Starting phenix.real_space_refine on Wed Mar 4 08:06:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6s3s_10096/03_2026/6s3s_10096.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s3s_10096/03_2026/6s3s_10096.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/6s3s_10096/03_2026/6s3s_10096.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s3s_10096/03_2026/6s3s_10096.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6s3s_10096/03_2026/6s3s_10096.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s3s_10096/03_2026/6s3s_10096.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= 0.006 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: 4 Type Number sf(0) Gaussians S 138 5.16 5 C 8224 2.51 5 N 1870 2.21 5 O 2089 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12321 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1482 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 10, 'TRANS': 180} Chain: "B" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1513 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "C" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1520 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 10, 'TRANS': 185} Chain: "D" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1520 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 10, 'TRANS': 185} Chain: "E" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1454 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 9, 'TRANS': 177} Chain: "F" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2000 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "G" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 724 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 4, 'TRANS': 84} Chain: "H" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 724 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 4, 'TRANS': 84} Chain: "I" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 724 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 4, 'TRANS': 84} Chain: "J" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 660 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain breaks: 1 Time building chain proxies: 2.93, per 1000 atoms: 0.24 Number of scatterers: 12321 At special positions: 0 Unit cell: (100.284, 100.284, 123.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 138 16.00 O 2089 8.00 N 1870 7.00 C 8224 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 626.7 milliseconds 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3008 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 0 sheets defined 83.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 110 through 117 removed outlier: 4.204A pdb=" N ILE A 114 " --> pdb=" O PRO A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 133 removed outlier: 3.616A pdb=" N MET A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 156 Processing helix chain 'A' and resid 156 through 165 Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 177 through 195 removed outlier: 3.534A pdb=" N ALA A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU A 187 " --> pdb=" O ASP A 183 " (cutoff:3.500A) Proline residue: A 188 - end of helix Processing helix chain 'A' and resid 198 through 210 removed outlier: 3.521A pdb=" N GLY A 210 " --> pdb=" O VAL A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 262 Proline residue: A 226 - end of helix Proline residue: A 246 - end of helix removed outlier: 3.690A pdb=" N ASP A 251 " --> pdb=" O PHE A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 283 removed outlier: 3.791A pdb=" N VAL A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 296 removed outlier: 4.337A pdb=" N SER A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 115 removed outlier: 3.585A pdb=" N LEU B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 133 removed outlier: 3.647A pdb=" N ILE B 122 " --> pdb=" O SER B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 156 removed outlier: 4.165A pdb=" N GLY B 146 " --> pdb=" O GLN B 142 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 149 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 167 Processing helix chain 'B' and resid 167 through 173 Processing helix chain 'B' and resid 179 through 195 removed outlier: 3.872A pdb=" N ASP B 183 " --> pdb=" O ARG B 179 " (cutoff:3.500A) Proline residue: B 188 - end of helix removed outlier: 3.674A pdb=" N LYS B 195 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 209 removed outlier: 3.823A pdb=" N LEU B 202 " --> pdb=" O ARG B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 219 removed outlier: 3.536A pdb=" N VAL B 219 " --> pdb=" O PRO B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 262 Proline residue: B 226 - end of helix removed outlier: 3.843A pdb=" N THR B 230 " --> pdb=" O PRO B 226 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) Proline residue: B 246 - end of helix removed outlier: 4.387A pdb=" N MET B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 272 removed outlier: 3.523A pdb=" N VAL B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 283 Processing helix chain 'B' and resid 285 through 296 Processing helix chain 'C' and resid 108 through 113 Processing helix chain 'C' and resid 119 through 133 removed outlier: 3.576A pdb=" N VAL C 123 " --> pdb=" O PHE C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 156 Processing helix chain 'C' and resid 156 through 167 removed outlier: 3.710A pdb=" N GLN C 162 " --> pdb=" O PRO C 158 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU C 165 " --> pdb=" O ASN C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 172 Processing helix chain 'C' and resid 179 through 185 removed outlier: 3.545A pdb=" N ASP C 183 " --> pdb=" O ARG C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 194 removed outlier: 4.015A pdb=" N MET C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 208 removed outlier: 4.052A pdb=" N THR C 204 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE C 205 " --> pdb=" O ASP C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 219 Processing helix chain 'C' and resid 220 through 261 Proline residue: C 226 - end of helix removed outlier: 4.015A pdb=" N LYS C 234 " --> pdb=" O THR C 230 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU C 245 " --> pdb=" O PHE C 241 " (cutoff:3.500A) Proline residue: C 246 - end of helix removed outlier: 3.542A pdb=" N ASP C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET C 261 " --> pdb=" O VAL C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 283 Processing helix chain 'C' and resid 285 through 297 Processing helix chain 'D' and resid 108 through 117 removed outlier: 3.655A pdb=" N MET D 112 " --> pdb=" O PHE D 108 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE D 114 " --> pdb=" O PRO D 110 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU D 115 " --> pdb=" O ALA D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 133 removed outlier: 4.729A pdb=" N ILE D 122 " --> pdb=" O SER D 118 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL D 123 " --> pdb=" O PHE D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 168 removed outlier: 3.931A pdb=" N ILE D 145 " --> pdb=" O ASN D 141 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY D 146 " --> pdb=" O GLN D 142 " (cutoff:3.500A) Proline residue: D 158 - end of helix Processing helix chain 'D' and resid 169 through 173 Processing helix chain 'D' and resid 181 through 195 removed outlier: 3.504A pdb=" N ALA D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU D 187 " --> pdb=" O ASP D 183 " (cutoff:3.500A) Proline residue: D 188 - end of helix removed outlier: 3.754A pdb=" N LYS D 195 " --> pdb=" O ALA D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 210 removed outlier: 3.906A pdb=" N LEU D 202 " --> pdb=" O ARG D 198 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET D 208 " --> pdb=" O THR D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 219 removed outlier: 3.551A pdb=" N VAL D 219 " --> pdb=" O PRO D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 262 Proline residue: D 226 - end of helix removed outlier: 3.746A pdb=" N THR D 230 " --> pdb=" O PRO D 226 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU D 245 " --> pdb=" O PHE D 241 " (cutoff:3.500A) Proline residue: D 246 - end of helix Processing helix chain 'D' and resid 271 through 283 removed outlier: 4.427A pdb=" N PHE D 275 " --> pdb=" O VAL D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 297 removed outlier: 3.516A pdb=" N PHE D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 133 removed outlier: 3.555A pdb=" N VAL E 124 " --> pdb=" O THR E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 167 removed outlier: 3.649A pdb=" N ILE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE E 153 " --> pdb=" O LEU E 149 " (cutoff:3.500A) Proline residue: E 158 - end of helix removed outlier: 3.951A pdb=" N ALA E 167 " --> pdb=" O ILE E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 173 Processing helix chain 'E' and resid 177 through 195 removed outlier: 3.644A pdb=" N GLN E 186 " --> pdb=" O PHE E 182 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU E 187 " --> pdb=" O ASP E 183 " (cutoff:3.500A) Proline residue: E 188 - end of helix removed outlier: 3.697A pdb=" N LYS E 195 " --> pdb=" O ALA E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 209 Processing helix chain 'E' and resid 215 through 219 Processing helix chain 'E' and resid 220 through 262 Proline residue: E 226 - end of helix removed outlier: 3.837A pdb=" N MET E 242 " --> pdb=" O GLN E 238 " (cutoff:3.500A) Proline residue: E 246 - end of helix Processing helix chain 'E' and resid 267 through 279 removed outlier: 3.675A pdb=" N VAL E 271 " --> pdb=" O SER E 267 " (cutoff:3.500A) Proline residue: E 274 - end of helix Processing helix chain 'E' and resid 285 through 296 removed outlier: 3.525A pdb=" N ILE E 289 " --> pdb=" O GLY E 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 27 Processing helix chain 'F' and resid 38 through 54 removed outlier: 3.575A pdb=" N ARG F 42 " --> pdb=" O PRO F 38 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE F 51 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 107 removed outlier: 3.597A pdb=" N ILE F 74 " --> pdb=" O GLN F 70 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE F 81 " --> pdb=" O GLU F 77 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL F 88 " --> pdb=" O ALA F 84 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR F 89 " --> pdb=" O MET F 85 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE F 96 " --> pdb=" O LEU F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 116 Processing helix chain 'F' and resid 125 through 141 removed outlier: 3.628A pdb=" N LEU F 132 " --> pdb=" O GLN F 128 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU F 139 " --> pdb=" O THR F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 158 removed outlier: 3.505A pdb=" N LYS F 146 " --> pdb=" O ASP F 142 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE F 155 " --> pdb=" O VAL F 151 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS F 156 " --> pdb=" O VAL F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 175 Processing helix chain 'F' and resid 175 through 208 removed outlier: 5.748A pdb=" N SER F 190 " --> pdb=" O ALA F 186 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N GLY F 191 " --> pdb=" O VAL F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 235 removed outlier: 3.550A pdb=" N SER F 235 " --> pdb=" O TRP F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 256 removed outlier: 4.373A pdb=" N HIS F 240 " --> pdb=" O GLY F 236 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE F 252 " --> pdb=" O THR F 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 42 removed outlier: 3.532A pdb=" N SER G 13 " --> pdb=" O LEU G 9 " (cutoff:3.500A) Proline residue: G 27 - end of helix removed outlier: 3.568A pdb=" N THR G 42 " --> pdb=" O PHE G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 65 removed outlier: 3.900A pdb=" N ARG G 54 " --> pdb=" O SER G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 89 removed outlier: 3.813A pdb=" N THR G 70 " --> pdb=" O GLY G 66 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU G 84 " --> pdb=" O MET G 80 " (cutoff:3.500A) Proline residue: G 85 - end of helix Processing helix chain 'H' and resid 4 through 42 removed outlier: 3.705A pdb=" N SER H 13 " --> pdb=" O LEU H 9 " (cutoff:3.500A) Proline residue: H 27 - end of helix Processing helix chain 'H' and resid 51 through 65 removed outlier: 3.827A pdb=" N LEU H 62 " --> pdb=" O THR H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 83 removed outlier: 3.825A pdb=" N ILE H 81 " --> pdb=" O PHE H 77 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG H 83 " --> pdb=" O SER H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 89 removed outlier: 3.518A pdb=" N TYR H 89 " --> pdb=" O PRO H 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 43 Proline residue: I 27 - end of helix Processing helix chain 'I' and resid 50 through 65 removed outlier: 3.868A pdb=" N MET I 63 " --> pdb=" O LEU I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 89 Proline residue: I 85 - end of helix removed outlier: 3.526A pdb=" N TYR I 89 " --> pdb=" O PRO I 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 39 removed outlier: 3.592A pdb=" N SER J 13 " --> pdb=" O LEU J 9 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA J 23 " --> pdb=" O ILE J 19 " (cutoff:3.500A) Proline residue: J 27 - end of helix Processing helix chain 'J' and resid 51 through 83 removed outlier: 3.595A pdb=" N THR J 58 " --> pdb=" O ARG J 54 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N HIS J 67 " --> pdb=" O MET J 63 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N TRP J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 89 removed outlier: 3.669A pdb=" N VAL J 87 " --> pdb=" O ARG J 83 " (cutoff:3.500A) 845 hydrogen bonds defined for protein. 2505 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3686 1.34 - 1.46: 2526 1.46 - 1.57: 6099 1.57 - 1.69: 0 1.69 - 1.81: 269 Bond restraints: 12580 Sorted by residual: bond pdb=" C GLU C 187 " pdb=" N PRO C 188 " ideal model delta sigma weight residual 1.336 1.362 -0.026 1.20e-02 6.94e+03 4.77e+00 bond pdb=" CA ILE D 176 " pdb=" CB ILE D 176 " ideal model delta sigma weight residual 1.553 1.540 0.013 7.40e-03 1.83e+04 2.95e+00 bond pdb=" CA VAL E 283 " pdb=" C VAL E 283 " ideal model delta sigma weight residual 1.530 1.513 0.017 1.12e-02 7.97e+03 2.40e+00 bond pdb=" C GLN E 166 " pdb=" N ALA E 167 " ideal model delta sigma weight residual 1.332 1.311 0.021 1.40e-02 5.10e+03 2.32e+00 bond pdb=" CA LEU B 266 " pdb=" C LEU B 266 " ideal model delta sigma weight residual 1.532 1.518 0.014 9.60e-03 1.09e+04 2.21e+00 ... (remaining 12575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 16480 1.99 - 3.97: 465 3.97 - 5.96: 97 5.96 - 7.95: 21 7.95 - 9.93: 3 Bond angle restraints: 17066 Sorted by residual: angle pdb=" N GLN C 162 " pdb=" CA GLN C 162 " pdb=" C GLN C 162 " ideal model delta sigma weight residual 113.88 108.61 5.27 1.23e+00 6.61e-01 1.84e+01 angle pdb=" C ASN C 173 " pdb=" N GLU C 174 " pdb=" CA GLU C 174 " ideal model delta sigma weight residual 121.54 128.96 -7.42 1.91e+00 2.74e-01 1.51e+01 angle pdb=" N THR C 138 " pdb=" CA THR C 138 " pdb=" C THR C 138 " ideal model delta sigma weight residual 109.81 117.75 -7.94 2.21e+00 2.05e-01 1.29e+01 angle pdb=" N VAL A 223 " pdb=" CA VAL A 223 " pdb=" C VAL A 223 " ideal model delta sigma weight residual 113.16 107.90 5.26 1.49e+00 4.50e-01 1.25e+01 angle pdb=" C MET E 263 " pdb=" N MET E 264 " pdb=" CA MET E 264 " ideal model delta sigma weight residual 121.54 128.08 -6.54 1.91e+00 2.74e-01 1.17e+01 ... (remaining 17061 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 6781 17.47 - 34.93: 633 34.93 - 52.40: 119 52.40 - 69.86: 22 69.86 - 87.33: 9 Dihedral angle restraints: 7564 sinusoidal: 2976 harmonic: 4588 Sorted by residual: dihedral pdb=" CA THR C 138 " pdb=" C THR C 138 " pdb=" N PRO C 139 " pdb=" CA PRO C 139 " ideal model delta harmonic sigma weight residual 180.00 112.92 67.08 0 5.00e+00 4.00e-02 1.80e+02 dihedral pdb=" CA THR A 138 " pdb=" C THR A 138 " pdb=" N PRO A 139 " pdb=" CA PRO A 139 " ideal model delta harmonic sigma weight residual -180.00 -130.25 -49.75 0 5.00e+00 4.00e-02 9.90e+01 dihedral pdb=" CA ASN A 173 " pdb=" C ASN A 173 " pdb=" N GLU A 174 " pdb=" CA GLU A 174 " ideal model delta harmonic sigma weight residual -180.00 -144.78 -35.22 0 5.00e+00 4.00e-02 4.96e+01 ... (remaining 7561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1261 0.037 - 0.075: 644 0.075 - 0.112: 173 0.112 - 0.150: 20 0.150 - 0.187: 4 Chirality restraints: 2102 Sorted by residual: chirality pdb=" CB ILE E 128 " pdb=" CA ILE E 128 " pdb=" CG1 ILE E 128 " pdb=" CG2 ILE E 128 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.78e-01 chirality pdb=" CG LEU C 135 " pdb=" CB LEU C 135 " pdb=" CD1 LEU C 135 " pdb=" CD2 LEU C 135 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 7.78e-01 chirality pdb=" CA LEU B 245 " pdb=" N LEU B 245 " pdb=" C LEU B 245 " pdb=" CB LEU B 245 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.51e-01 ... (remaining 2099 not shown) Planarity restraints: 2069 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 138 " 0.074 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO C 139 " -0.194 5.00e-02 4.00e+02 pdb=" CA PRO C 139 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO C 139 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 138 " -0.061 5.00e-02 4.00e+02 9.36e-02 1.40e+01 pdb=" N PRO A 139 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO A 139 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 139 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 137 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.27e+00 pdb=" C GLN C 137 " 0.040 2.00e-02 2.50e+03 pdb=" O GLN C 137 " -0.015 2.00e-02 2.50e+03 pdb=" N THR C 138 " -0.014 2.00e-02 2.50e+03 ... (remaining 2066 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 365 2.69 - 3.24: 14500 3.24 - 3.80: 20368 3.80 - 4.35: 25906 4.35 - 4.90: 41670 Nonbonded interactions: 102809 Sorted by model distance: nonbonded pdb=" O LEU B 149 " pdb=" OG1 THR B 152 " model vdw 2.141 3.040 nonbonded pdb=" O ILE C 114 " pdb=" OG1 THR C 117 " model vdw 2.156 3.040 nonbonded pdb=" O LEU E 288 " pdb=" OG SER E 291 " model vdw 2.157 3.040 nonbonded pdb=" O GLU B 232 " pdb=" OG1 THR B 235 " model vdw 2.181 3.040 nonbonded pdb=" O ILE D 289 " pdb=" OG1 THR D 292 " model vdw 2.195 3.040 ... (remaining 102804 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 113 through 299) selection = (chain 'B' and resid 113 through 299) selection = (chain 'C' and resid 113 through 299) selection = (chain 'D' and resid 113 through 299) selection = chain 'E' } ncs_group { reference = (chain 'G' and (resid 1 through 39 or resid 49 through 89)) selection = (chain 'H' and (resid 1 through 39 or resid 49 through 89)) selection = (chain 'I' and (resid 1 through 39 or resid 49 through 89)) selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.820 Find NCS groups from input model: 0.190 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 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 : 0.007 0.050 12580 Z= 0.320 Angle : 0.871 9.934 17066 Z= 0.487 Chirality : 0.045 0.187 2102 Planarity : 0.005 0.112 2069 Dihedral : 14.287 87.331 4556 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.76 % Favored : 91.86 % Rotamer: Outliers : 0.07 % Allowed : 7.53 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.13 % 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: -3.54 (0.18), residues: 1547 helix: -1.82 (0.13), residues: 1210 sheet: None (None), residues: 0 loop : -3.65 (0.31), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 54 TYR 0.012 0.001 TYR F 241 PHE 0.022 0.002 PHE B 119 TRP 0.016 0.002 TRP E 286 HIS 0.004 0.002 HIS F 144 Details of bonding type rmsd covalent geometry : bond 0.00663 (12580) covalent geometry : angle 0.87071 (17066) hydrogen bonds : bond 0.17886 ( 845) hydrogen bonds : angle 7.03300 ( 2505) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 355 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8563 (tm-30) REVERT: A 263 MET cc_start: 0.7688 (mtt) cc_final: 0.7396 (mtt) REVERT: B 116 MET cc_start: 0.8254 (mtt) cc_final: 0.8033 (mtm) REVERT: B 183 ASP cc_start: 0.8740 (t0) cc_final: 0.8042 (t0) REVERT: B 193 MET cc_start: 0.8263 (mtp) cc_final: 0.5836 (mtp) REVERT: B 232 GLU cc_start: 0.8324 (tp30) cc_final: 0.7958 (tp30) REVERT: B 261 MET cc_start: 0.8188 (mtm) cc_final: 0.7596 (mtm) REVERT: B 269 MET cc_start: 0.7496 (mmm) cc_final: 0.7289 (tpp) REVERT: B 284 ASP cc_start: 0.8450 (t0) cc_final: 0.8242 (t0) REVERT: C 259 MET cc_start: 0.8416 (mmm) cc_final: 0.7862 (tpp) REVERT: D 116 MET cc_start: 0.7889 (ttm) cc_final: 0.7633 (mmt) REVERT: D 264 MET cc_start: 0.8117 (tmm) cc_final: 0.7896 (tmm) REVERT: D 265 MET cc_start: 0.8369 (tpp) cc_final: 0.6838 (tpp) REVERT: E 138 THR cc_start: 0.8675 (p) cc_final: 0.8414 (p) REVERT: E 142 GLN cc_start: 0.7883 (tt0) cc_final: 0.7680 (tm-30) REVERT: E 174 GLU cc_start: 0.7873 (tp30) cc_final: 0.7605 (tp30) REVERT: E 193 MET cc_start: 0.9014 (mtp) cc_final: 0.8638 (mtm) REVERT: E 245 LEU cc_start: 0.9514 (mt) cc_final: 0.9236 (mt) REVERT: E 264 MET cc_start: 0.7788 (tpp) cc_final: 0.6378 (tpp) REVERT: F 15 TYR cc_start: 0.8181 (m-80) cc_final: 0.6454 (m-10) REVERT: F 25 MET cc_start: 0.8869 (tmm) cc_final: 0.8660 (tmm) REVERT: G 30 LEU cc_start: 0.9491 (mm) cc_final: 0.9161 (tt) REVERT: H 44 ILE cc_start: 0.8684 (mt) cc_final: 0.8480 (mm) REVERT: H 45 ASN cc_start: 0.8346 (t0) cc_final: 0.7383 (t0) REVERT: H 54 ARG cc_start: 0.9006 (ttp-110) cc_final: 0.8691 (mtp-110) REVERT: I 20 MET cc_start: 0.8257 (mtt) cc_final: 0.8002 (mtp) outliers start: 1 outliers final: 1 residues processed: 356 average time/residue: 0.0990 time to fit residues: 52.0616 Evaluate side-chains 235 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 234 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN B 164 ASN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 GLN C 142 GLN ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 GLN ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 ASN F 94 GLN F 251 GLN ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.056780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.046787 restraints weight = 59743.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.048266 restraints weight = 34367.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.049208 restraints weight = 23361.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.049923 restraints weight = 18136.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.050142 restraints weight = 14903.663| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12580 Z= 0.172 Angle : 0.803 11.933 17066 Z= 0.395 Chirality : 0.046 0.185 2102 Planarity : 0.006 0.102 2069 Dihedral : 5.641 64.714 1616 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.62 % Favored : 94.18 % Rotamer: Outliers : 0.22 % Allowed : 6.08 % Favored : 93.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.13 % 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: -1.30 (0.20), residues: 1547 helix: -0.18 (0.14), residues: 1239 sheet: None (None), residues: 0 loop : -3.34 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 54 TYR 0.012 0.001 TYR F 241 PHE 0.033 0.002 PHE D 160 TRP 0.014 0.002 TRP E 286 HIS 0.006 0.001 HIS H 67 Details of bonding type rmsd covalent geometry : bond 0.00384 (12580) covalent geometry : angle 0.80293 (17066) hydrogen bonds : bond 0.04647 ( 845) hydrogen bonds : angle 4.53333 ( 2505) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 349 time to evaluate : 0.491 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: A 131 GLN cc_start: 0.8949 (tm-30) cc_final: 0.8676 (tm-30) REVERT: A 133 MET cc_start: 0.8595 (ptp) cc_final: 0.8393 (ptp) REVERT: A 141 ASN cc_start: 0.8448 (m-40) cc_final: 0.8218 (m-40) REVERT: A 259 MET cc_start: 0.9146 (mmm) cc_final: 0.8439 (mmt) REVERT: A 263 MET cc_start: 0.7188 (mtt) cc_final: 0.6712 (mtt) REVERT: B 193 MET cc_start: 0.8363 (mtp) cc_final: 0.7894 (mtm) REVERT: B 269 MET cc_start: 0.7797 (mmm) cc_final: 0.7488 (tpp) REVERT: C 116 MET cc_start: 0.8316 (ptt) cc_final: 0.7974 (tmm) REVERT: C 193 MET cc_start: 0.8956 (mtm) cc_final: 0.8685 (mtm) REVERT: C 207 GLU cc_start: 0.8499 (pp20) cc_final: 0.8133 (pp20) REVERT: C 221 MET cc_start: 0.7515 (pmm) cc_final: 0.7257 (pmm) REVERT: D 116 MET cc_start: 0.7994 (ttm) cc_final: 0.7709 (mmt) REVERT: D 232 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8171 (tp30) REVERT: E 138 THR cc_start: 0.8787 (p) cc_final: 0.8412 (p) REVERT: E 174 GLU cc_start: 0.7799 (tp30) cc_final: 0.7472 (tp30) REVERT: E 193 MET cc_start: 0.8802 (mtp) cc_final: 0.8286 (mtm) REVERT: E 208 MET cc_start: 0.8815 (mtt) cc_final: 0.8614 (mtt) REVERT: E 245 LEU cc_start: 0.9396 (mt) cc_final: 0.9176 (mt) REVERT: F 15 TYR cc_start: 0.8365 (m-80) cc_final: 0.7996 (m-10) REVERT: F 250 GLU cc_start: 0.8540 (pt0) cc_final: 0.8263 (pt0) REVERT: G 18 LEU cc_start: 0.9380 (tt) cc_final: 0.9133 (tt) REVERT: G 20 MET cc_start: 0.8706 (mtm) cc_final: 0.8068 (mtp) REVERT: G 63 MET cc_start: 0.8481 (tpt) cc_final: 0.7861 (tmm) REVERT: H 45 ASN cc_start: 0.8585 (t0) cc_final: 0.8365 (t0) REVERT: H 80 MET cc_start: 0.9035 (mmp) cc_final: 0.8620 (tpp) REVERT: J 25 ILE cc_start: 0.9546 (mm) cc_final: 0.9297 (mm) outliers start: 3 outliers final: 1 residues processed: 351 average time/residue: 0.0929 time to fit residues: 48.8112 Evaluate side-chains 247 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 246 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 143 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 45 optimal weight: 0.0020 chunk 65 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 43 optimal weight: 30.0000 overall best weight: 3.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 ASN ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN F 128 GLN I 86 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.056150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.046100 restraints weight = 60809.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.047536 restraints weight = 35525.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.048521 restraints weight = 24464.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.049209 restraints weight = 18670.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.049737 restraints weight = 15370.324| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 12580 Z= 0.201 Angle : 0.786 9.316 17066 Z= 0.386 Chirality : 0.046 0.195 2102 Planarity : 0.005 0.106 2069 Dihedral : 5.584 64.675 1616 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.82 % Favored : 94.05 % Rotamer: Outliers : 0.36 % Allowed : 4.92 % Favored : 94.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.07 % 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: -0.63 (0.21), residues: 1547 helix: 0.32 (0.14), residues: 1241 sheet: None (None), residues: 0 loop : -3.28 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 35 TYR 0.010 0.001 TYR F 170 PHE 0.032 0.002 PHE B 244 TRP 0.014 0.002 TRP G 68 HIS 0.003 0.001 HIS F 144 Details of bonding type rmsd covalent geometry : bond 0.00464 (12580) covalent geometry : angle 0.78564 (17066) hydrogen bonds : bond 0.04240 ( 845) hydrogen bonds : angle 4.41885 ( 2505) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 317 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8704 (ttm170) cc_final: 0.8267 (ttm-80) REVERT: A 131 GLN cc_start: 0.8987 (tm-30) cc_final: 0.8775 (tm-30) REVERT: A 141 ASN cc_start: 0.8487 (m-40) cc_final: 0.8210 (m-40) REVERT: A 232 GLU cc_start: 0.8841 (tp30) cc_final: 0.8553 (mm-30) REVERT: A 242 MET cc_start: 0.8025 (mtm) cc_final: 0.7688 (mtm) REVERT: A 259 MET cc_start: 0.9059 (mmm) cc_final: 0.8453 (mmt) REVERT: A 263 MET cc_start: 0.7341 (mtt) cc_final: 0.6692 (mtt) REVERT: A 264 MET cc_start: 0.8213 (ttp) cc_final: 0.7744 (ptm) REVERT: A 265 MET cc_start: 0.8117 (mmm) cc_final: 0.7869 (tpp) REVERT: A 277 LEU cc_start: 0.9272 (mt) cc_final: 0.9059 (mt) REVERT: B 193 MET cc_start: 0.8704 (mtp) cc_final: 0.8205 (mtm) REVERT: B 264 MET cc_start: 0.8298 (mtm) cc_final: 0.7849 (mtm) REVERT: B 269 MET cc_start: 0.7812 (mmm) cc_final: 0.7450 (tpp) REVERT: C 112 MET cc_start: 0.7544 (ptm) cc_final: 0.7304 (ptm) REVERT: C 116 MET cc_start: 0.8373 (ptt) cc_final: 0.8025 (tmm) REVERT: C 126 MET cc_start: 0.8566 (mtm) cc_final: 0.8304 (mtm) REVERT: C 156 MET cc_start: 0.8660 (mmm) cc_final: 0.8113 (mmm) REVERT: C 221 MET cc_start: 0.7570 (pmm) cc_final: 0.7341 (pmm) REVERT: C 279 LEU cc_start: 0.9242 (tp) cc_final: 0.8682 (mm) REVERT: D 116 MET cc_start: 0.7960 (ttm) cc_final: 0.7700 (mmt) REVERT: D 232 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8204 (mm-30) REVERT: D 278 MET cc_start: 0.8370 (ttt) cc_final: 0.8082 (ttp) REVERT: E 174 GLU cc_start: 0.7681 (tp30) cc_final: 0.7312 (tp30) REVERT: E 245 LEU cc_start: 0.9440 (mt) cc_final: 0.9200 (mt) REVERT: E 264 MET cc_start: 0.8032 (tpp) cc_final: 0.7738 (tpp) REVERT: F 15 TYR cc_start: 0.8261 (m-80) cc_final: 0.7853 (m-10) REVERT: F 22 ILE cc_start: 0.9509 (mt) cc_final: 0.9286 (tp) REVERT: F 25 MET cc_start: 0.8980 (tmm) cc_final: 0.8640 (tmm) REVERT: H 45 ASN cc_start: 0.8664 (t0) cc_final: 0.8389 (t0) REVERT: H 54 ARG cc_start: 0.9018 (ttp-110) cc_final: 0.8429 (mtp-110) REVERT: I 74 MET cc_start: 0.8530 (mmm) cc_final: 0.8067 (tpp) REVERT: J 25 ILE cc_start: 0.9538 (mm) cc_final: 0.9328 (mm) REVERT: J 54 ARG cc_start: 0.9002 (ttp-110) cc_final: 0.8329 (mtm110) REVERT: J 74 MET cc_start: 0.9157 (mtp) cc_final: 0.8934 (mmm) outliers start: 5 outliers final: 0 residues processed: 318 average time/residue: 0.0903 time to fit residues: 43.7420 Evaluate side-chains 241 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 124 optimal weight: 0.1980 chunk 129 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 45 optimal weight: 40.0000 chunk 0 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 41 optimal weight: 0.2980 chunk 110 optimal weight: 6.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.057104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.046882 restraints weight = 60244.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.048343 restraints weight = 35072.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.049328 restraints weight = 24183.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.050026 restraints weight = 18481.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.050552 restraints weight = 15319.753| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12580 Z= 0.171 Angle : 0.780 10.284 17066 Z= 0.377 Chirality : 0.045 0.207 2102 Planarity : 0.005 0.095 2069 Dihedral : 5.527 63.911 1616 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.82 % Favored : 93.99 % Rotamer: Outliers : 0.07 % Allowed : 3.98 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.07 % 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: -0.20 (0.21), residues: 1547 helix: 0.63 (0.15), residues: 1244 sheet: None (None), residues: 0 loop : -3.24 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 54 TYR 0.010 0.001 TYR F 170 PHE 0.030 0.002 PHE D 244 TRP 0.016 0.002 TRP G 68 HIS 0.002 0.001 HIS F 144 Details of bonding type rmsd covalent geometry : bond 0.00399 (12580) covalent geometry : angle 0.77959 (17066) hydrogen bonds : bond 0.03917 ( 845) hydrogen bonds : angle 4.27704 ( 2505) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 326 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8742 (ttm170) cc_final: 0.8299 (ttm-80) REVERT: A 131 GLN cc_start: 0.8967 (tm-30) cc_final: 0.8752 (tm-30) REVERT: A 141 ASN cc_start: 0.8272 (m-40) cc_final: 0.8023 (m-40) REVERT: A 232 GLU cc_start: 0.8865 (tp30) cc_final: 0.8601 (mm-30) REVERT: A 242 MET cc_start: 0.8108 (mtm) cc_final: 0.7857 (mtm) REVERT: A 259 MET cc_start: 0.9054 (mmm) cc_final: 0.8471 (mmt) REVERT: A 263 MET cc_start: 0.7585 (mtt) cc_final: 0.6912 (mtt) REVERT: A 264 MET cc_start: 0.8273 (ttp) cc_final: 0.7672 (ptm) REVERT: A 265 MET cc_start: 0.7958 (mmm) cc_final: 0.7726 (tpp) REVERT: A 277 LEU cc_start: 0.9260 (mt) cc_final: 0.9034 (mt) REVERT: B 193 MET cc_start: 0.8628 (mtp) cc_final: 0.8157 (mtm) REVERT: B 264 MET cc_start: 0.8287 (mtm) cc_final: 0.7670 (mtm) REVERT: B 269 MET cc_start: 0.7761 (mmm) cc_final: 0.7446 (tpp) REVERT: C 112 MET cc_start: 0.7388 (ptm) cc_final: 0.7188 (ptm) REVERT: C 116 MET cc_start: 0.8468 (ptt) cc_final: 0.7956 (tmm) REVERT: C 156 MET cc_start: 0.8663 (mmm) cc_final: 0.8125 (mmm) REVERT: C 208 MET cc_start: 0.8736 (mtp) cc_final: 0.8472 (mtp) REVERT: C 221 MET cc_start: 0.7625 (pmm) cc_final: 0.7419 (pmm) REVERT: C 232 GLU cc_start: 0.8897 (tp30) cc_final: 0.8555 (tp30) REVERT: C 279 LEU cc_start: 0.9181 (tp) cc_final: 0.8671 (mm) REVERT: D 116 MET cc_start: 0.7941 (ttm) cc_final: 0.7726 (mmt) REVERT: D 232 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8205 (mm-30) REVERT: D 278 MET cc_start: 0.8376 (ttt) cc_final: 0.8060 (ttp) REVERT: E 174 GLU cc_start: 0.7652 (tp30) cc_final: 0.7258 (tp30) REVERT: E 245 LEU cc_start: 0.9437 (mt) cc_final: 0.9186 (mt) REVERT: E 248 LEU cc_start: 0.9188 (tt) cc_final: 0.8949 (tt) REVERT: E 264 MET cc_start: 0.8041 (tpp) cc_final: 0.7784 (tpp) REVERT: F 15 TYR cc_start: 0.8401 (m-80) cc_final: 0.8107 (m-10) REVERT: F 22 ILE cc_start: 0.9477 (mt) cc_final: 0.9269 (tp) REVERT: F 25 MET cc_start: 0.8912 (tmm) cc_final: 0.8650 (tmm) REVERT: F 250 GLU cc_start: 0.8422 (pt0) cc_final: 0.8100 (pt0) REVERT: G 63 MET cc_start: 0.8670 (tpp) cc_final: 0.7739 (tmm) REVERT: H 45 ASN cc_start: 0.8677 (t0) cc_final: 0.8092 (t0) REVERT: H 52 LEU cc_start: 0.9124 (tt) cc_final: 0.8666 (tp) REVERT: H 54 ARG cc_start: 0.9069 (ttp-110) cc_final: 0.8795 (ttp-110) REVERT: I 59 LEU cc_start: 0.9140 (mt) cc_final: 0.8837 (mt) REVERT: I 74 MET cc_start: 0.8544 (mmm) cc_final: 0.8024 (tpp) REVERT: J 25 ILE cc_start: 0.9523 (mm) cc_final: 0.9306 (mm) REVERT: J 54 ARG cc_start: 0.9045 (ttp-110) cc_final: 0.8333 (mtm110) outliers start: 1 outliers final: 0 residues processed: 326 average time/residue: 0.0858 time to fit residues: 42.7704 Evaluate side-chains 247 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 66 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 chunk 129 optimal weight: 9.9990 chunk 19 optimal weight: 20.0000 chunk 64 optimal weight: 0.0470 chunk 16 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 GLN ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.057951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.047625 restraints weight = 59279.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.049100 restraints weight = 34651.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.050108 restraints weight = 23846.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.050811 restraints weight = 18283.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.051342 restraints weight = 15050.818| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 12580 Z= 0.155 Angle : 0.771 10.278 17066 Z= 0.376 Chirality : 0.044 0.194 2102 Planarity : 0.005 0.096 2069 Dihedral : 5.468 62.623 1616 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.24 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.07 % 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: 0.17 (0.22), residues: 1547 helix: 0.90 (0.15), residues: 1230 sheet: None (None), residues: 0 loop : -2.97 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 54 TYR 0.010 0.001 TYR F 44 PHE 0.018 0.001 PHE B 119 TRP 0.016 0.002 TRP H 68 HIS 0.002 0.001 HIS F 144 Details of bonding type rmsd covalent geometry : bond 0.00350 (12580) covalent geometry : angle 0.77059 (17066) hydrogen bonds : bond 0.03854 ( 845) hydrogen bonds : angle 4.19530 ( 2505) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8772 (ttm170) cc_final: 0.8322 (ttm-80) REVERT: A 131 GLN cc_start: 0.9024 (tm-30) cc_final: 0.8812 (tm-30) REVERT: A 141 ASN cc_start: 0.8162 (m-40) cc_final: 0.7881 (m-40) REVERT: A 232 GLU cc_start: 0.8884 (tp30) cc_final: 0.8663 (mm-30) REVERT: A 259 MET cc_start: 0.9006 (mmm) cc_final: 0.8432 (mmt) REVERT: A 263 MET cc_start: 0.7520 (mtt) cc_final: 0.6917 (mtt) REVERT: B 149 LEU cc_start: 0.9120 (tp) cc_final: 0.8843 (tt) REVERT: B 193 MET cc_start: 0.8528 (mtp) cc_final: 0.8054 (mtm) REVERT: B 261 MET cc_start: 0.7685 (mtm) cc_final: 0.7454 (mtp) REVERT: B 264 MET cc_start: 0.8007 (mtm) cc_final: 0.7777 (mtm) REVERT: B 269 MET cc_start: 0.7663 (mmm) cc_final: 0.7360 (tpp) REVERT: C 115 LEU cc_start: 0.9268 (mm) cc_final: 0.8925 (mt) REVERT: C 116 MET cc_start: 0.8377 (ptt) cc_final: 0.7937 (tmm) REVERT: C 232 GLU cc_start: 0.8863 (tp30) cc_final: 0.8518 (tp30) REVERT: C 259 MET cc_start: 0.8483 (tpp) cc_final: 0.8182 (tpp) REVERT: C 279 LEU cc_start: 0.9157 (tp) cc_final: 0.8655 (mm) REVERT: D 116 MET cc_start: 0.7893 (ttm) cc_final: 0.7654 (mmt) REVERT: D 232 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8179 (tp30) REVERT: D 278 MET cc_start: 0.8374 (ttt) cc_final: 0.8027 (ttp) REVERT: E 208 MET cc_start: 0.8884 (mtt) cc_final: 0.8498 (mtt) REVERT: E 245 LEU cc_start: 0.9411 (mt) cc_final: 0.9162 (mt) REVERT: F 22 ILE cc_start: 0.9482 (mt) cc_final: 0.9281 (tp) REVERT: F 98 MET cc_start: 0.8561 (mmt) cc_final: 0.8263 (mmt) REVERT: F 102 ILE cc_start: 0.9208 (mt) cc_final: 0.8887 (mt) REVERT: F 114 MET cc_start: 0.8677 (tmm) cc_final: 0.8348 (tmm) REVERT: F 250 GLU cc_start: 0.8501 (pt0) cc_final: 0.8190 (pt0) REVERT: G 30 LEU cc_start: 0.9541 (mm) cc_final: 0.9175 (tt) REVERT: H 45 ASN cc_start: 0.8576 (t0) cc_final: 0.8360 (t0) REVERT: H 52 LEU cc_start: 0.9149 (tt) cc_final: 0.8789 (tp) REVERT: H 74 MET cc_start: 0.8827 (mmm) cc_final: 0.8366 (mmm) REVERT: I 59 LEU cc_start: 0.9088 (mt) cc_final: 0.8753 (mt) REVERT: I 74 MET cc_start: 0.8539 (mmm) cc_final: 0.8037 (tpp) REVERT: J 20 MET cc_start: 0.9443 (mtp) cc_final: 0.8975 (mtt) REVERT: J 25 ILE cc_start: 0.9536 (mm) cc_final: 0.9327 (mm) REVERT: J 54 ARG cc_start: 0.9030 (ttp-110) cc_final: 0.8260 (mtm110) REVERT: J 57 ILE cc_start: 0.9273 (mp) cc_final: 0.9042 (mp) outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.0886 time to fit residues: 44.6268 Evaluate side-chains 249 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 5 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 127 optimal weight: 0.0470 chunk 58 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 overall best weight: 1.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 GLN C 180 GLN ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 GLN ** I 86 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 = 0.3293 r_free = 0.3293 target = 0.058337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.047905 restraints weight = 59710.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.049400 restraints weight = 34986.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.050406 restraints weight = 24135.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.051100 restraints weight = 18481.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.051415 restraints weight = 15339.236| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12580 Z= 0.154 Angle : 0.778 11.515 17066 Z= 0.379 Chirality : 0.045 0.229 2102 Planarity : 0.005 0.091 2069 Dihedral : 5.403 61.583 1616 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.62 % Favored : 94.25 % Rotamer: Outliers : 0.07 % Allowed : 2.82 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.07 % 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: 0.41 (0.22), residues: 1547 helix: 1.07 (0.15), residues: 1231 sheet: None (None), residues: 0 loop : -2.93 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 54 TYR 0.009 0.001 TYR F 241 PHE 0.037 0.001 PHE J 10 TRP 0.014 0.002 TRP G 68 HIS 0.002 0.001 HIS F 144 Details of bonding type rmsd covalent geometry : bond 0.00350 (12580) covalent geometry : angle 0.77808 (17066) hydrogen bonds : bond 0.03787 ( 845) hydrogen bonds : angle 4.12275 ( 2505) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 320 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8845 (ttm170) cc_final: 0.8322 (ttm-80) REVERT: A 232 GLU cc_start: 0.8848 (tp30) cc_final: 0.8586 (tp30) REVERT: A 259 MET cc_start: 0.8980 (mmm) cc_final: 0.8461 (mmt) REVERT: A 263 MET cc_start: 0.7603 (mtt) cc_final: 0.7180 (mtt) REVERT: A 277 LEU cc_start: 0.9169 (mt) cc_final: 0.8948 (mt) REVERT: B 149 LEU cc_start: 0.9084 (tp) cc_final: 0.8777 (tt) REVERT: B 193 MET cc_start: 0.8479 (mtp) cc_final: 0.7994 (mtm) REVERT: B 269 MET cc_start: 0.7692 (mmm) cc_final: 0.7407 (tpp) REVERT: C 115 LEU cc_start: 0.9280 (mm) cc_final: 0.8931 (mt) REVERT: C 116 MET cc_start: 0.8482 (ptt) cc_final: 0.7984 (tmm) REVERT: C 232 GLU cc_start: 0.8796 (tp30) cc_final: 0.8457 (tp30) REVERT: C 259 MET cc_start: 0.8595 (tpp) cc_final: 0.8034 (mmm) REVERT: C 279 LEU cc_start: 0.9218 (tp) cc_final: 0.8679 (mm) REVERT: D 116 MET cc_start: 0.7899 (ttm) cc_final: 0.7657 (mmt) REVERT: D 232 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8180 (mm-30) REVERT: D 278 MET cc_start: 0.8267 (ttt) cc_final: 0.7946 (ttp) REVERT: E 138 THR cc_start: 0.8872 (p) cc_final: 0.8537 (p) REVERT: E 208 MET cc_start: 0.8892 (mtt) cc_final: 0.8494 (mtm) REVERT: E 245 LEU cc_start: 0.9395 (mt) cc_final: 0.9158 (mt) REVERT: F 25 MET cc_start: 0.8862 (tmm) cc_final: 0.8394 (tmm) REVERT: F 29 MET cc_start: 0.7637 (ttt) cc_final: 0.7208 (ttt) REVERT: F 77 GLU cc_start: 0.8652 (pp20) cc_final: 0.8359 (pp20) REVERT: F 94 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8364 (mm-40) REVERT: F 102 ILE cc_start: 0.9159 (mt) cc_final: 0.8928 (mt) REVERT: F 114 MET cc_start: 0.8769 (tmm) cc_final: 0.8351 (tmm) REVERT: G 63 MET cc_start: 0.8685 (tpp) cc_final: 0.7725 (tmm) REVERT: H 45 ASN cc_start: 0.8565 (t0) cc_final: 0.8310 (t0) REVERT: H 74 MET cc_start: 0.8889 (mmm) cc_final: 0.8437 (mmm) REVERT: J 25 ILE cc_start: 0.9495 (mm) cc_final: 0.9258 (mm) REVERT: J 54 ARG cc_start: 0.8909 (ttp-110) cc_final: 0.8326 (mtm110) REVERT: J 57 ILE cc_start: 0.9291 (mp) cc_final: 0.9064 (mp) outliers start: 1 outliers final: 0 residues processed: 321 average time/residue: 0.0859 time to fit residues: 42.6753 Evaluate side-chains 252 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 122 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 GLN ** I 86 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 = 0.3250 r_free = 0.3250 target = 0.056818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.046623 restraints weight = 60182.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.048041 restraints weight = 35298.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.049013 restraints weight = 24444.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.049670 restraints weight = 18732.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.049904 restraints weight = 15662.159| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 12580 Z= 0.206 Angle : 0.815 10.662 17066 Z= 0.399 Chirality : 0.046 0.190 2102 Planarity : 0.005 0.095 2069 Dihedral : 5.509 63.054 1616 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.88 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.07 % 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: 0.28 (0.22), residues: 1547 helix: 1.01 (0.15), residues: 1229 sheet: None (None), residues: 0 loop : -3.09 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 54 TYR 0.011 0.001 TYR F 238 PHE 0.017 0.002 PHE B 119 TRP 0.019 0.002 TRP F 176 HIS 0.004 0.001 HIS F 144 Details of bonding type rmsd covalent geometry : bond 0.00479 (12580) covalent geometry : angle 0.81462 (17066) hydrogen bonds : bond 0.03835 ( 845) hydrogen bonds : angle 4.29868 ( 2505) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8881 (ttm170) cc_final: 0.8294 (ttm-80) REVERT: A 193 MET cc_start: 0.8966 (mtm) cc_final: 0.8655 (mtm) REVERT: A 232 GLU cc_start: 0.8827 (tp30) cc_final: 0.8544 (tp30) REVERT: A 259 MET cc_start: 0.8965 (mmm) cc_final: 0.8509 (mmt) REVERT: A 263 MET cc_start: 0.7717 (mtt) cc_final: 0.7427 (mtt) REVERT: B 126 MET cc_start: 0.8982 (mtp) cc_final: 0.8749 (mtm) REVERT: B 149 LEU cc_start: 0.9122 (tp) cc_final: 0.8770 (tt) REVERT: B 193 MET cc_start: 0.8558 (mtp) cc_final: 0.8200 (mtm) REVERT: B 263 MET cc_start: 0.7505 (mpp) cc_final: 0.7100 (mpp) REVERT: B 264 MET cc_start: 0.8118 (mtm) cc_final: 0.7635 (mtm) REVERT: B 269 MET cc_start: 0.7767 (mmm) cc_final: 0.7542 (tpp) REVERT: C 116 MET cc_start: 0.8465 (ptt) cc_final: 0.8080 (tmm) REVERT: C 232 GLU cc_start: 0.8794 (tp30) cc_final: 0.8421 (tp30) REVERT: C 279 LEU cc_start: 0.9225 (tp) cc_final: 0.8720 (mm) REVERT: D 116 MET cc_start: 0.7951 (ttm) cc_final: 0.7705 (mmt) REVERT: D 232 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8211 (mm-30) REVERT: D 278 MET cc_start: 0.8264 (ttt) cc_final: 0.7992 (tmm) REVERT: E 138 THR cc_start: 0.8800 (p) cc_final: 0.8191 (p) REVERT: E 208 MET cc_start: 0.8894 (mtt) cc_final: 0.8583 (mtt) REVERT: E 245 LEU cc_start: 0.9444 (mt) cc_final: 0.9190 (mt) REVERT: F 25 MET cc_start: 0.8894 (tmm) cc_final: 0.8492 (tmm) REVERT: F 29 MET cc_start: 0.7832 (ttt) cc_final: 0.7362 (ttt) REVERT: F 77 GLU cc_start: 0.8714 (pp20) cc_final: 0.8431 (pp20) REVERT: F 98 MET cc_start: 0.8605 (mmt) cc_final: 0.8354 (mmt) REVERT: F 102 ILE cc_start: 0.9130 (mt) cc_final: 0.8900 (mt) REVERT: F 114 MET cc_start: 0.8707 (tmm) cc_final: 0.8361 (tmm) REVERT: F 250 GLU cc_start: 0.8590 (pt0) cc_final: 0.8237 (pt0) REVERT: G 18 LEU cc_start: 0.9386 (tt) cc_final: 0.9057 (tt) REVERT: G 30 LEU cc_start: 0.9539 (mm) cc_final: 0.9183 (tt) REVERT: G 63 MET cc_start: 0.8658 (tpp) cc_final: 0.7856 (tmm) REVERT: H 45 ASN cc_start: 0.8492 (t0) cc_final: 0.8246 (t0) REVERT: H 72 MET cc_start: 0.8839 (pmm) cc_final: 0.8639 (pmm) REVERT: J 25 ILE cc_start: 0.9529 (mm) cc_final: 0.9301 (mm) REVERT: J 54 ARG cc_start: 0.8887 (ttp-110) cc_final: 0.8455 (mtm110) REVERT: J 57 ILE cc_start: 0.9285 (mp) cc_final: 0.9071 (mp) REVERT: J 82 GLU cc_start: 0.8797 (mp0) cc_final: 0.8554 (mp0) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.0847 time to fit residues: 41.3829 Evaluate side-chains 248 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 57 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 109 optimal weight: 0.0040 chunk 66 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.058286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.048179 restraints weight = 59859.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.049623 restraints weight = 35537.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.050546 restraints weight = 24436.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.051352 restraints weight = 19168.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.051871 restraints weight = 15554.757| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 12580 Z= 0.152 Angle : 0.817 10.787 17066 Z= 0.392 Chirality : 0.045 0.177 2102 Planarity : 0.005 0.090 2069 Dihedral : 5.420 60.707 1616 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.72 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.07 % 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: 0.38 (0.22), residues: 1547 helix: 1.07 (0.15), residues: 1226 sheet: None (None), residues: 0 loop : -2.96 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 54 TYR 0.011 0.001 TYR F 19 PHE 0.018 0.001 PHE B 119 TRP 0.012 0.001 TRP I 68 HIS 0.001 0.000 HIS F 144 Details of bonding type rmsd covalent geometry : bond 0.00346 (12580) covalent geometry : angle 0.81720 (17066) hydrogen bonds : bond 0.03723 ( 845) hydrogen bonds : angle 4.16681 ( 2505) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8838 (ttm170) cc_final: 0.8347 (ttm-80) REVERT: A 232 GLU cc_start: 0.8830 (tp30) cc_final: 0.8354 (mm-30) REVERT: A 259 MET cc_start: 0.8933 (mmm) cc_final: 0.8443 (mmt) REVERT: A 263 MET cc_start: 0.7543 (mtt) cc_final: 0.7113 (mtm) REVERT: A 277 LEU cc_start: 0.9151 (mt) cc_final: 0.8938 (mt) REVERT: B 149 LEU cc_start: 0.9110 (tp) cc_final: 0.8795 (tt) REVERT: B 193 MET cc_start: 0.8441 (mtp) cc_final: 0.7775 (mtm) REVERT: B 269 MET cc_start: 0.7733 (mmm) cc_final: 0.7494 (tpp) REVERT: C 116 MET cc_start: 0.8317 (ptt) cc_final: 0.7959 (tmm) REVERT: C 232 GLU cc_start: 0.8764 (tp30) cc_final: 0.8379 (tp30) REVERT: C 279 LEU cc_start: 0.9236 (tp) cc_final: 0.8719 (mm) REVERT: D 232 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8163 (mm-30) REVERT: D 278 MET cc_start: 0.8224 (ttt) cc_final: 0.7954 (tmm) REVERT: E 138 THR cc_start: 0.8794 (p) cc_final: 0.8291 (p) REVERT: E 208 MET cc_start: 0.8827 (mtt) cc_final: 0.8451 (mtm) REVERT: E 245 LEU cc_start: 0.9406 (mt) cc_final: 0.9169 (mt) REVERT: F 25 MET cc_start: 0.8852 (tmm) cc_final: 0.8477 (tmm) REVERT: F 29 MET cc_start: 0.7578 (ttt) cc_final: 0.7135 (ttt) REVERT: F 77 GLU cc_start: 0.8700 (pp20) cc_final: 0.8392 (pp20) REVERT: F 114 MET cc_start: 0.8659 (tmm) cc_final: 0.8352 (tmm) REVERT: F 250 GLU cc_start: 0.8467 (pt0) cc_final: 0.8066 (pt0) REVERT: F 258 LEU cc_start: 0.8899 (tp) cc_final: 0.8691 (tp) REVERT: G 16 LEU cc_start: 0.9215 (tp) cc_final: 0.8996 (tp) REVERT: G 30 LEU cc_start: 0.9501 (mm) cc_final: 0.9152 (tt) REVERT: G 63 MET cc_start: 0.8636 (tpp) cc_final: 0.7737 (tmm) REVERT: H 38 PHE cc_start: 0.8977 (t80) cc_final: 0.8358 (t80) REVERT: H 45 ASN cc_start: 0.8435 (t0) cc_final: 0.8205 (t0) REVERT: H 74 MET cc_start: 0.8767 (mmm) cc_final: 0.8409 (mmm) REVERT: I 44 ILE cc_start: 0.8657 (mm) cc_final: 0.8380 (mm) REVERT: I 45 ASN cc_start: 0.8366 (m-40) cc_final: 0.7556 (p0) REVERT: J 25 ILE cc_start: 0.9485 (mm) cc_final: 0.9232 (mm) REVERT: J 54 ARG cc_start: 0.9056 (ttp-110) cc_final: 0.8336 (mtm110) outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.0877 time to fit residues: 43.8144 Evaluate side-chains 256 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 107 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 GLN ** I 86 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 = 0.3254 r_free = 0.3254 target = 0.056933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.046780 restraints weight = 60838.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.048194 restraints weight = 35998.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.049151 restraints weight = 25026.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.049794 restraints weight = 19284.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.050080 restraints weight = 16144.167| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.137 12580 Z= 0.223 Angle : 0.850 10.300 17066 Z= 0.414 Chirality : 0.047 0.176 2102 Planarity : 0.005 0.094 2069 Dihedral : 5.455 62.796 1616 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.01 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.07 % 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: 0.28 (0.22), residues: 1547 helix: 0.97 (0.15), residues: 1236 sheet: None (None), residues: 0 loop : -2.93 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 54 TYR 0.011 0.001 TYR G 89 PHE 0.060 0.002 PHE B 244 TRP 0.016 0.002 TRP G 68 HIS 0.003 0.001 HIS F 144 Details of bonding type rmsd covalent geometry : bond 0.00533 (12580) covalent geometry : angle 0.84958 (17066) hydrogen bonds : bond 0.03818 ( 845) hydrogen bonds : angle 4.31206 ( 2505) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8884 (ttm170) cc_final: 0.8496 (ttm-80) REVERT: A 193 MET cc_start: 0.8928 (mtm) cc_final: 0.8630 (mtm) REVERT: A 232 GLU cc_start: 0.8812 (tp30) cc_final: 0.8570 (tp30) REVERT: A 259 MET cc_start: 0.8927 (mmm) cc_final: 0.8383 (mmt) REVERT: B 149 LEU cc_start: 0.9147 (tp) cc_final: 0.8818 (tt) REVERT: B 193 MET cc_start: 0.8553 (mtp) cc_final: 0.8093 (mtm) REVERT: B 269 MET cc_start: 0.7793 (mmm) cc_final: 0.7583 (tpp) REVERT: B 287 ASN cc_start: 0.8139 (t0) cc_final: 0.7781 (t0) REVERT: C 116 MET cc_start: 0.8405 (ptt) cc_final: 0.8200 (tmm) REVERT: C 193 MET cc_start: 0.8853 (mtt) cc_final: 0.8648 (mtt) REVERT: C 232 GLU cc_start: 0.8768 (tp30) cc_final: 0.8371 (tp30) REVERT: C 279 LEU cc_start: 0.9245 (tp) cc_final: 0.8751 (mm) REVERT: D 232 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8208 (mm-30) REVERT: D 278 MET cc_start: 0.8235 (ttt) cc_final: 0.7997 (tmm) REVERT: E 138 THR cc_start: 0.8785 (p) cc_final: 0.8367 (p) REVERT: E 208 MET cc_start: 0.8897 (mtt) cc_final: 0.8561 (mtt) REVERT: E 245 LEU cc_start: 0.9450 (mt) cc_final: 0.9203 (mt) REVERT: F 25 MET cc_start: 0.8941 (tmm) cc_final: 0.8501 (tmm) REVERT: F 29 MET cc_start: 0.7923 (ttt) cc_final: 0.7442 (ttt) REVERT: F 77 GLU cc_start: 0.8775 (pp20) cc_final: 0.8436 (pp20) REVERT: F 98 MET cc_start: 0.8831 (mmt) cc_final: 0.8569 (mmt) REVERT: F 114 MET cc_start: 0.8692 (tmm) cc_final: 0.8422 (tmm) REVERT: F 250 GLU cc_start: 0.8690 (pt0) cc_final: 0.8141 (pt0) REVERT: G 30 LEU cc_start: 0.9538 (mm) cc_final: 0.9177 (tt) REVERT: G 58 THR cc_start: 0.9317 (t) cc_final: 0.9081 (m) REVERT: G 63 MET cc_start: 0.8666 (tpp) cc_final: 0.7909 (tmm) REVERT: H 5 ILE cc_start: 0.8884 (tp) cc_final: 0.7957 (tp) REVERT: H 38 PHE cc_start: 0.9008 (t80) cc_final: 0.8420 (t80) REVERT: H 45 ASN cc_start: 0.8532 (t0) cc_final: 0.8316 (t0) REVERT: H 74 MET cc_start: 0.8860 (mmm) cc_final: 0.8424 (mmm) REVERT: J 25 ILE cc_start: 0.9511 (mm) cc_final: 0.9257 (mm) REVERT: J 82 GLU cc_start: 0.8744 (mp0) cc_final: 0.8533 (mp0) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.0873 time to fit residues: 40.9690 Evaluate side-chains 239 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 113 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.058017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.047991 restraints weight = 60713.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.049436 restraints weight = 35503.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.050434 restraints weight = 24528.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.051172 restraints weight = 18841.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.051715 restraints weight = 15353.524| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 12580 Z= 0.167 Angle : 0.845 13.684 17066 Z= 0.407 Chirality : 0.046 0.198 2102 Planarity : 0.005 0.091 2069 Dihedral : 5.453 60.966 1616 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.04 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.22), residues: 1547 helix: 1.07 (0.15), residues: 1226 sheet: None (None), residues: 0 loop : -3.00 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 54 TYR 0.010 0.001 TYR F 241 PHE 0.053 0.002 PHE B 244 TRP 0.015 0.001 TRP G 68 HIS 0.002 0.000 HIS F 144 Details of bonding type rmsd covalent geometry : bond 0.00400 (12580) covalent geometry : angle 0.84524 (17066) hydrogen bonds : bond 0.03795 ( 845) hydrogen bonds : angle 4.25708 ( 2505) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8851 (ttm170) cc_final: 0.8229 (ttm-80) REVERT: A 193 MET cc_start: 0.8869 (mtm) cc_final: 0.8644 (mtm) REVERT: A 232 GLU cc_start: 0.8780 (tp30) cc_final: 0.8542 (tp30) REVERT: A 259 MET cc_start: 0.8919 (mmm) cc_final: 0.8325 (mmt) REVERT: B 149 LEU cc_start: 0.9149 (tp) cc_final: 0.8800 (tt) REVERT: B 193 MET cc_start: 0.8569 (mtp) cc_final: 0.8012 (mtm) REVERT: B 269 MET cc_start: 0.7801 (mmm) cc_final: 0.7571 (tpp) REVERT: B 287 ASN cc_start: 0.8110 (t0) cc_final: 0.7609 (t0) REVERT: C 115 LEU cc_start: 0.9218 (mm) cc_final: 0.8873 (mp) REVERT: C 116 MET cc_start: 0.8404 (ptt) cc_final: 0.8185 (tmm) REVERT: C 129 LEU cc_start: 0.9622 (tt) cc_final: 0.9240 (pp) REVERT: C 193 MET cc_start: 0.8808 (mtt) cc_final: 0.8595 (mtt) REVERT: C 232 GLU cc_start: 0.8757 (tp30) cc_final: 0.8375 (tp30) REVERT: C 279 LEU cc_start: 0.9187 (tp) cc_final: 0.8700 (mm) REVERT: D 232 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8191 (mm-30) REVERT: D 278 MET cc_start: 0.8226 (ttt) cc_final: 0.7933 (tmm) REVERT: E 138 THR cc_start: 0.8811 (p) cc_final: 0.8374 (p) REVERT: E 208 MET cc_start: 0.8825 (mtt) cc_final: 0.8449 (mtm) REVERT: E 245 LEU cc_start: 0.9419 (mt) cc_final: 0.9189 (mt) REVERT: E 263 MET cc_start: 0.8086 (tpp) cc_final: 0.7835 (tpp) REVERT: F 25 MET cc_start: 0.8948 (tmm) cc_final: 0.8491 (tmm) REVERT: F 29 MET cc_start: 0.7711 (ttt) cc_final: 0.7220 (ttt) REVERT: F 77 GLU cc_start: 0.8764 (pp20) cc_final: 0.8418 (pp20) REVERT: F 114 MET cc_start: 0.8724 (tmm) cc_final: 0.8419 (tmm) REVERT: F 250 GLU cc_start: 0.8547 (pt0) cc_final: 0.8197 (pt0) REVERT: F 258 LEU cc_start: 0.8896 (tp) cc_final: 0.8674 (tp) REVERT: G 1 MET cc_start: 0.6835 (mmm) cc_final: 0.6590 (mmm) REVERT: G 30 LEU cc_start: 0.9562 (mm) cc_final: 0.9204 (tt) REVERT: G 58 THR cc_start: 0.9302 (t) cc_final: 0.9089 (m) REVERT: G 63 MET cc_start: 0.8651 (tpp) cc_final: 0.7825 (tmm) REVERT: H 5 ILE cc_start: 0.8793 (tp) cc_final: 0.7985 (tp) REVERT: H 38 PHE cc_start: 0.8991 (t80) cc_final: 0.8396 (t80) REVERT: H 45 ASN cc_start: 0.8478 (t0) cc_final: 0.8271 (t0) REVERT: H 72 MET cc_start: 0.8839 (pmm) cc_final: 0.8566 (pmm) REVERT: H 74 MET cc_start: 0.8772 (mmm) cc_final: 0.8422 (mmm) REVERT: I 44 ILE cc_start: 0.8654 (mm) cc_final: 0.8376 (mm) REVERT: I 45 ASN cc_start: 0.8339 (m-40) cc_final: 0.7550 (p0) REVERT: J 25 ILE cc_start: 0.9483 (mm) cc_final: 0.9196 (mm) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.0883 time to fit residues: 42.7903 Evaluate side-chains 246 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 129 optimal weight: 0.8980 chunk 139 optimal weight: 0.3980 chunk 50 optimal weight: 0.0040 chunk 77 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 20 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 110 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.059531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.049466 restraints weight = 59476.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.050936 restraints weight = 35010.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.051998 restraints weight = 24195.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.052730 restraints weight = 18278.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.053147 restraints weight = 15079.865| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 12580 Z= 0.153 Angle : 0.832 12.087 17066 Z= 0.400 Chirality : 0.045 0.168 2102 Planarity : 0.005 0.091 2069 Dihedral : 5.378 58.580 1616 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.17 % Favored : 94.76 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.22), residues: 1547 helix: 1.06 (0.15), residues: 1231 sheet: None (None), residues: 0 loop : -3.02 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 54 TYR 0.010 0.001 TYR F 241 PHE 0.048 0.002 PHE B 244 TRP 0.016 0.001 TRP I 68 HIS 0.003 0.001 HIS J 67 Details of bonding type rmsd covalent geometry : bond 0.00348 (12580) covalent geometry : angle 0.83238 (17066) hydrogen bonds : bond 0.03815 ( 845) hydrogen bonds : angle 4.21119 ( 2505) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1734.93 seconds wall clock time: 30 minutes 50.75 seconds (1850.75 seconds total)