Starting phenix.real_space_refine on Fri Jul 3 13:55:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fyc_29564/07_2026/8fyc_29564.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fyc_29564/07_2026/8fyc_29564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fyc_29564/07_2026/8fyc_29564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fyc_29564/07_2026/8fyc_29564.map" model { file = "/net/cci-nas-00/data/ceres_data/8fyc_29564/07_2026/8fyc_29564.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fyc_29564/07_2026/8fyc_29564.cif" } resolution = 4.1 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= 0.017 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 143 5.49 5 S 34 5.16 5 C 8774 2.51 5 N 2623 2.21 5 O 3001 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14575 Number of models: 1 Model: "" Number of chains: 11 Chain: "K" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1314 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 3, 'TRANS': 160} Chain: "J" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 881 Classifications: {'DNA': 43} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 42} Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 746 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "A" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 746 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "B" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2295 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 11, 'TRANS': 280} Chain: "C" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2423 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain: "E" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2295 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 11, 'TRANS': 280} Chain: "F" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1770 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 1 Chain: "G" Number of atoms: 1187 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 57, 1165 Classifications: {'DNA': 57} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 56} Conformer: "B" Number of residues, atoms: 57, 1165 Classifications: {'DNA': 57} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 56} bond proxies already assigned to first conformer: 1279 Chain: "H" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 632 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Chain: "I" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 286 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P A DG G 29 " occ=0.74 ... (42 atoms not shown) pdb=" C4 B DG G 29 " occ=0.26 Time building chain proxies: 2.87, per 1000 atoms: 0.20 Number of scatterers: 14575 At special positions: 0 Unit cell: (107.04, 95.89, 157.215, 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 34 16.00 P 143 15.00 O 3001 8.00 N 2623 7.00 C 8774 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: 1.00 Conformation dependent library (CDL) restraints added in 574.7 milliseconds 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2724 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 9 sheets defined 50.2% alpha, 13.7% beta 44 base pairs and 103 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'K' and resid 171 through 178 Processing helix chain 'K' and resid 181 through 189 Processing helix chain 'K' and resid 191 through 203 Processing helix chain 'K' and resid 212 through 228 removed outlier: 3.929A pdb=" N ASP K 216 " --> pdb=" O HIS K 212 " (cutoff:3.500A) Processing helix chain 'K' and resid 238 through 246 removed outlier: 3.922A pdb=" N ILE K 242 " --> pdb=" O ASP K 238 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU K 246 " --> pdb=" O ILE K 242 " (cutoff:3.500A) Processing helix chain 'K' and resid 254 through 262 Processing helix chain 'K' and resid 271 through 287 Processing helix chain 'D' and resid 12 through 19 Processing helix chain 'D' and resid 20 through 22 No H-bonds generated for 'chain 'D' and resid 20 through 22' Processing helix chain 'D' and resid 36 through 51 removed outlier: 4.057A pdb=" N GLU D 41 " --> pdb=" O SER D 37 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR D 42 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET D 51 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 19 Processing helix chain 'A' and resid 20 through 22 No H-bonds generated for 'chain 'A' and resid 20 through 22' Processing helix chain 'A' and resid 36 through 49 removed outlier: 3.577A pdb=" N GLU A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 77 removed outlier: 3.755A pdb=" N THR B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 89 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 102 through 114 Processing helix chain 'B' and resid 114 through 129 removed outlier: 3.532A pdb=" N ARG B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 163 removed outlier: 3.533A pdb=" N ARG B 144 " --> pdb=" O MET B 140 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER B 145 " --> pdb=" O GLN B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 205 removed outlier: 3.938A pdb=" N LEU B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 227 Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 250 through 265 removed outlier: 4.337A pdb=" N ASP B 265 " --> pdb=" O ASP B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 280 removed outlier: 4.380A pdb=" N GLN B 277 " --> pdb=" O VAL B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 298 through 303 removed outlier: 3.642A pdb=" N VAL B 303 " --> pdb=" O LYS B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'C' and resid 17 through 21 removed outlier: 3.883A pdb=" N ARG C 21 " --> pdb=" O VAL C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 55 Processing helix chain 'C' and resid 68 through 77 removed outlier: 3.897A pdb=" N THR C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 114 removed outlier: 3.910A pdb=" N ASN C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 130 removed outlier: 3.572A pdb=" N ARG C 129 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 141 No H-bonds generated for 'chain 'C' and resid 139 through 141' Processing helix chain 'C' and resid 142 through 163 Processing helix chain 'C' and resid 180 through 205 removed outlier: 3.693A pdb=" N GLN C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA C 192 " --> pdb=" O ALA C 188 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU C 193 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA C 202 " --> pdb=" O HIS C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 231 removed outlier: 3.748A pdb=" N TYR C 223 " --> pdb=" O ARG C 219 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA C 231 " --> pdb=" O ASP C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 245 Processing helix chain 'C' and resid 250 through 266 removed outlier: 3.722A pdb=" N ARG C 260 " --> pdb=" O ARG C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 281 Processing helix chain 'E' and resid 68 through 77 removed outlier: 4.483A pdb=" N LEU E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.799A pdb=" N ARG E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 114 removed outlier: 3.954A pdb=" N LYS E 107 " --> pdb=" O ARG E 103 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL E 112 " --> pdb=" O GLN E 108 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 130 Processing helix chain 'E' and resid 139 through 162 removed outlier: 3.761A pdb=" N LYS E 160 " --> pdb=" O ARG E 156 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS E 161 " --> pdb=" O GLU E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 205 removed outlier: 4.077A pdb=" N GLN E 184 " --> pdb=" O ASP E 180 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU E 196 " --> pdb=" O ALA E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 224 Processing helix chain 'E' and resid 226 through 231 removed outlier: 4.625A pdb=" N ALA E 231 " --> pdb=" O ASP E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 244 Processing helix chain 'E' and resid 250 through 265 removed outlier: 4.199A pdb=" N ASP E 265 " --> pdb=" O ASP E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 280 Processing helix chain 'E' and resid 298 through 303 Processing helix chain 'F' and resid 51 through 53 No H-bonds generated for 'chain 'F' and resid 51 through 53' Processing helix chain 'F' and resid 68 through 78 removed outlier: 3.560A pdb=" N THR F 77 " --> pdb=" O LEU F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 114 removed outlier: 3.704A pdb=" N ASN F 114 " --> pdb=" O GLU F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 130 removed outlier: 3.753A pdb=" N GLN F 127 " --> pdb=" O ARG F 123 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N MET F 128 " --> pdb=" O ARG F 124 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG F 129 " --> pdb=" O MET F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 204 Processing helix chain 'F' and resid 219 through 226 Processing helix chain 'F' and resid 226 through 231 removed outlier: 4.306A pdb=" N ALA F 231 " --> pdb=" O ASP F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 244 Processing helix chain 'F' and resid 250 through 267 removed outlier: 3.534A pdb=" N ARG F 256 " --> pdb=" O GLY F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 280 removed outlier: 4.024A pdb=" N VAL F 273 " --> pdb=" O LEU F 269 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS F 274 " --> pdb=" O LYS F 270 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 161 through 164 removed outlier: 3.655A pdb=" N PHE K 161 " --> pdb=" O ALA K 150 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU K 147 " --> pdb=" O GLU K 134 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU K 134 " --> pdb=" O GLU K 147 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR K 128 " --> pdb=" O CYS K 153 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N VAL K 129 " --> pdb=" O VAL K 209 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 24 through 25 removed outlier: 4.485A pdb=" N ALA D 56 " --> pdb=" O GLU D 73 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU D 73 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE D 60 " --> pdb=" O ASP D 69 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP D 69 " --> pdb=" O PHE D 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 78 through 81 removed outlier: 5.591A pdb=" N ILE D 88 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ARG C 49 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER C 67 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ARG C 34 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA B 30 " --> pdb=" O ASP B 65 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N SER B 67 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE B 32 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY B 46 " --> pdb=" O GLU B 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 24 through 27 removed outlier: 5.679A pdb=" N GLU A 25 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL A 32 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA A 27 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A 56 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 78 through 82 removed outlier: 6.773A pdb=" N ARG F 34 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N ILE E 32 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 289 through 291 removed outlier: 7.773A pdb=" N VAL B 57 " --> pdb=" O ARG B 21 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N THR B 23 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU B 59 " --> pdb=" O THR B 23 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE B 25 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL B 82 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LEU B 81 " --> pdb=" O GLY B 95 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY C 88 " --> pdb=" O GLY C 85 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY C 85 " --> pdb=" O GLY C 88 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N TRP C 83 " --> pdb=" O ARG C 90 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N TYR C 92 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU C 81 " --> pdb=" O TYR C 92 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU C 58 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N VAL C 84 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LEU C 60 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE C 25 " --> pdb=" O LEU C 59 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 214 through 215 Processing sheet with id=AA8, first strand: chain 'E' and resid 289 through 292 removed outlier: 6.293A pdb=" N ALA E 22 " --> pdb=" O GLU E 291 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N VAL E 57 " --> pdb=" O ARG E 21 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N THR E 23 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU E 59 " --> pdb=" O THR E 23 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE E 25 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU E 58 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL E 84 " --> pdb=" O LEU E 58 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LEU E 60 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEU E 81 " --> pdb=" O GLY E 95 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR F 91 " --> pdb=" O TRP F 83 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU F 81 " --> pdb=" O ALA F 93 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL F 82 " --> pdb=" O LEU F 58 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N THR F 23 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU F 59 " --> pdb=" O THR F 23 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE F 25 " --> pdb=" O LEU F 59 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 47 through 48 568 hydrogen bonds defined for protein. 1635 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 104 hydrogen bonds 196 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 103 stacking parallelities Total time for adding SS restraints: 2.39 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2152 1.32 - 1.44: 4712 1.44 - 1.57: 7932 1.57 - 1.69: 286 1.69 - 1.82: 64 Bond restraints: 15146 Sorted by residual: bond pdb=" C ASP E 250 " pdb=" O ASP E 250 " ideal model delta sigma weight residual 1.234 1.311 -0.077 1.14e-02 7.69e+03 4.55e+01 bond pdb=" C SER C 159 " pdb=" O SER C 159 " ideal model delta sigma weight residual 1.236 1.192 0.044 1.15e-02 7.56e+03 1.47e+01 bond pdb=" N THR B 102 " pdb=" CA THR B 102 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.06e-02 8.90e+03 1.30e+01 bond pdb=" C3' DC G 24 " pdb=" C2' DC G 24 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" C3' DA G 43 " pdb=" C2' DA G 43 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 ... (remaining 15141 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 19978 1.62 - 3.24: 995 3.24 - 4.86: 106 4.86 - 6.49: 26 6.49 - 8.11: 5 Bond angle restraints: 21110 Sorted by residual: angle pdb=" C ARG E 260 " pdb=" CA ARG E 260 " pdb=" CB ARG E 260 " ideal model delta sigma weight residual 110.79 102.68 8.11 1.66e+00 3.63e-01 2.39e+01 angle pdb=" N GLU C 147 " pdb=" CA GLU C 147 " pdb=" C GLU C 147 " ideal model delta sigma weight residual 111.28 105.98 5.30 1.09e+00 8.42e-01 2.36e+01 angle pdb=" N SER C 159 " pdb=" CA SER C 159 " pdb=" C SER C 159 " ideal model delta sigma weight residual 111.07 106.33 4.74 1.07e+00 8.73e-01 1.96e+01 angle pdb=" N TYR C 155 " pdb=" CA TYR C 155 " pdb=" C TYR C 155 " ideal model delta sigma weight residual 111.07 106.47 4.60 1.07e+00 8.73e-01 1.85e+01 angle pdb=" CA LYS C 160 " pdb=" C LYS C 160 " pdb=" O LYS C 160 " ideal model delta sigma weight residual 120.82 116.37 4.45 1.05e+00 9.07e-01 1.79e+01 ... (remaining 21105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 8083 35.72 - 71.45: 594 71.45 - 107.17: 21 107.17 - 142.90: 4 142.90 - 178.62: 4 Dihedral angle restraints: 8706 sinusoidal: 4458 harmonic: 4248 Sorted by residual: dihedral pdb=" C ARG E 260 " pdb=" N ARG E 260 " pdb=" CA ARG E 260 " pdb=" CB ARG E 260 " ideal model delta harmonic sigma weight residual -122.60 -111.60 -11.00 0 2.50e+00 1.60e-01 1.94e+01 dihedral pdb=" CA THR C 139 " pdb=" C THR C 139 " pdb=" N MET C 140 " pdb=" CA MET C 140 " ideal model delta harmonic sigma weight residual 180.00 -160.20 -19.80 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" C4' DA J 31 " pdb=" C3' DA J 31 " pdb=" O3' DA J 31 " pdb=" P DA J 32 " ideal model delta sinusoidal sigma weight residual 220.00 41.38 178.62 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 8703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1978 0.066 - 0.132: 357 0.132 - 0.199: 33 0.199 - 0.265: 10 0.265 - 0.331: 1 Chirality restraints: 2379 Sorted by residual: chirality pdb=" CA ARG E 260 " pdb=" N ARG E 260 " pdb=" C ARG E 260 " pdb=" CB ARG E 260 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CA TYR C 155 " pdb=" N TYR C 155 " pdb=" C TYR C 155 " pdb=" CB TYR C 155 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA LYS F 9 " pdb=" N LYS F 9 " pdb=" C LYS F 9 " pdb=" CB LYS F 9 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 2376 not shown) Planarity restraints: 2203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 159 " -0.025 2.00e-02 2.50e+03 5.06e-02 2.56e+01 pdb=" C SER C 159 " 0.087 2.00e-02 2.50e+03 pdb=" O SER C 159 " -0.033 2.00e-02 2.50e+03 pdb=" N LYS C 160 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 249 " -0.019 2.00e-02 2.50e+03 3.88e-02 1.51e+01 pdb=" C GLN E 249 " 0.067 2.00e-02 2.50e+03 pdb=" O GLN E 249 " -0.025 2.00e-02 2.50e+03 pdb=" N ASP E 250 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 250 " 0.014 2.00e-02 2.50e+03 2.83e-02 8.02e+00 pdb=" C ASP E 250 " -0.049 2.00e-02 2.50e+03 pdb=" O ASP E 250 " 0.018 2.00e-02 2.50e+03 pdb=" N ILE E 251 " 0.017 2.00e-02 2.50e+03 ... (remaining 2200 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1245 2.74 - 3.28: 15722 3.28 - 3.82: 27656 3.82 - 4.36: 31538 4.36 - 4.90: 48790 Nonbonded interactions: 124951 Sorted by model distance: nonbonded pdb=" O GLY D 17 " pdb=" OG1 THR D 20 " model vdw 2.196 3.040 nonbonded pdb=" OH TYR E 223 " pdb=" N2 DG G 27 " model vdw 2.229 3.120 nonbonded pdb=" NH1 ARG E 34 " pdb=" O ARG E 69 " model vdw 2.229 3.120 nonbonded pdb=" OH TYR C 229 " pdb=" OD2 ASP C 275 " model vdw 2.231 3.040 nonbonded pdb=" O ARG C 256 " pdb=" OG1 THR C 259 " model vdw 2.233 3.040 ... (remaining 124946 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = (chain 'C' and resid 20 through 311) selection = chain 'E' } 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=0.26 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.870 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 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 : 0.005 0.077 15146 Z= 0.411 Angle : 0.750 8.108 21110 Z= 0.565 Chirality : 0.051 0.331 2379 Planarity : 0.004 0.051 2203 Dihedral : 20.674 178.623 5982 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.22 % Favored : 96.71 % Rotamer: Outliers : 0.25 % Allowed : 1.16 % Favored : 98.60 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.21), residues: 1459 helix: 0.48 (0.21), residues: 624 sheet: -0.95 (0.34), residues: 211 loop : -1.00 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 116 TYR 0.012 0.001 TYR F 91 PHE 0.019 0.001 PHE K 224 TRP 0.017 0.002 TRP A 44 HIS 0.005 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.41 (15146) covalent geometry : angle 0.74968 / 0.56 (21110) hydrogen bonds : bond 0.29180 / 20.13 ( 672) hydrogen bonds : angle 8.80156 / 7.04 ( 1831) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 301 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 271 ARG cc_start: 0.7809 (mtt180) cc_final: 0.7533 (mmt180) REVERT: D 69 ASP cc_start: 0.8191 (t70) cc_final: 0.7957 (t70) REVERT: A 49 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8269 (mt-10) REVERT: B 81 LEU cc_start: 0.8752 (tt) cc_final: 0.8507 (tt) REVERT: B 86 GLU cc_start: 0.8038 (tp30) cc_final: 0.7832 (tp30) REVERT: B 141 GLN cc_start: 0.9381 (tm-30) cc_final: 0.8875 (tm-30) REVERT: B 163 ASN cc_start: 0.8846 (m-40) cc_final: 0.8543 (m-40) REVERT: B 217 HIS cc_start: 0.9200 (t-90) cc_final: 0.8844 (t70) REVERT: C 156 ARG cc_start: 0.9251 (mtt180) cc_final: 0.8567 (tpp80) REVERT: C 197 VAL cc_start: 0.8996 (t) cc_final: 0.8762 (p) REVERT: C 253 GLN cc_start: 0.7502 (tm-30) cc_final: 0.7148 (tp40) REVERT: C 282 ILE cc_start: 0.9182 (mm) cc_final: 0.8981 (mm) REVERT: C 295 LEU cc_start: 0.9372 (mm) cc_final: 0.9144 (mm) REVERT: E 69 ARG cc_start: 0.7745 (tpm170) cc_final: 0.7099 (tpm170) REVERT: E 272 MET cc_start: 0.9143 (mpp) cc_final: 0.8934 (mpp) REVERT: F 114 ASN cc_start: 0.9107 (m110) cc_final: 0.8903 (t0) REVERT: F 125 MET cc_start: 0.8866 (ttt) cc_final: 0.8263 (tmm) REVERT: F 190 HIS cc_start: 0.7674 (m170) cc_final: 0.7452 (m-70) outliers start: 3 outliers final: 0 residues processed: 301 average time/residue: 0.1228 time to fit residues: 53.1580 Evaluate side-chains 223 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 186 GLN ** K 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 222 GLN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN F 127 GLN F 183 ASN F 184 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.099312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.076946 restraints weight = 74008.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.079046 restraints weight = 43361.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.080321 restraints weight = 30671.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.081286 restraints weight = 24641.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.081802 restraints weight = 21297.000| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3584 r_free = 0.3584 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3584 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15146 Z= 0.199 Angle : 0.690 9.866 21110 Z= 0.397 Chirality : 0.047 0.294 2379 Planarity : 0.005 0.047 2203 Dihedral : 23.958 178.761 3215 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.21), residues: 1459 helix: 0.38 (0.19), residues: 665 sheet: -1.24 (0.33), residues: 218 loop : -1.24 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 129 TYR 0.025 0.002 TYR C 126 PHE 0.022 0.002 PHE K 202 TRP 0.011 0.001 TRP D 44 HIS 0.005 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.20 (15146) covalent geometry : angle 0.69017 / 0.40 (21110) hydrogen bonds : bond 0.09029 / 6.11 ( 672) hydrogen bonds : angle 5.62147 / 4.01 ( 1831) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 148 ILE cc_start: 0.9257 (mt) cc_final: 0.9002 (mt) REVERT: K 271 ARG cc_start: 0.7929 (mtt180) cc_final: 0.7636 (mmt180) REVERT: D 69 ASP cc_start: 0.8293 (t70) cc_final: 0.8025 (t70) REVERT: A 45 ARG cc_start: 0.8529 (tpp80) cc_final: 0.8159 (mmm-85) REVERT: A 49 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8678 (mm-30) REVERT: B 83 TRP cc_start: 0.8956 (m100) cc_final: 0.8674 (m100) REVERT: B 125 MET cc_start: 0.8655 (mpp) cc_final: 0.8423 (mpp) REVERT: B 141 GLN cc_start: 0.9323 (tm-30) cc_final: 0.9042 (tm-30) REVERT: B 163 ASN cc_start: 0.8862 (m-40) cc_final: 0.8581 (m-40) REVERT: B 186 LEU cc_start: 0.9160 (tt) cc_final: 0.8946 (tt) REVERT: B 217 HIS cc_start: 0.9191 (t-90) cc_final: 0.8810 (t70) REVERT: C 184 GLN cc_start: 0.9166 (pm20) cc_final: 0.8825 (pm20) REVERT: C 282 ILE cc_start: 0.9197 (mm) cc_final: 0.8946 (mm) REVERT: E 69 ARG cc_start: 0.7659 (tpm170) cc_final: 0.7268 (tpm170) REVERT: E 83 TRP cc_start: 0.8325 (m-90) cc_final: 0.8034 (m-90) REVERT: E 272 MET cc_start: 0.9144 (mpp) cc_final: 0.8881 (mpp) REVERT: F 15 LEU cc_start: 0.9313 (mt) cc_final: 0.9082 (mt) REVERT: F 128 MET cc_start: 0.6477 (pmm) cc_final: 0.6252 (pmm) REVERT: F 190 HIS cc_start: 0.7428 (m170) cc_final: 0.7159 (m-70) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.1228 time to fit residues: 50.2476 Evaluate side-chains 214 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 55 optimal weight: 4.9990 chunk 158 optimal weight: 40.0000 chunk 143 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 124 optimal weight: 0.1980 chunk 132 optimal weight: 0.7980 chunk 87 optimal weight: 0.4980 chunk 105 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 222 GLN ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS C 253 GLN ** F 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 ASN F 184 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.100673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.078534 restraints weight = 67467.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.080593 restraints weight = 40202.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.081959 restraints weight = 28448.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.082749 restraints weight = 22744.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.083345 restraints weight = 19942.139| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 15146 Z= 0.163 Angle : 0.653 8.221 21110 Z= 0.371 Chirality : 0.046 0.239 2379 Planarity : 0.005 0.075 2203 Dihedral : 24.264 179.659 3215 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.21), residues: 1459 helix: 0.51 (0.19), residues: 667 sheet: -1.19 (0.34), residues: 209 loop : -1.33 (0.23), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG K 241 TYR 0.019 0.002 TYR K 231 PHE 0.023 0.002 PHE E 239 TRP 0.012 0.001 TRP D 44 HIS 0.006 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.16 (15146) covalent geometry : angle 0.65270 / 0.37 (21110) hydrogen bonds : bond 0.07156 / 4.73 ( 672) hydrogen bonds : angle 5.18185 / 3.68 ( 1831) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 271 ARG cc_start: 0.7946 (mtt180) cc_final: 0.7556 (mmt180) REVERT: D 69 ASP cc_start: 0.8305 (t70) cc_final: 0.7977 (t70) REVERT: A 20 THR cc_start: 0.9106 (p) cc_final: 0.8789 (t) REVERT: B 83 TRP cc_start: 0.9011 (m100) cc_final: 0.8803 (m100) REVERT: B 134 ASP cc_start: 0.8978 (m-30) cc_final: 0.8271 (t0) REVERT: B 141 GLN cc_start: 0.9391 (tm-30) cc_final: 0.9080 (tm-30) REVERT: B 217 HIS cc_start: 0.9243 (t-90) cc_final: 0.8907 (t70) REVERT: C 190 HIS cc_start: 0.7934 (m90) cc_final: 0.7722 (m170) REVERT: C 282 ILE cc_start: 0.9127 (mm) cc_final: 0.8869 (mm) REVERT: E 83 TRP cc_start: 0.8409 (m-90) cc_final: 0.7756 (m-90) REVERT: E 260 ARG cc_start: 0.8894 (ptt90) cc_final: 0.8550 (ptt90) REVERT: F 15 LEU cc_start: 0.9283 (mt) cc_final: 0.9066 (mt) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.1135 time to fit residues: 47.3053 Evaluate side-chains 214 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 107 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 222 GLN K 237 HIS ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN C 214 HIS C 253 GLN F 33 ASN ** F 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 ASN F 184 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.098576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.076596 restraints weight = 71037.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.078516 restraints weight = 42882.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.079834 restraints weight = 30634.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.080527 restraints weight = 24681.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.081056 restraints weight = 21760.185| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3562 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 15146 Z= 0.217 Angle : 0.679 6.812 21110 Z= 0.382 Chirality : 0.045 0.250 2379 Planarity : 0.005 0.147 2203 Dihedral : 24.493 177.782 3215 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.21), residues: 1459 helix: 0.33 (0.19), residues: 672 sheet: -1.56 (0.32), residues: 217 loop : -1.37 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 241 TYR 0.015 0.002 TYR C 126 PHE 0.018 0.002 PHE K 202 TRP 0.013 0.002 TRP D 44 HIS 0.006 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.22 (15146) covalent geometry : angle 0.67935 / 0.38 (21110) hydrogen bonds : bond 0.07124 / 4.61 ( 672) hydrogen bonds : angle 5.06114 / 3.58 ( 1831) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 220 LEU cc_start: 0.6310 (tt) cc_final: 0.6087 (tt) REVERT: K 271 ARG cc_start: 0.8132 (mtt180) cc_final: 0.7750 (mmt180) REVERT: D 41 GLU cc_start: 0.8638 (mp0) cc_final: 0.8347 (mp0) REVERT: D 51 MET cc_start: 0.8142 (ptm) cc_final: 0.7849 (ptm) REVERT: D 69 ASP cc_start: 0.8397 (t70) cc_final: 0.8006 (t70) REVERT: A 20 THR cc_start: 0.9183 (p) cc_final: 0.8892 (t) REVERT: B 83 TRP cc_start: 0.9027 (m100) cc_final: 0.8801 (m100) REVERT: B 134 ASP cc_start: 0.8989 (m-30) cc_final: 0.8134 (t0) REVERT: B 137 LYS cc_start: 0.9545 (mppt) cc_final: 0.9311 (mmtm) REVERT: B 217 HIS cc_start: 0.9187 (t-90) cc_final: 0.8825 (t70) REVERT: C 141 GLN cc_start: 0.8953 (mp10) cc_final: 0.8718 (mp10) REVERT: C 282 ILE cc_start: 0.9200 (mm) cc_final: 0.8753 (mm) REVERT: E 69 ARG cc_start: 0.7535 (tpm170) cc_final: 0.7239 (tpm170) REVERT: E 128 MET cc_start: 0.8933 (tpp) cc_final: 0.8620 (tpp) REVERT: E 272 MET cc_start: 0.9164 (mpp) cc_final: 0.8960 (mpp) REVERT: F 15 LEU cc_start: 0.9273 (mt) cc_final: 0.9047 (mt) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.1134 time to fit residues: 44.0338 Evaluate side-chains 208 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 143 optimal weight: 10.0000 chunk 147 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 18 optimal weight: 30.0000 chunk 52 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 222 GLN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN ** C 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.094747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.072211 restraints weight = 101132.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.074375 restraints weight = 53554.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.075811 restraints weight = 35810.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.076744 restraints weight = 27798.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.077285 restraints weight = 23639.956| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3480 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3480 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 15146 Z= 0.344 Angle : 0.810 12.713 21110 Z= 0.447 Chirality : 0.049 0.250 2379 Planarity : 0.006 0.127 2203 Dihedral : 24.840 174.945 3215 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 26.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.08 % Allowed : 5.45 % Favored : 94.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.20), residues: 1459 helix: -0.12 (0.19), residues: 670 sheet: -1.85 (0.32), residues: 217 loop : -1.65 (0.23), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG D 77 TYR 0.022 0.002 TYR C 162 PHE 0.045 0.003 PHE B 24 TRP 0.012 0.002 TRP C 83 HIS 0.006 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00704 / 0.34 (15146) covalent geometry : angle 0.81048 / 0.45 (21110) hydrogen bonds : bond 0.08602 / 5.57 ( 672) hydrogen bonds : angle 5.37955 / 3.79 ( 1831) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 239 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 158 GLU cc_start: 0.6787 (mp0) cc_final: 0.6552 (mp0) REVERT: K 271 ARG cc_start: 0.8187 (mtt180) cc_final: 0.7778 (mmt180) REVERT: D 41 GLU cc_start: 0.8632 (mp0) cc_final: 0.7939 (mp0) REVERT: D 63 ARG cc_start: 0.8266 (mmt180) cc_final: 0.7563 (mmm160) REVERT: D 69 ASP cc_start: 0.8493 (t70) cc_final: 0.8023 (t70) REVERT: D 70 PHE cc_start: 0.8383 (m-10) cc_final: 0.8177 (m-10) REVERT: A 20 THR cc_start: 0.9155 (p) cc_final: 0.8882 (t) REVERT: B 134 ASP cc_start: 0.9118 (m-30) cc_final: 0.8332 (t0) REVERT: B 217 HIS cc_start: 0.9203 (t-90) cc_final: 0.8900 (t70) REVERT: C 141 GLN cc_start: 0.9031 (mp10) cc_final: 0.8808 (mp10) REVERT: C 156 ARG cc_start: 0.9139 (mpt-90) cc_final: 0.8917 (mpp80) REVERT: E 128 MET cc_start: 0.8956 (tpp) cc_final: 0.8724 (tpp) REVERT: F 15 LEU cc_start: 0.9376 (mt) cc_final: 0.9128 (mt) REVERT: F 198 HIS cc_start: 0.8322 (t-90) cc_final: 0.7905 (t-90) outliers start: 1 outliers final: 1 residues processed: 240 average time/residue: 0.1117 time to fit residues: 39.6200 Evaluate side-chains 194 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 141 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 ASN ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 ASN ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 GLN ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN ** F 184 GLN ** 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 = 0.3983 r_free = 0.3983 target = 0.099538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.076046 restraints weight = 104630.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.078528 restraints weight = 52900.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.080184 restraints weight = 34215.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.081317 restraints weight = 26097.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.081988 restraints weight = 21828.941| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15146 Z= 0.159 Angle : 0.684 10.942 21110 Z= 0.377 Chirality : 0.047 0.260 2379 Planarity : 0.005 0.110 2203 Dihedral : 24.814 179.522 3215 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.21), residues: 1459 helix: 0.21 (0.19), residues: 672 sheet: -1.70 (0.32), residues: 223 loop : -1.44 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 241 TYR 0.020 0.002 TYR C 126 PHE 0.023 0.002 PHE K 224 TRP 0.017 0.002 TRP D 44 HIS 0.005 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 (15146) covalent geometry : angle 0.68361 / 0.38 (21110) hydrogen bonds : bond 0.06052 / 3.97 ( 672) hydrogen bonds : angle 4.84696 / 3.40 ( 1831) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 142 ARG cc_start: 0.6432 (mtt180) cc_final: 0.4211 (mtm110) REVERT: K 220 LEU cc_start: 0.6281 (tt) cc_final: 0.5980 (tt) REVERT: K 271 ARG cc_start: 0.8233 (mtt180) cc_final: 0.7798 (mmt180) REVERT: D 4 THR cc_start: 0.8033 (t) cc_final: 0.7761 (t) REVERT: D 21 ARG cc_start: 0.8539 (ttm110) cc_final: 0.7935 (ttm110) REVERT: D 38 ARG cc_start: 0.8589 (tmm-80) cc_final: 0.8105 (tmm-80) REVERT: D 41 GLU cc_start: 0.8626 (mp0) cc_final: 0.7966 (mp0) REVERT: A 20 THR cc_start: 0.9101 (p) cc_final: 0.8833 (t) REVERT: B 84 VAL cc_start: 0.8120 (m) cc_final: 0.6876 (m) REVERT: B 134 ASP cc_start: 0.9080 (m-30) cc_final: 0.8298 (t0) REVERT: B 217 HIS cc_start: 0.9157 (t-90) cc_final: 0.8805 (t70) REVERT: C 141 GLN cc_start: 0.9034 (mp10) cc_final: 0.8809 (mp10) REVERT: C 156 ARG cc_start: 0.9127 (mtt180) cc_final: 0.8775 (tpp80) REVERT: C 160 LYS cc_start: 0.9294 (mptt) cc_final: 0.9049 (mmtt) REVERT: C 190 HIS cc_start: 0.7901 (m90) cc_final: 0.7624 (m170) REVERT: E 258 ARG cc_start: 0.9495 (mmt180) cc_final: 0.9248 (tpp80) REVERT: F 15 LEU cc_start: 0.9349 (mt) cc_final: 0.9112 (mt) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.1220 time to fit residues: 45.0724 Evaluate side-chains 203 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 113 optimal weight: 8.9990 chunk 153 optimal weight: 30.0000 chunk 31 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 14 optimal weight: 30.0000 chunk 84 optimal weight: 0.9990 chunk 150 optimal weight: 20.0000 chunk 114 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 222 GLN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN F 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.098639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.076668 restraints weight = 72905.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.078573 restraints weight = 43127.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.079937 restraints weight = 30625.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.080763 restraints weight = 24433.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.081106 restraints weight = 21259.459| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3563 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3563 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15146 Z= 0.187 Angle : 0.672 8.876 21110 Z= 0.374 Chirality : 0.045 0.254 2379 Planarity : 0.005 0.072 2203 Dihedral : 24.823 179.754 3215 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.21), residues: 1459 helix: 0.26 (0.19), residues: 671 sheet: -1.65 (0.31), residues: 223 loop : -1.44 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 241 TYR 0.022 0.002 TYR C 126 PHE 0.019 0.002 PHE K 224 TRP 0.040 0.002 TRP B 83 HIS 0.007 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.19 (15146) covalent geometry : angle 0.67156 / 0.37 (21110) hydrogen bonds : bond 0.06282 / 4.07 ( 672) hydrogen bonds : angle 4.77181 / 3.34 ( 1831) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 142 ARG cc_start: 0.6239 (mtt180) cc_final: 0.4317 (mtm180) REVERT: K 220 LEU cc_start: 0.6391 (tt) cc_final: 0.6082 (tt) REVERT: K 271 ARG cc_start: 0.8268 (mtt180) cc_final: 0.7791 (mmt180) REVERT: D 38 ARG cc_start: 0.8651 (tmm-80) cc_final: 0.8386 (tmm-80) REVERT: D 41 GLU cc_start: 0.8469 (mp0) cc_final: 0.8164 (mp0) REVERT: D 69 ASP cc_start: 0.8080 (t70) cc_final: 0.7863 (t0) REVERT: A 20 THR cc_start: 0.9153 (p) cc_final: 0.8919 (t) REVERT: B 84 VAL cc_start: 0.8191 (m) cc_final: 0.7281 (m) REVERT: B 134 ASP cc_start: 0.9059 (m-30) cc_final: 0.8328 (t0) REVERT: B 163 ASN cc_start: 0.8973 (m-40) cc_final: 0.8753 (m-40) REVERT: B 217 HIS cc_start: 0.9152 (t-90) cc_final: 0.8804 (t70) REVERT: C 156 ARG cc_start: 0.9109 (mtt180) cc_final: 0.8715 (tpp80) REVERT: C 160 LYS cc_start: 0.9265 (mptt) cc_final: 0.9035 (mmtt) REVERT: C 190 HIS cc_start: 0.8124 (m90) cc_final: 0.7874 (m170) REVERT: E 258 ARG cc_start: 0.9516 (mmt180) cc_final: 0.9277 (tpp80) REVERT: F 15 LEU cc_start: 0.9306 (mt) cc_final: 0.9103 (mt) REVERT: F 19 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7595 (mm-30) REVERT: F 128 MET cc_start: 0.7272 (pmm) cc_final: 0.7068 (pmm) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.1157 time to fit residues: 41.1047 Evaluate side-chains 201 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 52 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 chunk 155 optimal weight: 20.0000 chunk 156 optimal weight: 20.0000 chunk 150 optimal weight: 20.0000 chunk 147 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 90 optimal weight: 0.0000 chunk 22 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 overall best weight: 1.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN E 249 GLN F 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.099774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.077193 restraints weight = 82560.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.079379 restraints weight = 45891.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.080829 restraints weight = 31349.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.081757 restraints weight = 24617.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.082278 restraints weight = 21103.440| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3590 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3590 r_free = 0.3590 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3590 r_free = 0.3590 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3590 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15146 Z= 0.161 Angle : 0.660 6.872 21110 Z= 0.368 Chirality : 0.045 0.255 2379 Planarity : 0.005 0.104 2203 Dihedral : 24.817 179.823 3215 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.21), residues: 1459 helix: 0.35 (0.19), residues: 673 sheet: -1.54 (0.32), residues: 223 loop : -1.42 (0.24), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 69 TYR 0.025 0.002 TYR E 229 PHE 0.020 0.002 PHE K 224 TRP 0.063 0.002 TRP B 83 HIS 0.008 0.001 HIS C 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 (15146) covalent geometry : angle 0.65953 / 0.37 (21110) hydrogen bonds : bond 0.05873 / 3.79 ( 672) hydrogen bonds : angle 4.69549 / 3.30 ( 1831) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 142 ARG cc_start: 0.6251 (mtt180) cc_final: 0.4347 (mtm180) REVERT: K 151 ILE cc_start: 0.4696 (tp) cc_final: 0.4440 (tp) REVERT: K 220 LEU cc_start: 0.6438 (tt) cc_final: 0.6104 (tt) REVERT: K 271 ARG cc_start: 0.8338 (mtt180) cc_final: 0.7851 (mmt180) REVERT: D 38 ARG cc_start: 0.8612 (tmm-80) cc_final: 0.8344 (tmm-80) REVERT: D 41 GLU cc_start: 0.8442 (mp0) cc_final: 0.8107 (mp0) REVERT: D 69 ASP cc_start: 0.8033 (t70) cc_final: 0.7816 (t0) REVERT: A 58 MET cc_start: 0.8097 (mtp) cc_final: 0.7704 (mtp) REVERT: B 84 VAL cc_start: 0.8215 (m) cc_final: 0.7207 (m) REVERT: B 134 ASP cc_start: 0.9060 (m-30) cc_final: 0.8335 (t0) REVERT: B 163 ASN cc_start: 0.8956 (m-40) cc_final: 0.8730 (m-40) REVERT: B 217 HIS cc_start: 0.9145 (t-90) cc_final: 0.8842 (t70) REVERT: C 156 ARG cc_start: 0.9118 (mtt180) cc_final: 0.8701 (tpp80) REVERT: C 160 LYS cc_start: 0.9287 (mptt) cc_final: 0.9048 (mmtt) REVERT: C 190 HIS cc_start: 0.8107 (m90) cc_final: 0.7871 (m170) REVERT: E 258 ARG cc_start: 0.9504 (mmt180) cc_final: 0.9258 (tpp80) REVERT: E 272 MET cc_start: 0.8856 (mpp) cc_final: 0.8626 (mpp) REVERT: F 19 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7599 (mm-30) REVERT: F 54 MET cc_start: 0.8462 (mmm) cc_final: 0.8171 (mmt) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.1171 time to fit residues: 44.3258 Evaluate side-chains 205 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 152 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 127 optimal weight: 8.9990 chunk 23 optimal weight: 0.8980 chunk 128 optimal weight: 0.0570 chunk 14 optimal weight: 7.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN E 249 GLN F 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.100791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.077805 restraints weight = 86983.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.080153 restraints weight = 47510.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.081675 restraints weight = 32036.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.082699 restraints weight = 25013.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.083285 restraints weight = 21338.283| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3614 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3614 r_free = 0.3614 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3614 r_free = 0.3614 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3614 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15146 Z= 0.149 Angle : 0.664 8.851 21110 Z= 0.369 Chirality : 0.045 0.253 2379 Planarity : 0.005 0.128 2203 Dihedral : 24.804 179.343 3215 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.21), residues: 1459 helix: 0.38 (0.19), residues: 673 sheet: -1.51 (0.32), residues: 222 loop : -1.36 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG D 77 TYR 0.024 0.002 TYR E 229 PHE 0.020 0.001 PHE K 224 TRP 0.015 0.002 TRP B 83 HIS 0.007 0.001 HIS C 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.15 (15146) covalent geometry : angle 0.66401 / 0.37 (21110) hydrogen bonds : bond 0.05762 / 3.69 ( 672) hydrogen bonds : angle 4.61723 / 3.25 ( 1831) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 142 ARG cc_start: 0.6226 (mtt180) cc_final: 0.4226 (mtm180) REVERT: K 220 LEU cc_start: 0.6438 (tt) cc_final: 0.6122 (tt) REVERT: K 271 ARG cc_start: 0.8388 (mtt180) cc_final: 0.7871 (mmt180) REVERT: D 38 ARG cc_start: 0.8554 (tmm-80) cc_final: 0.8265 (tmm-80) REVERT: D 41 GLU cc_start: 0.8462 (mp0) cc_final: 0.8086 (mp0) REVERT: B 84 VAL cc_start: 0.8217 (m) cc_final: 0.7224 (m) REVERT: B 134 ASP cc_start: 0.9039 (m-30) cc_final: 0.8329 (t0) REVERT: B 163 ASN cc_start: 0.8964 (m-40) cc_final: 0.8730 (m-40) REVERT: B 194 TYR cc_start: 0.7731 (m-10) cc_final: 0.7492 (m-80) REVERT: B 217 HIS cc_start: 0.9158 (t-90) cc_final: 0.8851 (t70) REVERT: B 223 TYR cc_start: 0.7973 (m-80) cc_final: 0.7562 (m-80) REVERT: C 156 ARG cc_start: 0.9128 (mtt180) cc_final: 0.8774 (tpp80) REVERT: C 160 LYS cc_start: 0.9287 (mptt) cc_final: 0.9046 (mmtt) REVERT: E 258 ARG cc_start: 0.9501 (mmt180) cc_final: 0.9259 (tpp80) REVERT: E 272 MET cc_start: 0.8858 (mpp) cc_final: 0.8646 (mpp) REVERT: F 15 LEU cc_start: 0.9265 (mt) cc_final: 0.8999 (mt) REVERT: F 19 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7435 (tp30) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.1109 time to fit residues: 41.0608 Evaluate side-chains 208 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 59 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 0.0870 chunk 151 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 128 optimal weight: 1.9990 chunk 37 optimal weight: 0.0980 chunk 85 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 117 optimal weight: 0.0270 overall best weight: 0.4420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN ** F 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.101939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.077699 restraints weight = 117535.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.080379 restraints weight = 57629.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.082173 restraints weight = 36687.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.083378 restraints weight = 27507.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.084165 restraints weight = 22674.209| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15146 Z= 0.147 Angle : 0.677 9.500 21110 Z= 0.373 Chirality : 0.046 0.257 2379 Planarity : 0.005 0.134 2203 Dihedral : 24.775 178.764 3215 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % 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: -0.93 (0.21), residues: 1459 helix: 0.34 (0.19), residues: 679 sheet: -1.39 (0.32), residues: 222 loop : -1.36 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 241 TYR 0.022 0.001 TYR E 229 PHE 0.022 0.001 PHE K 224 TRP 0.044 0.002 TRP B 83 HIS 0.006 0.001 HIS C 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.15 (15146) covalent geometry : angle 0.67743 / 0.37 (21110) hydrogen bonds : bond 0.05659 / 3.63 ( 672) hydrogen bonds : angle 4.56226 / 3.22 ( 1831) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2918 Ramachandran restraints generated. 1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 142 ARG cc_start: 0.6213 (mtt180) cc_final: 0.4334 (mtm180) REVERT: K 161 PHE cc_start: 0.8012 (t80) cc_final: 0.7606 (t80) REVERT: K 220 LEU cc_start: 0.6474 (tt) cc_final: 0.6126 (tt) REVERT: K 271 ARG cc_start: 0.8381 (mtt180) cc_final: 0.7864 (mmt180) REVERT: D 28 THR cc_start: 0.9197 (p) cc_final: 0.8990 (t) REVERT: D 38 ARG cc_start: 0.8574 (tmm-80) cc_final: 0.8287 (tmm-80) REVERT: D 41 GLU cc_start: 0.8521 (mp0) cc_final: 0.8142 (mp0) REVERT: A 20 THR cc_start: 0.9094 (p) cc_final: 0.8873 (t) REVERT: B 84 VAL cc_start: 0.8118 (m) cc_final: 0.7296 (m) REVERT: B 134 ASP cc_start: 0.8992 (m-30) cc_final: 0.8302 (t0) REVERT: B 163 ASN cc_start: 0.8925 (m-40) cc_final: 0.8686 (m-40) REVERT: B 217 HIS cc_start: 0.9138 (t-90) cc_final: 0.8839 (t70) REVERT: B 223 TYR cc_start: 0.7969 (m-80) cc_final: 0.7590 (m-80) REVERT: C 60 LEU cc_start: 0.8983 (mt) cc_final: 0.8716 (mt) REVERT: C 83 TRP cc_start: 0.8344 (m100) cc_final: 0.8076 (m100) REVERT: C 156 ARG cc_start: 0.9116 (mtt180) cc_final: 0.8710 (tpp80) REVERT: C 160 LYS cc_start: 0.9244 (mptt) cc_final: 0.9004 (mmtt) REVERT: C 190 HIS cc_start: 0.7791 (m90) cc_final: 0.7324 (m170) REVERT: E 258 ARG cc_start: 0.9483 (mmt180) cc_final: 0.9254 (tpp80) REVERT: E 272 MET cc_start: 0.8816 (mpp) cc_final: 0.8607 (mpp) REVERT: F 15 LEU cc_start: 0.9220 (mt) cc_final: 0.8948 (mt) REVERT: F 19 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7384 (tp30) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.1104 time to fit residues: 42.4528 Evaluate side-chains 210 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 93 optimal weight: 0.9990 chunk 104 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 122 optimal weight: 0.8980 chunk 155 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 112 optimal weight: 0.0030 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN F 68 HIS F 184 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.101422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.077392 restraints weight = 108209.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.079950 restraints weight = 54184.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.081652 restraints weight = 35078.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.082807 restraints weight = 26551.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.083573 restraints weight = 22165.869| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15146 Z= 0.154 Angle : 0.674 9.492 21110 Z= 0.374 Chirality : 0.045 0.249 2379 Planarity : 0.005 0.139 2203 Dihedral : 24.768 179.661 3215 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: -0.93 (0.21), residues: 1459 helix: 0.36 (0.19), residues: 676 sheet: -1.45 (0.32), residues: 220 loop : -1.36 (0.24), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 241 TYR 0.034 0.002 TYR B 194 PHE 0.025 0.002 PHE K 224 TRP 0.021 0.002 TRP E 83 HIS 0.005 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (15146) covalent geometry : angle 0.67444 / 0.37 (21110) hydrogen bonds : bond 0.05656 / 3.62 ( 672) hydrogen bonds : angle 4.62913 / 3.28 ( 1831) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2799.74 seconds wall clock time: 49 minutes 3.88 seconds (2943.88 seconds total)