Starting phenix.real_space_refine on Fri Jul 3 04:49:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8evu_28637/07_2026/8evu_28637.cif Found real_map, /net/cci-nas-00/data/ceres_data/8evu_28637/07_2026/8evu_28637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5804 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8evu_28637/07_2026/8evu_28637.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8evu_28637/07_2026/8evu_28637.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8evu_28637/07_2026/8evu_28637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8evu_28637/07_2026/8evu_28637.map" model { file = "/net/cci-nas-00/data/ceres_data/8evu_28637/07_2026/8evu_28637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8evu_28637/07_2026/8evu_28637.cif" } resolution = 2.5804 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians Fe 2 7.16 5 P 2 5.49 5 S 68 5.16 5 C 7746 2.51 5 N 1949 2.21 5 O 2135 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11902 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3416 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 422} Chain: "B" Number of atoms: 3182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3182 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 15, 'TRANS': 396} Chain: "C" Number of atoms: 1894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1894 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 7, 'TRANS': 242} Chain: "D" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1545 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 9, 'TRANS': 192} Chain: "E" Number of atoms: 1512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1512 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "F" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 244 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {'FMN': 1, 'RBF': 1, 'UQ1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9290 SG CYS D 112 65.958 42.181 63.643 1.00 79.57 S ATOM 10247 SG CYS E 26 64.578 45.018 65.377 1.00 65.74 S ATOM 8651 SG CYS D 29 62.336 42.626 69.152 1.00 69.87 S ATOM 10969 SG CYS E 120 64.405 39.385 68.240 1.00 75.41 S Time building chain proxies: 2.45, per 1000 atoms: 0.21 Number of scatterers: 11902 At special positions: 0 Unit cell: (99.324, 110.004, 133.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 S 68 16.00 P 2 15.00 O 2135 8.00 N 1949 7.00 C 7746 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 536.1 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS D 112 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 26 " pdb="FE2 FES E 301 " - pdb=" SG CYS D 29 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 120 " Number of angles added : 6 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2784 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 8 sheets defined 60.7% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 109 through 113 Processing helix chain 'A' and resid 114 through 125 Processing helix chain 'A' and resid 126 through 131 removed outlier: 3.596A pdb=" N THR A 129 " --> pdb=" O GLY A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 170 removed outlier: 3.919A pdb=" N VAL A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 219 through 228 Processing helix chain 'A' and resid 241 through 254 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 335 through 339 Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.737A pdb=" N HIS A 354 " --> pdb=" O PHE A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 384 removed outlier: 3.866A pdb=" N LYS A 382 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 383 " --> pdb=" O ASN A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 401 through 408 Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 415 through 417 No H-bonds generated for 'chain 'A' and resid 415 through 417' Processing helix chain 'A' and resid 418 through 424 Processing helix chain 'A' and resid 430 through 446 removed outlier: 3.622A pdb=" N LEU A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 10 Processing helix chain 'B' and resid 10 through 15 removed outlier: 3.906A pdb=" N PHE B 14 " --> pdb=" O ILE B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 23 through 35 removed outlier: 3.694A pdb=" N LEU B 33 " --> pdb=" O ALA B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.569A pdb=" N VAL B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 87 Processing helix chain 'B' and resid 89 through 99 Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 117 through 152 Proline residue: B 131 - end of helix Processing helix chain 'B' and resid 158 through 169 Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 191 through 195 Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 236 through 245 Processing helix chain 'B' and resid 246 through 249 Processing helix chain 'B' and resid 259 through 266 Processing helix chain 'B' and resid 276 through 290 Processing helix chain 'B' and resid 294 through 316 Processing helix chain 'B' and resid 320 through 325 removed outlier: 3.542A pdb=" N MET B 325 " --> pdb=" O MET B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 333 removed outlier: 3.528A pdb=" N VAL B 332 " --> pdb=" O HIS B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 353 through 375 Processing helix chain 'B' and resid 381 through 410 removed outlier: 3.585A pdb=" N LEU B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Proline residue: B 394 - end of helix Processing helix chain 'B' and resid 411 through 414 Processing helix chain 'C' and resid 8 through 33 Processing helix chain 'C' and resid 33 through 54 removed outlier: 3.529A pdb=" N LYS C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 70 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 92 through 98 Processing helix chain 'C' and resid 99 through 101 No H-bonds generated for 'chain 'C' and resid 99 through 101' Processing helix chain 'C' and resid 177 through 181 Processing helix chain 'C' and resid 182 through 188 removed outlier: 3.777A pdb=" N GLN C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 239 Processing helix chain 'C' and resid 244 through 253 Processing helix chain 'D' and resid 9 through 17 Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 27 through 34 removed outlier: 3.652A pdb=" N ALA D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA D 33 " --> pdb=" O CYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 62 Processing helix chain 'D' and resid 70 through 94 Processing helix chain 'D' and resid 94 through 102 Processing helix chain 'D' and resid 103 through 109 Processing helix chain 'D' and resid 111 through 121 Processing helix chain 'D' and resid 122 through 125 removed outlier: 3.615A pdb=" N SER D 125 " --> pdb=" O ALA D 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 122 through 125' Processing helix chain 'D' and resid 126 through 158 Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 178 through 182 Processing helix chain 'D' and resid 183 through 202 removed outlier: 4.233A pdb=" N ALA D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 206 Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 24 through 31 Processing helix chain 'E' and resid 34 through 63 Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 75 through 77 No H-bonds generated for 'chain 'E' and resid 75 through 77' Processing helix chain 'E' and resid 78 through 102 removed outlier: 3.575A pdb=" N GLN E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG E 100 " --> pdb=" O MET E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 109 Processing helix chain 'E' and resid 110 through 113 Processing helix chain 'E' and resid 119 through 133 Processing helix chain 'E' and resid 135 through 164 Processing helix chain 'E' and resid 165 through 167 No H-bonds generated for 'chain 'E' and resid 165 through 167' Processing helix chain 'E' and resid 175 through 191 Processing helix chain 'E' and resid 192 through 194 No H-bonds generated for 'chain 'E' and resid 192 through 194' Processing helix chain 'F' and resid 2 through 30 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 6.245A pdb=" N ILE A 2 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL A 189 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N HIS A 209 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL A 191 " --> pdb=" O HIS A 209 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N PHE A 211 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LYS A 193 " --> pdb=" O PHE A 211 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 22 removed outlier: 3.519A pdb=" N LEU A 274 " --> pdb=" O SER A 17 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N VAL A 19 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ARG A 276 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N SER A 21 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 9.729A pdb=" N VAL A 278 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL A 323 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N SER A 263 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL A 325 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA A 265 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N ARG A 327 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N GLN A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 32 removed outlier: 6.962A pdb=" N LEU A 87 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ARG A 81 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N SER A 89 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ILE A 79 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL A 91 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 43 removed outlier: 7.130A pdb=" N PHE A 68 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 83 through 84 removed outlier: 3.959A pdb=" N LEU C 75 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 14.780A pdb=" N VAL C 121 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N VAL C 140 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N VAL C 123 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU C 138 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR C 125 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL C 136 " --> pdb=" O TYR C 125 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL C 127 " --> pdb=" O SER C 134 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS C 132 " --> pdb=" O ASP C 129 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N MET C 148 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLU C 169 " --> pdb=" O MET C 148 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TYR C 150 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR C 167 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE C 152 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU C 165 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA C 154 " --> pdb=" O SER C 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 103 through 105 Processing sheet with id=AA7, first strand: chain 'C' and resid 204 through 206 Processing sheet with id=AA8, first strand: chain 'D' and resid 159 through 160 668 hydrogen bonds defined for protein. 1890 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.97 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.42: 5002 1.42 - 1.61: 7044 1.61 - 1.81: 120 1.81 - 2.01: 0 2.01 - 2.20: 4 Bond restraints: 12170 Sorted by residual: bond pdb=" C2 UQ1 B 602 " pdb=" C3 UQ1 B 602 " ideal model delta sigma weight residual 1.339 1.425 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C1 UQ1 B 602 " pdb=" C2 UQ1 B 602 " ideal model delta sigma weight residual 1.485 1.408 0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C4 RBF B 601 " pdb=" C4A RBF B 601 " ideal model delta sigma weight residual 1.481 1.406 0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C1 UQ1 B 602 " pdb=" C6 UQ1 B 602 " ideal model delta sigma weight residual 1.485 1.411 0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C4A FMN B 600 " pdb=" N5 FMN B 600 " ideal model delta sigma weight residual 1.380 1.307 0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 12165 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 16295 1.51 - 3.02: 163 3.02 - 4.54: 43 4.54 - 6.05: 15 6.05 - 7.56: 1 Bond angle restraints: 16517 Sorted by residual: angle pdb=" C3 UQ1 B 602 " pdb=" C2 UQ1 B 602 " pdb=" O2 UQ1 B 602 " ideal model delta sigma weight residual 122.52 130.08 -7.56 3.00e+00 1.11e-01 6.35e+00 angle pdb=" N VAL A 287 " pdb=" CA VAL A 287 " pdb=" CB VAL A 287 " ideal model delta sigma weight residual 111.81 107.07 4.74 2.24e+00 1.99e-01 4.47e+00 angle pdb=" C ILE C 115 " pdb=" N GLN C 116 " pdb=" CA GLN C 116 " ideal model delta sigma weight residual 121.54 125.54 -4.00 1.91e+00 2.74e-01 4.39e+00 angle pdb=" C1 UQ1 B 602 " pdb=" C2 UQ1 B 602 " pdb=" O2 UQ1 B 602 " ideal model delta sigma weight residual 117.10 111.14 5.96 3.00e+00 1.11e-01 3.95e+00 angle pdb=" CA TRP B 103 " pdb=" CB TRP B 103 " pdb=" CG TRP B 103 " ideal model delta sigma weight residual 113.60 117.23 -3.63 1.90e+00 2.77e-01 3.66e+00 ... (remaining 16512 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 7057 35.54 - 71.07: 30 71.07 - 106.61: 4 106.61 - 142.15: 1 142.15 - 177.68: 3 Dihedral angle restraints: 7095 sinusoidal: 2738 harmonic: 4357 Sorted by residual: dihedral pdb=" C10 FMN C 301 " pdb=" C1' FMN C 301 " pdb=" N10 FMN C 301 " pdb=" C2' FMN C 301 " ideal model delta sinusoidal sigma weight residual 257.59 79.91 177.68 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' FMN C 301 " pdb=" O5' FMN C 301 " pdb=" P FMN C 301 " pdb=" O1P FMN C 301 " ideal model delta sinusoidal sigma weight residual 75.26 -113.98 -170.76 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C10 FMN B 600 " pdb=" C1' FMN B 600 " pdb=" N10 FMN B 600 " pdb=" C2' FMN B 600 " ideal model delta sinusoidal sigma weight residual 257.59 89.21 168.38 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 7092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1366 0.039 - 0.078: 409 0.078 - 0.116: 110 0.116 - 0.155: 13 0.155 - 0.194: 1 Chirality restraints: 1899 Sorted by residual: chirality pdb=" C4' RBF B 601 " pdb=" C3' RBF B 601 " pdb=" C5' RBF B 601 " pdb=" O4' RBF B 601 " both_signs ideal model delta sigma weight residual False -2.27 -2.47 0.19 2.00e-01 2.50e+01 9.41e-01 chirality pdb=" CA ILE C 205 " pdb=" N ILE C 205 " pdb=" C ILE C 205 " pdb=" CB ILE C 205 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.93e-01 chirality pdb=" CA ILE A 92 " pdb=" N ILE A 92 " pdb=" C ILE A 92 " pdb=" CB ILE A 92 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 ... (remaining 1896 not shown) Planarity restraints: 2060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ1 B 602 " 0.028 2.00e-02 2.50e+03 6.15e-02 1.14e+02 pdb=" C2 UQ1 B 602 " 0.011 2.00e-02 2.50e+03 pdb=" C3 UQ1 B 602 " 0.012 2.00e-02 2.50e+03 pdb=" C4 UQ1 B 602 " 0.056 2.00e-02 2.50e+03 pdb=" C5 UQ1 B 602 " 0.004 2.00e-02 2.50e+03 pdb=" C6 UQ1 B 602 " -0.001 2.00e-02 2.50e+03 pdb=" C7 UQ1 B 602 " -0.070 2.00e-02 2.50e+03 pdb=" CM5 UQ1 B 602 " -0.064 2.00e-02 2.50e+03 pdb=" O1 UQ1 B 602 " 0.074 2.00e-02 2.50e+03 pdb=" O2 UQ1 B 602 " -0.031 2.00e-02 2.50e+03 pdb=" O3 UQ1 B 602 " -0.124 2.00e-02 2.50e+03 pdb=" O4 UQ1 B 602 " 0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ1 B 602 " 0.007 2.00e-02 2.50e+03 4.18e-02 2.18e+01 pdb=" C11 UQ1 B 602 " -0.042 2.00e-02 2.50e+03 pdb=" C7 UQ1 B 602 " -0.050 2.00e-02 2.50e+03 pdb=" C8 UQ1 B 602 " 0.062 2.00e-02 2.50e+03 pdb=" C9 UQ1 B 602 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FMN C 301 " 0.013 2.00e-02 2.50e+03 7.11e-03 2.40e+00 pdb=" C10 FMN C 301 " 0.004 2.00e-02 2.50e+03 pdb=" C2 FMN C 301 " -0.007 2.00e-02 2.50e+03 pdb=" C4 FMN C 301 " 0.002 2.00e-02 2.50e+03 pdb=" C4A FMN C 301 " 0.006 2.00e-02 2.50e+03 pdb=" C5A FMN C 301 " 0.004 2.00e-02 2.50e+03 pdb=" C6 FMN C 301 " 0.002 2.00e-02 2.50e+03 pdb=" C7 FMN C 301 " -0.004 2.00e-02 2.50e+03 pdb=" C7M FMN C 301 " -0.007 2.00e-02 2.50e+03 pdb=" C8 FMN C 301 " -0.006 2.00e-02 2.50e+03 pdb=" C8M FMN C 301 " -0.009 2.00e-02 2.50e+03 pdb=" C9 FMN C 301 " 0.003 2.00e-02 2.50e+03 pdb=" C9A FMN C 301 " 0.003 2.00e-02 2.50e+03 pdb=" N1 FMN C 301 " 0.002 2.00e-02 2.50e+03 pdb=" N10 FMN C 301 " 0.006 2.00e-02 2.50e+03 pdb=" N3 FMN C 301 " -0.004 2.00e-02 2.50e+03 pdb=" N5 FMN C 301 " 0.008 2.00e-02 2.50e+03 pdb=" O2 FMN C 301 " -0.019 2.00e-02 2.50e+03 pdb=" O4 FMN C 301 " 0.003 2.00e-02 2.50e+03 ... (remaining 2057 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3125 2.80 - 3.33: 11271 3.33 - 3.85: 20185 3.85 - 4.38: 24700 4.38 - 4.90: 41563 Nonbonded interactions: 100844 Sorted by model distance: nonbonded pdb=" O GLU C 99 " pdb=" OG SER C 103 " model vdw 2.279 3.040 nonbonded pdb=" O GLU B 28 " pdb=" OG1 THR B 32 " model vdw 2.283 3.040 nonbonded pdb=" O ILE E 46 " pdb=" OG1 THR E 50 " model vdw 2.317 3.040 nonbonded pdb=" NH1 ARG B 199 " pdb=" O TYR E 166 " model vdw 2.329 3.120 nonbonded pdb=" O ASN E 57 " pdb=" ND2 ASN E 61 " model vdw 2.342 3.120 ... (remaining 100839 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.470 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: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.980 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:6.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9164 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 12176 Z= 0.207 Angle : 0.454 10.329 16523 Z= 0.216 Chirality : 0.039 0.194 1899 Planarity : 0.004 0.062 2060 Dihedral : 10.092 177.684 4311 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.08 % Allowed : 1.35 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.21), residues: 1528 helix: 1.47 (0.18), residues: 786 sheet: 0.62 (0.58), residues: 74 loop : 0.05 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 174 TYR 0.010 0.001 TYR D 141 PHE 0.020 0.001 PHE E 22 TRP 0.014 0.001 TRP B 103 HIS 0.003 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (12170) covalent geometry : angle 0.44448 / 0.22 (16517) hydrogen bonds : bond 0.21006 / 13.93 ( 668) hydrogen bonds : angle 6.70307 / 4.67 ( 1890) metal coordination : bond 0.00700 / 0.34 ( 4) metal coordination : angle 4.93056 / 2.33 ( 6) Misc. bond : bond 0.10783 / 5.42 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.9352 (mmm) cc_final: 0.9125 (tpp) REVERT: E 138 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8523 (mt-10) REVERT: F 26 LYS cc_start: 0.9033 (tttt) cc_final: 0.8630 (tmmt) outliers start: 1 outliers final: 0 residues processed: 159 average time/residue: 0.7474 time to fit residues: 126.6149 Evaluate side-chains 119 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 7.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 91 GLN E 79 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.057656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.043353 restraints weight = 30908.261| |-----------------------------------------------------------------------------| r_work (start): 0.2585 rms_B_bonded: 2.23 r_work: 0.2475 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2362 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 12176 Z= 0.241 Angle : 0.575 9.542 16523 Z= 0.304 Chirality : 0.044 0.168 1899 Planarity : 0.004 0.040 2060 Dihedral : 9.238 173.312 1646 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.80 % Allowed : 6.69 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.22), residues: 1528 helix: 1.88 (0.19), residues: 787 sheet: -0.04 (0.53), residues: 89 loop : 0.06 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 71 TYR 0.013 0.001 TYR B 360 PHE 0.024 0.002 PHE E 22 TRP 0.018 0.002 TRP B 103 HIS 0.006 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.24 (12170) covalent geometry : angle 0.56888 / 0.30 (16517) hydrogen bonds : bond 0.06075 / 4.08 ( 668) hydrogen bonds : angle 4.90380 / 3.39 ( 1890) metal coordination : bond 0.02009 / 0.99 ( 4) metal coordination : angle 4.36233 / 1.96 ( 6) Misc. bond : bond 0.00121 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.9483 (mmm) cc_final: 0.9221 (tpp) REVERT: B 13 HIS cc_start: 0.7430 (m-70) cc_final: 0.6787 (m-70) REVERT: D 9 LYS cc_start: 0.8924 (pptt) cc_final: 0.8123 (mppt) REVERT: D 96 ASP cc_start: 0.8501 (p0) cc_final: 0.8143 (p0) REVERT: E 138 GLU cc_start: 0.9318 (mt-10) cc_final: 0.9060 (mt-10) REVERT: E 186 MET cc_start: 0.9398 (mtp) cc_final: 0.9163 (mtp) REVERT: F 26 LYS cc_start: 0.9333 (tttt) cc_final: 0.8663 (tmmt) outliers start: 10 outliers final: 4 residues processed: 120 average time/residue: 0.6110 time to fit residues: 78.6429 Evaluate side-chains 116 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain E residue 1 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 59 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 29 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 130 optimal weight: 4.9990 chunk 33 optimal weight: 0.4980 chunk 43 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.058129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.043937 restraints weight = 31077.848| |-----------------------------------------------------------------------------| r_work (start): 0.2604 rms_B_bonded: 2.24 r_work: 0.2493 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2381 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9058 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12176 Z= 0.172 Angle : 0.513 10.377 16523 Z= 0.269 Chirality : 0.042 0.166 1899 Planarity : 0.004 0.038 2060 Dihedral : 8.809 172.824 1646 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.96 % Allowed : 7.17 % Favored : 91.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.22), residues: 1528 helix: 1.88 (0.18), residues: 796 sheet: -0.06 (0.54), residues: 89 loop : -0.01 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 71 TYR 0.014 0.001 TYR B 360 PHE 0.020 0.001 PHE E 22 TRP 0.020 0.001 TRP B 103 HIS 0.005 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (12170) covalent geometry : angle 0.50592 / 0.27 (16517) hydrogen bonds : bond 0.05154 / 3.48 ( 668) hydrogen bonds : angle 4.58888 / 3.18 ( 1890) metal coordination : bond 0.01352 / 0.66 ( 4) metal coordination : angle 4.58127 / 2.08 ( 6) Misc. bond : bond 0.00090 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.9494 (mmm) cc_final: 0.9221 (tpp) REVERT: B 153 HIS cc_start: 0.7595 (m90) cc_final: 0.7105 (m90) REVERT: D 9 LYS cc_start: 0.8917 (pptt) cc_final: 0.8168 (mppt) REVERT: D 96 ASP cc_start: 0.8540 (p0) cc_final: 0.8155 (p0) REVERT: E 17 MET cc_start: 0.9217 (mmm) cc_final: 0.8832 (tpp) REVERT: E 138 GLU cc_start: 0.9291 (mt-10) cc_final: 0.9038 (mt-10) REVERT: F 26 LYS cc_start: 0.9351 (tttt) cc_final: 0.8649 (tmmt) outliers start: 12 outliers final: 5 residues processed: 122 average time/residue: 0.6293 time to fit residues: 82.6797 Evaluate side-chains 120 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain E residue 1 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 21 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.056719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.042431 restraints weight = 31239.145| |-----------------------------------------------------------------------------| r_work (start): 0.2564 rms_B_bonded: 2.25 r_work: 0.2453 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2341 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9101 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 12176 Z= 0.297 Angle : 0.594 9.094 16523 Z= 0.311 Chirality : 0.045 0.178 1899 Planarity : 0.004 0.058 2060 Dihedral : 8.756 174.132 1646 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.19 % Allowed : 7.96 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.22), residues: 1528 helix: 1.74 (0.18), residues: 800 sheet: -0.31 (0.53), residues: 99 loop : -0.02 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 318 TYR 0.019 0.002 TYR D 141 PHE 0.026 0.002 PHE E 22 TRP 0.022 0.002 TRP B 103 HIS 0.004 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00689 / 0.30 (12170) covalent geometry : angle 0.58938 / 0.31 (16517) hydrogen bonds : bond 0.05672 / 3.83 ( 668) hydrogen bonds : angle 4.68662 / 3.24 ( 1890) metal coordination : bond 0.02297 / 1.14 ( 4) metal coordination : angle 3.95787 / 1.78 ( 6) Misc. bond : bond 0.00213 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.9491 (mmm) cc_final: 0.9230 (tpp) REVERT: D 9 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8146 (mppt) REVERT: D 96 ASP cc_start: 0.8610 (p0) cc_final: 0.8280 (p0) REVERT: E 138 GLU cc_start: 0.9308 (mt-10) cc_final: 0.9089 (mt-10) REVERT: E 186 MET cc_start: 0.9449 (mtp) cc_final: 0.9177 (mtp) REVERT: F 26 LYS cc_start: 0.9403 (tttt) cc_final: 0.8699 (tmmt) outliers start: 15 outliers final: 4 residues processed: 119 average time/residue: 0.6426 time to fit residues: 82.2265 Evaluate side-chains 120 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 9 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 92 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 149 optimal weight: 0.0270 chunk 91 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.058194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.044046 restraints weight = 31047.088| |-----------------------------------------------------------------------------| r_work (start): 0.2606 rms_B_bonded: 2.25 r_work: 0.2496 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2384 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12176 Z= 0.142 Angle : 0.507 8.338 16523 Z= 0.267 Chirality : 0.041 0.161 1899 Planarity : 0.004 0.050 2060 Dihedral : 8.548 173.321 1646 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.19 % Allowed : 8.60 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.22), residues: 1528 helix: 1.89 (0.18), residues: 798 sheet: -0.25 (0.53), residues: 97 loop : -0.04 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 71 TYR 0.017 0.001 TYR D 141 PHE 0.019 0.001 PHE E 22 TRP 0.023 0.001 TRP B 103 HIS 0.004 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (12170) covalent geometry : angle 0.50208 / 0.27 (16517) hydrogen bonds : bond 0.04755 / 3.22 ( 668) hydrogen bonds : angle 4.47964 / 3.10 ( 1890) metal coordination : bond 0.00868 / 0.42 ( 4) metal coordination : angle 3.83835 / 1.76 ( 6) Misc. bond : bond 0.00070 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.9509 (mmm) cc_final: 0.9249 (tpp) REVERT: B 34 PHE cc_start: 0.8883 (m-80) cc_final: 0.8663 (m-80) REVERT: B 68 MET cc_start: 0.9528 (OUTLIER) cc_final: 0.9297 (ttp) REVERT: B 122 MET cc_start: 0.9338 (OUTLIER) cc_final: 0.9092 (ttm) REVERT: D 9 LYS cc_start: 0.8896 (pptt) cc_final: 0.8208 (mppt) REVERT: D 96 ASP cc_start: 0.8579 (p0) cc_final: 0.8285 (p0) REVERT: E 17 MET cc_start: 0.9229 (mmm) cc_final: 0.8830 (tpp) REVERT: E 138 GLU cc_start: 0.9287 (mt-10) cc_final: 0.9041 (mt-10) REVERT: F 26 LYS cc_start: 0.9384 (tttt) cc_final: 0.8653 (tmmt) outliers start: 15 outliers final: 6 residues processed: 120 average time/residue: 0.6549 time to fit residues: 84.2163 Evaluate side-chains 121 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 133 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 43 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 97 optimal weight: 0.0020 chunk 122 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.057182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.042916 restraints weight = 31342.512| |-----------------------------------------------------------------------------| r_work (start): 0.2578 rms_B_bonded: 2.26 r_work: 0.2466 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2354 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9090 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12176 Z= 0.236 Angle : 0.555 8.220 16523 Z= 0.289 Chirality : 0.043 0.170 1899 Planarity : 0.004 0.039 2060 Dihedral : 8.529 173.252 1646 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.11 % Allowed : 9.39 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.22), residues: 1528 helix: 1.81 (0.18), residues: 803 sheet: -0.34 (0.53), residues: 99 loop : -0.06 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 318 TYR 0.019 0.001 TYR D 141 PHE 0.023 0.002 PHE E 22 TRP 0.023 0.002 TRP B 103 HIS 0.004 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.24 (12170) covalent geometry : angle 0.55101 / 0.29 (16517) hydrogen bonds : bond 0.05202 / 3.52 ( 668) hydrogen bonds : angle 4.53705 / 3.14 ( 1890) metal coordination : bond 0.01724 / 0.86 ( 4) metal coordination : angle 3.60368 / 1.64 ( 6) Misc. bond : bond 0.00141 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.9494 (mmm) cc_final: 0.9220 (tpp) REVERT: B 15 GLU cc_start: 0.8860 (tp30) cc_final: 0.8068 (pp20) REVERT: B 34 PHE cc_start: 0.8922 (m-80) cc_final: 0.8669 (m-80) REVERT: B 122 MET cc_start: 0.9396 (OUTLIER) cc_final: 0.9156 (ttm) REVERT: D 9 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8216 (mppt) REVERT: D 96 ASP cc_start: 0.8620 (p0) cc_final: 0.8367 (p0) REVERT: E 17 MET cc_start: 0.9234 (OUTLIER) cc_final: 0.8837 (tpp) REVERT: E 138 GLU cc_start: 0.9305 (mt-10) cc_final: 0.9092 (mt-10) REVERT: F 26 LYS cc_start: 0.9409 (tttt) cc_final: 0.8707 (tmmt) outliers start: 14 outliers final: 7 residues processed: 117 average time/residue: 0.6722 time to fit residues: 84.5072 Evaluate side-chains 122 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 9 LYS Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 17 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 116 optimal weight: 3.9990 chunk 135 optimal weight: 0.1980 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.058460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.044326 restraints weight = 30949.492| |-----------------------------------------------------------------------------| r_work (start): 0.2616 rms_B_bonded: 2.24 r_work: 0.2506 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2394 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9048 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12176 Z= 0.138 Angle : 0.508 8.788 16523 Z= 0.265 Chirality : 0.041 0.160 1899 Planarity : 0.004 0.038 2060 Dihedral : 8.373 173.501 1646 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.27 % Allowed : 9.63 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.22), residues: 1528 helix: 1.95 (0.19), residues: 798 sheet: -0.29 (0.54), residues: 97 loop : -0.08 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 71 TYR 0.017 0.001 TYR D 141 PHE 0.019 0.001 PHE E 22 TRP 0.023 0.001 TRP B 103 HIS 0.003 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (12170) covalent geometry : angle 0.50260 / 0.26 (16517) hydrogen bonds : bond 0.04541 / 3.07 ( 668) hydrogen bonds : angle 4.39911 / 3.05 ( 1890) metal coordination : bond 0.00817 / 0.40 ( 4) metal coordination : angle 3.79243 / 1.77 ( 6) Misc. bond : bond 0.00055 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.9516 (mmm) cc_final: 0.9254 (tpp) REVERT: B 15 GLU cc_start: 0.8844 (tp30) cc_final: 0.8023 (pp20) REVERT: B 34 PHE cc_start: 0.8927 (m-80) cc_final: 0.8673 (m-80) REVERT: B 122 MET cc_start: 0.9357 (OUTLIER) cc_final: 0.9099 (ttm) REVERT: D 9 LYS cc_start: 0.8919 (pptt) cc_final: 0.8244 (mppt) REVERT: D 96 ASP cc_start: 0.8630 (p0) cc_final: 0.8404 (p0) REVERT: D 119 GLU cc_start: 0.8789 (tp30) cc_final: 0.8542 (tp30) REVERT: D 124 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8935 (ptpt) REVERT: E 17 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8827 (tpp) REVERT: E 138 GLU cc_start: 0.9286 (mt-10) cc_final: 0.9081 (mt-10) REVERT: F 26 LYS cc_start: 0.9394 (tttt) cc_final: 0.8663 (tmmt) outliers start: 16 outliers final: 6 residues processed: 118 average time/residue: 0.6863 time to fit residues: 86.8915 Evaluate side-chains 120 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain E residue 17 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 117 optimal weight: 0.8980 chunk 147 optimal weight: 0.3980 chunk 66 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.058450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.044194 restraints weight = 30818.290| |-----------------------------------------------------------------------------| r_work (start): 0.2615 rms_B_bonded: 2.26 r_work: 0.2505 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2392 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9064 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12176 Z= 0.144 Angle : 0.509 9.333 16523 Z= 0.266 Chirality : 0.041 0.162 1899 Planarity : 0.004 0.038 2060 Dihedral : 8.317 173.469 1646 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.72 % Allowed : 10.35 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.22), residues: 1528 helix: 1.95 (0.18), residues: 804 sheet: -0.27 (0.54), residues: 97 loop : -0.05 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 71 TYR 0.018 0.001 TYR D 141 PHE 0.033 0.001 PHE E 22 TRP 0.023 0.001 TRP B 103 HIS 0.002 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (12170) covalent geometry : angle 0.50431 / 0.27 (16517) hydrogen bonds : bond 0.04546 / 3.07 ( 668) hydrogen bonds : angle 4.38282 / 3.04 ( 1890) metal coordination : bond 0.00882 / 0.43 ( 4) metal coordination : angle 3.74170 / 1.76 ( 6) Misc. bond : bond 0.00060 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.482 Fit side-chains REVERT: A 43 MET cc_start: 0.9507 (mmm) cc_final: 0.9246 (tpp) REVERT: B 8 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6901 (pm20) REVERT: B 34 PHE cc_start: 0.8937 (m-80) cc_final: 0.8661 (m-80) REVERT: B 122 MET cc_start: 0.9381 (OUTLIER) cc_final: 0.9135 (ttm) REVERT: D 9 LYS cc_start: 0.8909 (pptt) cc_final: 0.8233 (mppt) REVERT: D 96 ASP cc_start: 0.8643 (p0) cc_final: 0.8425 (p0) REVERT: D 119 GLU cc_start: 0.8790 (tp30) cc_final: 0.8479 (tp30) REVERT: E 138 GLU cc_start: 0.9278 (mt-10) cc_final: 0.9050 (mt-10) REVERT: F 26 LYS cc_start: 0.9402 (tttt) cc_final: 0.8691 (tmmt) outliers start: 9 outliers final: 4 residues processed: 115 average time/residue: 0.7014 time to fit residues: 86.6961 Evaluate side-chains 118 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 112 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 123 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 139 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 111 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.058946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.044811 restraints weight = 30692.564| |-----------------------------------------------------------------------------| r_work (start): 0.2630 rms_B_bonded: 2.25 r_work: 0.2520 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2409 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9040 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12176 Z= 0.126 Angle : 0.506 9.732 16523 Z= 0.264 Chirality : 0.040 0.158 1899 Planarity : 0.004 0.037 2060 Dihedral : 8.240 173.838 1646 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.72 % Allowed : 10.43 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.22), residues: 1528 helix: 2.01 (0.18), residues: 804 sheet: -0.20 (0.54), residues: 95 loop : -0.05 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 71 TYR 0.020 0.001 TYR D 141 PHE 0.027 0.001 PHE E 22 TRP 0.024 0.001 TRP B 103 HIS 0.002 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (12170) covalent geometry : angle 0.50108 / 0.26 (16517) hydrogen bonds : bond 0.04331 / 2.93 ( 668) hydrogen bonds : angle 4.32801 / 3.00 ( 1890) metal coordination : bond 0.00803 / 0.39 ( 4) metal coordination : angle 3.65381 / 1.73 ( 6) Misc. bond : bond 0.00036 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.472 Fit side-chains REVERT: A 43 MET cc_start: 0.9515 (mmm) cc_final: 0.9260 (tpp) REVERT: B 8 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6892 (pm20) REVERT: B 12 HIS cc_start: 0.8104 (p90) cc_final: 0.7786 (p90) REVERT: B 15 GLU cc_start: 0.8897 (tp30) cc_final: 0.8185 (pp20) REVERT: B 34 PHE cc_start: 0.8926 (m-80) cc_final: 0.8631 (m-80) REVERT: B 122 MET cc_start: 0.9367 (OUTLIER) cc_final: 0.9115 (ttm) REVERT: D 9 LYS cc_start: 0.8902 (pptt) cc_final: 0.8199 (mppt) REVERT: D 96 ASP cc_start: 0.8624 (p0) cc_final: 0.8407 (p0) REVERT: D 119 GLU cc_start: 0.8782 (tp30) cc_final: 0.8336 (tp30) REVERT: E 138 GLU cc_start: 0.9278 (mt-10) cc_final: 0.9052 (mt-10) REVERT: F 26 LYS cc_start: 0.9373 (tttt) cc_final: 0.8651 (tmmt) outliers start: 9 outliers final: 2 residues processed: 116 average time/residue: 0.7190 time to fit residues: 89.5887 Evaluate side-chains 116 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain C residue 123 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 63 optimal weight: 1.9990 chunk 126 optimal weight: 0.0170 chunk 39 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.059200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.045095 restraints weight = 30884.021| |-----------------------------------------------------------------------------| r_work (start): 0.2636 rms_B_bonded: 2.26 r_work: 0.2525 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2413 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9024 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12176 Z= 0.120 Angle : 0.509 9.909 16523 Z= 0.263 Chirality : 0.040 0.155 1899 Planarity : 0.004 0.037 2060 Dihedral : 8.209 174.083 1646 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.48 % Allowed : 10.99 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.22), residues: 1528 helix: 2.03 (0.18), residues: 804 sheet: 0.14 (0.57), residues: 85 loop : -0.05 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 199 TYR 0.016 0.001 TYR D 141 PHE 0.028 0.001 PHE E 22 TRP 0.024 0.001 TRP B 103 HIS 0.002 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (12170) covalent geometry : angle 0.50406 / 0.26 (16517) hydrogen bonds : bond 0.04248 / 2.87 ( 668) hydrogen bonds : angle 4.29936 / 2.99 ( 1890) metal coordination : bond 0.00681 / 0.33 ( 4) metal coordination : angle 3.79891 / 1.78 ( 6) Misc. bond : bond 0.00034 / 0.02 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 112 time to evaluate : 0.559 Fit side-chains REVERT: A 43 MET cc_start: 0.9517 (mmm) cc_final: 0.9291 (tpp) REVERT: B 15 GLU cc_start: 0.8897 (tp30) cc_final: 0.8130 (pp20) REVERT: B 34 PHE cc_start: 0.8909 (m-80) cc_final: 0.8649 (m-80) REVERT: B 68 MET cc_start: 0.9493 (ttp) cc_final: 0.9281 (ttp) REVERT: B 122 MET cc_start: 0.9373 (OUTLIER) cc_final: 0.9160 (ttm) REVERT: B 256 GLN cc_start: 0.8691 (mm-40) cc_final: 0.8344 (mm-40) REVERT: D 9 LYS cc_start: 0.8876 (pptt) cc_final: 0.8200 (mppt) REVERT: D 96 ASP cc_start: 0.8619 (p0) cc_final: 0.8408 (p0) REVERT: D 207 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8551 (mt-10) REVERT: E 117 THR cc_start: 0.8825 (m) cc_final: 0.8574 (m) REVERT: E 138 GLU cc_start: 0.9268 (mt-10) cc_final: 0.9051 (mt-10) REVERT: F 26 LYS cc_start: 0.9379 (tttt) cc_final: 0.8674 (tmmt) outliers start: 6 outliers final: 2 residues processed: 116 average time/residue: 0.6966 time to fit residues: 86.8712 Evaluate side-chains 114 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 111 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain F residue 15 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.058143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.043855 restraints weight = 31047.132| |-----------------------------------------------------------------------------| r_work (start): 0.2608 rms_B_bonded: 2.27 r_work: 0.2497 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2385 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9071 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12176 Z= 0.178 Angle : 0.546 9.525 16523 Z= 0.283 Chirality : 0.042 0.161 1899 Planarity : 0.004 0.037 2060 Dihedral : 8.258 173.840 1646 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.56 % Allowed : 11.15 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.22), residues: 1528 helix: 1.95 (0.18), residues: 805 sheet: -0.34 (0.53), residues: 99 loop : -0.04 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 71 TYR 0.021 0.001 TYR D 141 PHE 0.032 0.001 PHE E 22 TRP 0.025 0.001 TRP B 103 HIS 0.003 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (12170) covalent geometry : angle 0.54201 / 0.28 (16517) hydrogen bonds : bond 0.04683 / 3.17 ( 668) hydrogen bonds : angle 4.39575 / 3.05 ( 1890) metal coordination : bond 0.01007 / 0.50 ( 4) metal coordination : angle 3.53146 / 1.66 ( 6) Misc. bond : bond 0.00085 / 0.04 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3926.27 seconds wall clock time: 67 minutes 42.44 seconds (4062.44 seconds total)