Starting phenix.real_space_refine on Wed Jul 30 05:37:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6s3s_10096/07_2025/6s3s_10096.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s3s_10096/07_2025/6s3s_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6s3s_10096/07_2025/6s3s_10096.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s3s_10096/07_2025/6s3s_10096.map" model { file = "/net/cci-nas-00/data/ceres_data/6s3s_10096/07_2025/6s3s_10096.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s3s_10096/07_2025/6s3s_10096.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.24, per 1000 atoms: 0.67 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: 3.16 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.28 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: 3.58 Time building geometry restraints manager: 3.75 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: 1.350 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: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 31.230 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.060 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.050 ------------------------------------------------------------------------------- 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 : 18.71 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.016 0.002 TRP E 286 HIS 0.004 0.002 HIS F 144 PHE 0.022 0.002 PHE B 119 TYR 0.012 0.001 TYR F 241 ARG 0.004 0.000 ARG H 54 Details of bonding type rmsd hydrogen bonds : bond 0.17886 ( 845) hydrogen bonds : angle 7.03300 ( 2505) covalent geometry : bond 0.00663 (12580) covalent geometry : angle 0.87071 (17066) *********************** 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 : 1.496 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: 0.8264 (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: 0.8243 (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: 0.6837 (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: 0.2324 time to fit residues: 119.2322 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 : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 8.9990 chunk 114 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 45 optimal weight: 30.0000 chunk 71 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 128 GLN F 251 GLN ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.056258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.046326 restraints weight = 59678.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.047728 restraints weight = 35097.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.048684 restraints weight = 24373.792| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12580 Z= 0.189 Angle : 0.812 12.039 17066 Z= 0.400 Chirality : 0.047 0.182 2102 Planarity : 0.006 0.103 2069 Dihedral : 5.665 65.288 1616 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.82 % Favored : 93.99 % Rotamer: Outliers : 0.22 % Allowed : 6.44 % Favored : 93.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.20), residues: 1547 helix: -0.21 (0.14), residues: 1238 sheet: None (None), residues: 0 loop : -3.36 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 286 HIS 0.007 0.001 HIS H 67 PHE 0.035 0.002 PHE D 160 TYR 0.012 0.001 TYR F 241 ARG 0.011 0.001 ARG G 54 Details of bonding type rmsd hydrogen bonds : bond 0.04685 ( 845) hydrogen bonds : angle 4.58257 ( 2505) covalent geometry : bond 0.00423 (12580) covalent geometry : angle 0.81229 (17066) *********************** 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 343 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 340 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLN cc_start: 0.8947 (tm-30) cc_final: 0.8682 (tm-30) REVERT: A 133 MET cc_start: 0.8621 (ptp) cc_final: 0.8414 (ptp) REVERT: A 141 ASN cc_start: 0.8503 (m-40) cc_final: 0.8274 (m-40) REVERT: A 259 MET cc_start: 0.9158 (mmm) cc_final: 0.8506 (mmt) REVERT: A 263 MET cc_start: 0.7231 (mtt) cc_final: 0.6749 (mtt) REVERT: A 277 LEU cc_start: 0.9335 (mt) cc_final: 0.9080 (mt) REVERT: B 116 MET cc_start: 0.8162 (mtt) cc_final: 0.7792 (mtm) REVERT: B 269 MET cc_start: 0.7806 (mmm) cc_final: 0.7549 (tpp) REVERT: C 116 MET cc_start: 0.8312 (ptt) cc_final: 0.7922 (tmm) REVERT: C 207 GLU cc_start: 0.8559 (pp20) cc_final: 0.8265 (pp20) REVERT: C 221 MET cc_start: 0.7533 (pmm) cc_final: 0.7281 (pmm) REVERT: D 116 MET cc_start: 0.8021 (ttm) cc_final: 0.7726 (mmt) REVERT: D 232 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8145 (tp30) REVERT: D 264 MET cc_start: 0.8010 (tmm) cc_final: 0.7622 (tmm) REVERT: D 265 MET cc_start: 0.8509 (tpp) cc_final: 0.7891 (tpp) REVERT: E 138 THR cc_start: 0.8827 (p) cc_final: 0.8625 (p) REVERT: E 174 GLU cc_start: 0.7941 (tp30) cc_final: 0.7596 (tp30) REVERT: E 193 MET cc_start: 0.8821 (mtp) cc_final: 0.8273 (mtm) REVERT: E 245 LEU cc_start: 0.9406 (mt) cc_final: 0.9190 (mt) REVERT: E 264 MET cc_start: 0.7425 (tpp) cc_final: 0.6672 (tpp) REVERT: F 15 TYR cc_start: 0.8380 (m-80) cc_final: 0.7718 (m-10) REVERT: F 54 MET cc_start: 0.8206 (tmm) cc_final: 0.7943 (tmm) REVERT: F 98 MET cc_start: 0.8477 (mmt) cc_final: 0.8231 (mmt) REVERT: F 250 GLU cc_start: 0.8585 (pt0) cc_final: 0.8300 (pt0) REVERT: G 20 MET cc_start: 0.8742 (mtm) cc_final: 0.8090 (mtp) REVERT: G 63 MET cc_start: 0.8507 (tpt) cc_final: 0.7890 (tmm) REVERT: H 80 MET cc_start: 0.9051 (mmp) cc_final: 0.8641 (tpp) REVERT: I 86 GLN cc_start: 0.8521 (pp30) cc_final: 0.8286 (pp30) REVERT: J 25 ILE cc_start: 0.9561 (mm) cc_final: 0.9320 (mm) REVERT: J 54 ARG cc_start: 0.8944 (mtm110) cc_final: 0.8707 (mtm-85) outliers start: 3 outliers final: 1 residues processed: 342 average time/residue: 0.2115 time to fit residues: 106.3561 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 : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 113 optimal weight: 8.9990 chunk 96 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 46 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.055136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.044938 restraints weight = 62157.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.046328 restraints weight = 36691.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.047255 restraints weight = 25388.519| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 12580 Z= 0.247 Angle : 0.822 10.022 17066 Z= 0.403 Chirality : 0.047 0.198 2102 Planarity : 0.006 0.109 2069 Dihedral : 5.677 65.908 1616 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.46 % Favored : 93.41 % Rotamer: Outliers : 0.29 % Allowed : 5.72 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.21), residues: 1547 helix: 0.29 (0.14), residues: 1237 sheet: None (None), residues: 0 loop : -3.29 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 286 HIS 0.004 0.002 HIS F 144 PHE 0.029 0.002 PHE B 244 TYR 0.011 0.001 TYR F 238 ARG 0.004 0.000 ARG F 35 Details of bonding type rmsd hydrogen bonds : bond 0.04368 ( 845) hydrogen bonds : angle 4.53816 ( 2505) covalent geometry : bond 0.00567 (12580) covalent geometry : angle 0.82153 (17066) *********************** 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: 4 poor density : 318 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLN cc_start: 0.8991 (tm-30) cc_final: 0.8766 (tm-30) REVERT: A 141 ASN cc_start: 0.8583 (m-40) cc_final: 0.8351 (m-40) REVERT: A 259 MET cc_start: 0.9040 (mmm) cc_final: 0.8466 (mmt) REVERT: A 263 MET cc_start: 0.7505 (mtt) cc_final: 0.6967 (mtt) REVERT: A 264 MET cc_start: 0.8470 (ttp) cc_final: 0.8004 (ptm) REVERT: B 116 MET cc_start: 0.8171 (mtt) cc_final: 0.7813 (mtm) REVERT: B 264 MET cc_start: 0.8304 (mtm) cc_final: 0.7870 (mtm) REVERT: B 269 MET cc_start: 0.7862 (mmm) cc_final: 0.7558 (tpp) REVERT: C 112 MET cc_start: 0.7599 (ptm) cc_final: 0.7357 (ptm) REVERT: C 116 MET cc_start: 0.8616 (ptt) cc_final: 0.8216 (tmm) REVERT: C 126 MET cc_start: 0.8623 (mtm) cc_final: 0.8379 (mtm) REVERT: C 156 MET cc_start: 0.8738 (mmm) cc_final: 0.8190 (mmm) REVERT: C 259 MET cc_start: 0.8685 (tpp) cc_final: 0.8255 (tpp) REVERT: C 279 LEU cc_start: 0.9256 (tp) cc_final: 0.8730 (mm) REVERT: D 116 MET cc_start: 0.8015 (ttm) cc_final: 0.7739 (mmt) REVERT: D 232 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8241 (mm-30) REVERT: D 265 MET cc_start: 0.8509 (tpp) cc_final: 0.8023 (mmt) REVERT: E 174 GLU cc_start: 0.7853 (tp30) cc_final: 0.7482 (tp30) REVERT: E 245 LEU cc_start: 0.9455 (mt) cc_final: 0.9213 (mt) REVERT: E 264 MET cc_start: 0.7562 (tpp) cc_final: 0.7029 (tpp) REVERT: F 15 TYR cc_start: 0.8498 (m-80) cc_final: 0.8060 (m-10) REVERT: F 22 ILE cc_start: 0.9509 (mt) cc_final: 0.9298 (tp) REVERT: F 25 MET cc_start: 0.8993 (tmm) cc_final: 0.8657 (tmm) REVERT: F 54 MET cc_start: 0.8259 (tmm) cc_final: 0.8045 (tmm) REVERT: F 205 MET cc_start: 0.8900 (mtm) cc_final: 0.8696 (mtm) REVERT: H 54 ARG cc_start: 0.9043 (ttp-110) cc_final: 0.8494 (mtp-110) REVERT: I 59 LEU cc_start: 0.9208 (mt) cc_final: 0.8944 (mt) REVERT: I 74 MET cc_start: 0.8607 (mmm) cc_final: 0.8132 (tpp) REVERT: I 86 GLN cc_start: 0.8606 (pp30) cc_final: 0.8392 (pp30) REVERT: J 25 ILE cc_start: 0.9576 (mm) cc_final: 0.9376 (mm) REVERT: J 54 ARG cc_start: 0.9090 (mtm110) cc_final: 0.8665 (mtp-110) REVERT: J 82 GLU cc_start: 0.8897 (mp0) cc_final: 0.8692 (mp0) outliers start: 4 outliers final: 1 residues processed: 319 average time/residue: 0.2166 time to fit residues: 102.9431 Evaluate side-chains 240 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 239 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 5 optimal weight: 8.9990 chunk 86 optimal weight: 0.0870 chunk 140 optimal weight: 7.9990 chunk 114 optimal weight: 20.0000 chunk 101 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 90 optimal weight: 9.9990 chunk 118 optimal weight: 0.8980 chunk 141 optimal weight: 7.9990 overall best weight: 2.1760 ------------------------------------------------------------------------------- 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 H 39 GLN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.056625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.046507 restraints weight = 59824.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.047991 restraints weight = 34566.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.048929 restraints weight = 23555.265| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 12580 Z= 0.164 Angle : 0.778 10.454 17066 Z= 0.380 Chirality : 0.045 0.206 2102 Planarity : 0.005 0.096 2069 Dihedral : 5.563 64.288 1616 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.82 % Favored : 93.99 % Rotamer: Outliers : 0.07 % Allowed : 3.77 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.21), residues: 1547 helix: 0.61 (0.15), residues: 1232 sheet: None (None), residues: 0 loop : -3.07 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 68 HIS 0.002 0.001 HIS F 144 PHE 0.029 0.002 PHE D 244 TYR 0.017 0.001 TYR I 89 ARG 0.004 0.001 ARG I 54 Details of bonding type rmsd hydrogen bonds : bond 0.03976 ( 845) hydrogen bonds : angle 4.30281 ( 2505) covalent geometry : bond 0.00377 (12580) covalent geometry : angle 0.77753 (17066) *********************** 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 325 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 324 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8717 (ttm170) cc_final: 0.8330 (ttm-80) REVERT: A 131 GLN cc_start: 0.8957 (tm-30) cc_final: 0.8738 (tm-30) REVERT: A 141 ASN cc_start: 0.8324 (m-40) cc_final: 0.8053 (m-40) REVERT: A 232 GLU cc_start: 0.8842 (tp30) cc_final: 0.8579 (mm-30) REVERT: A 259 MET cc_start: 0.8993 (mmm) cc_final: 0.8464 (mmt) REVERT: A 263 MET cc_start: 0.7538 (mtt) cc_final: 0.6908 (mtt) REVERT: B 116 MET cc_start: 0.8055 (mtt) cc_final: 0.7821 (mtm) REVERT: B 264 MET cc_start: 0.8360 (mtm) cc_final: 0.8081 (mtm) REVERT: B 269 MET cc_start: 0.7801 (tpt) cc_final: 0.7571 (tpp) REVERT: C 115 LEU cc_start: 0.9344 (mm) cc_final: 0.9002 (mt) REVERT: C 279 LEU cc_start: 0.9178 (tp) cc_final: 0.8598 (mm) REVERT: D 116 MET cc_start: 0.7961 (ttm) cc_final: 0.7709 (mmt) REVERT: D 232 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8199 (mm-30) REVERT: D 278 MET cc_start: 0.8388 (ttt) cc_final: 0.8068 (ttp) REVERT: E 174 GLU cc_start: 0.7746 (tp30) cc_final: 0.7355 (tp30) REVERT: E 245 LEU cc_start: 0.9427 (mt) cc_final: 0.9194 (mt) REVERT: E 264 MET cc_start: 0.7493 (tpp) cc_final: 0.7206 (tpp) REVERT: F 15 TYR cc_start: 0.8477 (m-80) cc_final: 0.8079 (m-10) REVERT: F 25 MET cc_start: 0.8954 (tmm) cc_final: 0.8684 (tmm) REVERT: F 54 MET cc_start: 0.8176 (tmm) cc_final: 0.7972 (tmm) REVERT: F 114 MET cc_start: 0.8441 (ttt) cc_final: 0.8161 (tmm) REVERT: F 250 GLU cc_start: 0.8562 (pt0) cc_final: 0.8198 (pt0) REVERT: I 54 ARG cc_start: 0.9225 (ttm-80) cc_final: 0.8704 (ttm-80) REVERT: I 59 LEU cc_start: 0.9172 (mt) cc_final: 0.8865 (mt) REVERT: I 74 MET cc_start: 0.8551 (mmm) cc_final: 0.8089 (tpp) REVERT: J 25 ILE cc_start: 0.9532 (mm) cc_final: 0.9304 (mm) REVERT: J 54 ARG cc_start: 0.9057 (mtm110) cc_final: 0.8615 (mtp-110) outliers start: 1 outliers final: 0 residues processed: 324 average time/residue: 0.2182 time to fit residues: 104.0135 Evaluate side-chains 242 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 114 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 145 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 213 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.057823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.047586 restraints weight = 59037.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.049047 restraints weight = 34409.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.050027 restraints weight = 23676.589| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12580 Z= 0.155 Angle : 0.775 9.264 17066 Z= 0.380 Chirality : 0.046 0.231 2102 Planarity : 0.005 0.097 2069 Dihedral : 5.464 62.768 1616 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.88 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.22), residues: 1547 helix: 0.82 (0.15), residues: 1238 sheet: None (None), residues: 0 loop : -2.97 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 68 HIS 0.001 0.001 HIS F 144 PHE 0.017 0.001 PHE H 10 TYR 0.010 0.001 TYR F 241 ARG 0.004 0.001 ARG I 54 Details of bonding type rmsd hydrogen bonds : bond 0.03852 ( 845) hydrogen bonds : angle 4.24697 ( 2505) covalent geometry : bond 0.00346 (12580) covalent geometry : angle 0.77538 (17066) *********************** 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 316 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8702 (ttm170) cc_final: 0.8279 (ttm-80) REVERT: A 131 GLN cc_start: 0.9006 (tm-30) cc_final: 0.8792 (tm-30) REVERT: A 141 ASN cc_start: 0.8202 (m-40) cc_final: 0.7905 (m-40) REVERT: A 232 GLU cc_start: 0.8898 (tp30) cc_final: 0.8629 (mm-30) REVERT: A 259 MET cc_start: 0.8946 (mmm) cc_final: 0.8425 (mmt) REVERT: A 263 MET cc_start: 0.7622 (mtt) cc_final: 0.6919 (mtt) REVERT: A 264 MET cc_start: 0.8491 (ttp) cc_final: 0.7897 (ptm) REVERT: B 261 MET cc_start: 0.7715 (mtm) cc_final: 0.7473 (mtp) REVERT: B 264 MET cc_start: 0.8367 (mtm) cc_final: 0.7993 (mtm) REVERT: B 269 MET cc_start: 0.7787 (tpt) cc_final: 0.7428 (tpt) REVERT: C 115 LEU cc_start: 0.9314 (mm) cc_final: 0.9022 (mt) REVERT: C 156 MET cc_start: 0.8600 (mmm) cc_final: 0.8037 (mmm) REVERT: C 279 LEU cc_start: 0.9173 (tp) cc_final: 0.8617 (mm) REVERT: D 116 MET cc_start: 0.7921 (ttm) cc_final: 0.7652 (mmt) REVERT: D 232 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8203 (tp30) REVERT: D 264 MET cc_start: 0.7811 (tmm) cc_final: 0.7315 (tmm) REVERT: D 278 MET cc_start: 0.8349 (ttt) cc_final: 0.8003 (ttp) REVERT: E 245 LEU cc_start: 0.9403 (mt) cc_final: 0.9172 (mt) REVERT: E 264 MET cc_start: 0.7748 (tpp) cc_final: 0.7180 (tpp) REVERT: F 15 TYR cc_start: 0.8514 (m-80) cc_final: 0.8274 (m-10) REVERT: F 25 MET cc_start: 0.8962 (tmm) cc_final: 0.8626 (tmm) REVERT: F 54 MET cc_start: 0.8182 (tmm) cc_final: 0.7978 (tmm) REVERT: F 77 GLU cc_start: 0.8702 (pp20) cc_final: 0.8466 (pp20) REVERT: F 102 ILE cc_start: 0.9223 (mt) cc_final: 0.8902 (mt) REVERT: G 30 LEU cc_start: 0.9553 (mm) cc_final: 0.9193 (tt) REVERT: G 63 MET cc_start: 0.8582 (tpt) cc_final: 0.7668 (tmm) REVERT: H 74 MET cc_start: 0.8903 (mmm) cc_final: 0.8445 (mmm) REVERT: I 59 LEU cc_start: 0.9128 (mt) cc_final: 0.8814 (mt) REVERT: J 25 ILE cc_start: 0.9533 (mm) cc_final: 0.9315 (mm) REVERT: J 54 ARG cc_start: 0.9066 (mtm110) cc_final: 0.8406 (mtm110) REVERT: J 74 MET cc_start: 0.9194 (mtp) cc_final: 0.8912 (mtp) REVERT: J 82 GLU cc_start: 0.8811 (mp0) cc_final: 0.8602 (mp0) outliers start: 0 outliers final: 0 residues processed: 316 average time/residue: 0.2131 time to fit residues: 100.3785 Evaluate side-chains 245 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 37 optimal weight: 4.9990 chunk 7 optimal weight: 0.0570 chunk 11 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 115 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 43 optimal weight: 0.0010 overall best weight: 1.4108 ------------------------------------------------------------------------------- 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 ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.058282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.048158 restraints weight = 59529.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.049648 restraints weight = 34377.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.050665 restraints weight = 23520.176| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12580 Z= 0.156 Angle : 0.774 11.625 17066 Z= 0.379 Chirality : 0.045 0.214 2102 Planarity : 0.005 0.090 2069 Dihedral : 5.449 61.672 1616 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.49 % Favored : 94.38 % Rotamer: Outliers : 0.07 % Allowed : 2.75 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.22), residues: 1547 helix: 0.94 (0.15), residues: 1236 sheet: None (None), residues: 0 loop : -2.98 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 68 HIS 0.002 0.001 HIS F 144 PHE 0.036 0.001 PHE J 10 TYR 0.009 0.001 TYR F 241 ARG 0.006 0.000 ARG I 54 Details of bonding type rmsd hydrogen bonds : bond 0.03828 ( 845) hydrogen bonds : angle 4.21863 ( 2505) covalent geometry : bond 0.00355 (12580) covalent geometry : angle 0.77373 (17066) *********************** 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 324 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 323 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8776 (ttm170) cc_final: 0.8317 (ttm-80) REVERT: A 141 ASN cc_start: 0.8245 (m-40) cc_final: 0.8017 (m-40) REVERT: A 232 GLU cc_start: 0.8881 (tp30) cc_final: 0.8644 (mm-30) REVERT: A 259 MET cc_start: 0.8904 (mmm) cc_final: 0.8417 (mmt) REVERT: A 263 MET cc_start: 0.7628 (mtt) cc_final: 0.6974 (mtt) REVERT: A 264 MET cc_start: 0.8564 (ttp) cc_final: 0.7939 (ptm) REVERT: B 149 LEU cc_start: 0.9136 (tp) cc_final: 0.8837 (tt) REVERT: B 261 MET cc_start: 0.7631 (mtm) cc_final: 0.7334 (mtp) REVERT: B 264 MET cc_start: 0.8474 (mtm) cc_final: 0.8131 (mtm) REVERT: B 269 MET cc_start: 0.7859 (tpt) cc_final: 0.7597 (tpp) REVERT: C 115 LEU cc_start: 0.9236 (mm) cc_final: 0.8884 (mt) REVERT: C 116 MET cc_start: 0.8452 (ttp) cc_final: 0.8095 (tmm) REVERT: C 259 MET cc_start: 0.8485 (tpp) cc_final: 0.7480 (mmm) REVERT: C 279 LEU cc_start: 0.9153 (tp) cc_final: 0.8642 (mm) REVERT: D 116 MET cc_start: 0.7929 (ttm) cc_final: 0.7660 (mmt) REVERT: D 232 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8169 (tp30) REVERT: D 278 MET cc_start: 0.8309 (ttt) cc_final: 0.7988 (ttp) REVERT: E 133 MET cc_start: 0.8804 (tpt) cc_final: 0.8564 (tpt) REVERT: E 138 THR cc_start: 0.8835 (p) cc_final: 0.8596 (p) REVERT: E 245 LEU cc_start: 0.9405 (mt) cc_final: 0.9163 (mt) REVERT: F 77 GLU cc_start: 0.8722 (pp20) cc_final: 0.8366 (pp20) REVERT: F 78 GLN cc_start: 0.8746 (mt0) cc_final: 0.8193 (mt0) REVERT: F 114 MET cc_start: 0.8482 (ttt) cc_final: 0.8082 (tmm) REVERT: F 149 GLN cc_start: 0.9305 (mt0) cc_final: 0.8984 (mt0) REVERT: F 205 MET cc_start: 0.8896 (mtm) cc_final: 0.8629 (mtm) REVERT: F 250 GLU cc_start: 0.8585 (pt0) cc_final: 0.8251 (pt0) REVERT: G 63 MET cc_start: 0.8573 (tpt) cc_final: 0.7624 (tmm) REVERT: I 59 LEU cc_start: 0.9110 (mt) cc_final: 0.8815 (mt) REVERT: J 10 PHE cc_start: 0.9013 (t80) cc_final: 0.8699 (t80) REVERT: J 25 ILE cc_start: 0.9497 (mm) cc_final: 0.9241 (mm) REVERT: J 54 ARG cc_start: 0.9042 (mtm110) cc_final: 0.8668 (mtm-85) outliers start: 1 outliers final: 0 residues processed: 324 average time/residue: 0.2095 time to fit residues: 101.2516 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 : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 55 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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** G 39 GLN H 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.058498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.048346 restraints weight = 60218.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.049825 restraints weight = 35391.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.050808 restraints weight = 24516.120| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12580 Z= 0.153 Angle : 0.805 10.759 17066 Z= 0.390 Chirality : 0.045 0.184 2102 Planarity : 0.005 0.091 2069 Dihedral : 5.454 60.279 1616 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.30 % Favored : 94.57 % Rotamer: Outliers : 0.07 % Allowed : 1.74 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.22), residues: 1547 helix: 1.03 (0.15), residues: 1230 sheet: None (None), residues: 0 loop : -2.97 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 68 HIS 0.002 0.001 HIS F 144 PHE 0.031 0.001 PHE J 10 TYR 0.010 0.001 TYR D 171 ARG 0.009 0.001 ARG I 54 Details of bonding type rmsd hydrogen bonds : bond 0.03756 ( 845) hydrogen bonds : angle 4.21245 ( 2505) covalent geometry : bond 0.00345 (12580) covalent geometry : angle 0.80450 (17066) *********************** 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 326 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 325 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8766 (ttm170) cc_final: 0.8331 (ttm-80) REVERT: A 141 ASN cc_start: 0.8225 (m-40) cc_final: 0.7999 (m-40) REVERT: A 232 GLU cc_start: 0.8909 (tp30) cc_final: 0.8673 (mm-30) REVERT: A 259 MET cc_start: 0.8910 (mmm) cc_final: 0.8392 (mmt) REVERT: B 116 MET cc_start: 0.8085 (mtt) cc_final: 0.7864 (mtm) REVERT: B 149 LEU cc_start: 0.9150 (tp) cc_final: 0.8846 (tt) REVERT: B 261 MET cc_start: 0.7553 (mtm) cc_final: 0.7242 (mtp) REVERT: B 269 MET cc_start: 0.7795 (tpt) cc_final: 0.7526 (tpp) REVERT: C 115 LEU cc_start: 0.9215 (mm) cc_final: 0.8876 (mp) REVERT: C 116 MET cc_start: 0.8473 (ttp) cc_final: 0.8134 (tmm) REVERT: C 259 MET cc_start: 0.8578 (tpp) cc_final: 0.7573 (mmm) REVERT: C 279 LEU cc_start: 0.9260 (tp) cc_final: 0.8710 (mm) REVERT: D 116 MET cc_start: 0.7953 (ttm) cc_final: 0.7701 (mmt) REVERT: D 232 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8141 (mm-30) REVERT: D 265 MET cc_start: 0.7812 (ptm) cc_final: 0.7582 (ptm) REVERT: D 278 MET cc_start: 0.8276 (ttt) cc_final: 0.7994 (tmm) REVERT: E 138 THR cc_start: 0.8946 (p) cc_final: 0.8135 (p) REVERT: E 245 LEU cc_start: 0.9381 (mt) cc_final: 0.9157 (mt) REVERT: E 264 MET cc_start: 0.8638 (tpp) cc_final: 0.8253 (tpt) REVERT: F 25 MET cc_start: 0.8817 (tmm) cc_final: 0.8450 (tmm) REVERT: F 29 MET cc_start: 0.7700 (ttt) cc_final: 0.7278 (ttt) REVERT: F 77 GLU cc_start: 0.8707 (pp20) cc_final: 0.8373 (pp20) REVERT: F 78 GLN cc_start: 0.8742 (mt0) cc_final: 0.8206 (mt0) REVERT: F 87 MET cc_start: 0.7437 (mmt) cc_final: 0.7227 (mmt) REVERT: F 114 MET cc_start: 0.8484 (ttt) cc_final: 0.8141 (tmm) REVERT: F 149 GLN cc_start: 0.9321 (mt0) cc_final: 0.8954 (mt0) REVERT: F 250 GLU cc_start: 0.8479 (pt0) cc_final: 0.8161 (pt0) REVERT: G 30 LEU cc_start: 0.9523 (mm) cc_final: 0.9157 (tt) REVERT: G 58 THR cc_start: 0.9282 (t) cc_final: 0.9052 (m) REVERT: G 63 MET cc_start: 0.8522 (tpt) cc_final: 0.7586 (tmm) REVERT: H 74 MET cc_start: 0.8816 (mmm) cc_final: 0.8411 (mmm) REVERT: H 86 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8444 (pp30) REVERT: I 59 LEU cc_start: 0.9092 (mt) cc_final: 0.8765 (mt) REVERT: J 25 ILE cc_start: 0.9510 (mm) cc_final: 0.9226 (mm) REVERT: J 54 ARG cc_start: 0.9037 (mtm110) cc_final: 0.8659 (mtm-85) outliers start: 1 outliers final: 0 residues processed: 326 average time/residue: 0.2102 time to fit residues: 101.7283 Evaluate side-chains 254 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 253 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 70 optimal weight: 0.8980 chunk 22 optimal weight: 0.0270 chunk 136 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 chunk 87 optimal weight: 0.4980 chunk 108 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 10 optimal weight: 0.0470 chunk 33 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 overall best weight: 0.4736 ------------------------------------------------------------------------------- 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 142 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 = 0.3319 r_free = 0.3319 target = 0.059282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.049072 restraints weight = 60101.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.050604 restraints weight = 34861.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.051547 restraints weight = 23971.413| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 12580 Z= 0.155 Angle : 0.822 10.629 17066 Z= 0.396 Chirality : 0.045 0.221 2102 Planarity : 0.005 0.087 2069 Dihedral : 5.352 59.191 1616 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.04 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.22), residues: 1547 helix: 1.04 (0.15), residues: 1229 sheet: None (None), residues: 0 loop : -2.99 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 68 HIS 0.001 0.000 HIS F 144 PHE 0.058 0.002 PHE B 244 TYR 0.010 0.001 TYR D 171 ARG 0.006 0.000 ARG I 54 Details of bonding type rmsd hydrogen bonds : bond 0.03765 ( 845) hydrogen bonds : angle 4.18097 ( 2505) covalent geometry : bond 0.00353 (12580) covalent geometry : angle 0.82199 (17066) *********************** 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 333 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8776 (ttm170) cc_final: 0.8391 (ttm-80) REVERT: A 193 MET cc_start: 0.8830 (mtm) cc_final: 0.8620 (mtm) REVERT: A 232 GLU cc_start: 0.8869 (tp30) cc_final: 0.8652 (mm-30) REVERT: A 259 MET cc_start: 0.8936 (mmm) cc_final: 0.8328 (mmt) REVERT: B 261 MET cc_start: 0.7523 (mtm) cc_final: 0.7209 (mtp) REVERT: B 269 MET cc_start: 0.7659 (tpt) cc_final: 0.7418 (tpp) REVERT: C 115 LEU cc_start: 0.9149 (mm) cc_final: 0.8838 (mt) REVERT: C 116 MET cc_start: 0.8345 (ttp) cc_final: 0.8070 (tmm) REVERT: C 129 LEU cc_start: 0.9596 (tt) cc_final: 0.9259 (pp) REVERT: C 232 GLU cc_start: 0.8851 (tp30) cc_final: 0.8451 (tp30) REVERT: C 259 MET cc_start: 0.8462 (tpp) cc_final: 0.8029 (mmm) REVERT: C 279 LEU cc_start: 0.9209 (tp) cc_final: 0.8687 (mm) REVERT: D 116 MET cc_start: 0.7884 (ttm) cc_final: 0.7656 (mmt) REVERT: D 232 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8027 (mm-30) REVERT: D 278 MET cc_start: 0.8184 (ttt) cc_final: 0.7937 (tmm) REVERT: E 138 THR cc_start: 0.8795 (p) cc_final: 0.7860 (p) REVERT: E 245 LEU cc_start: 0.9363 (mt) cc_final: 0.9131 (mt) REVERT: F 19 TYR cc_start: 0.8907 (t80) cc_final: 0.8626 (t80) REVERT: F 25 MET cc_start: 0.8795 (tmm) cc_final: 0.8427 (tmm) REVERT: F 29 MET cc_start: 0.7713 (ttt) cc_final: 0.7266 (ttt) REVERT: F 77 GLU cc_start: 0.8714 (pp20) cc_final: 0.8343 (pp20) REVERT: F 78 GLN cc_start: 0.8716 (mt0) cc_final: 0.8168 (mt0) REVERT: F 98 MET cc_start: 0.8893 (mmt) cc_final: 0.8435 (mmm) REVERT: F 102 ILE cc_start: 0.9021 (mt) cc_final: 0.8588 (mt) REVERT: F 114 MET cc_start: 0.8478 (ttt) cc_final: 0.8094 (tmm) REVERT: F 149 GLN cc_start: 0.9250 (mt0) cc_final: 0.8877 (mt0) REVERT: F 205 MET cc_start: 0.8920 (mtm) cc_final: 0.8197 (tpp) REVERT: F 250 GLU cc_start: 0.8541 (pt0) cc_final: 0.8202 (pt0) REVERT: F 258 LEU cc_start: 0.8895 (tp) cc_final: 0.8690 (tp) REVERT: G 16 LEU cc_start: 0.9176 (tp) cc_final: 0.8899 (tp) REVERT: G 63 MET cc_start: 0.8490 (tpt) cc_final: 0.7581 (tmm) REVERT: H 38 PHE cc_start: 0.8975 (t80) cc_final: 0.8360 (t80) REVERT: H 72 MET cc_start: 0.8819 (pmm) cc_final: 0.8579 (pmm) REVERT: H 74 MET cc_start: 0.8715 (mmm) cc_final: 0.8395 (mmm) REVERT: I 44 ILE cc_start: 0.8618 (mm) cc_final: 0.8316 (mm) REVERT: I 45 ASN cc_start: 0.8491 (m-40) cc_final: 0.7698 (p0) REVERT: I 59 LEU cc_start: 0.9055 (mt) cc_final: 0.8785 (mt) REVERT: J 25 ILE cc_start: 0.9477 (mm) cc_final: 0.9171 (mm) REVERT: J 54 ARG cc_start: 0.9007 (mtm110) cc_final: 0.8581 (mtm-85) REVERT: J 82 GLU cc_start: 0.8757 (mp0) cc_final: 0.8534 (mp0) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.2161 time to fit residues: 108.0839 Evaluate side-chains 257 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 51 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 81 optimal weight: 20.0000 chunk 23 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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** ** 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 = 0.3305 r_free = 0.3305 target = 0.058630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.048491 restraints weight = 60013.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.049989 restraints weight = 35456.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.050966 restraints weight = 24401.623| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 12580 Z= 0.159 Angle : 0.821 10.370 17066 Z= 0.396 Chirality : 0.045 0.176 2102 Planarity : 0.005 0.089 2069 Dihedral : 5.345 59.122 1616 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.24 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.22), residues: 1547 helix: 1.08 (0.15), residues: 1227 sheet: None (None), residues: 0 loop : -3.00 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 68 HIS 0.002 0.001 HIS F 144 PHE 0.047 0.002 PHE B 244 TYR 0.010 0.001 TYR G 89 ARG 0.009 0.001 ARG I 54 Details of bonding type rmsd hydrogen bonds : bond 0.03758 ( 845) hydrogen bonds : angle 4.21655 ( 2505) covalent geometry : bond 0.00380 (12580) covalent geometry : angle 0.82055 (17066) *********************** 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 318 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8825 (ttm170) cc_final: 0.8411 (ttm-80) REVERT: A 259 MET cc_start: 0.8919 (mmm) cc_final: 0.8243 (mmt) REVERT: A 284 ASP cc_start: 0.8229 (m-30) cc_final: 0.7798 (m-30) REVERT: B 149 LEU cc_start: 0.9105 (tp) cc_final: 0.8766 (tt) REVERT: B 263 MET cc_start: 0.8509 (mpp) cc_final: 0.8300 (ptp) REVERT: B 264 MET cc_start: 0.8147 (mtm) cc_final: 0.7937 (mtm) REVERT: B 269 MET cc_start: 0.7767 (tpt) cc_final: 0.7560 (tpp) REVERT: B 287 ASN cc_start: 0.8072 (t0) cc_final: 0.7843 (t0) REVERT: C 115 LEU cc_start: 0.9163 (mm) cc_final: 0.8849 (mt) REVERT: C 116 MET cc_start: 0.8373 (ttp) cc_final: 0.8120 (tmm) REVERT: C 129 LEU cc_start: 0.9544 (tt) cc_final: 0.9249 (pp) REVERT: C 232 GLU cc_start: 0.8812 (tp30) cc_final: 0.8592 (tp30) REVERT: C 279 LEU cc_start: 0.9215 (tp) cc_final: 0.8692 (mm) REVERT: D 116 MET cc_start: 0.7932 (ttm) cc_final: 0.7705 (mmt) REVERT: D 232 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8107 (mm-30) REVERT: D 278 MET cc_start: 0.8200 (ttt) cc_final: 0.7931 (tmm) REVERT: E 138 THR cc_start: 0.8805 (p) cc_final: 0.8156 (p) REVERT: E 140 SER cc_start: 0.8384 (t) cc_final: 0.8130 (p) REVERT: E 245 LEU cc_start: 0.9392 (mt) cc_final: 0.9157 (mt) REVERT: F 19 TYR cc_start: 0.8945 (t80) cc_final: 0.8695 (t80) REVERT: F 25 MET cc_start: 0.8877 (tmm) cc_final: 0.8462 (tmm) REVERT: F 29 MET cc_start: 0.7820 (ttt) cc_final: 0.7444 (ttt) REVERT: F 77 GLU cc_start: 0.8732 (pp20) cc_final: 0.8480 (pp20) REVERT: F 98 MET cc_start: 0.8865 (mmt) cc_final: 0.8652 (mmm) REVERT: F 114 MET cc_start: 0.8468 (ttt) cc_final: 0.8093 (tmm) REVERT: F 205 MET cc_start: 0.8894 (mtm) cc_final: 0.8131 (tpp) REVERT: F 250 GLU cc_start: 0.8569 (pt0) cc_final: 0.8211 (pt0) REVERT: F 258 LEU cc_start: 0.8907 (tp) cc_final: 0.8689 (tp) REVERT: G 30 LEU cc_start: 0.9523 (mm) cc_final: 0.9137 (tt) REVERT: G 63 MET cc_start: 0.8493 (tpt) cc_final: 0.7647 (tmm) REVERT: H 38 PHE cc_start: 0.8965 (t80) cc_final: 0.8365 (t80) REVERT: H 74 MET cc_start: 0.8729 (mmm) cc_final: 0.8391 (mmm) REVERT: I 54 ARG cc_start: 0.9285 (ttm-80) cc_final: 0.9081 (tpp80) REVERT: I 59 LEU cc_start: 0.9070 (mt) cc_final: 0.8794 (mt) REVERT: J 25 ILE cc_start: 0.9467 (mm) cc_final: 0.9182 (mm) REVERT: J 54 ARG cc_start: 0.8933 (mtm110) cc_final: 0.8640 (mtm-85) REVERT: J 82 GLU cc_start: 0.8770 (mp0) cc_final: 0.8518 (mp0) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.2323 time to fit residues: 110.5699 Evaluate side-chains 253 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 40 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- 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 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.057249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.047139 restraints weight = 61122.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.048527 restraints weight = 36387.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.049504 restraints weight = 25399.864| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 12580 Z= 0.210 Angle : 0.860 11.177 17066 Z= 0.418 Chirality : 0.047 0.184 2102 Planarity : 0.005 0.090 2069 Dihedral : 5.449 61.289 1616 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.75 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.22), residues: 1547 helix: 1.06 (0.15), residues: 1234 sheet: None (None), residues: 0 loop : -3.05 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 68 HIS 0.004 0.001 HIS F 144 PHE 0.046 0.002 PHE B 244 TYR 0.012 0.001 TYR G 89 ARG 0.009 0.001 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.03944 ( 845) hydrogen bonds : angle 4.34111 ( 2505) covalent geometry : bond 0.00498 (12580) covalent geometry : angle 0.85951 (17066) ********************** 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 301 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8843 (ttm170) cc_final: 0.8295 (ttm170) REVERT: A 193 MET cc_start: 0.8944 (mtm) cc_final: 0.8661 (mtm) REVERT: A 232 GLU cc_start: 0.8908 (tp30) cc_final: 0.7699 (tp30) REVERT: A 259 MET cc_start: 0.8779 (mmm) cc_final: 0.8122 (mmt) REVERT: A 284 ASP cc_start: 0.7985 (m-30) cc_final: 0.7771 (m-30) REVERT: B 116 MET cc_start: 0.7881 (mtm) cc_final: 0.7622 (mtm) REVERT: B 149 LEU cc_start: 0.9130 (tp) cc_final: 0.8788 (tt) REVERT: B 287 ASN cc_start: 0.8085 (t0) cc_final: 0.7560 (t0) REVERT: C 115 LEU cc_start: 0.9241 (mm) cc_final: 0.8905 (mt) REVERT: C 116 MET cc_start: 0.8443 (ttp) cc_final: 0.8191 (tmm) REVERT: C 232 GLU cc_start: 0.8822 (tp30) cc_final: 0.8585 (tp30) REVERT: C 259 MET cc_start: 0.8720 (mmm) cc_final: 0.8323 (mmm) REVERT: C 279 LEU cc_start: 0.9259 (tp) cc_final: 0.8786 (mm) REVERT: D 116 MET cc_start: 0.7961 (ttm) cc_final: 0.7748 (mmt) REVERT: D 232 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8148 (mm-30) REVERT: D 278 MET cc_start: 0.8183 (ttt) cc_final: 0.7927 (tmm) REVERT: E 138 THR cc_start: 0.8806 (p) cc_final: 0.8091 (p) REVERT: E 140 SER cc_start: 0.8597 (t) cc_final: 0.8350 (p) REVERT: E 245 LEU cc_start: 0.9403 (mt) cc_final: 0.9158 (mt) REVERT: F 25 MET cc_start: 0.8923 (tmm) cc_final: 0.8508 (tmm) REVERT: F 29 MET cc_start: 0.7897 (ttt) cc_final: 0.7535 (ttt) REVERT: F 77 GLU cc_start: 0.8776 (pp20) cc_final: 0.8514 (pp20) REVERT: F 98 MET cc_start: 0.8948 (mmt) cc_final: 0.8580 (mmm) REVERT: F 114 MET cc_start: 0.8576 (ttt) cc_final: 0.8170 (tmm) REVERT: F 116 ASP cc_start: 0.8909 (t70) cc_final: 0.8685 (t0) REVERT: F 205 MET cc_start: 0.8900 (mtm) cc_final: 0.8113 (tpp) REVERT: F 250 GLU cc_start: 0.8535 (pt0) cc_final: 0.8179 (pt0) REVERT: G 30 LEU cc_start: 0.9531 (mm) cc_final: 0.9168 (tt) REVERT: G 63 MET cc_start: 0.8531 (tpt) cc_final: 0.7712 (tmm) REVERT: H 38 PHE cc_start: 0.8976 (t80) cc_final: 0.8384 (t80) REVERT: H 72 MET cc_start: 0.8922 (pmm) cc_final: 0.8682 (pmm) REVERT: H 74 MET cc_start: 0.8832 (mmm) cc_final: 0.8424 (mmm) REVERT: I 44 ILE cc_start: 0.8690 (mm) cc_final: 0.8387 (mm) REVERT: I 45 ASN cc_start: 0.8477 (m-40) cc_final: 0.7708 (p0) REVERT: I 74 MET cc_start: 0.8426 (mmm) cc_final: 0.7916 (tpp) REVERT: J 25 ILE cc_start: 0.9482 (mm) cc_final: 0.9214 (mm) REVERT: J 54 ARG cc_start: 0.8981 (mtm110) cc_final: 0.8344 (mtm110) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.2556 time to fit residues: 116.6712 Evaluate side-chains 236 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 80 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 90 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 86 optimal weight: 0.0370 chunk 75 optimal weight: 6.9990 chunk 37 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 chunk 142 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.059006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.048843 restraints weight = 59680.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.050327 restraints weight = 35047.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.051303 restraints weight = 24087.695| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 12580 Z= 0.154 Angle : 0.833 11.242 17066 Z= 0.403 Chirality : 0.046 0.192 2102 Planarity : 0.005 0.087 2069 Dihedral : 5.335 58.211 1616 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.49 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.22), residues: 1547 helix: 1.09 (0.15), residues: 1237 sheet: None (None), residues: 0 loop : -3.07 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 68 HIS 0.001 0.000 HIS G 67 PHE 0.041 0.002 PHE B 244 TYR 0.010 0.001 TYR F 241 ARG 0.008 0.001 ARG I 54 Details of bonding type rmsd hydrogen bonds : bond 0.03792 ( 845) hydrogen bonds : angle 4.23006 ( 2505) covalent geometry : bond 0.00350 (12580) covalent geometry : angle 0.83293 (17066) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4188.75 seconds wall clock time: 75 minutes 27.22 seconds (4527.22 seconds total)