Starting phenix.real_space_refine on Sun Oct 25 19:22:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/37uo_78494/10_2026/37uo_78494.cif Found real_map, /net/cci-nas-00/data/ceres_data/37uo_78494/10_2026/37uo_78494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/37uo_78494/10_2026/37uo_78494.map" default_real_map = "/net/cci-nas-00/data/ceres_data/37uo_78494/10_2026/37uo_78494.map" model { file = "/net/cci-nas-00/data/ceres_data/37uo_78494/10_2026/37uo_78494.cif" } default_model = "/net/cci-nas-00/data/ceres_data/37uo_78494/10_2026/37uo_78494.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.046 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 70 5.49 5 S 66 5.16 5 C 10999 2.51 5 N 2911 2.21 5 O 3593 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: 17639 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2694 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain: "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: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'RNA': 16} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 14} Chain: "H" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 387 Classifications: {'RNA': 18} Modifications used: {'rna3p_pur': 13, 'rna3p_pyr': 5} Link IDs: {'rna3p': 17} Chain: "B" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2694 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain: "I" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 356 Classifications: {'RNA': 17} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 6, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 15} Chain: "J" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 407 Classifications: {'RNA': 19} Modifications used: {'rna3p_pur': 13, 'rna3p_pyr': 6} Link IDs: {'rna3p': 18} Time building chain proxies: 4.08, per 1000 atoms: 0.23 Number of scatterers: 17639 At special positions: 0 Unit cell: (111.72, 123.424, 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 70 15.00 O 3593 8.00 N 2911 7.00 C 10999 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: 1.62 Conformation dependent library (CDL) restraints added in 750.0 milliseconds 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3778 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 42 sheets defined 29.3% alpha, 27.0% beta 27 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 1.85 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 '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: 3.592A 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: 3.567A pdb=" N ALA F 249 " --> pdb=" O ARG F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 303 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 75 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 216 Processing helix chain 'B' and resid 220 through 226 Processing helix chain 'B' and resid 239 through 249 removed outlier: 3.582A pdb=" N ALA B 249 " --> pdb=" O ARG B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 302 Processing helix chain 'B' and resid 326 through 329 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 removed outlier: 6.898A pdb=" N VAL A 31 " --> pdb=" O VAL A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 67 Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 99 removed outlier: 6.548A pdb=" N THR A 80 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 5.354A 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: 6.548A pdb=" N THR A 80 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 5.354A 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: 6.279A 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 'C' and resid 24 through 27 removed outlier: 6.864A pdb=" N VAL C 31 " --> pdb=" O VAL C 42 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 66 through 67 Processing sheet with id=AB1, first strand: chain 'C' and resid 98 through 99 removed outlier: 6.795A pdb=" N THR C 80 " --> pdb=" O VAL C 99 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ASP C 117 " --> pdb=" O ASN C 81 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL C 114 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N VAL C 135 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TYR C 116 " --> pdb=" O VAL C 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 98 through 99 removed outlier: 6.795A pdb=" N THR C 80 " --> pdb=" O VAL C 99 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ASP C 117 " --> pdb=" O ASN C 81 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL C 114 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N VAL C 135 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TYR C 116 " --> pdb=" O VAL C 135 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 86 through 87 Processing sheet with id=AB4, 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=AB5, 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=AB6, 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=AB7, first strand: chain 'D' and resid 65 through 67 Processing sheet with id=AB8, first strand: chain 'D' and resid 98 through 99 removed outlier: 6.660A pdb=" N THR D 80 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL D 79 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N ASP D 117 " --> pdb=" O VAL D 79 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N ASN D 81 " --> pdb=" O ASP D 117 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU D 166 " --> pdb=" O ILE D 148 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 98 through 99 removed outlier: 6.660A pdb=" N THR D 80 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL D 79 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N ASP D 117 " --> pdb=" O VAL D 79 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N ASN D 81 " --> pdb=" O ASP D 117 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 86 through 87 Processing sheet with id=AC2, 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=AC3, 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: 5.156A pdb=" N ILE D 330 " --> pdb=" O GLU D 326 " (cutoff:3.500A) Processing sheet with id=AC4, 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=AC5, first strand: chain 'E' and resid 65 through 67 Processing sheet with id=AC6, 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: 5.426A 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=AC7, 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: 5.426A pdb=" N ASP E 117 " --> pdb=" O ASN E 81 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 86 through 87 Processing sheet with id=AC9, 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: 4.283A pdb=" N THR E 282 " --> pdb=" O GLN E 266 " (cutoff:3.500A) removed outlier: 6.112A 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=AD1, 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=AD2, 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=AD3, first strand: chain 'F' and resid 65 through 67 Processing sheet with id=AD4, first strand: chain 'F' and resid 98 through 99 removed outlier: 6.665A pdb=" N THR F 80 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ASP F 117 " --> pdb=" O ASN F 81 " (cutoff:3.500A) removed outlier: 6.424A 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=AD5, first strand: chain 'F' and resid 98 through 99 removed outlier: 6.665A pdb=" N THR F 80 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ASP F 117 " --> pdb=" O ASN F 81 " (cutoff:3.500A) removed outlier: 6.424A 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=AD6, first strand: chain 'F' and resid 86 through 87 Processing sheet with id=AD7, first strand: chain 'F' and resid 252 through 256 removed outlier: 6.419A pdb=" N GLN F 266 " --> pdb=" O THR F 282 " (cutoff:3.500A) removed outlier: 4.069A 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: 3.981A pdb=" N VAL F 280 " --> pdb=" O TYR F 268 " (cutoff:3.500A) Processing sheet with id=AD8, 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: 6.456A pdb=" N GLU F 326 " --> pdb=" O ILE F 330 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ILE F 330 " --> pdb=" O GLU F 326 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 24 through 27 removed outlier: 6.899A pdb=" N VAL B 31 " --> pdb=" O VAL B 42 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 65 through 67 Processing sheet with id=AE2, first strand: chain 'B' and resid 98 through 99 removed outlier: 6.548A pdb=" N THR B 80 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ASP B 117 " --> pdb=" O ASN B 81 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 98 through 99 removed outlier: 6.548A pdb=" N THR B 80 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ASP B 117 " --> pdb=" O ASN B 81 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AE5, first strand: chain 'B' and resid 252 through 256 removed outlier: 6.613A pdb=" N GLN B 266 " --> pdb=" O THR B 282 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR B 282 " --> pdb=" O GLN B 266 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR B 268 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL B 280 " --> pdb=" O TYR B 268 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 307 through 312 removed outlier: 3.502A pdb=" N LYS B 308 " --> pdb=" O THR B 323 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL B 310 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR B 332 " --> pdb=" O TRP B 324 " (cutoff:3.500A) 671 hydrogen bonds defined for protein. 1821 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 61 hydrogen bonds 122 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 3.44 Time building geometry restraints manager: 2.07 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: 5409 1.34 - 1.46: 3628 1.46 - 1.58: 8863 1.58 - 1.70: 134 1.70 - 1.82: 102 Bond restraints: 18136 Sorted by residual: bond pdb=" P A J 15 " pdb=" O5' A J 15 " ideal model delta sigma weight residual 1.593 1.546 0.047 1.00e-02 1.00e+04 2.21e+01 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 2.18e+01 bond pdb=" P G I 9 " pdb=" O5' G I 9 " ideal model delta sigma weight residual 1.593 1.625 -0.032 1.00e-02 1.00e+04 1.05e+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 1.02e+01 bond pdb=" P C J 14 " pdb=" O5' C J 14 " ideal model delta sigma weight residual 1.593 1.618 -0.025 1.00e-02 1.00e+04 6.27e+00 ... (remaining 18131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 24311 1.78 - 3.56: 515 3.56 - 5.33: 68 5.33 - 7.11: 50 7.11 - 8.89: 10 Bond angle restraints: 24954 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 108.20 112.57 -4.37 8.00e-01 1.56e+00 2.98e+01 angle pdb=" O4' U I 8 " pdb=" C1' U I 8 " pdb=" N1 U I 8 " ideal model delta sigma weight residual 108.20 112.47 -4.27 8.00e-01 1.56e+00 2.85e+01 angle pdb=" N LEU C 271 " pdb=" CA LEU C 271 " pdb=" CB LEU C 271 " ideal model delta sigma weight residual 110.90 105.10 5.80 1.56e+00 4.11e-01 1.38e+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=" N1 U I 8 " pdb=" C2 U I 8 " pdb=" O2 U I 8 " ideal model delta sigma weight residual 122.80 125.34 -2.54 7.00e-01 2.04e+00 1.32e+01 ... (remaining 24949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.52: 10043 23.52 - 47.03: 615 47.03 - 70.55: 119 70.55 - 94.07: 28 94.07 - 117.58: 2 Dihedral angle restraints: 10807 sinusoidal: 4864 harmonic: 5943 Sorted by residual: dihedral pdb=" O4' U I 8 " pdb=" C1' U I 8 " pdb=" N1 U I 8 " pdb=" C2 U I 8 " ideal model delta sinusoidal sigma weight residual -128.00 -10.42 -117.58 1 1.70e+01 3.46e-03 4.86e+01 dihedral pdb=" 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 -10.45 -117.55 1 1.70e+01 3.46e-03 4.86e+01 dihedral pdb=" CA TYR E 215 " pdb=" C TYR E 215 " pdb=" N GLY E 216 " pdb=" CA GLY E 216 " ideal model delta harmonic sigma weight residual 180.00 154.69 25.31 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 10804 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 2742 0.115 - 0.231: 106 0.231 - 0.346: 1 0.346 - 0.461: 19 0.461 - 0.577: 18 Chirality restraints: 2886 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 C J 14 " pdb=" OP1 C J 14 " pdb=" OP2 C J 14 " pdb=" O5' C J 14 " both_signs ideal model delta sigma weight residual True 2.41 -2.99 -0.57 2.00e-01 2.50e+01 8.26e+00 chirality pdb=" P G I 17 " pdb=" OP1 G I 17 " pdb=" OP2 G I 17 " pdb=" O5' G I 17 " both_signs ideal model delta sigma weight residual True 2.41 -2.94 -0.53 2.00e-01 2.50e+01 6.96e+00 ... (remaining 2883 not shown) Planarity restraints: 2955 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 215 " -0.064 2.00e-02 2.50e+03 3.36e-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 " -0.045 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 1.88e-02 3.54e+00 pdb=" C TYR E 215 " 0.033 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 delta sigma weight rms_deltas residual plane pdb=" C1' U G 6 " -0.020 2.00e-02 2.50e+03 1.03e-02 2.41e+00 pdb=" N1 U G 6 " 0.023 2.00e-02 2.50e+03 pdb=" C2 U G 6 " 0.001 2.00e-02 2.50e+03 pdb=" O2 U G 6 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U G 6 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U G 6 " -0.002 2.00e-02 2.50e+03 pdb=" O4 U G 6 " -0.006 2.00e-02 2.50e+03 pdb=" C5 U G 6 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U G 6 " 0.004 2.00e-02 2.50e+03 ... (remaining 2952 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 5331 2.83 - 3.35: 14744 3.35 - 3.86: 28635 3.86 - 4.38: 34091 4.38 - 4.90: 57680 Nonbonded interactions: 140481 Sorted by model distance: nonbonded pdb=" OE2 GLU A 39 " pdb=" NH1 ARG B 96 " model vdw 2.310 3.120 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 ARG B 201 " pdb=" OD2 ASP B 205 " model vdw 2.414 3.040 nonbonded pdb=" O ASN F 259 " pdb=" OD1 ASN F 259 " model vdw 2.436 3.040 ... (remaining 140476 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' } ncs_group { reference = chain 'G' selection = (chain 'I' and resid 5 through 20) } ncs_group { reference = chain 'H' selection = (chain 'J' and resid 1 through 18) } 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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.320 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18136 Z= 0.242 Angle : 0.650 8.891 24954 Z= 0.392 Chirality : 0.071 0.577 2886 Planarity : 0.003 0.050 2955 Dihedral : 15.571 117.584 7029 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % 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: 2021 helix: 1.83 (0.25), residues: 508 sheet: -0.13 (0.27), residues: 373 loop : -0.32 (0.19), residues: 1140 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 0.004 0.001 PHE E 211 TRP 0.003 0.001 TRP D 86 HIS 0.002 0.001 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.24 (18136) covalent geometry : angle 0.64959 / 0.39 (24954) hydrogen bonds : bond 0.18921 / 12.78 ( 674) hydrogen bonds : angle 7.12148 / 4.83 ( 1943) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 MET cc_start: 0.8501 (mmm) cc_final: 0.8293 (mmm) REVERT: C 38 VAL cc_start: 0.8860 (t) cc_final: 0.8615 (m) REVERT: D 209 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6675 (pm20) REVERT: D 334 TYR cc_start: 0.6017 (p90) cc_final: 0.5799 (p90) REVERT: F 106 ASP cc_start: 0.8289 (m-30) cc_final: 0.7922 (m-30) REVERT: F 138 GLN cc_start: 0.7213 (mm-40) cc_final: 0.6931 (mt0) REVERT: F 243 MET cc_start: 0.5099 (ttp) cc_final: 0.4891 (ttp) REVERT: F 293 GLU cc_start: 0.4865 (tt0) cc_final: 0.4523 (tp30) REVERT: F 314 ILE cc_start: 0.5999 (mt) cc_final: 0.5773 (tt) REVERT: B 92 THR cc_start: 0.8610 (m) cc_final: 0.8401 (p) REVERT: B 122 ASP cc_start: 0.8561 (m-30) cc_final: 0.8144 (m-30) REVERT: B 250 ASN cc_start: 0.8319 (m-40) cc_final: 0.7959 (t0) outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.1446 time to fit residues: 69.3759 Evaluate side-chains 170 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [98, 194, 107, 10, 66, 130, 124, 103, 200, 77, 122] chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 50.0000 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 4.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 ASN C 222 GLN C 317 HIS D 4 ASN D 62 ASN D 222 GLN E 4 ASN E 156 ASN E 274 ASN F 69 ASN F 90 ASN F 110 ASN F 184 ASN F 317 HIS B 4 ASN B 110 ASN B 165 ASN B 336 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.179464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.129356 restraints weight = 24687.374| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.52 r_work: 0.3257 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18136 Z= 0.215 Angle : 0.601 7.526 24954 Z= 0.326 Chirality : 0.047 0.176 2886 Planarity : 0.004 0.035 2955 Dihedral : 12.238 112.081 3257 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.85 % Allowed : 10.46 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.19), residues: 2021 helix: 1.26 (0.23), residues: 543 sheet: 0.14 (0.26), residues: 367 loop : -0.29 (0.19), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 142 TYR 0.021 0.002 TYR E 190 PHE 0.024 0.002 PHE E 211 TRP 0.012 0.002 TRP A 86 HIS 0.005 0.002 HIS E 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.21 (18136) covalent geometry : angle 0.60066 / 0.33 (24954) hydrogen bonds : bond 0.04707 / 3.14 ( 674) hydrogen bonds : angle 5.16654 / 3.50 ( 1943) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 9 MET cc_start: 0.8854 (mmm) cc_final: 0.8632 (mmm) REVERT: D 62 ASN cc_start: 0.7727 (OUTLIER) cc_final: 0.7318 (t0) REVERT: D 209 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6754 (pm20) REVERT: D 259 ASN cc_start: 0.7495 (p0) cc_final: 0.7130 (p0) REVERT: D 279 GLN cc_start: 0.7151 (tt0) cc_final: 0.6577 (mt0) REVERT: E 96 ARG cc_start: 0.6287 (ttm110) cc_final: 0.5877 (ttm110) REVERT: E 156 ASN cc_start: 0.7830 (OUTLIER) cc_final: 0.7489 (t0) REVERT: F 138 GLN cc_start: 0.7241 (mm-40) cc_final: 0.6720 (mt0) REVERT: F 243 MET cc_start: 0.4774 (ttp) cc_final: 0.4448 (ttp) REVERT: F 245 ARG cc_start: 0.5871 (tpt-90) cc_final: 0.4284 (tpp-160) REVERT: B 250 ASN cc_start: 0.8494 (OUTLIER) cc_final: 0.8012 (t0) REVERT: B 252 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8948 (tt) outliers start: 33 outliers final: 14 residues processed: 194 average time/residue: 0.1356 time to fit residues: 40.0130 Evaluate side-chains 156 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 252 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [192, 111, 34, 165, 45, 29, 20, 123, 13, 84, 18] chunk 192 optimal weight: 0.8980 chunk 111 optimal weight: 9.9990 chunk 34 optimal weight: 0.6980 chunk 165 optimal weight: 50.0000 chunk 45 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 123 optimal weight: 20.0000 chunk 13 optimal weight: 4.9990 chunk 84 optimal weight: 0.0370 chunk 18 optimal weight: 6.9990 overall best weight: 1.5262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN D 62 ASN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 ASN E 156 ASN F 68 ASN F 110 ASN F 238 HIS F 279 GLN B 186 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.179400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.130290 restraints weight = 25096.221| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.56 r_work: 0.3268 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18136 Z= 0.126 Angle : 0.481 6.451 24954 Z= 0.264 Chirality : 0.042 0.144 2886 Planarity : 0.003 0.035 2955 Dihedral : 12.120 111.314 3257 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.40 % Allowed : 11.70 % Favored : 86.91 % 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: 0.39 (0.19), residues: 2021 helix: 1.28 (0.23), residues: 548 sheet: 0.10 (0.28), residues: 317 loop : -0.12 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 64 TYR 0.021 0.001 TYR E 190 PHE 0.010 0.001 PHE F 211 TRP 0.007 0.001 TRP D 324 HIS 0.008 0.001 HIS F 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (18136) covalent geometry : angle 0.48066 / 0.26 (24954) hydrogen bonds : bond 0.03681 / 2.45 ( 674) hydrogen bonds : angle 4.79094 / 3.25 ( 1943) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 9 MET cc_start: 0.8833 (mmm) cc_final: 0.8621 (mmm) REVERT: D 209 GLU cc_start: 0.7388 (mt-10) cc_final: 0.6840 (pm20) REVERT: D 279 GLN cc_start: 0.7018 (tt0) cc_final: 0.6680 (mt0) REVERT: D 334 TYR cc_start: 0.5607 (p90) cc_final: 0.4820 (p90) REVERT: E 96 ARG cc_start: 0.6180 (ttm110) cc_final: 0.5754 (ttm110) REVERT: E 156 ASN cc_start: 0.7917 (OUTLIER) cc_final: 0.7303 (t0) REVERT: E 206 MET cc_start: 0.7181 (ppp) cc_final: 0.6647 (ppp) REVERT: E 243 MET cc_start: 0.6975 (mtm) cc_final: 0.6764 (mtt) REVERT: E 321 PHE cc_start: 0.6047 (m-80) cc_final: 0.5665 (m-80) REVERT: F 138 GLN cc_start: 0.7167 (mm-40) cc_final: 0.6686 (mt0) REVERT: F 243 MET cc_start: 0.4618 (ttp) cc_final: 0.4253 (ttp) REVERT: F 245 ARG cc_start: 0.5862 (tpt-90) cc_final: 0.4283 (tpp-160) REVERT: B 250 ASN cc_start: 0.8465 (OUTLIER) cc_final: 0.8076 (t0) outliers start: 25 outliers final: 17 residues processed: 162 average time/residue: 0.1338 time to fit residues: 33.0287 Evaluate side-chains 157 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 250 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [69, 91, 93, 159, 7, 105, 171, 191, 187, 89, 81] chunk 69 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 159 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 chunk 191 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 89 optimal weight: 0.1980 chunk 81 optimal weight: 9.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 36 GLN C 222 GLN ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN F 68 ASN F 110 ASN ** F 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.178518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.128668 restraints weight = 24975.437| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.48 r_work: 0.3257 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18136 Z= 0.137 Angle : 0.471 6.469 24954 Z= 0.257 Chirality : 0.041 0.143 2886 Planarity : 0.003 0.036 2955 Dihedral : 12.080 110.214 3257 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.73 % Allowed : 12.42 % Favored : 85.84 % 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: 0.40 (0.19), residues: 2021 helix: 1.31 (0.23), residues: 548 sheet: 0.06 (0.28), residues: 319 loop : -0.11 (0.19), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 61 TYR 0.021 0.001 TYR E 190 PHE 0.012 0.001 PHE E 203 TRP 0.006 0.001 TRP A 86 HIS 0.013 0.001 HIS F 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (18136) covalent geometry : angle 0.47064 / 0.26 (24954) hydrogen bonds : bond 0.03445 / 2.30 ( 674) hydrogen bonds : angle 4.61852 / 3.12 ( 1943) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 MET cc_start: 0.7061 (mmm) cc_final: 0.6652 (mmm) REVERT: C 9 MET cc_start: 0.8810 (mmm) cc_final: 0.8601 (mmm) REVERT: D 209 GLU cc_start: 0.7389 (mt-10) cc_final: 0.6828 (pm20) REVERT: D 273 ASP cc_start: 0.6470 (m-30) cc_final: 0.5747 (t0) REVERT: D 279 GLN cc_start: 0.7052 (tt0) cc_final: 0.6586 (mt0) REVERT: D 334 TYR cc_start: 0.5619 (p90) cc_final: 0.4817 (p90) REVERT: E 156 ASN cc_start: 0.7890 (OUTLIER) cc_final: 0.7361 (t0) REVERT: E 204 LEU cc_start: 0.5353 (OUTLIER) cc_final: 0.5135 (mp) REVERT: E 206 MET cc_start: 0.7270 (ppp) cc_final: 0.6899 (ppp) REVERT: F 108 GLU cc_start: 0.6818 (tp30) cc_final: 0.6525 (tp30) REVERT: F 138 GLN cc_start: 0.7286 (mm-40) cc_final: 0.6840 (mt0) REVERT: F 243 MET cc_start: 0.4885 (ttp) cc_final: 0.4530 (ttp) REVERT: F 245 ARG cc_start: 0.5776 (tpt-90) cc_final: 0.4181 (tpp-160) REVERT: F 293 GLU cc_start: 0.4152 (tt0) cc_final: 0.3851 (tp30) REVERT: B 250 ASN cc_start: 0.8491 (OUTLIER) cc_final: 0.8114 (t0) outliers start: 31 outliers final: 20 residues processed: 169 average time/residue: 0.1310 time to fit residues: 33.8057 Evaluate side-chains 164 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 250 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [43, 167, 131, 8, 143, 31, 132, 134, 144, 36, 9] chunk 43 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 144 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 62 ASN ** D 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 ASN F 110 ASN ** F 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.177190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.127043 restraints weight = 24889.321| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.51 r_work: 0.3250 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 18136 Z= 0.164 Angle : 0.491 7.192 24954 Z= 0.266 Chirality : 0.042 0.141 2886 Planarity : 0.004 0.040 2955 Dihedral : 12.085 109.079 3257 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.07 % Allowed : 12.42 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.19), residues: 2021 helix: 1.27 (0.23), residues: 548 sheet: -0.14 (0.28), residues: 329 loop : -0.13 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 119 TYR 0.021 0.001 TYR E 190 PHE 0.013 0.001 PHE E 203 TRP 0.006 0.001 TRP D 324 HIS 0.009 0.001 HIS F 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.16 (18136) covalent geometry : angle 0.49106 / 0.27 (24954) hydrogen bonds : bond 0.03539 / 2.37 ( 674) hydrogen bonds : angle 4.57781 / 3.09 ( 1943) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 LYS cc_start: 0.8339 (mtmt) cc_final: 0.8113 (mtpt) REVERT: D 209 GLU cc_start: 0.7435 (mt-10) cc_final: 0.6820 (pm20) REVERT: D 273 ASP cc_start: 0.6526 (m-30) cc_final: 0.5843 (t0) REVERT: D 279 GLN cc_start: 0.7062 (tt0) cc_final: 0.6529 (mt0) REVERT: D 334 TYR cc_start: 0.5579 (p90) cc_final: 0.4756 (p90) REVERT: E 204 LEU cc_start: 0.5275 (OUTLIER) cc_final: 0.5032 (mp) REVERT: F 108 GLU cc_start: 0.6828 (tp30) cc_final: 0.6458 (tp30) REVERT: F 138 GLN cc_start: 0.7392 (mm-40) cc_final: 0.6972 (mt0) REVERT: F 243 MET cc_start: 0.4954 (ttp) cc_final: 0.4604 (ttp) REVERT: F 245 ARG cc_start: 0.5739 (tpt-90) cc_final: 0.4124 (tpp-160) outliers start: 37 outliers final: 28 residues processed: 174 average time/residue: 0.1282 time to fit residues: 34.6768 Evaluate side-chains 168 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 182 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [87, 33, 179, 176, 165, 36, 53, 46, 43, 57, 77] chunk 87 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 179 optimal weight: 0.9980 chunk 176 optimal weight: 5.9990 chunk 165 optimal weight: 50.0000 chunk 36 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 36 GLN C 90 ASN ** D 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN F 68 ASN ** F 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.176724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.126254 restraints weight = 24698.809| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.40 r_work: 0.3245 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 18136 Z= 0.159 Angle : 0.488 8.337 24954 Z= 0.263 Chirality : 0.042 0.143 2886 Planarity : 0.004 0.036 2955 Dihedral : 12.071 108.376 3257 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.24 % Allowed : 12.87 % Favored : 84.89 % 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: 0.30 (0.19), residues: 2021 helix: 1.24 (0.23), residues: 553 sheet: -0.18 (0.28), residues: 331 loop : -0.13 (0.19), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 64 TYR 0.022 0.001 TYR E 190 PHE 0.014 0.001 PHE E 203 TRP 0.006 0.001 TRP A 86 HIS 0.006 0.001 HIS F 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (18136) covalent geometry : angle 0.48837 / 0.26 (24954) hydrogen bonds : bond 0.03485 / 2.34 ( 674) hydrogen bonds : angle 4.53142 / 3.06 ( 1943) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 322 MET cc_start: 0.7088 (mmm) cc_final: 0.6568 (mmm) REVERT: C 205 ASP cc_start: 0.8458 (m-30) cc_final: 0.8239 (m-30) REVERT: D 122 ASP cc_start: 0.7803 (m-30) cc_final: 0.6917 (p0) REVERT: D 209 GLU cc_start: 0.7499 (mt-10) cc_final: 0.6847 (pm20) REVERT: D 273 ASP cc_start: 0.6655 (OUTLIER) cc_final: 0.6227 (t0) REVERT: D 279 GLN cc_start: 0.7077 (tt0) cc_final: 0.6498 (mt0) REVERT: D 334 TYR cc_start: 0.5605 (p90) cc_final: 0.4757 (p90) REVERT: E 156 ASN cc_start: 0.8112 (OUTLIER) cc_final: 0.7545 (t0) REVERT: E 161 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7936 (mtmm) REVERT: E 204 LEU cc_start: 0.5350 (OUTLIER) cc_final: 0.5084 (mp) REVERT: F 108 GLU cc_start: 0.6888 (tp30) cc_final: 0.6628 (tp30) REVERT: F 138 GLN cc_start: 0.7390 (mm-40) cc_final: 0.7008 (mt0) REVERT: F 243 MET cc_start: 0.4960 (ttp) cc_final: 0.4618 (ttp) REVERT: F 245 ARG cc_start: 0.5796 (tpt-90) cc_final: 0.4170 (tpp-160) outliers start: 40 outliers final: 29 residues processed: 177 average time/residue: 0.1233 time to fit residues: 33.7627 Evaluate side-chains 174 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 182 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [131, 56, 105, 119, 111, 34, 99, 114, 66, 116, 158] chunk 131 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 119 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 99 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 158 optimal weight: 20.0000 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 ASN ** F 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.175058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.124279 restraints weight = 24744.313| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.40 r_work: 0.3214 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 18136 Z= 0.215 Angle : 0.537 9.002 24954 Z= 0.287 Chirality : 0.043 0.153 2886 Planarity : 0.004 0.037 2955 Dihedral : 12.099 107.900 3257 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.57 % Allowed : 13.15 % Favored : 84.28 % 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: 0.13 (0.19), residues: 2021 helix: 1.14 (0.23), residues: 553 sheet: -0.22 (0.25), residues: 386 loop : -0.27 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 70 TYR 0.022 0.002 TYR E 190 PHE 0.012 0.002 PHE F 55 TRP 0.007 0.001 TRP A 86 HIS 0.005 0.002 HIS A 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.21 (18136) covalent geometry : angle 0.53705 / 0.29 (24954) hydrogen bonds : bond 0.03880 / 2.62 ( 674) hydrogen bonds : angle 4.61116 / 3.12 ( 1943) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 147 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: A 322 MET cc_start: 0.7222 (mmm) cc_final: 0.7012 (mmt) REVERT: D 122 ASP cc_start: 0.7799 (m-30) cc_final: 0.6813 (p0) REVERT: D 209 GLU cc_start: 0.7476 (mt-10) cc_final: 0.6822 (pm20) REVERT: D 273 ASP cc_start: 0.6854 (OUTLIER) cc_final: 0.6297 (t0) REVERT: D 279 GLN cc_start: 0.7210 (tt0) cc_final: 0.6706 (mt0) REVERT: D 323 THR cc_start: 0.8073 (OUTLIER) cc_final: 0.7586 (t) REVERT: D 334 TYR cc_start: 0.5602 (p90) cc_final: 0.4743 (p90) REVERT: E 204 LEU cc_start: 0.5335 (OUTLIER) cc_final: 0.5044 (mp) REVERT: E 206 MET cc_start: 0.7236 (OUTLIER) cc_final: 0.6608 (ppp) REVERT: E 219 LEU cc_start: 0.6510 (OUTLIER) cc_final: 0.6249 (mt) REVERT: F 108 GLU cc_start: 0.7049 (tp30) cc_final: 0.6808 (tp30) REVERT: F 138 GLN cc_start: 0.7389 (mm-40) cc_final: 0.7027 (mt0) REVERT: F 243 MET cc_start: 0.5120 (ttp) cc_final: 0.4715 (ttp) REVERT: F 245 ARG cc_start: 0.5912 (tpt-90) cc_final: 0.4161 (tpp-160) REVERT: B 243 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8688 (mtm) REVERT: B 331 LYS cc_start: 0.7834 (tttt) cc_final: 0.7574 (ttpp) outliers start: 46 outliers final: 34 residues processed: 178 average time/residue: 0.1162 time to fit residues: 32.7047 Evaluate side-chains 183 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 143 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 243 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [157, 66, 53, 44, 74, 76, 184, 68, 174, 180, 11] chunk 157 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 74 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 184 optimal weight: 0.0050 chunk 68 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 HIS C 131 ASN ** D 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 ASN F 238 HIS ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.178409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.128672 restraints weight = 24740.907| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.43 r_work: 0.3265 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18136 Z= 0.083 Angle : 0.443 11.215 24954 Z= 0.242 Chirality : 0.040 0.150 2886 Planarity : 0.003 0.035 2955 Dihedral : 11.952 107.352 3257 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.34 % Allowed : 14.49 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.19), residues: 2021 helix: 1.36 (0.24), residues: 548 sheet: -0.05 (0.30), residues: 291 loop : -0.21 (0.19), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 96 TYR 0.016 0.001 TYR E 190 PHE 0.014 0.001 PHE E 203 TRP 0.008 0.001 TRP F 86 HIS 0.003 0.001 HIS F 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00175 / 0.08 (18136) covalent geometry : angle 0.44342 / 0.24 (24954) hydrogen bonds : bond 0.02825 / 1.88 ( 674) hydrogen bonds : angle 4.35713 / 2.96 ( 1943) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 322 MET cc_start: 0.7103 (mmm) cc_final: 0.6606 (mmm) REVERT: D 122 ASP cc_start: 0.7807 (m-30) cc_final: 0.6884 (p0) REVERT: D 209 GLU cc_start: 0.7525 (mt-10) cc_final: 0.6844 (pm20) REVERT: D 273 ASP cc_start: 0.6528 (m-30) cc_final: 0.6175 (t0) REVERT: D 279 GLN cc_start: 0.7090 (tt0) cc_final: 0.6598 (mt0) REVERT: D 323 THR cc_start: 0.8104 (OUTLIER) cc_final: 0.7715 (t) REVERT: D 334 TYR cc_start: 0.5670 (p90) cc_final: 0.4773 (p90) REVERT: E 204 LEU cc_start: 0.5427 (OUTLIER) cc_final: 0.5131 (mp) REVERT: E 206 MET cc_start: 0.7428 (OUTLIER) cc_final: 0.6642 (ppp) REVERT: F 108 GLU cc_start: 0.7066 (tp30) cc_final: 0.6809 (tp30) REVERT: F 138 GLN cc_start: 0.7358 (mm-40) cc_final: 0.7032 (mt0) REVERT: F 230 ASP cc_start: 0.4391 (p0) cc_final: 0.3935 (m-30) REVERT: F 243 MET cc_start: 0.5360 (ttp) cc_final: 0.4999 (ttp) outliers start: 24 outliers final: 16 residues processed: 175 average time/residue: 0.1265 time to fit residues: 34.8201 Evaluate side-chains 162 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain F residue 238 HIS Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain B residue 92 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [155, 97, 165, 136, 83, 181, 66, 148, 16, 19, 151] chunk 155 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 165 optimal weight: 50.0000 chunk 136 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 181 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 148 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 151 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.175074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.125305 restraints weight = 24675.592| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.43 r_work: 0.3213 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 18136 Z= 0.220 Angle : 0.544 11.526 24954 Z= 0.290 Chirality : 0.043 0.145 2886 Planarity : 0.004 0.037 2955 Dihedral : 11.993 106.738 3257 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.57 % Allowed : 15.00 % Favored : 83.44 % 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: 0.12 (0.19), residues: 2021 helix: 1.20 (0.23), residues: 553 sheet: -0.09 (0.26), residues: 344 loop : -0.39 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 70 TYR 0.035 0.002 TYR A 302 PHE 0.017 0.002 PHE F 126 TRP 0.006 0.001 TRP D 324 HIS 0.044 0.003 HIS F 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.22 (18136) covalent geometry : angle 0.54393 / 0.29 (24954) hydrogen bonds : bond 0.03813 / 2.57 ( 674) hydrogen bonds : angle 4.51506 / 3.06 ( 1943) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: A 302 TYR cc_start: 0.8070 (m-10) cc_final: 0.7779 (m-10) REVERT: D 122 ASP cc_start: 0.7778 (m-30) cc_final: 0.6795 (p0) REVERT: D 209 GLU cc_start: 0.7512 (mt-10) cc_final: 0.6836 (pm20) REVERT: D 273 ASP cc_start: 0.6677 (OUTLIER) cc_final: 0.6207 (t0) REVERT: D 279 GLN cc_start: 0.7228 (tt0) cc_final: 0.6746 (mt0) REVERT: D 323 THR cc_start: 0.8153 (OUTLIER) cc_final: 0.7711 (t) REVERT: E 204 LEU cc_start: 0.5343 (OUTLIER) cc_final: 0.5020 (mp) REVERT: E 206 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6367 (ppp) REVERT: E 210 SER cc_start: 0.7912 (m) cc_final: 0.7331 (t) REVERT: F 138 GLN cc_start: 0.7365 (mm-40) cc_final: 0.6989 (mt0) REVERT: F 243 MET cc_start: 0.5272 (ttp) cc_final: 0.4892 (ttp) REVERT: F 245 ARG cc_start: 0.5922 (tpt-90) cc_final: 0.4209 (tpp-160) outliers start: 28 outliers final: 19 residues processed: 165 average time/residue: 0.1201 time to fit residues: 31.6219 Evaluate side-chains 163 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain B residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [58, 66, 169, 195, 177, 162, 11, 13, 40, 68, 180] chunk 58 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 chunk 195 optimal weight: 0.7980 chunk 177 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 180 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.176369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.125638 restraints weight = 24450.880| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.38 r_work: 0.3233 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18136 Z= 0.137 Angle : 0.489 12.755 24954 Z= 0.262 Chirality : 0.041 0.153 2886 Planarity : 0.003 0.035 2955 Dihedral : 11.950 106.913 3257 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.34 % Allowed : 15.33 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.19), residues: 2021 helix: 1.23 (0.23), residues: 553 sheet: -0.08 (0.26), residues: 344 loop : -0.35 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 70 TYR 0.022 0.001 TYR A 302 PHE 0.010 0.001 PHE E 203 TRP 0.008 0.001 TRP D 324 HIS 0.010 0.001 HIS F 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (18136) covalent geometry : angle 0.48880 / 0.26 (24954) hydrogen bonds : bond 0.03283 / 2.21 ( 674) hydrogen bonds : angle 4.42274 / 3.00 ( 1943) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: D 122 ASP cc_start: 0.7566 (m-30) cc_final: 0.6740 (p0) REVERT: D 209 GLU cc_start: 0.7524 (mt-10) cc_final: 0.6829 (pm20) REVERT: D 273 ASP cc_start: 0.6655 (m-30) cc_final: 0.6269 (t0) REVERT: D 279 GLN cc_start: 0.7160 (tt0) cc_final: 0.6703 (mt0) REVERT: D 323 THR cc_start: 0.8141 (OUTLIER) cc_final: 0.7714 (t) REVERT: D 331 LYS cc_start: 0.6121 (tptt) cc_final: 0.5682 (mmmt) REVERT: E 204 LEU cc_start: 0.5369 (OUTLIER) cc_final: 0.5045 (mp) REVERT: E 206 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.6379 (ppp) REVERT: E 210 SER cc_start: 0.7954 (m) cc_final: 0.7337 (t) REVERT: F 138 GLN cc_start: 0.7404 (mm-40) cc_final: 0.7040 (mt0) REVERT: F 243 MET cc_start: 0.5416 (ttp) cc_final: 0.5043 (ttp) REVERT: F 245 ARG cc_start: 0.5920 (tpt-90) cc_final: 0.4198 (tpp-160) outliers start: 24 outliers final: 19 residues processed: 161 average time/residue: 0.1240 time to fit residues: 31.5235 Evaluate side-chains 163 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [21, 58, 36, 69, 158, 3, 197, 42, 113, 136, 184] chunk 21 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 197 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 113 optimal weight: 8.9990 chunk 136 optimal weight: 0.9980 chunk 184 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.175547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.125128 restraints weight = 24703.074| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.43 r_work: 0.3216 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18136 Z= 0.168 Angle : 0.516 12.272 24954 Z= 0.275 Chirality : 0.042 0.169 2886 Planarity : 0.004 0.035 2955 Dihedral : 11.949 106.789 3257 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.62 % Allowed : 15.05 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.19), residues: 2021 helix: 1.20 (0.23), residues: 553 sheet: -0.08 (0.26), residues: 342 loop : -0.42 (0.19), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 70 TYR 0.018 0.001 TYR E 190 PHE 0.010 0.001 PHE B 269 TRP 0.007 0.001 TRP D 324 HIS 0.005 0.001 HIS F 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (18136) covalent geometry : angle 0.51615 / 0.28 (24954) hydrogen bonds : bond 0.03566 / 2.40 ( 674) hydrogen bonds : angle 4.46420 / 3.03 ( 1943) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4243.02 seconds wall clock time: 73 minutes 17.81 seconds (4397.81 seconds total)