Starting phenix.real_space_refine on Sun Oct 25 16:10:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/37kx_78244/10_2026/37kx_78244.cif Found real_map, /net/cci-nas-00/data/ceres_data/37kx_78244/10_2026/37kx_78244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/37kx_78244/10_2026/37kx_78244.map" default_real_map = "/net/cci-nas-00/data/ceres_data/37kx_78244/10_2026/37kx_78244.map" model { file = "/net/cci-nas-00/data/ceres_data/37kx_78244/10_2026/37kx_78244.cif" } default_model = "/net/cci-nas-00/data/ceres_data/37kx_78244/10_2026/37kx_78244.cif" } resolution = 3.0 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= 0.053 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 42 5.49 5 S 66 5.16 5 C 10737 2.51 5 N 2809 2.21 5 O 3402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17056 Number of models: 1 Model: "" Number of chains: 8 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: "F" Number of atoms: 2686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2686 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 11, 'TRANS': 326} Chain: "G" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 421 Classifications: {'RNA': 20} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 11} Link IDs: {'rna2p': 1, 'rna3p': 18} Chain: "H" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 469 Classifications: {'RNA': 22} Modifications used: {'rna3p_pur': 14, 'rna3p_pyr': 8} Link IDs: {'rna3p': 21} Time building chain proxies: 3.67, per 1000 atoms: 0.22 Number of scatterers: 17056 At special positions: 0 Unit cell: (114.912, 118.104, 127.68, 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 42 15.00 O 3402 8.00 N 2809 7.00 C 10737 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: 1.36 Conformation dependent library (CDL) restraints added in 682.6 milliseconds 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3780 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 42 sheets defined 29.3% alpha, 27.4% beta 17 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 1.68 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: 3.547A 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: 3.556A 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: 3.669A 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: 4.019A 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: 3.502A 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 76 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 239 through 249 removed outlier: 3.568A pdb=" N ALA F 249 " --> pdb=" O ARG F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 303 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: 4.123A 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: 3.502A pdb=" N LYS A 308 " --> pdb=" O THR A 323 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 310 " --> pdb=" O PHE A 321 " (cutoff:3.500A) removed outlier: 4.056A 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: 6.542A pdb=" N GLN B 266 " --> pdb=" O THR B 282 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR B 282 " --> pdb=" O GLN B 266 " (cutoff:3.500A) removed outlier: 6.131A 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: 8.017A 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: 8.017A 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: 6.024A pdb=" N TYR C 268 " --> pdb=" O VAL C 280 " (cutoff:3.500A) removed outlier: 3.880A 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: 3.735A pdb=" N LYS C 308 " --> pdb=" O THR C 323 " (cutoff:3.500A) removed outlier: 6.907A 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: 6.703A 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: 6.781A 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: 8.977A 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: 8.977A 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: 6.714A 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: 3.982A 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: 3.643A 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: 6.835A 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: 6.664A pdb=" N THR F 80 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASP F 117 " --> pdb=" O ASN F 81 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL F 114 " --> pdb=" O VAL F 133 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N VAL F 135 " --> pdb=" O VAL F 114 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N TYR F 116 " --> pdb=" O VAL F 135 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU F 166 " --> pdb=" O ILE F 148 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 98 through 99 removed outlier: 6.664A pdb=" N THR F 80 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASP F 117 " --> pdb=" O ASN F 81 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL F 114 " --> pdb=" O VAL F 133 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N VAL F 135 " --> pdb=" O VAL F 114 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N TYR F 116 " --> pdb=" O VAL F 135 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LYS F 170 " --> pdb=" O VAL F 177 " (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: 6.418A pdb=" N GLN F 266 " --> pdb=" O THR F 282 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THR F 282 " --> pdb=" O GLN F 266 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N TYR F 268 " --> pdb=" O VAL F 280 " (cutoff:3.500A) removed outlier: 3.980A 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 314 removed outlier: 3.603A pdb=" N LYS F 308 " --> pdb=" O THR F 323 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR F 332 " --> pdb=" O TRP F 324 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLU F 326 " --> pdb=" O ILE F 330 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ILE F 330 " --> pdb=" O GLU F 326 " (cutoff:3.500A) 675 hydrogen bonds defined for protein. 1836 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 39 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 3.23 Time building geometry restraints manager: 1.84 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: 5352 1.34 - 1.46: 3470 1.46 - 1.58: 8479 1.58 - 1.70: 81 1.70 - 1.82: 102 Bond restraints: 17484 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 2.19e+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=" 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 8.77e+00 bond pdb=" C GLY B 242 " pdb=" N MET B 243 " ideal model delta sigma weight residual 1.335 1.295 0.040 1.38e-02 5.25e+03 8.49e+00 bond pdb=" P C H 14 " pdb=" O5' C H 14 " ideal model delta sigma weight residual 1.593 1.618 -0.025 1.00e-02 1.00e+04 6.18e+00 ... (remaining 17479 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 23471 1.78 - 3.56: 391 3.56 - 5.33: 49 5.33 - 7.11: 27 7.11 - 8.89: 5 Bond angle restraints: 23943 Sorted by residual: 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 G 8 " pdb=" C2 U G 8 " pdb=" O2 U G 8 " ideal model delta sigma weight residual 122.80 125.36 -2.56 7.00e-01 2.04e+00 1.34e+01 angle pdb=" OE1 GLN E 222 " pdb=" CD GLN E 222 " pdb=" NE2 GLN E 222 " ideal model delta sigma weight residual 122.60 119.03 3.57 1.00e+00 1.00e+00 1.28e+01 angle pdb=" C4' A G 18 " pdb=" C3' A G 18 " pdb=" C2' A G 18 " ideal model delta sigma weight residual 102.60 99.04 3.56 1.00e+00 1.00e+00 1.27e+01 angle pdb=" CA MET A 322 " pdb=" C MET A 322 " pdb=" O MET A 322 " ideal model delta sigma weight residual 121.19 117.31 3.88 1.10e+00 8.26e-01 1.24e+01 ... (remaining 23938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.52: 9734 23.52 - 47.04: 560 47.04 - 70.57: 98 70.57 - 94.09: 21 94.09 - 117.61: 1 Dihedral angle restraints: 10414 sinusoidal: 4468 harmonic: 5946 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 -10.39 -117.61 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 180.00 154.67 25.33 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" C4' U G 8 " pdb=" O4' U G 8 " pdb=" C1' U G 8 " pdb=" C2' U G 8 " ideal model delta sinusoidal sigma weight residual -21.00 8.04 -29.04 1 8.00e+00 1.56e-02 1.89e+01 ... (remaining 10411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 2635 0.115 - 0.231: 91 0.231 - 0.346: 1 0.346 - 0.462: 11 0.462 - 0.577: 9 Chirality restraints: 2747 Sorted by residual: 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 8.32e+00 chirality pdb=" P G G 17 " pdb=" OP1 G G 17 " pdb=" OP2 G G 17 " pdb=" O5' G G 17 " both_signs ideal model delta sigma weight residual True 2.41 -2.93 -0.52 2.00e-01 2.50e+01 6.85e+00 chirality pdb=" P G H 13 " pdb=" OP1 G H 13 " pdb=" OP2 G H 13 " pdb=" O5' G H 13 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.53e+00 ... (remaining 2744 not shown) Planarity restraints: 2930 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 215 " -0.064 2.00e-02 2.50e+03 3.35e-02 2.25e+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 " 0.030 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 2.43e-02 5.92e+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 " -0.014 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 1.86e-02 3.48e+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 2927 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 6432 2.90 - 3.40: 14871 3.40 - 3.90: 27596 3.90 - 4.40: 31996 4.40 - 4.90: 54216 Nonbonded interactions: 135111 Sorted by model distance: nonbonded pdb=" O CYS D 102 " pdb=" OD1 ASP D 106 " model vdw 2.397 3.040 nonbonded pdb=" O ARG A 201 " pdb=" OD2 ASP A 205 " model vdw 2.414 3.040 nonbonded pdb=" O ASN F 259 " pdb=" OD1 ASN F 259 " model vdw 2.435 3.040 nonbonded pdb=" O ASP F 273 " pdb=" OD1 ASP F 273 " model vdw 2.458 3.040 nonbonded pdb=" O ASP A 198 " pdb=" OD1 ASP A 202 " model vdw 2.467 3.040 ... (remaining 135106 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid -1 through 336) selection = (chain 'B' and resid -1 through 336) selection = (chain 'C' and resid -1 through 336) selection = (chain 'D' and resid -1 through 336) selection = (chain 'E' and resid -1 through 336) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.860 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 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 : 0.003 0.047 17484 Z= 0.201 Angle : 0.575 8.892 23943 Z= 0.346 Chirality : 0.060 0.577 2747 Planarity : 0.003 0.050 2930 Dihedral : 14.981 117.611 6634 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.19), residues: 2022 helix: 1.67 (0.25), residues: 518 sheet: -0.05 (0.27), residues: 377 loop : -0.18 (0.19), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 142 TYR 0.064 0.001 TYR E 215 PHE 0.005 0.001 PHE B 211 TRP 0.003 0.001 TRP D 86 HIS 0.002 0.001 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.20 (17484) covalent geometry : angle 0.57469 / 0.35 (23943) hydrogen bonds : bond 0.18941 / 12.73 ( 656) hydrogen bonds : angle 7.20199 / 5.05 ( 1914) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.609 Fit side-chains REVERT: A 92 THR cc_start: 0.9148 (m) cc_final: 0.8922 (p) REVERT: A 142 ARG cc_start: 0.8610 (ttm110) cc_final: 0.8266 (ttp-110) REVERT: A 324 TRP cc_start: 0.7900 (m100) cc_final: 0.7166 (m-10) REVERT: C 300 LYS cc_start: 0.7227 (ttpp) cc_final: 0.7008 (ttpp) REVERT: C 334 TYR cc_start: 0.8285 (p90) cc_final: 0.7918 (p90) REVERT: D 233 GLN cc_start: 0.7142 (tt0) cc_final: 0.6777 (mm-40) REVERT: D 289 ASP cc_start: 0.6771 (t0) cc_final: 0.6463 (m-30) REVERT: E 268 TYR cc_start: 0.8561 (m-80) cc_final: 0.8327 (m-80) REVERT: F 106 ASP cc_start: 0.8379 (m-30) cc_final: 0.8038 (m-30) REVERT: F 140 TYR cc_start: 0.8422 (m-80) cc_final: 0.8082 (m-80) REVERT: F 297 ASN cc_start: 0.5836 (m-40) cc_final: 0.5403 (t0) outliers start: 0 outliers final: 1 residues processed: 151 average time/residue: 0.5588 time to fit residues: 94.5603 Evaluate side-chains 132 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 198 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: [98, 194, 107, 10, 66, 130, 124, 103, 200, 77, 122] chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.0170 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 40.0000 chunk 77 optimal weight: 0.0670 chunk 122 optimal weight: 9.9990 overall best weight: 2.1760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 ASN B 250 ASN D 4 ASN E 4 ASN E 131 ASN E 222 GLN F 62 ASN F 250 ASN F 336 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.157326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.112947 restraints weight = 20068.704| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.99 r_work: 0.3021 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17484 Z= 0.172 Angle : 0.518 8.685 23943 Z= 0.283 Chirality : 0.045 0.174 2747 Planarity : 0.004 0.041 2930 Dihedral : 10.378 108.767 2861 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.01 % Allowed : 9.45 % Favored : 88.53 % 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: 2022 helix: 1.32 (0.24), residues: 545 sheet: 0.01 (0.28), residues: 327 loop : -0.06 (0.19), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 142 TYR 0.019 0.001 TYR B 302 PHE 0.012 0.001 PHE C 32 TRP 0.009 0.002 TRP D 86 HIS 0.004 0.001 HIS F 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 (17484) covalent geometry : angle 0.51804 / 0.28 (23943) hydrogen bonds : bond 0.04399 / 2.93 ( 656) hydrogen bonds : angle 5.27707 / 3.75 ( 1914) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: A 327 ASP cc_start: 0.8344 (p0) cc_final: 0.7856 (p0) REVERT: B 322 MET cc_start: 0.5816 (OUTLIER) cc_final: 0.4585 (mmt) REVERT: D 11 LYS cc_start: 0.8128 (mmtt) cc_final: 0.7928 (mmtm) REVERT: D 39 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8108 (mt-10) REVERT: D 106 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8342 (m-30) REVERT: D 206 MET cc_start: 0.7534 (mtm) cc_final: 0.7332 (mtm) REVERT: D 233 GLN cc_start: 0.6835 (tt0) cc_final: 0.6396 (mm-40) REVERT: D 289 ASP cc_start: 0.6641 (t0) cc_final: 0.6406 (m-30) REVERT: E 268 TYR cc_start: 0.8389 (m-80) cc_final: 0.8099 (m-80) REVERT: F 106 ASP cc_start: 0.8400 (m-30) cc_final: 0.8083 (m-30) REVERT: F 140 TYR cc_start: 0.8355 (m-80) cc_final: 0.7945 (m-80) REVERT: F 273 ASP cc_start: 0.7537 (t0) cc_final: 0.7167 (p0) REVERT: F 297 ASN cc_start: 0.5601 (m-40) cc_final: 0.5201 (t0) outliers start: 36 outliers final: 16 residues processed: 162 average time/residue: 0.5469 time to fit residues: 99.6827 Evaluate side-chains 146 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain F residue 22 MET Chi-restraints excluded: chain F residue 142 ARG Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain F residue 259 ASN Chi-restraints excluded: chain F residue 281 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: [35, 194, 33, 152, 59, 91, 120, 153, 140, 114, 90] chunk 35 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 152 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 GLN B 90 ASN B 250 ASN E 138 GLN E 222 GLN F 250 ASN F 336 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.158124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.113292 restraints weight = 20199.880| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.10 r_work: 0.3033 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17484 Z= 0.126 Angle : 0.456 6.979 23943 Z= 0.250 Chirality : 0.043 0.148 2747 Planarity : 0.003 0.040 2930 Dihedral : 10.196 110.775 2859 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.29 % Allowed : 9.90 % Favored : 87.81 % 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: 2022 helix: 1.31 (0.23), residues: 546 sheet: 0.21 (0.29), residues: 316 loop : -0.07 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 142 TYR 0.026 0.001 TYR C 302 PHE 0.007 0.001 PHE A 32 TRP 0.009 0.001 TRP D 86 HIS 0.003 0.001 HIS F 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (17484) covalent geometry : angle 0.45613 / 0.25 (23943) hydrogen bonds : bond 0.03746 / 2.52 ( 656) hydrogen bonds : angle 4.79167 / 3.41 ( 1914) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 138 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: A 201 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.6846 (mtm110) REVERT: A 327 ASP cc_start: 0.8323 (p0) cc_final: 0.7850 (p0) REVERT: B 322 MET cc_start: 0.5870 (OUTLIER) cc_final: 0.4649 (mmt) REVERT: C 326 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6998 (mp0) REVERT: C 334 TYR cc_start: 0.8344 (p90) cc_final: 0.7844 (p90) REVERT: D 11 LYS cc_start: 0.8147 (mmtt) cc_final: 0.7933 (mmtm) REVERT: D 39 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8085 (mt-10) REVERT: D 106 ASP cc_start: 0.8708 (OUTLIER) cc_final: 0.8357 (m-30) REVERT: D 206 MET cc_start: 0.7666 (mtm) cc_final: 0.7196 (mtm) REVERT: D 233 GLN cc_start: 0.6920 (tt0) cc_final: 0.6453 (mm-40) REVERT: D 322 MET cc_start: 0.6809 (OUTLIER) cc_final: 0.6471 (mmt) REVERT: E 206 MET cc_start: 0.6904 (OUTLIER) cc_final: 0.6491 (ptp) REVERT: E 322 MET cc_start: 0.5329 (mmt) cc_final: 0.4703 (mmm) REVERT: F 106 ASP cc_start: 0.8392 (m-30) cc_final: 0.8044 (m-30) REVERT: F 140 TYR cc_start: 0.8367 (m-80) cc_final: 0.7950 (m-80) REVERT: F 273 ASP cc_start: 0.7506 (t0) cc_final: 0.7148 (p0) REVERT: F 297 ASN cc_start: 0.5507 (m-40) cc_final: 0.5088 (t0) outliers start: 41 outliers final: 14 residues processed: 161 average time/residue: 0.5586 time to fit residues: 100.9942 Evaluate side-chains 154 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain F residue 142 ARG Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain F residue 259 ASN Chi-restraints excluded: chain F residue 281 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: [106, 74, 91, 132, 169, 103, 192, 113, 78, 76, 153] chunk 106 optimal weight: 0.0470 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 132 optimal weight: 9.9990 chunk 169 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 192 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 153 optimal weight: 10.0000 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 250 ASN E 222 GLN F 46 GLN F 250 ASN F 336 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.158732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.114328 restraints weight = 20157.944| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.02 r_work: 0.3099 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17484 Z= 0.102 Angle : 0.438 8.822 23943 Z= 0.240 Chirality : 0.042 0.162 2747 Planarity : 0.003 0.039 2930 Dihedral : 10.163 108.413 2859 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.96 % Allowed : 11.30 % Favored : 86.74 % 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: 0.55 (0.19), residues: 2022 helix: 1.34 (0.23), residues: 549 sheet: 0.33 (0.29), residues: 310 loop : -0.02 (0.18), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 142 TYR 0.023 0.001 TYR A 302 PHE 0.006 0.001 PHE A 32 TRP 0.008 0.001 TRP D 86 HIS 0.003 0.001 HIS C 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (17484) covalent geometry : angle 0.43834 / 0.24 (23943) hydrogen bonds : bond 0.03181 / 2.13 ( 656) hydrogen bonds : angle 4.58560 / 3.26 ( 1914) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: A 201 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7104 (mtm110) REVERT: A 327 ASP cc_start: 0.8328 (p0) cc_final: 0.7887 (p0) REVERT: B 322 MET cc_start: 0.6117 (OUTLIER) cc_final: 0.4807 (mmt) REVERT: C 302 TYR cc_start: 0.6713 (m-80) cc_final: 0.6361 (m-80) REVERT: C 326 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6983 (mp0) REVERT: C 334 TYR cc_start: 0.8475 (p90) cc_final: 0.8013 (p90) REVERT: D 39 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8037 (mt-10) REVERT: D 106 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8383 (m-30) REVERT: D 206 MET cc_start: 0.7676 (mtm) cc_final: 0.7271 (mtm) REVERT: D 233 GLN cc_start: 0.7038 (tt0) cc_final: 0.6591 (mm-40) REVERT: D 322 MET cc_start: 0.6965 (mpt) cc_final: 0.6623 (mmt) REVERT: E 206 MET cc_start: 0.7165 (OUTLIER) cc_final: 0.6689 (ptp) REVERT: F 140 TYR cc_start: 0.8497 (m-80) cc_final: 0.8115 (m-80) REVERT: F 273 ASP cc_start: 0.7540 (t0) cc_final: 0.7202 (p0) REVERT: F 297 ASN cc_start: 0.5575 (m-40) cc_final: 0.5127 (t0) outliers start: 35 outliers final: 18 residues processed: 164 average time/residue: 0.5470 time to fit residues: 100.5202 Evaluate side-chains 148 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain F residue 142 ARG Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain F residue 259 ASN Chi-restraints excluded: chain F residue 281 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: [26, 174, 191, 86, 18, 199, 17, 142, 192, 30, 5] chunk 26 optimal weight: 6.9990 chunk 174 optimal weight: 2.9990 chunk 191 optimal weight: 10.0000 chunk 86 optimal weight: 0.0050 chunk 18 optimal weight: 1.9990 chunk 199 optimal weight: 40.0000 chunk 17 optimal weight: 0.7980 chunk 142 optimal weight: 0.4980 chunk 192 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN A 317 HIS B 238 HIS B 250 ASN E 222 GLN F 250 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.159564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.114530 restraints weight = 20081.103| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.10 r_work: 0.3125 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17484 Z= 0.085 Angle : 0.415 7.281 23943 Z= 0.229 Chirality : 0.041 0.181 2747 Planarity : 0.003 0.038 2930 Dihedral : 10.132 106.895 2859 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.01 % Allowed : 12.19 % Favored : 85.79 % 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: 0.64 (0.19), residues: 2022 helix: 1.41 (0.23), residues: 549 sheet: 0.38 (0.29), residues: 310 loop : 0.04 (0.18), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 142 TYR 0.027 0.001 TYR A 302 PHE 0.008 0.001 PHE A 211 TRP 0.008 0.001 TRP A 324 HIS 0.003 0.001 HIS C 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00190 / 0.09 (17484) covalent geometry : angle 0.41458 / 0.23 (23943) hydrogen bonds : bond 0.02917 / 1.95 ( 656) hydrogen bonds : angle 4.45531 / 3.17 ( 1914) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: A 201 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.6912 (mtm110) REVERT: A 327 ASP cc_start: 0.8343 (p0) cc_final: 0.7924 (p0) REVERT: B 322 MET cc_start: 0.5944 (OUTLIER) cc_final: 0.4695 (mmt) REVERT: C 326 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7061 (mp0) REVERT: C 334 TYR cc_start: 0.8386 (p90) cc_final: 0.8001 (p90) REVERT: D 39 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.8021 (mt-10) REVERT: D 106 ASP cc_start: 0.8709 (OUTLIER) cc_final: 0.8369 (m-30) REVERT: D 206 MET cc_start: 0.7640 (mtm) cc_final: 0.7205 (mtm) REVERT: D 233 GLN cc_start: 0.6984 (tt0) cc_final: 0.6592 (mm-40) REVERT: D 322 MET cc_start: 0.6840 (mpt) cc_final: 0.6486 (mmt) REVERT: E 206 MET cc_start: 0.6927 (OUTLIER) cc_final: 0.6496 (ptp) REVERT: E 322 MET cc_start: 0.5490 (mmt) cc_final: 0.4882 (mmm) REVERT: F 106 ASP cc_start: 0.8393 (m-30) cc_final: 0.7963 (m-30) REVERT: F 140 TYR cc_start: 0.8457 (m-80) cc_final: 0.8078 (m-80) REVERT: F 273 ASP cc_start: 0.7558 (t0) cc_final: 0.7171 (p0) outliers start: 36 outliers final: 19 residues processed: 152 average time/residue: 0.5426 time to fit residues: 92.7011 Evaluate side-chains 149 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 265 MET Chi-restraints excluded: chain F residue 22 MET Chi-restraints excluded: chain F residue 142 ARG Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain F residue 259 ASN Chi-restraints excluded: chain F residue 281 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: [74, 24, 70, 106, 148, 201, 71, 12, 2, 72, 149] chunk 74 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 201 optimal weight: 40.0000 chunk 71 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 250 ASN E 222 GLN F 250 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.158599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.113291 restraints weight = 20093.996| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.12 r_work: 0.3074 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17484 Z= 0.114 Angle : 0.437 8.459 23943 Z= 0.238 Chirality : 0.042 0.141 2747 Planarity : 0.003 0.039 2930 Dihedral : 10.146 105.239 2859 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.07 % Allowed : 12.64 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.19), residues: 2022 helix: 1.40 (0.23), residues: 549 sheet: 0.41 (0.29), residues: 310 loop : 0.03 (0.18), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 142 TYR 0.028 0.001 TYR C 302 PHE 0.007 0.001 PHE F 211 TRP 0.008 0.001 TRP D 86 HIS 0.004 0.001 HIS D 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.11 (17484) covalent geometry : angle 0.43688 / 0.24 (23943) hydrogen bonds : bond 0.03157 / 2.11 ( 656) hydrogen bonds : angle 4.42478 / 3.15 ( 1914) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 126 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 201 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.6947 (mtm110) REVERT: A 327 ASP cc_start: 0.8352 (p0) cc_final: 0.7944 (p0) REVERT: B 322 MET cc_start: 0.5864 (OUTLIER) cc_final: 0.4612 (mmt) REVERT: C 326 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.7069 (mp0) REVERT: C 334 TYR cc_start: 0.8361 (p90) cc_final: 0.7960 (p90) REVERT: D 39 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8044 (mt-10) REVERT: D 106 ASP cc_start: 0.8714 (OUTLIER) cc_final: 0.8361 (m-30) REVERT: D 206 MET cc_start: 0.7640 (mtm) cc_final: 0.7168 (mtm) REVERT: D 233 GLN cc_start: 0.6880 (tt0) cc_final: 0.6504 (mm-40) REVERT: D 300 LYS cc_start: 0.5614 (tttt) cc_final: 0.5329 (tppp) REVERT: D 322 MET cc_start: 0.6829 (mpt) cc_final: 0.6464 (mmt) REVERT: E 141 LYS cc_start: 0.8186 (mmtm) cc_final: 0.7829 (tppt) REVERT: E 151 ASN cc_start: 0.8682 (OUTLIER) cc_final: 0.8206 (p0) REVERT: E 206 MET cc_start: 0.6916 (OUTLIER) cc_final: 0.6459 (ptp) REVERT: E 322 MET cc_start: 0.5291 (mmt) cc_final: 0.4525 (mmm) REVERT: F 140 TYR cc_start: 0.8426 (m-80) cc_final: 0.7962 (m-80) REVERT: F 273 ASP cc_start: 0.7572 (t0) cc_final: 0.7195 (p0) outliers start: 37 outliers final: 20 residues processed: 151 average time/residue: 0.5418 time to fit residues: 91.6117 Evaluate side-chains 150 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain F residue 142 ARG Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain F residue 259 ASN Chi-restraints excluded: chain F residue 281 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: [82, 146, 0, 109, 174, 198, 19, 128, 5, 75, 125] chunk 82 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 198 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 5 optimal weight: 0.2980 chunk 75 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 250 ASN C 155 GLN E 222 GLN F 250 ASN F 336 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.155534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.110622 restraints weight = 20082.785| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.08 r_work: 0.3031 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 17484 Z= 0.228 Angle : 0.545 9.582 23943 Z= 0.290 Chirality : 0.046 0.155 2747 Planarity : 0.004 0.047 2930 Dihedral : 10.284 104.556 2859 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.35 % Allowed : 12.64 % Favored : 85.01 % 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: 0.37 (0.19), residues: 2022 helix: 1.30 (0.23), residues: 541 sheet: 0.22 (0.29), residues: 310 loop : -0.20 (0.18), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 142 TYR 0.035 0.002 TYR C 302 PHE 0.010 0.002 PHE C 32 TRP 0.009 0.002 TRP B 86 HIS 0.007 0.002 HIS D 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.23 (17484) covalent geometry : angle 0.54501 / 0.29 (23943) hydrogen bonds : bond 0.04154 / 2.78 ( 656) hydrogen bonds : angle 4.63142 / 3.29 ( 1914) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 125 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: A 201 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.6906 (mtm110) REVERT: A 322 MET cc_start: 0.6667 (mmm) cc_final: 0.6376 (tpt) REVERT: B 205 ASP cc_start: 0.8112 (m-30) cc_final: 0.7721 (m-30) REVERT: B 322 MET cc_start: 0.5858 (OUTLIER) cc_final: 0.4609 (mmt) REVERT: C 300 LYS cc_start: 0.7270 (ttpt) cc_final: 0.7022 (ttpp) REVERT: D 39 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8112 (mt-10) REVERT: D 106 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.8456 (m-30) REVERT: D 206 MET cc_start: 0.7793 (mtm) cc_final: 0.7431 (mtm) REVERT: D 233 GLN cc_start: 0.6916 (tt0) cc_final: 0.6546 (mm-40) REVERT: D 300 LYS cc_start: 0.5666 (tttt) cc_final: 0.5406 (ttpt) REVERT: D 322 MET cc_start: 0.6936 (OUTLIER) cc_final: 0.6624 (mmt) REVERT: E 151 ASN cc_start: 0.8657 (OUTLIER) cc_final: 0.8163 (p0) REVERT: E 206 MET cc_start: 0.6923 (OUTLIER) cc_final: 0.6366 (ptp) REVERT: E 266 GLN cc_start: 0.7901 (mp10) cc_final: 0.7559 (mt0) REVERT: E 299 LEU cc_start: 0.6329 (OUTLIER) cc_final: 0.5703 (tp) REVERT: F 273 ASP cc_start: 0.7586 (t0) cc_final: 0.7223 (p0) outliers start: 42 outliers final: 22 residues processed: 153 average time/residue: 0.5163 time to fit residues: 89.1260 Evaluate side-chains 151 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain F residue 259 ASN Chi-restraints excluded: chain F residue 281 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: [57, 105, 73, 190, 11, 130, 144, 87, 193, 107, 52] chunk 57 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 190 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 130 optimal weight: 0.0970 chunk 144 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 193 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 250 ASN C 138 GLN E 222 GLN ** E 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 250 ASN F 336 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.157092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.111722 restraints weight = 20116.025| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.09 r_work: 0.3033 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17484 Z= 0.133 Angle : 0.465 8.387 23943 Z= 0.253 Chirality : 0.042 0.165 2747 Planarity : 0.003 0.042 2930 Dihedral : 10.212 104.891 2859 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.79 % Allowed : 13.26 % Favored : 84.96 % 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: 0.45 (0.19), residues: 2022 helix: 1.37 (0.23), residues: 541 sheet: 0.38 (0.29), residues: 310 loop : -0.18 (0.18), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 142 TYR 0.040 0.001 TYR C 302 PHE 0.007 0.001 PHE F 211 TRP 0.008 0.001 TRP D 86 HIS 0.004 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.13 (17484) covalent geometry : angle 0.46508 / 0.25 (23943) hydrogen bonds : bond 0.03362 / 2.25 ( 656) hydrogen bonds : angle 4.50680 / 3.21 ( 1914) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 0.663 Fit side-chains revert: symmetry clash REVERT: A 201 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7044 (mtm110) REVERT: B 36 GLN cc_start: 0.8429 (mm-40) cc_final: 0.8088 (mp10) REVERT: B 205 ASP cc_start: 0.8130 (m-30) cc_final: 0.7755 (m-30) REVERT: B 322 MET cc_start: 0.5943 (OUTLIER) cc_final: 0.4681 (mmt) REVERT: C 300 LYS cc_start: 0.7248 (ttpt) cc_final: 0.6981 (ttpp) REVERT: D 39 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8104 (mt-10) REVERT: D 106 ASP cc_start: 0.8792 (OUTLIER) cc_final: 0.8479 (m-30) REVERT: D 206 MET cc_start: 0.7779 (mtm) cc_final: 0.7391 (mtm) REVERT: D 233 GLN cc_start: 0.6971 (tt0) cc_final: 0.6606 (mm-40) REVERT: D 300 LYS cc_start: 0.5672 (tttt) cc_final: 0.5406 (ttpt) REVERT: D 322 MET cc_start: 0.6941 (mpt) cc_final: 0.6626 (mmt) REVERT: E 151 ASN cc_start: 0.8663 (OUTLIER) cc_final: 0.8156 (p0) REVERT: E 206 MET cc_start: 0.7043 (OUTLIER) cc_final: 0.6571 (ptp) REVERT: E 266 GLN cc_start: 0.7927 (mp10) cc_final: 0.7583 (mt0) REVERT: E 322 MET cc_start: 0.5132 (mmt) cc_final: 0.4433 (mmm) REVERT: F 273 ASP cc_start: 0.7616 (t0) cc_final: 0.7221 (p0) outliers start: 32 outliers final: 20 residues processed: 145 average time/residue: 0.5440 time to fit residues: 88.3500 Evaluate side-chains 147 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain F residue 259 ASN Chi-restraints excluded: chain F residue 281 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: [50, 196, 48, 86, 82, 34, 119, 33, 151, 146, 105] chunk 50 optimal weight: 0.7980 chunk 196 optimal weight: 0.2980 chunk 48 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 250 ASN E 222 GLN F 250 ASN F 317 HIS F 336 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.159129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.113943 restraints weight = 20102.848| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.10 r_work: 0.3079 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17484 Z= 0.084 Angle : 0.424 9.731 23943 Z= 0.231 Chirality : 0.041 0.170 2747 Planarity : 0.003 0.039 2930 Dihedral : 10.088 103.109 2859 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.51 % Allowed : 13.53 % Favored : 84.96 % 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: 0.60 (0.19), residues: 2022 helix: 1.41 (0.24), residues: 545 sheet: 0.41 (0.29), residues: 310 loop : -0.02 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 142 TYR 0.036 0.001 TYR C 302 PHE 0.006 0.001 PHE B 193 TRP 0.009 0.001 TRP D 86 HIS 0.003 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00184 / 0.08 (17484) covalent geometry : angle 0.42380 / 0.23 (23943) hydrogen bonds : bond 0.02785 / 1.86 ( 656) hydrogen bonds : angle 4.34806 / 3.09 ( 1914) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: A 142 ARG cc_start: 0.8760 (ttm110) cc_final: 0.8420 (ttp-110) REVERT: A 201 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.6988 (mtm110) REVERT: B 322 MET cc_start: 0.5910 (OUTLIER) cc_final: 0.4641 (mmt) REVERT: C 300 LYS cc_start: 0.7217 (ttpt) cc_final: 0.6945 (ttpp) REVERT: C 334 TYR cc_start: 0.8459 (p90) cc_final: 0.8065 (p90) REVERT: D 106 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.8400 (m-30) REVERT: D 206 MET cc_start: 0.7728 (mtm) cc_final: 0.7274 (mtm) REVERT: D 233 GLN cc_start: 0.6911 (tt0) cc_final: 0.6412 (mm110) REVERT: D 300 LYS cc_start: 0.5477 (tttt) cc_final: 0.5210 (ttpt) REVERT: D 322 MET cc_start: 0.6832 (mpt) cc_final: 0.6442 (mmt) REVERT: E 206 MET cc_start: 0.7024 (OUTLIER) cc_final: 0.6599 (ptp) REVERT: E 266 GLN cc_start: 0.7943 (mp10) cc_final: 0.7563 (mt0) REVERT: E 322 MET cc_start: 0.5188 (mmt) cc_final: 0.4348 (mmm) REVERT: F 140 TYR cc_start: 0.8450 (m-80) cc_final: 0.8076 (m-80) REVERT: F 273 ASP cc_start: 0.7608 (t0) cc_final: 0.7235 (p0) outliers start: 27 outliers final: 16 residues processed: 144 average time/residue: 0.5629 time to fit residues: 90.7077 Evaluate side-chains 143 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain F residue 259 ASN Chi-restraints excluded: chain F residue 281 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: [77, 152, 166, 44, 38, 51, 111, 41, 139, 11, 61] chunk 77 optimal weight: 0.0010 chunk 152 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 51 optimal weight: 0.0060 chunk 111 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 139 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 overall best weight: 0.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 250 ASN C 317 HIS E 222 GLN E 259 ASN F 250 ASN F 336 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.160364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.115491 restraints weight = 19964.321| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.10 r_work: 0.3119 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17484 Z= 0.075 Angle : 0.414 9.810 23943 Z= 0.227 Chirality : 0.041 0.157 2747 Planarity : 0.003 0.038 2930 Dihedral : 10.002 101.516 2859 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.34 % Allowed : 13.81 % Favored : 84.84 % 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: 0.75 (0.19), residues: 2022 helix: 1.52 (0.24), residues: 545 sheet: 0.47 (0.29), residues: 310 loop : 0.09 (0.19), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 142 TYR 0.034 0.001 TYR C 302 PHE 0.005 0.001 PHE E 269 TRP 0.009 0.001 TRP D 86 HIS 0.003 0.001 HIS C 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00160 / 0.08 (17484) covalent geometry : angle 0.41392 / 0.23 (23943) hydrogen bonds : bond 0.02593 / 1.73 ( 656) hydrogen bonds : angle 4.24601 / 3.02 ( 1914) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: A 142 ARG cc_start: 0.8752 (ttm110) cc_final: 0.8394 (ttp-110) REVERT: A 201 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.6961 (mtm110) REVERT: B 322 MET cc_start: 0.5764 (OUTLIER) cc_final: 0.4499 (mmt) REVERT: C 201 ARG cc_start: 0.7215 (mtm110) cc_final: 0.6636 (mtt-85) REVERT: C 334 TYR cc_start: 0.8384 (p90) cc_final: 0.8019 (p90) REVERT: D 106 ASP cc_start: 0.8710 (OUTLIER) cc_final: 0.8397 (m-30) REVERT: D 233 GLN cc_start: 0.6867 (tt0) cc_final: 0.6371 (mm110) REVERT: D 300 LYS cc_start: 0.5639 (tttt) cc_final: 0.5390 (ttpt) REVERT: D 322 MET cc_start: 0.6745 (mpt) cc_final: 0.6432 (mmt) REVERT: E 206 MET cc_start: 0.6963 (OUTLIER) cc_final: 0.6552 (ptp) REVERT: E 266 GLN cc_start: 0.7920 (mp10) cc_final: 0.7589 (mt0) REVERT: E 322 MET cc_start: 0.5161 (mmt) cc_final: 0.4382 (mmm) REVERT: F 140 TYR cc_start: 0.8420 (m-80) cc_final: 0.7970 (m-80) REVERT: F 273 ASP cc_start: 0.7605 (t0) cc_final: 0.7194 (p0) outliers start: 24 outliers final: 16 residues processed: 141 average time/residue: 0.5599 time to fit residues: 88.6735 Evaluate side-chains 142 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain F residue 259 ASN Chi-restraints excluded: chain F residue 281 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: [129, 90, 157, 34, 186, 153, 2, 103, 77, 63, 173] chunk 129 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 157 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 186 optimal weight: 0.6980 chunk 153 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.2980 chunk 63 optimal weight: 9.9990 chunk 173 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 250 ASN E 222 GLN E 259 ASN F 250 ASN F 336 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.160377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.115768 restraints weight = 20136.962| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.06 r_work: 0.3125 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17484 Z= 0.079 Angle : 0.412 8.362 23943 Z= 0.225 Chirality : 0.041 0.160 2747 Planarity : 0.003 0.039 2930 Dihedral : 9.973 100.618 2859 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.23 % Allowed : 14.09 % Favored : 84.68 % 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: 0.82 (0.19), residues: 2022 helix: 1.58 (0.24), residues: 545 sheet: 0.52 (0.29), residues: 310 loop : 0.14 (0.19), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 142 TYR 0.038 0.001 TYR C 302 PHE 0.005 0.001 PHE E 269 TRP 0.008 0.001 TRP D 86 HIS 0.002 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00176 / 0.08 (17484) covalent geometry : angle 0.41237 / 0.23 (23943) hydrogen bonds : bond 0.02622 / 1.75 ( 656) hydrogen bonds : angle 4.20330 / 2.98 ( 1914) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5142.54 seconds wall clock time: 88 minutes 25.62 seconds (5305.62 seconds total)