_final: 0.6063 (ttt) REVERT: A 686 ASP cc_start: 0.7296 (p0) cc_final: 0.6907 (p0) REVERT: A 743 LYS cc_start: 0.8977 (tttt) cc_final: 0.8722 (tttm) REVERT: F 23 PHE cc_start: 0.7818 (m-10) cc_final: 0.6523 (t80) REVERT: H 31 LYS cc_start: 0.8285 (mttm) cc_final: 0.8036 (mtpt) REVERT: H 63 ASP cc_start: 0.8528 (m-30) cc_final: 0.8231 (m-30) REVERT: B 67 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7678 (m-30) REVERT: B 72 MET cc_start: 0.8750 (tpp) cc_final: 0.8464 (mmt) REVERT: B 176 LEU cc_start: 0.8393 (mm) cc_final: 0.7971 (tp) REVERT: B 197 GLN cc_start: 0.7965 (tm-30) cc_final: 0.7722 (tm-30) REVERT: B 369 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7708 (mm-30) REVERT: B 429 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8425 (mm-30) REVERT: B 903 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7807 (ttm) REVERT: C 1 MET cc_start: 0.5500 (ppp) cc_final: 0.5146 (ppp) REVERT: D 4 THR cc_start: 0.8458 (t) cc_final: 0.8069 (p) REVERT: E 99 ARG cc_start: 0.7897 (mtm110) cc_final: 0.7588 (mpp80) REVERT: E 183 LYS cc_start: 0.7851 (mmtm) cc_final: 0.7581 (mtpt) REVERT: E 196 GLN cc_start: 0.8499 (tt0) cc_final: 0.8258 (tt0) REVERT: E 198 GLN cc_start: 0.7830 (pt0) cc_final: 0.7153 (tm130) REVERT: E 201 ASP cc_start: 0.6962 (m-30) cc_final: 0.6505 (p0) REVERT: E 232 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.7183 (tmt) REVERT: E 373 MET cc_start: 0.6919 (mmp) cc_final: 0.6690 (tpt) REVERT: E 903 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.6739 (ttp) REVERT: G 1 MET cc_start: 0.4862 (OUTLIER) cc_final: 0.4296 (ttm) REVERT: G 23 PHE cc_start: 0.7396 (m-10) cc_final: 0.6221 (t80) REVERT: I 1 MET cc_start: 0.2782 (mmt) cc_final: 0.1983 (mmt) REVERT: I 17 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7373 (tp30) REVERT: I 31 LYS cc_start: 0.8760 (mttm) cc_final: 0.8319 (mmmm) REVERT: I 58 LYS cc_start: 0.9269 (ttmt) cc_final: 0.8799 (tttp) outliers start: 41 outliers final: 28 residues processed: 274 average time/residue: 0.6453 time to fit residues: 199.6148 Evaluate side-chains 281 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 246 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 67 ASP 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 413 THR 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 903 MET Chi-restraints excluded: chain B residue 917 ASP Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain E residue 95 LEU 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 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 G residue 1 MET Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 33 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 255 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 137 optimal weight: 9.9990 chunk 15 optimal weight: 0.5980 chunk 142 optimal weight: 0.7980 chunk 216 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 GLN B 419 ASN E 58 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.130075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.103469 restraints weight = 28798.115| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.33 r_work: 0.3125 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2224 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= 0.128 Angle : 0.521 10.619 28980 Z= 0.260 Chirality : 0.041 0.207 3372 Planarity : 0.004 0.060 3582 Dihedral : 12.133 119.671 3690 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.84 % Allowed : 16.69 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.17), residues: 2643 helix: 1.76 (0.12), residues: 1803 sheet: 0.14 (0.43), residues: 156 loop : 0.39 (0.26), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 68 TYR 0.007 0.001 TYR I 76 PHE 0.020 0.001 PHE E 438 TRP 0.010 0.001 TRP A 379 HIS 0.003 0.001 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00304 (21459) covalent geometry : angle 0.52098 (28980) hydrogen bonds : bond 0.03463 ( 1354) hydrogen bonds : angle 3.84267 ( 3969) Misc. bond : bond 0.00053 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6363.29 seconds wall clock time: 109 minutes 8.15 seconds (6548.15 seconds total)