Starting phenix.real_space_refine on Thu Aug 6 08:48:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fyc_29564/08_2026/8fyc_29564.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fyc_29564/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8fyc_29564/08_2026/8fyc_29564.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fyc_29564/08_2026/8fyc_29564.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fyc_29564/08_2026/8fyc_29564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fyc_29564/08_2026/8fyc_29564.map" } 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-2.2rc3-6140/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: 3.20, per 1000 atoms: 0.22 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: 0.99 Conformation dependent library (CDL) restraints added in 391.7 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: 1.55 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: 2.53 Time building geometry restraints manager: 1.39 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: 19977 1.62 - 3.24: 996 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: 0.910 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.320 Find NCS groups from input model: 0.130 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.770 ------------------------------------------------------------------------------- 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 : 0.752 8.108 21110 Z= 0.568 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 0.75204 / 0.57 (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 : 0.467 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: K 271 ARG cc_start: 0.7809 (mtt180) cc_final: 0.7533 (mmt180) REVERT: D 69 ASP cc_start: 0.8191 (t70) cc_final: 0.7956 (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: 0.7831 (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: 0.8544 (m-40) REVERT: B 217 HIS cc_start: 0.9200 (t-90) cc_final: 0.8843 (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: 0.7453 (m-70) outliers start: 3 outliers final: 0 residues processed: 301 average time/residue: 0.1195 time to fit residues: 51.5031 Evaluate side-chains 222 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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: 0.0970 chunk 66 optimal weight: 7.9990 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: 1.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- 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** ** E 253 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 = 0.3970 r_free = 0.3970 target = 0.098958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.076652 restraints weight = 74920.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.078673 restraints weight = 43992.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.080057 restraints weight = 31092.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.080836 restraints weight = 24703.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.081469 restraints weight = 21626.397| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 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 = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15146 Z= 0.206 Angle : 0.710 9.440 21110 Z= 0.405 Chirality : 0.048 0.319 2379 Planarity : 0.005 0.047 2203 Dihedral : 23.990 179.598 3215 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % 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: -0.84 (0.21), residues: 1459 helix: 0.36 (0.19), residues: 665 sheet: -1.26 (0.33), residues: 218 loop : -1.25 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 129 TYR 0.023 0.002 TYR C 126 PHE 0.022 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 0.00396 / 0.21 (15146) covalent geometry : angle 0.70991 / 0.40 (21110) hydrogen bonds : bond 0.08674 / 5.84 ( 672) hydrogen bonds : angle 5.60430 / 3.99 ( 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 272 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 148 ILE cc_start: 0.9256 (mt) cc_final: 0.9004 (mt) REVERT: K 271 ARG cc_start: 0.7939 (mtt180) cc_final: 0.7645 (mmt180) REVERT: D 69 ASP cc_start: 0.8350 (t70) cc_final: 0.8093 (t70) REVERT: A 20 THR cc_start: 0.9099 (p) cc_final: 0.8778 (t) REVERT: A 45 ARG cc_start: 0.8523 (tpp80) cc_final: 0.8172 (mmm-85) REVERT: A 49 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8688 (mm-30) REVERT: B 83 TRP cc_start: 0.8960 (m100) cc_final: 0.8692 (m100) REVERT: B 125 MET cc_start: 0.8648 (mpp) cc_final: 0.8420 (mpp) REVERT: B 141 GLN cc_start: 0.9308 (tm-30) cc_final: 0.9009 (tm-30) REVERT: B 186 LEU cc_start: 0.9150 (tt) cc_final: 0.8943 (tt) REVERT: B 217 HIS cc_start: 0.9166 (t-90) cc_final: 0.8777 (t70) REVERT: C 184 GLN cc_start: 0.9166 (pm20) cc_final: 0.8830 (pm20) REVERT: C 282 ILE cc_start: 0.9163 (mm) cc_final: 0.8909 (mm) REVERT: E 69 ARG cc_start: 0.7686 (tpm170) cc_final: 0.7306 (tpm170) REVERT: E 83 TRP cc_start: 0.8354 (m-90) cc_final: 0.7924 (m-90) REVERT: E 272 MET cc_start: 0.9137 (mpp) cc_final: 0.8861 (mpp) REVERT: F 15 LEU cc_start: 0.9318 (mt) cc_final: 0.9085 (mt) REVERT: F 128 MET cc_start: 0.6526 (pmm) cc_final: 0.6298 (pmm) REVERT: F 190 HIS cc_start: 0.7437 (m170) cc_final: 0.7162 (m-70) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.0952 time to fit residues: 38.7353 Evaluate side-chains 211 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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: 9.9990 chunk 37 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 132 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 155 optimal weight: 20.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 212 HIS K 222 GLN D 48 GLN ** 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 ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS C 214 HIS C 253 GLN F 33 ASN F 183 ASN F 184 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.099185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.077157 restraints weight = 69654.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.079056 restraints weight = 41708.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.080398 restraints weight = 29836.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.081172 restraints weight = 24020.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.081594 restraints weight = 21081.636| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15146 Z= 0.189 Angle : 0.671 6.703 21110 Z= 0.380 Chirality : 0.046 0.255 2379 Planarity : 0.005 0.049 2203 Dihedral : 24.315 178.547 3215 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.08 % Allowed : 6.12 % Favored : 93.80 % 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: -0.89 (0.21), residues: 1459 helix: 0.38 (0.19), residues: 668 sheet: -1.36 (0.34), residues: 207 loop : -1.34 (0.23), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 156 TYR 0.018 0.002 TYR K 231 PHE 0.019 0.002 PHE K 202 TRP 0.014 0.002 TRP D 44 HIS 0.006 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.19 (15146) covalent geometry : angle 0.67068 / 0.38 (21110) hydrogen bonds : bond 0.07381 / 4.85 ( 672) hydrogen bonds : angle 5.27663 / 3.74 ( 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 271 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 270 time to evaluate : 0.418 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: K 271 ARG cc_start: 0.8027 (mtt180) cc_final: 0.7645 (mmt180) REVERT: D 48 GLN cc_start: 0.9472 (OUTLIER) cc_final: 0.8958 (mm110) REVERT: D 69 ASP cc_start: 0.8327 (t70) cc_final: 0.7993 (t70) REVERT: A 20 THR cc_start: 0.9153 (p) cc_final: 0.8860 (t) REVERT: A 45 ARG cc_start: 0.8484 (tpp80) cc_final: 0.8184 (mmm-85) REVERT: B 83 TRP cc_start: 0.9040 (m100) cc_final: 0.8818 (m100) REVERT: B 134 ASP cc_start: 0.8979 (m-30) cc_final: 0.8163 (t0) REVERT: B 137 LYS cc_start: 0.9534 (mppt) cc_final: 0.9325 (mmtm) REVERT: B 141 GLN cc_start: 0.9383 (tm-30) cc_final: 0.9062 (tm-30) REVERT: B 217 HIS cc_start: 0.9193 (t-90) cc_final: 0.8828 (t70) REVERT: C 190 HIS cc_start: 0.8020 (m90) cc_final: 0.7760 (m170) REVERT: C 282 ILE cc_start: 0.9140 (mm) cc_final: 0.8856 (mm) REVERT: E 260 ARG cc_start: 0.8923 (ptt90) cc_final: 0.8562 (ptt90) REVERT: E 272 MET cc_start: 0.9189 (mpp) cc_final: 0.8806 (mmt) REVERT: F 15 LEU cc_start: 0.9303 (mt) cc_final: 0.9076 (mt) outliers start: 1 outliers final: 0 residues processed: 271 average time/residue: 0.1054 time to fit residues: 42.3151 Evaluate side-chains 206 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 205 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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: 8.9990 chunk 75 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 36 optimal weight: 0.2980 chunk 96 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 chunk 141 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 222 GLN K 237 HIS ** 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 253 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 = 0.3989 r_free = 0.3989 target = 0.099676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.077495 restraints weight = 71212.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.079486 restraints weight = 42470.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.080839 restraints weight = 30132.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.081737 restraints weight = 24116.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.082196 restraints weight = 20893.990| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3598 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 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 = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3598 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15146 Z= 0.165 Angle : 0.661 10.581 21110 Z= 0.368 Chirality : 0.046 0.277 2379 Planarity : 0.004 0.055 2203 Dihedral : 24.441 179.232 3215 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.21), residues: 1459 helix: 0.37 (0.19), residues: 672 sheet: -1.40 (0.33), residues: 214 loop : -1.33 (0.24), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 144 TYR 0.016 0.002 TYR C 126 PHE 0.032 0.002 PHE K 224 TRP 0.013 0.001 TRP D 44 HIS 0.005 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 (15146) covalent geometry : angle 0.66119 / 0.37 (21110) hydrogen bonds : bond 0.06589 / 4.31 ( 672) hydrogen bonds : angle 5.00074 / 3.53 ( 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 280 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 220 LEU cc_start: 0.6374 (tt) cc_final: 0.5902 (tt) REVERT: K 271 ARG cc_start: 0.8083 (mtt180) cc_final: 0.7715 (mmt180) REVERT: D 41 GLU cc_start: 0.8616 (mp0) cc_final: 0.8350 (mp0) REVERT: D 69 ASP cc_start: 0.8336 (t70) cc_final: 0.8013 (t70) REVERT: A 45 ARG cc_start: 0.8469 (tpp80) cc_final: 0.8166 (mmm-85) REVERT: A 49 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8642 (mm-30) REVERT: B 83 TRP cc_start: 0.9000 (m100) cc_final: 0.8752 (m100) REVERT: B 125 MET cc_start: 0.8635 (mpp) cc_final: 0.8392 (mpp) REVERT: B 134 ASP cc_start: 0.8989 (m-30) cc_final: 0.8149 (t0) REVERT: B 137 LYS cc_start: 0.9536 (mppt) cc_final: 0.9323 (mmtm) REVERT: B 210 LEU cc_start: 0.8924 (mm) cc_final: 0.8678 (mm) REVERT: B 217 HIS cc_start: 0.9181 (t-90) cc_final: 0.8810 (t70) REVERT: C 23 THR cc_start: 0.9379 (p) cc_final: 0.9171 (t) REVERT: C 141 GLN cc_start: 0.8968 (mp10) cc_final: 0.8735 (mp10) REVERT: C 190 HIS cc_start: 0.8060 (m90) cc_final: 0.7836 (m90) REVERT: C 282 ILE cc_start: 0.9177 (mm) cc_final: 0.8746 (mm) REVERT: E 69 ARG cc_start: 0.7443 (tpm170) cc_final: 0.7143 (tpm170) REVERT: F 15 LEU cc_start: 0.9238 (mt) cc_final: 0.9028 (mt) REVERT: F 190 HIS cc_start: 0.7481 (m170) cc_final: 0.7217 (m-70) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.1245 time to fit residues: 51.6715 Evaluate side-chains 212 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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: 9.9990 chunk 147 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 18 optimal weight: 30.0000 chunk 52 optimal weight: 0.0060 chunk 57 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 overall best weight: 4.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 212 HIS K 222 GLN ** 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 ** F 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.097735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.074611 restraints weight = 101472.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.076936 restraints weight = 53891.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.078532 restraints weight = 35615.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.079591 restraints weight = 27364.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.080240 restraints weight = 23083.113| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3544 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3544 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 15146 Z= 0.236 Angle : 0.705 9.658 21110 Z= 0.392 Chirality : 0.046 0.271 2379 Planarity : 0.005 0.060 2203 Dihedral : 24.576 177.454 3215 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 20.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % 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: -1.07 (0.21), residues: 1459 helix: 0.26 (0.19), residues: 672 sheet: -1.62 (0.32), residues: 217 loop : -1.40 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 40 TYR 0.011 0.002 TYR C 162 PHE 0.029 0.002 PHE K 224 TRP 0.020 0.002 TRP A 44 HIS 0.005 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.24 (15146) covalent geometry : angle 0.70529 / 0.39 (21110) hydrogen bonds : bond 0.07018 / 4.52 ( 672) hydrogen bonds : angle 5.04454 / 3.56 ( 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 257 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 192 GLU cc_start: 0.7627 (pt0) cc_final: 0.7060 (mp0) REVERT: K 220 LEU cc_start: 0.6551 (tt) cc_final: 0.6097 (tt) REVERT: K 241 ARG cc_start: 0.3974 (ttm170) cc_final: 0.3742 (ttm170) REVERT: K 271 ARG cc_start: 0.8049 (mtt180) cc_final: 0.7660 (mmt180) REVERT: D 41 GLU cc_start: 0.8613 (mp0) cc_final: 0.7928 (mp0) REVERT: D 69 ASP cc_start: 0.8301 (t70) cc_final: 0.8024 (t70) REVERT: A 3 MET cc_start: 0.7660 (mmm) cc_final: 0.7219 (tpt) REVERT: A 20 THR cc_start: 0.9101 (p) cc_final: 0.8850 (t) REVERT: A 45 ARG cc_start: 0.8467 (tpp80) cc_final: 0.8231 (mmm-85) REVERT: A 77 ARG cc_start: 0.7834 (mtt180) cc_final: 0.7606 (mtt180) REVERT: B 134 ASP cc_start: 0.9032 (m-30) cc_final: 0.8181 (t0) REVERT: B 137 LYS cc_start: 0.9543 (mppt) cc_final: 0.9303 (mmtm) REVERT: B 217 HIS cc_start: 0.9150 (t-90) cc_final: 0.8847 (t70) REVERT: B 230 LYS cc_start: 0.8657 (tttt) cc_final: 0.8313 (tttt) REVERT: C 156 ARG cc_start: 0.9005 (mtt180) cc_final: 0.8777 (mtt90) REVERT: C 253 GLN cc_start: 0.8187 (tp40) cc_final: 0.7732 (tp40) REVERT: C 282 ILE cc_start: 0.9209 (mm) cc_final: 0.8837 (mm) REVERT: E 128 MET cc_start: 0.8892 (tpp) cc_final: 0.8610 (tpp) REVERT: E 258 ARG cc_start: 0.9481 (mmt180) cc_final: 0.9248 (tpp80) REVERT: E 272 MET cc_start: 0.9143 (mpp) cc_final: 0.8925 (mpp) REVERT: F 15 LEU cc_start: 0.9284 (mt) cc_final: 0.9078 (mt) REVERT: F 190 HIS cc_start: 0.7510 (m170) cc_final: 0.7260 (m-70) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.1033 time to fit residues: 39.5481 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 : 0.493 ------------------------------------------------------------------------------- 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: 0.9980 chunk 52 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 121 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 143 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.098747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.075318 restraints weight = 114297.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.077874 restraints weight = 56348.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.079571 restraints weight = 35906.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.080667 restraints weight = 27056.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.081327 restraints weight = 22442.632| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15146 Z= 0.171 Angle : 0.661 6.975 21110 Z= 0.370 Chirality : 0.045 0.276 2379 Planarity : 0.004 0.060 2203 Dihedral : 24.644 178.795 3215 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.21), residues: 1459 helix: 0.33 (0.19), residues: 673 sheet: -1.66 (0.32), residues: 216 loop : -1.37 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 96 TYR 0.015 0.002 TYR C 162 PHE 0.029 0.002 PHE B 24 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 0.00339 / 0.17 (15146) covalent geometry : angle 0.66070 / 0.37 (21110) hydrogen bonds : bond 0.06241 / 4.05 ( 672) hydrogen bonds : angle 4.82964 / 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 260 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.390 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: K 158 GLU cc_start: 0.6855 (mp0) cc_final: 0.6614 (mp0) REVERT: K 220 LEU cc_start: 0.6357 (tt) cc_final: 0.5966 (tt) REVERT: K 271 ARG cc_start: 0.8095 (mtt180) cc_final: 0.7657 (mmt180) REVERT: D 38 ARG cc_start: 0.8615 (tmm-80) cc_final: 0.8111 (tmm-80) REVERT: D 41 GLU cc_start: 0.8625 (mp0) cc_final: 0.7955 (mp0) REVERT: A 3 MET cc_start: 0.7724 (mmm) cc_final: 0.7404 (tpt) REVERT: A 45 ARG cc_start: 0.8486 (tpp80) cc_final: 0.8206 (mmm-85) REVERT: A 77 ARG cc_start: 0.7769 (mtt180) cc_final: 0.7411 (mtt180) REVERT: B 134 ASP cc_start: 0.9063 (m-30) cc_final: 0.8308 (t0) REVERT: B 217 HIS cc_start: 0.9211 (t-90) cc_final: 0.8897 (t70) REVERT: C 190 HIS cc_start: 0.8040 (m90) cc_final: 0.7794 (m170) REVERT: C 253 GLN cc_start: 0.8093 (tp40) cc_final: 0.7824 (tp40) REVERT: E 258 ARG cc_start: 0.9502 (mmt180) cc_final: 0.9181 (tpp80) REVERT: F 190 HIS cc_start: 0.7718 (m170) cc_final: 0.7414 (m-70) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.1133 time to fit residues: 43.6945 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 : 0.488 ------------------------------------------------------------------------------- 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: 0.4980 chunk 153 optimal weight: 30.0000 chunk 31 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 84 optimal weight: 8.9990 chunk 150 optimal weight: 20.0000 chunk 114 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 212 HIS K 222 GLN 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** ** 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 = 0.3938 r_free = 0.3938 target = 0.096882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.074895 restraints weight = 73522.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.076837 restraints weight = 44069.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.078155 restraints weight = 31252.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.078964 restraints weight = 25051.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.079445 restraints weight = 21810.143| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15146 Z= 0.257 Angle : 0.733 8.066 21110 Z= 0.406 Chirality : 0.047 0.272 2379 Planarity : 0.005 0.073 2203 Dihedral : 24.783 177.116 3215 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 21.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.21), residues: 1459 helix: 0.15 (0.19), residues: 671 sheet: -1.65 (0.32), residues: 217 loop : -1.47 (0.24), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 150 TYR 0.024 0.002 TYR C 126 PHE 0.025 0.002 PHE B 24 TRP 0.035 0.002 TRP B 83 HIS 0.010 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.26 (15146) covalent geometry : angle 0.73293 / 0.41 (21110) hydrogen bonds : bond 0.07028 / 4.54 ( 672) hydrogen bonds : angle 4.97980 / 3.51 ( 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 255 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.465 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: 0.6366 (tt) cc_final: 0.6062 (tt) REVERT: K 271 ARG cc_start: 0.8237 (mtt180) cc_final: 0.7783 (mmt180) REVERT: D 38 ARG cc_start: 0.8716 (tmm-80) cc_final: 0.8467 (tmm-80) REVERT: D 41 GLU cc_start: 0.8449 (mp0) cc_final: 0.8138 (mp0) REVERT: A 20 THR cc_start: 0.9112 (p) cc_final: 0.8890 (t) REVERT: A 45 ARG cc_start: 0.8466 (tpp80) cc_final: 0.8257 (mmm-85) REVERT: B 134 ASP cc_start: 0.9104 (m-30) cc_final: 0.8324 (t0) REVERT: B 217 HIS cc_start: 0.9180 (t-90) cc_final: 0.8889 (t70) REVERT: C 72 GLU cc_start: 0.8655 (tt0) cc_final: 0.8022 (tp30) REVERT: C 190 HIS cc_start: 0.8010 (m90) cc_final: 0.7794 (m170) REVERT: C 282 ILE cc_start: 0.9254 (mm) cc_final: 0.9032 (mm) REVERT: C 295 LEU cc_start: 0.9260 (mm) cc_final: 0.8980 (mt) REVERT: E 128 MET cc_start: 0.8857 (tpp) cc_final: 0.8626 (tpp) REVERT: E 258 ARG cc_start: 0.9498 (mmt180) cc_final: 0.9257 (tpp80) REVERT: F 15 LEU cc_start: 0.9324 (mt) cc_final: 0.9084 (mt) REVERT: F 19 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7546 (mm-30) REVERT: F 190 HIS cc_start: 0.7606 (m170) cc_final: 0.7327 (m-70) REVERT: F 198 HIS cc_start: 0.8246 (t-90) cc_final: 0.7892 (t-90) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.1211 time to fit residues: 45.4296 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 : 0.489 ------------------------------------------------------------------------------- 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: 0.0050 chunk 25 optimal weight: 6.9990 chunk 155 optimal weight: 20.0000 chunk 156 optimal weight: 20.0000 chunk 150 optimal weight: 20.0000 chunk 147 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 overall best weight: 3.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 48 GLN ** 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 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.097871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.075371 restraints weight = 82363.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.077475 restraints weight = 46840.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.078901 restraints weight = 32370.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.079809 restraints weight = 25555.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.080176 restraints weight = 21915.799| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15146 Z= 0.202 Angle : 0.695 8.452 21110 Z= 0.386 Chirality : 0.046 0.274 2379 Planarity : 0.005 0.061 2203 Dihedral : 24.843 178.125 3215 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 20.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.21), residues: 1459 helix: 0.13 (0.19), residues: 672 sheet: -1.56 (0.33), residues: 211 loop : -1.46 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 144 TYR 0.035 0.002 TYR E 229 PHE 0.021 0.002 PHE B 24 TRP 0.061 0.003 TRP B 83 HIS 0.008 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.20 (15146) covalent geometry : angle 0.69488 / 0.39 (21110) hydrogen bonds : bond 0.06292 / 4.06 ( 672) hydrogen bonds : angle 4.90244 / 3.46 ( 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 259 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.395 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 188 GLU cc_start: 0.5431 (mm-30) cc_final: 0.5190 (tp30) REVERT: K 192 GLU cc_start: 0.7745 (pt0) cc_final: 0.7472 (mt-10) REVERT: K 220 LEU cc_start: 0.6350 (tt) cc_final: 0.6030 (tt) REVERT: K 271 ARG cc_start: 0.8285 (mtt180) cc_final: 0.7812 (mmt180) REVERT: D 38 ARG cc_start: 0.8703 (tmm-80) cc_final: 0.8158 (tmm-80) REVERT: D 41 GLU cc_start: 0.8453 (mp0) cc_final: 0.7787 (mp0) REVERT: D 51 MET cc_start: 0.8096 (ptm) cc_final: 0.7768 (ptm) REVERT: A 20 THR cc_start: 0.9072 (p) cc_final: 0.8833 (t) REVERT: A 45 ARG cc_start: 0.8464 (tpp80) cc_final: 0.8243 (mmm-85) REVERT: B 134 ASP cc_start: 0.9088 (m-30) cc_final: 0.8345 (t0) REVERT: B 217 HIS cc_start: 0.9146 (t-90) cc_final: 0.8828 (t70) REVERT: C 141 GLN cc_start: 0.8951 (mp10) cc_final: 0.8705 (mp10) REVERT: E 128 MET cc_start: 0.8837 (tpp) cc_final: 0.8580 (tpp) REVERT: E 258 ARG cc_start: 0.9517 (mmt180) cc_final: 0.9255 (tpp80) REVERT: F 15 LEU cc_start: 0.9310 (mt) cc_final: 0.9046 (mt) REVERT: F 19 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7611 (mm-30) REVERT: F 128 MET cc_start: 0.7298 (pmm) cc_final: 0.7093 (pmm) REVERT: F 190 HIS cc_start: 0.7783 (m170) cc_final: 0.7443 (m-70) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.1155 time to fit residues: 43.9505 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 : 0.404 ------------------------------------------------------------------------------- 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: 30.0000 chunk 56 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 119 optimal weight: 0.4980 chunk 20 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 128 optimal weight: 0.0050 chunk 14 optimal weight: 20.0000 overall best weight: 1.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 212 HIS D 48 GLN ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN C 253 GLN E 249 GLN F 184 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.099815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.076832 restraints weight = 88962.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.079095 restraints weight = 47852.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.080577 restraints weight = 32387.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.081468 restraints weight = 25226.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.082162 restraints weight = 21769.850| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3596 r_free = 0.3596 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3596 r_free = 0.3596 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 15146 Z= 0.159 Angle : 0.678 10.255 21110 Z= 0.373 Chirality : 0.046 0.274 2379 Planarity : 0.004 0.060 2203 Dihedral : 24.814 179.788 3215 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % 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: -1.05 (0.21), residues: 1459 helix: 0.22 (0.19), residues: 672 sheet: -1.44 (0.33), residues: 211 loop : -1.39 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 153 TYR 0.030 0.002 TYR E 229 PHE 0.029 0.002 PHE B 221 TRP 0.017 0.002 TRP D 44 HIS 0.006 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.16 (15146) covalent geometry : angle 0.67800 / 0.37 (21110) hydrogen bonds : bond 0.05793 / 3.74 ( 672) hydrogen bonds : angle 4.77237 / 3.36 ( 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 259 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 159 THR cc_start: 0.7676 (t) cc_final: 0.7463 (t) REVERT: K 188 GLU cc_start: 0.5343 (mm-30) cc_final: 0.5080 (tp30) REVERT: K 192 GLU cc_start: 0.7680 (pt0) cc_final: 0.7411 (mt-10) REVERT: K 220 LEU cc_start: 0.6378 (tt) cc_final: 0.6062 (tt) REVERT: K 271 ARG cc_start: 0.8350 (mtt180) cc_final: 0.7859 (mmt180) REVERT: D 38 ARG cc_start: 0.8597 (tmm-80) cc_final: 0.8026 (tmm-80) REVERT: D 41 GLU cc_start: 0.8415 (mp0) cc_final: 0.7742 (mp0) REVERT: D 51 MET cc_start: 0.8051 (ptm) cc_final: 0.7797 (ptm) REVERT: A 45 ARG cc_start: 0.8496 (tpp80) cc_final: 0.8199 (mmm-85) REVERT: B 134 ASP cc_start: 0.9062 (m-30) cc_final: 0.8330 (t0) REVERT: B 163 ASN cc_start: 0.8983 (m-40) cc_final: 0.8751 (m-40) REVERT: B 206 LEU cc_start: 0.9039 (mp) cc_final: 0.8836 (mt) REVERT: B 217 HIS cc_start: 0.9181 (t-90) cc_final: 0.8854 (t70) REVERT: C 23 THR cc_start: 0.9420 (p) cc_final: 0.9179 (t) REVERT: C 156 ARG cc_start: 0.8788 (mpp80) cc_final: 0.8187 (mpt-90) REVERT: E 258 ARG cc_start: 0.9513 (mmt180) cc_final: 0.9246 (tpp80) REVERT: F 15 LEU cc_start: 0.9258 (mt) cc_final: 0.9006 (mt) REVERT: F 19 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7582 (tp30) REVERT: F 190 HIS cc_start: 0.7833 (m170) cc_final: 0.7535 (m-70) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.1099 time to fit residues: 42.2196 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 59 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 0.0270 chunk 151 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 44 optimal weight: 0.7980 chunk 117 optimal weight: 8.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 190 HIS ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN ** C 184 GLN ** 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 = 0.4015 r_free = 0.4015 target = 0.101121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.076969 restraints weight = 117123.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.079680 restraints weight = 56534.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.081460 restraints weight = 35589.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.082665 restraints weight = 26687.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.083367 restraints weight = 21994.539| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.30 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: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 15146 Z= 0.150 Angle : 0.690 9.107 21110 Z= 0.376 Chirality : 0.047 0.278 2379 Planarity : 0.004 0.062 2203 Dihedral : 24.772 179.192 3215 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % 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: -1.00 (0.21), residues: 1459 helix: 0.21 (0.19), residues: 676 sheet: -1.34 (0.33), residues: 216 loop : -1.34 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 153 TYR 0.027 0.002 TYR E 229 PHE 0.021 0.002 PHE K 224 TRP 0.038 0.002 TRP B 83 HIS 0.005 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 (15146) covalent geometry : angle 0.68951 / 0.38 (21110) hydrogen bonds : bond 0.05649 / 3.63 ( 672) hydrogen bonds : angle 4.67123 / 3.31 ( 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 268 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 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 159 THR cc_start: 0.7653 (t) cc_final: 0.7447 (t) REVERT: K 188 GLU cc_start: 0.5302 (mm-30) cc_final: 0.5026 (tp30) REVERT: K 192 GLU cc_start: 0.7598 (pt0) cc_final: 0.7393 (mt-10) REVERT: K 220 LEU cc_start: 0.6455 (tt) cc_final: 0.6090 (tt) REVERT: K 271 ARG cc_start: 0.8356 (mtt180) cc_final: 0.7848 (mmt180) REVERT: D 38 ARG cc_start: 0.8566 (tmm-80) cc_final: 0.7989 (tmm-80) REVERT: D 41 GLU cc_start: 0.8412 (mp0) cc_final: 0.7626 (mp0) REVERT: D 51 MET cc_start: 0.7920 (ptm) cc_final: 0.7679 (ptm) REVERT: A 20 THR cc_start: 0.9111 (p) cc_final: 0.8804 (t) REVERT: A 45 ARG cc_start: 0.8461 (tpp80) cc_final: 0.8182 (mmm-85) REVERT: B 134 ASP cc_start: 0.9060 (m-30) cc_final: 0.8346 (t0) REVERT: B 163 ASN cc_start: 0.8966 (m-40) cc_final: 0.8728 (m-40) REVERT: B 206 LEU cc_start: 0.8956 (mp) cc_final: 0.8693 (mt) REVERT: B 217 HIS cc_start: 0.9163 (t-90) cc_final: 0.8828 (t70) REVERT: B 223 TYR cc_start: 0.7974 (m-80) cc_final: 0.7539 (m-80) REVERT: C 23 THR cc_start: 0.9412 (p) cc_final: 0.9159 (t) REVERT: C 83 TRP cc_start: 0.8360 (m100) cc_final: 0.8060 (m100) REVERT: C 168 LYS cc_start: 0.9215 (mmpt) cc_final: 0.8780 (mtmm) REVERT: C 184 GLN cc_start: 0.9179 (pm20) cc_final: 0.8882 (pm20) REVERT: E 258 ARG cc_start: 0.9499 (mmt180) cc_final: 0.9223 (tpp80) REVERT: F 15 LEU cc_start: 0.9205 (mt) cc_final: 0.8970 (mt) REVERT: F 19 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7541 (tp30) REVERT: F 190 HIS cc_start: 0.7795 (m170) cc_final: 0.7555 (m-70) REVERT: F 270 LYS cc_start: 0.9578 (mmmt) cc_final: 0.9193 (tptp) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.1094 time to fit residues: 43.4296 Evaluate side-chains 219 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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: 0.9980 chunk 104 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 155 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 115 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 212 HIS ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 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 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 = 0.4021 r_free = 0.4021 target = 0.101387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.077541 restraints weight = 105687.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.080157 restraints weight = 52908.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.081861 restraints weight = 34261.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.083001 restraints weight = 26009.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.083705 restraints weight = 21772.131| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15146 Z= 0.147 Angle : 0.682 8.709 21110 Z= 0.373 Chirality : 0.046 0.278 2379 Planarity : 0.004 0.063 2203 Dihedral : 24.783 179.369 3215 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: 0.24 (0.19), residues: 677 sheet: -1.23 (0.32), residues: 228 loop : -1.32 (0.24), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 40 TYR 0.040 0.002 TYR B 194 PHE 0.021 0.002 PHE K 224 TRP 0.025 0.002 TRP E 83 HIS 0.005 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 (15146) covalent geometry : angle 0.68151 / 0.37 (21110) hydrogen bonds : bond 0.05591 / 3.57 ( 672) hydrogen bonds : angle 4.65999 / 3.31 ( 1831) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2724.70 seconds wall clock time: 47 minutes 40.01 seconds (2860.01 seconds total)