Starting phenix.real_space_refine on Sun Oct 25 19:34:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/37un_78493/10_2026/37un_78493.cif Found real_map, /net/cci-nas-00/data/ceres_data/37un_78493/10_2026/37un_78493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/37un_78493/10_2026/37un_78493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/37un_78493/10_2026/37un_78493.map" model { file = "/net/cci-nas-00/data/ceres_data/37un_78493/10_2026/37un_78493.cif" } default_model = "/net/cci-nas-00/data/ceres_data/37un_78493/10_2026/37un_78493.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 72 5.49 5 S 66 5.16 5 C 11027 2.51 5 N 2916 2.21 5 O 3613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17694 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2694 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain: "B" Number of atoms: 2704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2704 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 328} Chain: "C" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2694 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain: "D" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2694 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain: "E" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2694 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain: "G" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'RNA': 16} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 14} Chain: "H" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 427 Classifications: {'RNA': 20} Modifications used: {'rna3p_pur': 13, 'rna3p_pyr': 7} Link IDs: {'rna3p': 19} Chain: "F" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2694 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain: "I" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'RNA': 16} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 14} Chain: "J" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 427 Classifications: {'RNA': 20} Modifications used: {'rna3p_pur': 13, 'rna3p_pyr': 7} Link IDs: {'rna3p': 19} Time building chain proxies: 4.19, per 1000 atoms: 0.24 Number of scatterers: 17694 At special positions: 0 Unit cell: (112.784, 119.168, 126.616, 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 66 16.00 P 72 15.00 O 3613 8.00 N 2916 7.00 C 11027 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 703.4 milliseconds 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3782 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 42 sheets defined 29.7% alpha, 26.9% beta 26 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 50 through 60 Processing helix chain 'A' and resid 68 through 75 Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 122 through 129 Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 197 through 206 Processing helix chain 'A' and resid 207 through 216 Processing helix chain 'A' and resid 220 through 226 Processing helix chain 'A' and resid 239 through 249 removed outlier: 3.582A pdb=" N ALA A 249 " --> pdb=" O ARG A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 302 Processing helix chain 'A' and resid 326 through 329 Processing helix chain 'B' and resid 1 through 12 Processing helix chain 'B' and resid 50 through 60 Processing helix chain 'B' and resid 68 through 76 removed outlier: 3.546A pdb=" N GLY B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 121 No H-bonds generated for 'chain 'B' and resid 119 through 121' Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 197 through 206 Processing helix chain 'B' and resid 207 through 215 Processing helix chain 'B' and resid 216 through 219 removed outlier: 4.116A pdb=" N LEU B 219 " --> pdb=" O GLY B 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 216 through 219' Processing helix chain 'B' and resid 220 through 225 Processing helix chain 'B' and resid 239 through 249 removed outlier: 3.557A pdb=" N MET B 243 " --> pdb=" O THR B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 303 Processing helix chain 'C' and resid 1 through 12 Processing helix chain 'C' and resid 50 through 60 Processing helix chain 'C' and resid 68 through 76 removed outlier: 3.624A pdb=" N GLY C 76 " --> pdb=" O LEU C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 121 No H-bonds generated for 'chain 'C' and resid 119 through 121' Processing helix chain 'C' and resid 122 through 129 Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 197 through 206 Processing helix chain 'C' and resid 207 through 216 Processing helix chain 'C' and resid 220 through 225 Processing helix chain 'C' and resid 239 through 249 removed outlier: 3.668A pdb=" N ALA C 249 " --> pdb=" O ARG C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 303 Processing helix chain 'D' and resid 1 through 12 Processing helix chain 'D' and resid 50 through 60 Processing helix chain 'D' and resid 68 through 75 Processing helix chain 'D' and resid 119 through 121 No H-bonds generated for 'chain 'D' and resid 119 through 121' Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 149 through 151 No H-bonds generated for 'chain 'D' and resid 149 through 151' Processing helix chain 'D' and resid 189 through 193 removed outlier: 4.018A pdb=" N PHE D 193 " --> pdb=" O TYR D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 206 Processing helix chain 'D' and resid 207 through 215 Processing helix chain 'D' and resid 239 through 249 removed outlier: 3.503A pdb=" N ALA D 249 " --> pdb=" O ARG D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 303 Processing helix chain 'E' and resid 1 through 12 Processing helix chain 'E' and resid 50 through 60 Processing helix chain 'E' and resid 68 through 75 Processing helix chain 'E' and resid 119 through 121 No H-bonds generated for 'chain 'E' and resid 119 through 121' Processing helix chain 'E' and resid 122 through 129 Processing helix chain 'E' and resid 149 through 151 No H-bonds generated for 'chain 'E' and resid 149 through 151' Processing helix chain 'E' and resid 197 through 206 Processing helix chain 'E' and resid 207 through 216 removed outlier: 3.657A pdb=" N LYS E 214 " --> pdb=" O SER E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'E' and resid 239 through 249 removed outlier: 3.591A pdb=" N ALA E 249 " --> pdb=" O ARG E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 303 Processing helix chain 'F' and resid 1 through 12 Processing helix chain 'F' and resid 50 through 60 Processing helix chain 'F' and resid 68 through 75 Processing helix chain 'F' and resid 119 through 121 No H-bonds generated for 'chain 'F' and resid 119 through 121' Processing helix chain 'F' and resid 122 through 129 Processing helix chain 'F' and resid 149 through 151 No H-bonds generated for 'chain 'F' and resid 149 through 151' Processing helix chain 'F' and resid 197 through 206 Processing helix chain 'F' and resid 207 through 216 Processing helix chain 'F' and resid 220 through 226 Processing helix chain 'F' and resid 239 through 249 removed outlier: 3.581A pdb=" N ALA F 249 " --> pdb=" O ARG F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 302 Processing helix chain 'F' and resid 326 through 329 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 removed outlier: 6.898A pdb=" N VAL A 31 " --> pdb=" O VAL A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 67 Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 99 removed outlier: 6.549A pdb=" N THR A 80 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ASP A 117 " --> pdb=" O ASN A 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 98 through 99 removed outlier: 6.549A pdb=" N THR A 80 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ASP A 117 " --> pdb=" O ASN A 81 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA6, first strand: chain 'A' and resid 252 through 256 removed outlier: 6.613A pdb=" N GLN A 266 " --> pdb=" O THR A 282 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR A 282 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR A 268 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL A 280 " --> pdb=" O TYR A 268 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 307 through 312 removed outlier: 3.503A pdb=" N LYS A 308 " --> pdb=" O THR A 323 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 310 " --> pdb=" O PHE A 321 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR A 332 " --> pdb=" O TRP A 324 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 24 through 27 removed outlier: 6.728A pdb=" N VAL B 31 " --> pdb=" O VAL B 42 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 65 through 67 Processing sheet with id=AB1, first strand: chain 'B' and resid 98 through 99 removed outlier: 6.613A pdb=" N THR B 80 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ASP B 117 " --> pdb=" O ASN B 81 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 98 through 99 removed outlier: 6.613A pdb=" N THR B 80 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ASP B 117 " --> pdb=" O ASN B 81 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AB4, first strand: chain 'B' and resid 252 through 256 removed outlier: 6.541A pdb=" N GLN B 266 " --> pdb=" O THR B 282 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N THR B 282 " --> pdb=" O GLN B 266 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N TYR B 268 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL B 280 " --> pdb=" O TYR B 268 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 307 through 314 removed outlier: 3.904A pdb=" N THR B 332 " --> pdb=" O TRP B 324 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 24 through 27 removed outlier: 6.863A pdb=" N VAL C 31 " --> pdb=" O VAL C 42 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 66 through 67 Processing sheet with id=AB8, first strand: chain 'C' and resid 98 through 99 removed outlier: 6.796A pdb=" N THR C 80 " --> pdb=" O VAL C 99 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ASP C 117 " --> pdb=" O ASN C 81 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL C 114 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N VAL C 135 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TYR C 116 " --> pdb=" O VAL C 135 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 98 through 99 removed outlier: 6.796A pdb=" N THR C 80 " --> pdb=" O VAL C 99 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ASP C 117 " --> pdb=" O ASN C 81 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL C 114 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N VAL C 135 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TYR C 116 " --> pdb=" O VAL C 135 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 86 through 87 Processing sheet with id=AC2, first strand: chain 'C' and resid 252 through 256 removed outlier: 6.505A pdb=" N GLN C 266 " --> pdb=" O THR C 282 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N THR C 282 " --> pdb=" O GLN C 266 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TYR C 268 " --> pdb=" O VAL C 280 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL C 280 " --> pdb=" O TYR C 268 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 307 through 314 removed outlier: 3.736A pdb=" N LYS C 308 " --> pdb=" O THR C 323 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASN C 320 " --> pdb=" O PRO C 335 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N MET C 322 " --> pdb=" O CYS C 333 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N CYS C 333 " --> pdb=" O MET C 322 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TRP C 324 " --> pdb=" O LYS C 331 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 24 through 27 removed outlier: 6.780A pdb=" N VAL D 31 " --> pdb=" O VAL D 42 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 65 through 67 Processing sheet with id=AC6, first strand: chain 'D' and resid 98 through 99 removed outlier: 6.660A pdb=" N THR D 80 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL D 79 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N ASP D 117 " --> pdb=" O VAL D 79 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N ASN D 81 " --> pdb=" O ASP D 117 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU D 166 " --> pdb=" O ILE D 148 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 98 through 99 removed outlier: 6.660A pdb=" N THR D 80 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL D 79 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N ASP D 117 " --> pdb=" O VAL D 79 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N ASN D 81 " --> pdb=" O ASP D 117 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 86 through 87 Processing sheet with id=AC9, first strand: chain 'D' and resid 252 through 256 removed outlier: 4.749A pdb=" N VAL D 270 " --> pdb=" O GLN D 279 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N GLN D 279 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ALA D 272 " --> pdb=" O TYR D 277 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TYR D 277 " --> pdb=" O ALA D 272 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 307 through 314 removed outlier: 3.861A pdb=" N TYR D 334 " --> pdb=" O MET D 322 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR D 332 " --> pdb=" O TRP D 324 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N GLU D 326 " --> pdb=" O ILE D 330 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ILE D 330 " --> pdb=" O GLU D 326 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 24 through 27 removed outlier: 6.713A pdb=" N VAL E 31 " --> pdb=" O VAL E 42 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 65 through 67 Processing sheet with id=AD4, first strand: chain 'E' and resid 98 through 99 removed outlier: 6.623A pdb=" N THR E 80 " --> pdb=" O VAL E 99 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ASP E 117 " --> pdb=" O ASN E 81 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU E 166 " --> pdb=" O ILE E 148 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 98 through 99 removed outlier: 6.623A pdb=" N THR E 80 " --> pdb=" O VAL E 99 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ASP E 117 " --> pdb=" O ASN E 81 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 86 through 87 Processing sheet with id=AD7, first strand: chain 'E' and resid 252 through 256 removed outlier: 6.599A pdb=" N GLN E 266 " --> pdb=" O THR E 282 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR E 282 " --> pdb=" O GLN E 266 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N TYR E 268 " --> pdb=" O VAL E 280 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL E 280 " --> pdb=" O TYR E 268 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 307 through 314 removed outlier: 3.644A pdb=" N THR E 332 " --> pdb=" O TRP E 324 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 24 through 27 removed outlier: 6.899A pdb=" N VAL F 31 " --> pdb=" O VAL F 42 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 65 through 67 Processing sheet with id=AE2, first strand: chain 'F' and resid 98 through 99 removed outlier: 6.549A pdb=" N THR F 80 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ASP F 117 " --> pdb=" O ASN F 81 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 98 through 99 removed outlier: 6.549A pdb=" N THR F 80 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ASP F 117 " --> pdb=" O ASN F 81 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 86 through 87 Processing sheet with id=AE5, first strand: chain 'F' and resid 252 through 256 removed outlier: 6.614A pdb=" N GLN F 266 " --> pdb=" O THR F 282 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR F 282 " --> pdb=" O GLN F 266 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR F 268 " --> pdb=" O VAL F 280 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL F 280 " --> pdb=" O TYR F 268 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 307 through 312 removed outlier: 3.502A pdb=" N LYS F 308 " --> pdb=" O THR F 323 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL F 310 " --> pdb=" O PHE F 321 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR F 332 " --> pdb=" O TRP F 324 " (cutoff:3.500A) 680 hydrogen bonds defined for protein. 1845 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 58 hydrogen bonds 116 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 3.35 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5429 1.34 - 1.46: 3762 1.46 - 1.58: 8763 1.58 - 1.70: 138 1.70 - 1.82: 102 Bond restraints: 18194 Sorted by residual: bond pdb=" P A H 15 " pdb=" O5' A H 15 " ideal model delta sigma weight residual 1.593 1.546 0.047 1.00e-02 1.00e+04 2.23e+01 bond pdb=" P A J 15 " pdb=" O5' A J 15 " ideal model delta sigma weight residual 1.593 1.546 0.047 1.00e-02 1.00e+04 2.23e+01 bond pdb=" P G G 9 " pdb=" O5' G G 9 " ideal model delta sigma weight residual 1.593 1.625 -0.032 1.00e-02 1.00e+04 1.04e+01 bond pdb=" P G I 9 " pdb=" O5' G I 9 " ideal model delta sigma weight residual 1.593 1.625 -0.032 1.00e-02 1.00e+04 1.03e+01 bond pdb=" C MET B 243 " pdb=" N CYS B 244 " ideal model delta sigma weight residual 1.335 1.375 -0.040 1.36e-02 5.41e+03 8.73e+00 ... (remaining 18189 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 24385 1.78 - 3.57: 521 3.57 - 5.35: 71 5.35 - 7.14: 53 7.14 - 8.92: 10 Bond angle restraints: 25040 Sorted by residual: angle pdb=" O4' U I 8 " pdb=" C1' U I 8 " pdb=" N1 U I 8 " ideal model delta sigma weight residual 108.20 112.52 -4.32 8.00e-01 1.56e+00 2.92e+01 angle pdb=" O4' U G 8 " pdb=" C1' U G 8 " pdb=" N1 U G 8 " ideal model delta sigma weight residual 108.20 112.51 -4.31 8.00e-01 1.56e+00 2.90e+01 angle pdb=" N1 U I 8 " pdb=" C2 U I 8 " pdb=" O2 U I 8 " ideal model delta sigma weight residual 122.80 125.38 -2.58 7.00e-01 2.04e+00 1.36e+01 angle pdb=" N1 U G 8 " pdb=" C2 U G 8 " pdb=" O2 U G 8 " ideal model delta sigma weight residual 122.80 125.37 -2.57 7.00e-01 2.04e+00 1.35e+01 angle pdb=" C4' A I 18 " pdb=" C3' A I 18 " pdb=" C2' A I 18 " ideal model delta sigma weight residual 102.60 99.01 3.59 1.00e+00 1.00e+00 1.29e+01 ... (remaining 25035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.53: 10098 23.53 - 47.05: 606 47.05 - 70.57: 115 70.57 - 94.10: 28 94.10 - 117.62: 2 Dihedral angle restraints: 10849 sinusoidal: 4900 harmonic: 5949 Sorted by residual: dihedral pdb=" O4' U G 8 " pdb=" C1' U G 8 " pdb=" N1 U G 8 " pdb=" C2 U G 8 " ideal model delta sinusoidal sigma weight residual -128.00 -10.38 -117.62 1 1.70e+01 3.46e-03 4.86e+01 dihedral pdb=" O4' U I 8 " pdb=" C1' U I 8 " pdb=" N1 U I 8 " pdb=" C2 U I 8 " ideal model delta sinusoidal sigma weight residual -128.00 -10.42 -117.58 1 1.70e+01 3.46e-03 4.86e+01 dihedral pdb=" CA TYR E 215 " pdb=" C TYR E 215 " pdb=" N GLY E 216 " pdb=" CA GLY E 216 " ideal model delta harmonic sigma weight residual 180.00 154.69 25.31 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 10846 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 2753 0.116 - 0.231: 105 0.231 - 0.347: 1 0.347 - 0.462: 24 0.462 - 0.578: 16 Chirality restraints: 2899 Sorted by residual: chirality pdb=" P C J 14 " pdb=" OP1 C J 14 " pdb=" OP2 C J 14 " pdb=" O5' C J 14 " both_signs ideal model delta sigma weight residual True 2.41 -2.99 -0.58 2.00e-01 2.50e+01 8.35e+00 chirality pdb=" P C H 14 " pdb=" OP1 C H 14 " pdb=" OP2 C H 14 " pdb=" O5' C H 14 " both_signs ideal model delta sigma weight residual True 2.41 -2.99 -0.58 2.00e-01 2.50e+01 8.31e+00 chirality pdb=" P G I 17 " pdb=" OP1 G I 17 " pdb=" OP2 G I 17 " pdb=" O5' G I 17 " both_signs ideal model delta sigma weight residual True 2.41 -2.94 -0.53 2.00e-01 2.50e+01 6.91e+00 ... (remaining 2896 not shown) Planarity restraints: 2961 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 215 " -0.064 2.00e-02 2.50e+03 3.37e-02 2.27e+01 pdb=" CG TYR E 215 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR E 215 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR E 215 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR E 215 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR E 215 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR E 215 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 215 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 243 " -0.012 2.00e-02 2.50e+03 2.45e-02 6.02e+00 pdb=" C MET B 243 " 0.042 2.00e-02 2.50e+03 pdb=" O MET B 243 " -0.016 2.00e-02 2.50e+03 pdb=" N CYS B 244 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR E 215 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.49e+00 pdb=" C TYR E 215 " 0.032 2.00e-02 2.50e+03 pdb=" O TYR E 215 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY E 216 " -0.011 2.00e-02 2.50e+03 ... (remaining 2958 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 4205 2.80 - 3.32: 15059 3.32 - 3.85: 28414 3.85 - 4.37: 34626 4.37 - 4.90: 58675 Nonbonded interactions: 140979 Sorted by model distance: nonbonded pdb=" OE1 GLN D 138 " pdb=" O4' G I 17 " model vdw 2.272 3.040 nonbonded pdb=" OE2 GLU D 39 " pdb=" NH1 ARG F 96 " model vdw 2.313 3.120 nonbonded pdb=" O CYS D 102 " pdb=" OD1 ASP D 106 " model vdw 2.397 3.040 nonbonded pdb=" O ARG F 201 " pdb=" OD2 ASP F 205 " model vdw 2.414 3.040 nonbonded pdb=" O ARG A 201 " pdb=" OD2 ASP A 205 " model vdw 2.414 3.040 ... (remaining 140974 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' selection = (chain 'B' and resid -1 through 337) selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'H' selection = chain 'J' } 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: 0.010 Normalize map: mean=0, sd=1: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.260 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18194 Z= 0.249 Angle : 0.655 8.920 25040 Z= 0.394 Chirality : 0.072 0.578 2899 Planarity : 0.003 0.050 2961 Dihedral : 15.501 117.625 7067 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.19), residues: 2023 helix: 1.77 (0.25), residues: 508 sheet: -0.17 (0.27), residues: 376 loop : -0.33 (0.19), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 142 TYR 0.064 0.001 TYR E 215 PHE 0.006 0.001 PHE B 211 TRP 0.004 0.001 TRP E 86 HIS 0.002 0.001 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.25 (18194) covalent geometry : angle 0.65481 / 0.39 (25040) hydrogen bonds : bond 0.18998 / 12.74 ( 677) hydrogen bonds : angle 7.13271 / 5.00 ( 1961) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 LYS cc_start: 0.8613 (tptt) cc_final: 0.8278 (tmtt) REVERT: C 322 MET cc_start: 0.6304 (mpp) cc_final: 0.6025 (mmt) REVERT: D 312 VAL cc_start: 0.8870 (t) cc_final: 0.8574 (p) REVERT: E 73 LYS cc_start: 0.8062 (tptt) cc_final: 0.7792 (tttt) REVERT: E 161 LYS cc_start: 0.7279 (tptp) cc_final: 0.7066 (tttt) REVERT: F 208 GLU cc_start: 0.7951 (tt0) cc_final: 0.7451 (pm20) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.1387 time to fit residues: 63.4062 Evaluate side-chains 146 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: [98, 194, 107, 10, 66, 130, 124, 103, 200, 77, 122] chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.0020 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.0030 chunk 200 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 ASN A 90 ASN C 90 ASN C 131 ASN C 317 HIS D 4 ASN E 4 ASN E 131 ASN E 156 ASN F 4 ASN F 250 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.162879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.117783 restraints weight = 25491.789| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.40 r_work: 0.3400 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18194 Z= 0.109 Angle : 0.493 6.329 25040 Z= 0.276 Chirality : 0.043 0.174 2899 Planarity : 0.004 0.055 2961 Dihedral : 12.195 109.759 3290 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.51 % Allowed : 10.34 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.19), residues: 2023 helix: 1.37 (0.23), residues: 548 sheet: -0.15 (0.29), residues: 317 loop : 0.01 (0.19), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 142 TYR 0.021 0.001 TYR C 334 PHE 0.021 0.001 PHE C 211 TRP 0.005 0.001 TRP E 324 HIS 0.002 0.001 HIS B 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.11 (18194) covalent geometry : angle 0.49269 / 0.28 (25040) hydrogen bonds : bond 0.04046 / 2.64 ( 677) hydrogen bonds : angle 5.20378 / 3.61 ( 1961) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: A 263 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7701 (p0) REVERT: B 219 LEU cc_start: 0.6012 (mt) cc_final: 0.5800 (mp) REVERT: B 248 ARG cc_start: 0.7077 (mtm-85) cc_final: 0.6860 (mtm-85) REVERT: C 186 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8510 (mp10) REVERT: C 322 MET cc_start: 0.6843 (mpp) cc_final: 0.6548 (mmt) REVERT: C 326 GLU cc_start: 0.4121 (OUTLIER) cc_final: 0.3826 (pt0) REVERT: D 106 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8492 (m-30) REVERT: D 202 ASP cc_start: 0.6088 (m-30) cc_final: 0.5691 (m-30) REVERT: E 68 ASN cc_start: 0.7303 (p0) cc_final: 0.6974 (p0) REVERT: E 73 LYS cc_start: 0.8103 (tptt) cc_final: 0.7621 (tttt) REVERT: E 112 LEU cc_start: 0.7592 (mt) cc_final: 0.7329 (tp) REVERT: E 274 ASN cc_start: 0.8000 (t0) cc_final: 0.7652 (t0) REVERT: F 208 GLU cc_start: 0.7367 (tt0) cc_final: 0.6661 (pm20) REVERT: F 322 MET cc_start: 0.7343 (mmm) cc_final: 0.5879 (tpp) outliers start: 27 outliers final: 8 residues processed: 178 average time/residue: 0.1255 time to fit residues: 34.8800 Evaluate side-chains 146 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 79 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: [170, 2, 101, 164, 163, 32, 140, 194, 24, 193, 125] chunk 170 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 163 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 140 optimal weight: 0.7980 chunk 194 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 125 optimal weight: 8.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN A 317 HIS B 110 ASN E 156 ASN E 173 ASN F 250 ASN F 317 HIS F 336 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.157051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.110894 restraints weight = 25814.824| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.36 r_work: 0.3307 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18194 Z= 0.143 Angle : 0.495 6.276 25040 Z= 0.271 Chirality : 0.043 0.162 2899 Planarity : 0.004 0.041 2961 Dihedral : 12.140 111.161 3290 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.62 % Allowed : 11.85 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.19), residues: 2023 helix: 1.31 (0.23), residues: 547 sheet: 0.22 (0.29), residues: 317 loop : -0.13 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 201 TYR 0.022 0.002 TYR D 302 PHE 0.026 0.001 PHE C 211 TRP 0.009 0.001 TRP D 86 HIS 0.003 0.001 HIS B 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (18194) covalent geometry : angle 0.49487 / 0.27 (25040) hydrogen bonds : bond 0.03829 / 2.53 ( 677) hydrogen bonds : angle 4.71752 / 3.27 ( 1961) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: A 263 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7892 (p0) REVERT: B 110 ASN cc_start: 0.7625 (m-40) cc_final: 0.6536 (p0) REVERT: C 73 LYS cc_start: 0.8034 (mmtt) cc_final: 0.7776 (mmtt) REVERT: C 326 GLU cc_start: 0.4326 (OUTLIER) cc_final: 0.3889 (pt0) REVERT: D 106 ASP cc_start: 0.8799 (OUTLIER) cc_final: 0.8509 (m-30) REVERT: D 312 VAL cc_start: 0.8838 (t) cc_final: 0.8580 (m) REVERT: E 68 ASN cc_start: 0.7633 (p0) cc_final: 0.7346 (p0) REVERT: E 73 LYS cc_start: 0.8201 (tptt) cc_final: 0.7685 (ttmt) REVERT: E 78 ASP cc_start: 0.8833 (m-30) cc_final: 0.8476 (m-30) REVERT: E 112 LEU cc_start: 0.7610 (mt) cc_final: 0.7394 (tp) REVERT: E 142 ARG cc_start: 0.7167 (ptp90) cc_final: 0.6879 (ptp90) REVERT: E 255 LYS cc_start: 0.7083 (ttmt) cc_final: 0.6839 (ttpt) REVERT: E 274 ASN cc_start: 0.8187 (t0) cc_final: 0.7685 (t0) REVERT: F 250 ASN cc_start: 0.8539 (OUTLIER) cc_final: 0.8246 (t0) REVERT: F 322 MET cc_start: 0.7290 (mmm) cc_final: 0.6219 (tpp) outliers start: 29 outliers final: 18 residues processed: 162 average time/residue: 0.1329 time to fit residues: 33.0723 Evaluate side-chains 144 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 250 ASN Chi-restraints excluded: chain F residue 280 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: [96, 158, 104, 108, 181, 133, 191, 56, 159, 55, 91] chunk 96 optimal weight: 6.9990 chunk 158 optimal weight: 8.9990 chunk 104 optimal weight: 0.8980 chunk 108 optimal weight: 0.0270 chunk 181 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 191 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 159 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 overall best weight: 2.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 90 ASN B 274 ASN C 238 HIS E 250 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.154802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.108528 restraints weight = 25716.982| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.40 r_work: 0.3271 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18194 Z= 0.162 Angle : 0.486 6.439 25040 Z= 0.267 Chirality : 0.043 0.193 2899 Planarity : 0.004 0.037 2961 Dihedral : 12.167 108.334 3290 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.73 % Allowed : 12.69 % Favored : 85.58 % 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: 0.34 (0.18), residues: 2023 helix: 1.19 (0.23), residues: 548 sheet: 0.22 (0.29), residues: 317 loop : -0.17 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 248 TYR 0.026 0.001 TYR C 302 PHE 0.016 0.001 PHE C 211 TRP 0.008 0.001 TRP D 86 HIS 0.004 0.001 HIS C 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (18194) covalent geometry : angle 0.48589 / 0.27 (25040) hydrogen bonds : bond 0.03534 / 2.34 ( 677) hydrogen bonds : angle 4.58346 / 3.17 ( 1961) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: A 263 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.7928 (p0) REVERT: C 73 LYS cc_start: 0.8025 (mmtt) cc_final: 0.7777 (mmtt) REVERT: D 106 ASP cc_start: 0.8846 (OUTLIER) cc_final: 0.8572 (m-30) REVERT: D 294 LEU cc_start: 0.8515 (tp) cc_final: 0.8279 (tp) REVERT: D 312 VAL cc_start: 0.8701 (t) cc_final: 0.8399 (m) REVERT: E 68 ASN cc_start: 0.7716 (p0) cc_final: 0.7415 (p0) REVERT: E 73 LYS cc_start: 0.8144 (tptt) cc_final: 0.7640 (ttmt) REVERT: E 112 LEU cc_start: 0.7740 (mt) cc_final: 0.7455 (tp) REVERT: E 142 ARG cc_start: 0.7173 (ptp90) cc_final: 0.6720 (ptp90) REVERT: E 191 GLU cc_start: 0.7449 (mp0) cc_final: 0.6923 (mp0) REVERT: E 274 ASN cc_start: 0.8268 (t0) cc_final: 0.7747 (t0) REVERT: F 322 MET cc_start: 0.7347 (mmm) cc_final: 0.6419 (tpp) outliers start: 31 outliers final: 24 residues processed: 150 average time/residue: 0.1241 time to fit residues: 29.4895 Evaluate side-chains 144 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 323 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: [166, 73, 97, 99, 16, 75, 144, 198, 125, 164, 53] chunk 166 optimal weight: 50.0000 chunk 73 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 144 optimal weight: 9.9990 chunk 198 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.154396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.107905 restraints weight = 25681.468| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.38 r_work: 0.3262 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18194 Z= 0.137 Angle : 0.458 6.456 25040 Z= 0.252 Chirality : 0.042 0.213 2899 Planarity : 0.003 0.050 2961 Dihedral : 12.145 107.390 3290 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.73 % Allowed : 14.03 % Favored : 84.24 % 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: 0.36 (0.18), residues: 2023 helix: 1.19 (0.23), residues: 547 sheet: 0.39 (0.29), residues: 307 loop : -0.20 (0.18), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 142 TYR 0.021 0.001 TYR C 302 PHE 0.014 0.001 PHE C 211 TRP 0.009 0.001 TRP D 86 HIS 0.004 0.001 HIS C 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (18194) covalent geometry : angle 0.45828 / 0.25 (25040) hydrogen bonds : bond 0.03278 / 2.17 ( 677) hydrogen bonds : angle 4.47937 / 3.10 ( 1961) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: A 263 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.7952 (p0) REVERT: B 201 ARG cc_start: 0.6409 (mtm-85) cc_final: 0.6005 (mtp180) REVERT: C 73 LYS cc_start: 0.8073 (mmtt) cc_final: 0.7786 (mttt) REVERT: C 194 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7601 (mm-30) REVERT: D 106 ASP cc_start: 0.8843 (OUTLIER) cc_final: 0.8586 (m-30) REVERT: D 312 VAL cc_start: 0.8726 (t) cc_final: 0.8430 (m) REVERT: E 73 LYS cc_start: 0.8196 (tptt) cc_final: 0.7700 (ttmt) REVERT: E 112 LEU cc_start: 0.7782 (mt) cc_final: 0.7509 (tp) REVERT: E 274 ASN cc_start: 0.8309 (t0) cc_final: 0.7798 (t0) REVERT: F 322 MET cc_start: 0.7372 (mmm) cc_final: 0.6268 (tpp) outliers start: 31 outliers final: 23 residues processed: 150 average time/residue: 0.1320 time to fit residues: 30.3977 Evaluate side-chains 138 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 323 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: [191, 105, 93, 107, 103, 161, 154, 51, 106, 8, 37] chunk 191 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 93 optimal weight: 0.1980 chunk 107 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 161 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 274 ASN E 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.153999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.107857 restraints weight = 25525.718| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.35 r_work: 0.3257 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18194 Z= 0.128 Angle : 0.447 6.168 25040 Z= 0.246 Chirality : 0.041 0.164 2899 Planarity : 0.003 0.048 2961 Dihedral : 12.114 106.094 3290 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.57 % Allowed : 15.04 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.19), residues: 2023 helix: 1.20 (0.23), residues: 548 sheet: 0.20 (0.29), residues: 307 loop : -0.10 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 142 TYR 0.027 0.001 TYR F 167 PHE 0.015 0.001 PHE C 211 TRP 0.009 0.001 TRP D 86 HIS 0.003 0.001 HIS C 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (18194) covalent geometry : angle 0.44698 / 0.25 (25040) hydrogen bonds : bond 0.03174 / 2.08 ( 677) hydrogen bonds : angle 4.39260 / 3.03 ( 1961) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: A 219 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6427 (mt) REVERT: A 263 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.8036 (p0) REVERT: B 201 ARG cc_start: 0.6407 (mtm-85) cc_final: 0.6013 (mtp180) REVERT: C 73 LYS cc_start: 0.8107 (mmtt) cc_final: 0.7795 (mttt) REVERT: C 194 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7632 (mm-30) REVERT: D 106 ASP cc_start: 0.8862 (OUTLIER) cc_final: 0.8627 (m-30) REVERT: D 312 VAL cc_start: 0.8755 (t) cc_final: 0.8466 (m) REVERT: E 73 LYS cc_start: 0.8169 (tptt) cc_final: 0.7676 (ttmt) REVERT: E 112 LEU cc_start: 0.7769 (mt) cc_final: 0.7518 (tp) REVERT: E 191 GLU cc_start: 0.7512 (mp0) cc_final: 0.7141 (mp0) REVERT: E 274 ASN cc_start: 0.8323 (t0) cc_final: 0.7814 (t0) REVERT: F 302 TYR cc_start: 0.7044 (m-80) cc_final: 0.6844 (m-80) REVERT: F 322 MET cc_start: 0.7453 (mmm) cc_final: 0.6422 (tpp) outliers start: 28 outliers final: 20 residues processed: 144 average time/residue: 0.1338 time to fit residues: 29.3263 Evaluate side-chains 137 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 292 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: [77, 131, 177, 55, 144, 93, 31, 113, 73, 160, 117] chunk 77 optimal weight: 6.9990 chunk 131 optimal weight: 8.9990 chunk 177 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 31 optimal weight: 0.0970 chunk 113 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 160 optimal weight: 8.9990 chunk 117 optimal weight: 0.9980 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 274 ASN E 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.153088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.105990 restraints weight = 25809.369| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.32 r_work: 0.3244 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 18194 Z= 0.148 Angle : 0.465 7.009 25040 Z= 0.253 Chirality : 0.041 0.143 2899 Planarity : 0.003 0.053 2961 Dihedral : 12.120 106.032 3290 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.96 % Allowed : 15.20 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.19), residues: 2023 helix: 1.19 (0.23), residues: 548 sheet: 0.21 (0.29), residues: 307 loop : -0.16 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 142 TYR 0.020 0.001 TYR F 167 PHE 0.011 0.001 PHE C 211 TRP 0.009 0.001 TRP D 86 HIS 0.004 0.001 HIS C 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (18194) covalent geometry : angle 0.46480 / 0.25 (25040) hydrogen bonds : bond 0.03314 / 2.18 ( 677) hydrogen bonds : angle 4.39212 / 3.03 ( 1961) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 115 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: A 219 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.6486 (mt) REVERT: A 263 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.8054 (p0) REVERT: B 201 ARG cc_start: 0.6452 (mtm-85) cc_final: 0.6077 (mtp180) REVERT: C 73 LYS cc_start: 0.8105 (mmtt) cc_final: 0.7809 (mttt) REVERT: C 194 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7586 (mm-30) REVERT: D 312 VAL cc_start: 0.8789 (t) cc_final: 0.8505 (m) REVERT: E 73 LYS cc_start: 0.8209 (tptt) cc_final: 0.7712 (ttmt) REVERT: E 112 LEU cc_start: 0.7744 (mt) cc_final: 0.7504 (tp) REVERT: E 274 ASN cc_start: 0.8355 (t0) cc_final: 0.7854 (t0) REVERT: F 322 MET cc_start: 0.7498 (mmm) cc_final: 0.6473 (tpp) outliers start: 35 outliers final: 28 residues processed: 144 average time/residue: 0.1320 time to fit residues: 29.5605 Evaluate side-chains 139 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 274 ASN Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 292 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: [188, 184, 165, 17, 80, 123, 167, 0, 199, 39, 67] chunk 188 optimal weight: 4.9990 chunk 184 optimal weight: 0.9980 chunk 165 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 167 optimal weight: 50.0000 chunk 0 optimal weight: 7.9990 chunk 199 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 274 ASN B 297 ASN E 250 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.152972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.106007 restraints weight = 25616.136| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.30 r_work: 0.3243 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 18194 Z= 0.142 Angle : 0.461 7.293 25040 Z= 0.251 Chirality : 0.041 0.144 2899 Planarity : 0.003 0.044 2961 Dihedral : 12.120 105.909 3290 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.96 % Allowed : 15.71 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.19), residues: 2023 helix: 1.18 (0.23), residues: 548 sheet: 0.22 (0.29), residues: 307 loop : -0.15 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 142 TYR 0.018 0.001 TYR F 167 PHE 0.011 0.001 PHE C 211 TRP 0.009 0.001 TRP D 86 HIS 0.004 0.001 HIS C 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (18194) covalent geometry : angle 0.46059 / 0.25 (25040) hydrogen bonds : bond 0.03250 / 2.15 ( 677) hydrogen bonds : angle 4.35962 / 3.01 ( 1961) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: A 219 LEU cc_start: 0.6880 (OUTLIER) cc_final: 0.6424 (mt) REVERT: A 263 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.8026 (p0) REVERT: A 322 MET cc_start: 0.6984 (mmm) cc_final: 0.6674 (mmm) REVERT: B 73 LYS cc_start: 0.8451 (tptp) cc_final: 0.7707 (tmtt) REVERT: B 201 ARG cc_start: 0.6488 (mtm-85) cc_final: 0.6108 (mtp180) REVERT: B 274 ASN cc_start: 0.8204 (t160) cc_final: 0.7997 (t0) REVERT: C 73 LYS cc_start: 0.8106 (mmtt) cc_final: 0.7804 (mttt) REVERT: C 194 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7606 (mm-30) REVERT: D 312 VAL cc_start: 0.8777 (t) cc_final: 0.8491 (m) REVERT: E 73 LYS cc_start: 0.8221 (tptt) cc_final: 0.7696 (ttmt) REVERT: E 191 GLU cc_start: 0.7372 (mp0) cc_final: 0.6891 (mp0) REVERT: E 274 ASN cc_start: 0.8387 (t0) cc_final: 0.7905 (t0) REVERT: F 322 MET cc_start: 0.7531 (mmm) cc_final: 0.6527 (tpp) outliers start: 35 outliers final: 28 residues processed: 143 average time/residue: 0.1242 time to fit residues: 27.6814 Evaluate side-chains 142 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 292 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: [147, 113, 90, 2, 190, 61, 49, 107, 120, 52, 151] chunk 147 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 190 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 49 optimal weight: 0.2980 chunk 107 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 151 optimal weight: 0.0060 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 297 ASN E 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.154663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.107637 restraints weight = 25736.197| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.32 r_work: 0.3270 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 18194 Z= 0.084 Angle : 0.417 6.535 25040 Z= 0.231 Chirality : 0.040 0.143 2899 Planarity : 0.003 0.043 2961 Dihedral : 12.066 104.912 3290 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.17 % Allowed : 16.38 % Favored : 82.45 % 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: 0.48 (0.19), residues: 2023 helix: 1.29 (0.23), residues: 547 sheet: 0.18 (0.29), residues: 317 loop : -0.04 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 142 TYR 0.016 0.001 TYR F 167 PHE 0.012 0.001 PHE C 211 TRP 0.011 0.001 TRP A 324 HIS 0.002 0.001 HIS C 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00182 / 0.08 (18194) covalent geometry : angle 0.41662 / 0.23 (25040) hydrogen bonds : bond 0.02725 / 1.80 ( 677) hydrogen bonds : angle 4.24463 / 2.93 ( 1961) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 263 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.8024 (p0) REVERT: B 73 LYS cc_start: 0.8420 (tptp) cc_final: 0.7712 (ttpp) REVERT: B 201 ARG cc_start: 0.6450 (mtm-85) cc_final: 0.6077 (mtp180) REVERT: C 73 LYS cc_start: 0.8088 (mmtt) cc_final: 0.7796 (mttt) REVERT: C 194 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7618 (mm-30) REVERT: D 312 VAL cc_start: 0.8751 (t) cc_final: 0.8468 (m) REVERT: E 73 LYS cc_start: 0.8178 (tptt) cc_final: 0.7678 (ttmt) REVERT: E 142 ARG cc_start: 0.7362 (ptp90) cc_final: 0.6897 (ptp90) REVERT: E 161 LYS cc_start: 0.8391 (tttt) cc_final: 0.8169 (tttm) REVERT: E 191 GLU cc_start: 0.7347 (mp0) cc_final: 0.6882 (mp0) REVERT: E 274 ASN cc_start: 0.8404 (t0) cc_final: 0.7934 (t0) REVERT: F 322 MET cc_start: 0.7442 (mmm) cc_final: 0.6430 (tpp) outliers start: 21 outliers final: 19 residues processed: 138 average time/residue: 0.1287 time to fit residues: 26.9223 Evaluate side-chains 132 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 280 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: [5, 30, 185, 57, 143, 197, 124, 133, 8, 125, 16] chunk 5 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 185 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 197 optimal weight: 8.9990 chunk 124 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 274 ASN B 297 ASN E 250 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.153225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.106198 restraints weight = 25637.245| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.30 r_work: 0.3245 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18194 Z= 0.136 Angle : 0.458 8.964 25040 Z= 0.249 Chirality : 0.041 0.144 2899 Planarity : 0.003 0.041 2961 Dihedral : 12.069 104.943 3290 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.45 % Allowed : 16.15 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.19), residues: 2023 helix: 1.22 (0.23), residues: 548 sheet: 0.25 (0.29), residues: 307 loop : -0.09 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 142 TYR 0.016 0.001 TYR F 167 PHE 0.010 0.001 PHE C 211 TRP 0.008 0.001 TRP D 86 HIS 0.003 0.001 HIS C 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (18194) covalent geometry : angle 0.45766 / 0.25 (25040) hydrogen bonds : bond 0.03147 / 2.08 ( 677) hydrogen bonds : angle 4.27748 / 2.95 ( 1961) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: A 263 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.7996 (p0) REVERT: B 73 LYS cc_start: 0.8418 (tptp) cc_final: 0.7683 (tmtt) REVERT: B 201 ARG cc_start: 0.6468 (mtm-85) cc_final: 0.6099 (mtp180) REVERT: C 73 LYS cc_start: 0.8128 (mmtt) cc_final: 0.7814 (mttt) REVERT: C 194 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7564 (mm-30) REVERT: D 312 VAL cc_start: 0.8766 (t) cc_final: 0.8482 (m) REVERT: E 73 LYS cc_start: 0.8242 (tptt) cc_final: 0.7737 (ttmt) REVERT: E 78 ASP cc_start: 0.8674 (m-30) cc_final: 0.8429 (m-30) REVERT: E 191 GLU cc_start: 0.7355 (mp0) cc_final: 0.6881 (mp0) REVERT: E 274 ASN cc_start: 0.8459 (t0) cc_final: 0.7965 (t0) REVERT: F 322 MET cc_start: 0.7468 (mmm) cc_final: 0.6463 (tpp) outliers start: 26 outliers final: 21 residues processed: 135 average time/residue: 0.1342 time to fit residues: 28.4764 Evaluate side-chains 131 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 280 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: [169, 186, 96, 103, 202, 115, 69, 99, 175, 135, 191] chunk 169 optimal weight: 1.9990 chunk 186 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 202 optimal weight: 50.0000 chunk 115 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 99 optimal weight: 0.0980 chunk 175 optimal weight: 0.3980 chunk 135 optimal weight: 0.7980 chunk 191 optimal weight: 9.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 297 ASN E 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.155080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.108134 restraints weight = 25821.955| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.32 r_work: 0.3278 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18194 Z= 0.078 Angle : 0.414 8.132 25040 Z= 0.228 Chirality : 0.039 0.147 2899 Planarity : 0.003 0.041 2961 Dihedral : 12.024 104.033 3290 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.06 % Allowed : 16.71 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.19), residues: 2023 helix: 1.32 (0.23), residues: 547 sheet: 0.24 (0.30), residues: 307 loop : 0.03 (0.19), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 142 TYR 0.013 0.001 TYR F 167 PHE 0.012 0.001 PHE C 211 TRP 0.012 0.001 TRP A 324 HIS 0.002 0.001 HIS C 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00166 / 0.08 (18194) covalent geometry : angle 0.41366 / 0.23 (25040) hydrogen bonds : bond 0.02612 / 1.72 ( 677) hydrogen bonds : angle 4.17203 / 2.88 ( 1961) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4710.79 seconds wall clock time: 81 minutes 9.28 seconds (4869.28 seconds total)