Starting phenix.real_space_refine on Fri Jul 3 04:51:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ew3_28641/07_2026/8ew3_28641.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ew3_28641/07_2026/8ew3_28641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65159 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8ew3_28641/07_2026/8ew3_28641.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ew3_28641/07_2026/8ew3_28641.cif" model { file = "/net/cci-nas-00/data/ceres_data/8ew3_28641/07_2026/8ew3_28641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ew3_28641/07_2026/8ew3_28641.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ew3_28641/07_2026/8ew3_28641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ew3_28641/07_2026/8ew3_28641.map" } resolution = 2.65159 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 66.314 41.140 63.217 1.00 95.11 S ATOM 10247 SG CYS E 26 64.807 44.084 64.882 1.00 82.26 S ATOM 8651 SG CYS D 29 62.941 41.588 68.946 1.00104.84 S ATOM 10969 SG CYS E 120 64.555 38.368 67.743 1.00 78.16 S Time building chain proxies: 2.85, per 1000 atoms: 0.24 Number of scatterers: 11902 At special positions: 0 Unit cell: (99.324, 108.936, 132.432, 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: 0.97 Conformation dependent library (CDL) restraints added in 649.1 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: 77 helices and 8 sheets defined 60.0% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 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 114 through 125 Processing helix chain 'A' and resid 126 through 131 removed outlier: 3.599A pdb=" N THR A 129 " --> pdb=" O GLY A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 170 removed outlier: 3.907A pdb=" N VAL A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A 169 " --> pdb=" O VAL A 165 " (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: 3.755A pdb=" N HIS A 354 " --> pdb=" O PHE A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 384 removed outlier: 3.813A pdb=" N LYS A 382 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 3.678A 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: 3.613A 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: 3.924A 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: 3.729A pdb=" N LEU B 33 " --> pdb=" O ALA B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.538A 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: 3.515A pdb=" N MET B 325 " --> pdb=" O MET B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 333 removed outlier: 3.581A 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: 3.624A pdb=" N LEU B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.774A 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: 3.526A pdb=" N LYS C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS C 48 " --> pdb=" O ASP C 44 " (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 removed outlier: 3.510A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) 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: 3.758A 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: 3.636A pdb=" N ALA D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) removed outlier: 3.545A 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 removed outlier: 3.520A pdb=" N MET D 115 " --> pdb=" O ASN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 125 removed outlier: 3.629A 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: 4.222A pdb=" N ALA D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 3.780A 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 removed outlier: 3.518A pdb=" N ALA E 30 " --> pdb=" O CYS E 26 " (cutoff:3.500A) 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 Processing helix chain 'E' and resid 102 through 110 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 removed outlier: 3.513A pdb=" N ILE E 181 " --> pdb=" O GLY E 177 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY E 189 " --> pdb=" O LEU E 185 " (cutoff:3.500A) 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: 6.291A 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: 7.124A pdb=" N HIS A 209 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL A 191 " --> pdb=" O HIS A 209 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N PHE A 211 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 6.094A 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: 5.871A pdb=" N VAL A 19 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ARG A 276 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N SER A 21 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 9.737A pdb=" N VAL A 278 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N VAL A 323 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N SER A 263 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N VAL A 325 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ALA A 265 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N ARG A 327 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 5.606A 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: 6.958A pdb=" N LEU A 87 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ARG A 81 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N SER A 89 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE A 79 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 7.041A 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: 7.088A 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: 3.931A pdb=" N LEU C 75 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 14.754A pdb=" N VAL C 121 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 11.602A 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: 6.237A pdb=" N LEU C 138 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TYR C 125 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL C 136 " --> pdb=" O TYR C 125 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL C 127 " --> pdb=" O SER C 134 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS C 132 " --> pdb=" O ASP C 129 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N MET C 148 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLU C 169 " --> pdb=" O MET C 148 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N TYR C 150 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N TYR C 167 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N PHE C 152 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU C 165 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 6.235A 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 160 662 hydrogen bonds defined for protein. 1881 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: 2.05 Time building geometry restraints manager: 1.33 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: 5004 1.42 - 1.61: 7042 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 1.421 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C4 RBF B 601 " pdb=" C4A RBF B 601 " ideal model delta sigma weight residual 1.481 1.405 0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C4A FMN B 600 " pdb=" N5 FMN B 600 " ideal model delta sigma weight residual 1.380 1.306 0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C4A FMN C 301 " pdb=" N5 FMN C 301 " ideal model delta sigma weight residual 1.380 1.307 0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C1 UQ1 B 602 " pdb=" C2 UQ1 B 602 " ideal model delta sigma weight residual 1.485 1.412 0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 12165 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 16294 1.50 - 3.00: 163 3.00 - 4.51: 45 4.51 - 6.01: 12 6.01 - 7.51: 3 Bond angle restraints: 16517 Sorted by residual: angle pdb=" C ILE C 115 " pdb=" N GLN C 116 " pdb=" CA GLN C 116 " ideal model delta sigma weight residual 121.54 126.49 -4.95 1.91e+00 2.74e-01 6.73e+00 angle pdb=" C3 UQ1 B 602 " pdb=" C2 UQ1 B 602 " pdb=" O2 UQ1 B 602 " ideal model delta sigma weight residual 122.52 130.03 -7.51 3.00e+00 1.11e-01 6.26e+00 angle pdb=" C1 UQ1 B 602 " pdb=" C2 UQ1 B 602 " pdb=" O2 UQ1 B 602 " ideal model delta sigma weight residual 117.10 110.63 6.47 3.00e+00 1.11e-01 4.65e+00 angle pdb=" N VAL A 287 " pdb=" CA VAL A 287 " pdb=" CB VAL A 287 " ideal model delta sigma weight residual 111.81 107.29 4.52 2.24e+00 1.99e-01 4.07e+00 angle pdb=" CA TRP B 103 " pdb=" CB TRP B 103 " pdb=" CG TRP B 103 " ideal model delta sigma weight residual 113.60 116.95 -3.35 1.90e+00 2.77e-01 3.11e+00 ... (remaining 16512 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 7058 35.58 - 71.16: 29 71.16 - 106.75: 4 106.75 - 142.33: 1 142.33 - 177.91: 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 79.68 177.91 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 -115.18 -169.57 1 2.00e+01 2.50e-03 4.76e+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 89.23 168.37 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 7092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1330 0.036 - 0.072: 427 0.072 - 0.108: 117 0.108 - 0.144: 24 0.144 - 0.180: 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 -2.45 0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" CA VAL A 139 " pdb=" N VAL A 139 " pdb=" C VAL A 139 " pdb=" CB VAL A 139 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" CA VAL A 90 " pdb=" N VAL A 90 " pdb=" C VAL A 90 " pdb=" CB VAL A 90 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 ... (remaining 1896 not shown) Planarity restraints: 2060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ1 B 602 " 0.081 2.00e-02 2.50e+03 1.21e-01 4.42e+02 pdb=" C2 UQ1 B 602 " -0.017 2.00e-02 2.50e+03 pdb=" C3 UQ1 B 602 " -0.030 2.00e-02 2.50e+03 pdb=" C4 UQ1 B 602 " 0.093 2.00e-02 2.50e+03 pdb=" C5 UQ1 B 602 " -0.005 2.00e-02 2.50e+03 pdb=" C6 UQ1 B 602 " -0.032 2.00e-02 2.50e+03 pdb=" C7 UQ1 B 602 " -0.157 2.00e-02 2.50e+03 pdb=" CM5 UQ1 B 602 " -0.085 2.00e-02 2.50e+03 pdb=" O1 UQ1 B 602 " 0.202 2.00e-02 2.50e+03 pdb=" O2 UQ1 B 602 " -0.073 2.00e-02 2.50e+03 pdb=" O3 UQ1 B 602 " -0.190 2.00e-02 2.50e+03 pdb=" O4 UQ1 B 602 " 0.213 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ1 B 602 " 0.005 2.00e-02 2.50e+03 2.18e-02 5.92e+00 pdb=" C11 UQ1 B 602 " -0.019 2.00e-02 2.50e+03 pdb=" C7 UQ1 B 602 " -0.026 2.00e-02 2.50e+03 pdb=" C8 UQ1 B 602 " 0.036 2.00e-02 2.50e+03 pdb=" C9 UQ1 B 602 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FMN C 301 " 0.012 2.00e-02 2.50e+03 7.40e-03 2.60e+00 pdb=" C10 FMN C 301 " 0.006 2.00e-02 2.50e+03 pdb=" C2 FMN C 301 " -0.007 2.00e-02 2.50e+03 pdb=" C4 FMN C 301 " 0.003 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 " -0.005 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 " 0.002 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 " 0.008 2.00e-02 2.50e+03 pdb=" N3 FMN C 301 " -0.005 2.00e-02 2.50e+03 pdb=" N5 FMN C 301 " 0.009 2.00e-02 2.50e+03 pdb=" O2 FMN C 301 " -0.019 2.00e-02 2.50e+03 pdb=" O4 FMN C 301 " 0.002 2.00e-02 2.50e+03 ... (remaining 2057 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2783 2.79 - 3.32: 11247 3.32 - 3.84: 20053 3.84 - 4.37: 24722 4.37 - 4.90: 41643 Nonbonded interactions: 100448 Sorted by model distance: nonbonded pdb=" O GLU C 99 " pdb=" OG SER C 103 " model vdw 2.260 3.040 nonbonded pdb=" O ALA B 377 " pdb=" O2' FMN C 301 " model vdw 2.293 3.040 nonbonded pdb=" O GLU B 28 " pdb=" OG1 THR B 32 " model vdw 2.295 3.040 nonbonded pdb=" NH1 ARG C 118 " pdb=" O MET C 242 " model vdw 2.327 3.120 nonbonded pdb=" NH1 ARG B 199 " pdb=" O TYR E 166 " model vdw 2.335 3.120 ... (remaining 100443 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: 4.850 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.410 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9039 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 0.108 12176 Z= 0.206 Angle : 0.448 7.509 16523 Z= 0.217 Chirality : 0.039 0.180 1899 Planarity : 0.004 0.121 2060 Dihedral : 10.089 177.911 4311 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.16 % Allowed : 1.35 % Favored : 98.49 % 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: 1.12 (0.21), residues: 1528 helix: 1.44 (0.18), residues: 772 sheet: 0.54 (0.58), residues: 76 loop : 0.05 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 395 TYR 0.006 0.001 TYR A 429 PHE 0.013 0.001 PHE D 104 TRP 0.014 0.001 TRP B 103 HIS 0.003 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (12170) covalent geometry : angle 0.44605 / 0.22 (16517) hydrogen bonds : bond 0.21848 / 14.41 ( 662) hydrogen bonds : angle 6.85361 / 4.84 ( 1881) metal coordination : bond 0.00478 / 0.23 ( 4) metal coordination : angle 2.04330 / 0.82 ( 6) Misc. bond : bond 0.10732 / 5.39 ( 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 170 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 168 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 72 MET cc_start: 0.9473 (mtm) cc_final: 0.9250 (mtm) REVERT: D 87 ASP cc_start: 0.8625 (t70) cc_final: 0.8317 (t0) REVERT: D 95 TYR cc_start: 0.9140 (t80) cc_final: 0.8807 (t80) REVERT: D 202 LYS cc_start: 0.7725 (mmtt) cc_final: 0.7187 (mmmt) REVERT: E 82 THR cc_start: 0.9251 (m) cc_final: 0.9026 (m) REVERT: F 28 LYS cc_start: 0.5812 (mmmt) cc_final: 0.4756 (tttm) outliers start: 2 outliers final: 0 residues processed: 170 average time/residue: 0.7469 time to fit residues: 135.9121 Evaluate side-chains 116 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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: 0.6980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 79 ASN E 119 ASN E 197 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.064907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.048248 restraints weight = 31251.896| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 2.46 r_work: 0.2630 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2516 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12176 Z= 0.169 Angle : 0.546 8.231 16523 Z= 0.289 Chirality : 0.042 0.167 1899 Planarity : 0.004 0.057 2060 Dihedral : 9.130 172.849 1646 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.11 % Allowed : 6.61 % Favored : 92.28 % 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: 1.63 (0.22), residues: 1528 helix: 1.99 (0.19), residues: 786 sheet: 0.14 (0.55), residues: 86 loop : 0.17 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 71 TYR 0.013 0.001 TYR E 106 PHE 0.026 0.001 PHE E 22 TRP 0.018 0.001 TRP B 103 HIS 0.004 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (12170) covalent geometry : angle 0.54415 / 0.29 (16517) hydrogen bonds : bond 0.05832 / 3.90 ( 662) hydrogen bonds : angle 4.92093 / 3.46 ( 1881) metal coordination : bond 0.01259 / 0.63 ( 4) metal coordination : angle 2.70444 / 1.11 ( 6) Misc. bond : bond 0.00095 / 0.05 ( 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 131 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: B 72 MET cc_start: 0.9470 (mtm) cc_final: 0.9259 (mtm) REVERT: D 87 ASP cc_start: 0.9115 (t70) cc_final: 0.8805 (t0) REVERT: D 115 MET cc_start: 0.8581 (tpt) cc_final: 0.8122 (tmm) REVERT: D 202 LYS cc_start: 0.6724 (mmtt) cc_final: 0.6170 (mmmt) REVERT: E 71 GLU cc_start: 0.8903 (mp0) cc_final: 0.8506 (tt0) REVERT: E 82 THR cc_start: 0.9360 (m) cc_final: 0.9141 (m) REVERT: E 151 MET cc_start: 0.8905 (ttp) cc_final: 0.8401 (tpp) REVERT: F 16 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7825 (tm) REVERT: F 28 LYS cc_start: 0.4956 (mmmt) cc_final: 0.4339 (tttm) outliers start: 14 outliers final: 2 residues processed: 121 average time/residue: 0.7126 time to fit residues: 92.5191 Evaluate side-chains 113 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 110 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain F residue 16 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 59 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 29 optimal weight: 0.0170 chunk 1 optimal weight: 0.8980 chunk 130 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 0.0020 chunk 24 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.7830 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.063866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.047335 restraints weight = 31330.150| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 2.45 r_work: 0.2604 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2488 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 12176 Z= 0.206 Angle : 0.551 9.498 16523 Z= 0.287 Chirality : 0.043 0.165 1899 Planarity : 0.004 0.039 2060 Dihedral : 8.891 174.253 1646 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.43 % Allowed : 7.25 % Favored : 91.32 % 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: 1.56 (0.21), residues: 1528 helix: 1.95 (0.18), residues: 788 sheet: 0.28 (0.58), residues: 78 loop : 0.08 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 43 TYR 0.014 0.001 TYR B 360 PHE 0.017 0.002 PHE D 50 TRP 0.019 0.001 TRP B 103 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.21 (12170) covalent geometry : angle 0.54717 / 0.29 (16517) hydrogen bonds : bond 0.05303 / 3.55 ( 662) hydrogen bonds : angle 4.70125 / 3.30 ( 1881) metal coordination : bond 0.02025 / 1.03 ( 4) metal coordination : angle 3.47931 / 1.50 ( 6) Misc. bond : bond 0.00124 / 0.06 ( 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 133 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: B 72 MET cc_start: 0.9497 (mtm) cc_final: 0.9273 (mtm) REVERT: D 87 ASP cc_start: 0.9137 (t70) cc_final: 0.8851 (t0) REVERT: D 115 MET cc_start: 0.8568 (tpt) cc_final: 0.8184 (tmm) REVERT: D 202 LYS cc_start: 0.6977 (mmtt) cc_final: 0.6627 (mttp) REVERT: E 10 LYS cc_start: 0.8285 (ttpp) cc_final: 0.8015 (ttpt) REVERT: E 17 MET cc_start: 0.8707 (mmm) cc_final: 0.8306 (mtt) REVERT: E 82 THR cc_start: 0.9338 (m) cc_final: 0.9120 (m) REVERT: E 151 MET cc_start: 0.8984 (ttp) cc_final: 0.8424 (tpp) REVERT: F 6 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.8218 (t80) REVERT: F 16 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7851 (tm) REVERT: F 28 LYS cc_start: 0.4995 (mmmt) cc_final: 0.4367 (tttm) outliers start: 18 outliers final: 4 residues processed: 121 average time/residue: 0.7050 time to fit residues: 91.9178 Evaluate side-chains 114 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 16 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 21 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 107 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.064026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.047567 restraints weight = 31067.096| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 2.44 r_work: 0.2612 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2496 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 12176 Z= 0.172 Angle : 0.526 8.344 16523 Z= 0.273 Chirality : 0.042 0.163 1899 Planarity : 0.004 0.039 2060 Dihedral : 8.762 174.645 1646 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.27 % Allowed : 8.20 % Favored : 90.53 % 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: 1.60 (0.21), residues: 1528 helix: 2.03 (0.18), residues: 783 sheet: 0.39 (0.61), residues: 76 loop : 0.04 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 43 TYR 0.014 0.001 TYR B 360 PHE 0.016 0.001 PHE E 22 TRP 0.021 0.001 TRP B 103 HIS 0.003 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (12170) covalent geometry : angle 0.52295 / 0.27 (16517) hydrogen bonds : bond 0.04809 / 3.22 ( 662) hydrogen bonds : angle 4.56812 / 3.20 ( 1881) metal coordination : bond 0.01220 / 0.62 ( 4) metal coordination : angle 2.77931 / 1.19 ( 6) Misc. bond : bond 0.00111 / 0.05 ( 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 127 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: B 43 ARG cc_start: 0.8837 (mtm-85) cc_final: 0.8397 (mtm180) REVERT: B 72 MET cc_start: 0.9479 (mtm) cc_final: 0.9248 (mtm) REVERT: D 87 ASP cc_start: 0.9123 (t70) cc_final: 0.8844 (t0) REVERT: D 115 MET cc_start: 0.8481 (tpt) cc_final: 0.8172 (tmm) REVERT: D 202 LYS cc_start: 0.6965 (mmtt) cc_final: 0.6675 (mttp) REVERT: E 10 LYS cc_start: 0.8267 (ttpp) cc_final: 0.8008 (ttpt) REVERT: E 17 MET cc_start: 0.8693 (mmm) cc_final: 0.8315 (mtt) REVERT: E 71 GLU cc_start: 0.8952 (mp0) cc_final: 0.8611 (tt0) REVERT: E 82 THR cc_start: 0.9300 (m) cc_final: 0.9070 (m) REVERT: E 133 ASP cc_start: 0.8738 (t0) cc_final: 0.8427 (t0) REVERT: E 151 MET cc_start: 0.8927 (ttp) cc_final: 0.8367 (ttm) REVERT: F 6 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.8257 (t80) REVERT: F 16 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7954 (tm) REVERT: F 28 LYS cc_start: 0.5315 (mmmt) cc_final: 0.4780 (tttm) outliers start: 16 outliers final: 3 residues processed: 118 average time/residue: 0.6935 time to fit residues: 88.5556 Evaluate side-chains 115 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 16 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 92 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 149 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 134 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3151 r_free = 0.3151 target = 0.064834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.048516 restraints weight = 31193.085| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 2.45 r_work: 0.2639 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2523 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 12176 Z= 0.122 Angle : 0.492 9.702 16523 Z= 0.254 Chirality : 0.040 0.156 1899 Planarity : 0.004 0.036 2060 Dihedral : 8.557 174.799 1646 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.80 % Allowed : 9.08 % Favored : 90.13 % 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: 1.72 (0.22), residues: 1528 helix: 2.18 (0.19), residues: 783 sheet: 0.53 (0.63), residues: 74 loop : 0.01 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 43 TYR 0.014 0.001 TYR B 360 PHE 0.018 0.001 PHE E 22 TRP 0.022 0.001 TRP B 103 HIS 0.003 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (12170) covalent geometry : angle 0.49029 / 0.25 (16517) hydrogen bonds : bond 0.04336 / 2.91 ( 662) hydrogen bonds : angle 4.43489 / 3.10 ( 1881) metal coordination : bond 0.00967 / 0.49 ( 4) metal coordination : angle 2.28051 / 1.01 ( 6) Misc. bond : bond 0.00055 / 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 125 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: B 43 ARG cc_start: 0.8859 (mtm-85) cc_final: 0.8511 (mtm180) REVERT: B 72 MET cc_start: 0.9478 (mtm) cc_final: 0.9249 (mtm) REVERT: D 87 ASP cc_start: 0.9121 (t70) cc_final: 0.8855 (t0) REVERT: D 99 LYS cc_start: 0.9489 (mtpp) cc_final: 0.9181 (mtpp) REVERT: D 202 LYS cc_start: 0.6916 (mmtt) cc_final: 0.6677 (mttp) REVERT: E 10 LYS cc_start: 0.8187 (ttpp) cc_final: 0.7959 (ttpt) REVERT: E 17 MET cc_start: 0.8678 (mmm) cc_final: 0.8288 (mtt) REVERT: E 82 THR cc_start: 0.9295 (m) cc_final: 0.9064 (m) REVERT: E 119 ASN cc_start: 0.8690 (t0) cc_final: 0.8466 (t0) REVERT: E 133 ASP cc_start: 0.8726 (t0) cc_final: 0.8409 (t0) REVERT: E 151 MET cc_start: 0.8952 (ttp) cc_final: 0.8390 (tpp) REVERT: F 6 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.8237 (t80) REVERT: F 16 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7969 (tm) REVERT: F 28 LYS cc_start: 0.5318 (mmmt) cc_final: 0.4853 (tttm) outliers start: 10 outliers final: 3 residues processed: 119 average time/residue: 0.7406 time to fit residues: 94.6462 Evaluate side-chains 115 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 16 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 43 optimal weight: 0.0570 chunk 14 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 overall best weight: 1.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 116 GLN D 19 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.063158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.046802 restraints weight = 31380.031| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 2.44 r_work: 0.2595 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2479 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 12176 Z= 0.217 Angle : 0.553 10.484 16523 Z= 0.284 Chirality : 0.043 0.168 1899 Planarity : 0.004 0.037 2060 Dihedral : 8.621 175.204 1646 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.04 % Allowed : 9.95 % Favored : 89.01 % 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: 1.58 (0.21), residues: 1528 helix: 2.06 (0.18), residues: 787 sheet: 0.23 (0.62), residues: 78 loop : -0.02 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 43 TYR 0.015 0.001 TYR B 360 PHE 0.027 0.002 PHE E 22 TRP 0.023 0.001 TRP B 103 HIS 0.003 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.22 (12170) covalent geometry : angle 0.55019 / 0.28 (16517) hydrogen bonds : bond 0.04916 / 3.29 ( 662) hydrogen bonds : angle 4.54797 / 3.18 ( 1881) metal coordination : bond 0.01389 / 0.71 ( 4) metal coordination : angle 2.80411 / 1.22 ( 6) Misc. bond : bond 0.00131 / 0.06 ( 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 123 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 430 GLU cc_start: 0.9290 (OUTLIER) cc_final: 0.8859 (mt-10) REVERT: B 43 ARG cc_start: 0.8932 (mtm-85) cc_final: 0.8632 (mtm-85) REVERT: B 72 MET cc_start: 0.9511 (mtm) cc_final: 0.9299 (mtm) REVERT: D 87 ASP cc_start: 0.9124 (t70) cc_final: 0.8874 (t0) REVERT: D 99 LYS cc_start: 0.9500 (mtpp) cc_final: 0.9187 (mtpp) REVERT: D 202 LYS cc_start: 0.7033 (mmtt) cc_final: 0.6779 (mttp) REVERT: E 17 MET cc_start: 0.8706 (mmm) cc_final: 0.8341 (mtt) REVERT: E 71 GLU cc_start: 0.8970 (mp0) cc_final: 0.8634 (tt0) REVERT: E 82 THR cc_start: 0.9299 (m) cc_final: 0.9065 (m) REVERT: E 133 ASP cc_start: 0.8729 (t0) cc_final: 0.8443 (t0) REVERT: E 151 MET cc_start: 0.8993 (ttp) cc_final: 0.8393 (ttm) REVERT: F 6 PHE cc_start: 0.8654 (OUTLIER) cc_final: 0.8249 (t80) REVERT: F 16 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8001 (tm) REVERT: F 28 LYS cc_start: 0.5245 (mmmt) cc_final: 0.4694 (tttm) outliers start: 13 outliers final: 5 residues processed: 116 average time/residue: 0.6895 time to fit residues: 86.2247 Evaluate side-chains 118 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 16 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 116 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 0.0770 chunk 80 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 137 optimal weight: 7.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.064363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.048071 restraints weight = 31178.938| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 2.45 r_work: 0.2630 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2514 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12176 Z= 0.127 Angle : 0.504 11.343 16523 Z= 0.260 Chirality : 0.041 0.158 1899 Planarity : 0.004 0.035 2060 Dihedral : 8.447 175.705 1646 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.88 % Allowed : 10.03 % 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: 1.69 (0.22), residues: 1528 helix: 2.18 (0.18), residues: 790 sheet: 0.47 (0.63), residues: 74 loop : -0.05 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 43 TYR 0.014 0.001 TYR B 360 PHE 0.026 0.001 PHE E 22 TRP 0.023 0.001 TRP B 103 HIS 0.002 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (12170) covalent geometry : angle 0.50209 / 0.26 (16517) hydrogen bonds : bond 0.04319 / 2.90 ( 662) hydrogen bonds : angle 4.42000 / 3.09 ( 1881) metal coordination : bond 0.00822 / 0.42 ( 4) metal coordination : angle 2.17998 / 0.94 ( 6) Misc. bond : bond 0.00046 / 0.02 ( 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 125 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 430 GLU cc_start: 0.9279 (OUTLIER) cc_final: 0.8844 (mt-10) REVERT: B 42 LYS cc_start: 0.9458 (mttt) cc_final: 0.9250 (mmpt) REVERT: B 72 MET cc_start: 0.9480 (mtm) cc_final: 0.9258 (mtm) REVERT: D 87 ASP cc_start: 0.9105 (t70) cc_final: 0.8861 (t0) REVERT: D 99 LYS cc_start: 0.9506 (mtpp) cc_final: 0.9122 (mtpp) REVERT: D 164 GLU cc_start: 0.8782 (tt0) cc_final: 0.8375 (tm-30) REVERT: E 17 MET cc_start: 0.8645 (mmm) cc_final: 0.8287 (mtt) REVERT: E 71 GLU cc_start: 0.8945 (mp0) cc_final: 0.8603 (tt0) REVERT: E 82 THR cc_start: 0.9297 (m) cc_final: 0.9066 (m) REVERT: E 119 ASN cc_start: 0.8697 (t0) cc_final: 0.8443 (t0) REVERT: E 133 ASP cc_start: 0.8714 (t0) cc_final: 0.8427 (t0) REVERT: F 6 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.8256 (t80) REVERT: F 16 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8050 (tm) REVERT: F 28 LYS cc_start: 0.5304 (mmmt) cc_final: 0.4808 (tttm) outliers start: 11 outliers final: 5 residues processed: 118 average time/residue: 0.6514 time to fit residues: 82.4293 Evaluate side-chains 118 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 16 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 117 optimal weight: 2.9990 chunk 147 optimal weight: 0.1980 chunk 66 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 95 optimal weight: 0.0980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 19 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.064466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.048299 restraints weight = 31125.779| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 2.43 r_work: 0.2636 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2521 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12176 Z= 0.120 Angle : 0.502 11.818 16523 Z= 0.259 Chirality : 0.040 0.156 1899 Planarity : 0.004 0.034 2060 Dihedral : 8.285 176.356 1646 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.04 % Allowed : 10.43 % 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: 1.69 (0.22), residues: 1528 helix: 2.18 (0.18), residues: 792 sheet: 0.43 (0.63), residues: 74 loop : -0.07 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 43 TYR 0.015 0.001 TYR D 141 PHE 0.030 0.001 PHE E 22 TRP 0.024 0.001 TRP B 103 HIS 0.002 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (12170) covalent geometry : angle 0.50110 / 0.26 (16517) hydrogen bonds : bond 0.04158 / 2.80 ( 662) hydrogen bonds : angle 4.36572 / 3.06 ( 1881) metal coordination : bond 0.00818 / 0.42 ( 4) metal coordination : angle 2.00204 / 0.90 ( 6) Misc. bond : bond 0.00033 / 0.02 ( 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 128 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 430 GLU cc_start: 0.9281 (OUTLIER) cc_final: 0.8792 (mt-10) REVERT: B 72 MET cc_start: 0.9509 (mtm) cc_final: 0.9288 (mtm) REVERT: D 87 ASP cc_start: 0.9109 (t70) cc_final: 0.8880 (t0) REVERT: D 99 LYS cc_start: 0.9444 (mtpp) cc_final: 0.9173 (mtpp) REVERT: D 164 GLU cc_start: 0.8779 (tt0) cc_final: 0.8404 (tm-30) REVERT: E 17 MET cc_start: 0.8597 (mmm) cc_final: 0.8225 (mtt) REVERT: E 22 PHE cc_start: 0.8278 (m-10) cc_final: 0.7853 (m-10) REVERT: E 71 GLU cc_start: 0.8899 (mp0) cc_final: 0.8595 (tt0) REVERT: E 82 THR cc_start: 0.9317 (m) cc_final: 0.9088 (m) REVERT: E 119 ASN cc_start: 0.8590 (t0) cc_final: 0.8326 (t0) REVERT: F 6 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.8284 (t80) REVERT: F 10 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8399 (tpp) REVERT: F 16 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8073 (tm) REVERT: F 28 LYS cc_start: 0.4803 (mmmt) cc_final: 0.4336 (tttm) outliers start: 13 outliers final: 5 residues processed: 120 average time/residue: 0.6809 time to fit residues: 87.7278 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 : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 16 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 139 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 142 optimal weight: 0.7980 chunk 111 optimal weight: 0.3980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.064249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.048138 restraints weight = 31138.786| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 2.43 r_work: 0.2633 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2518 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12176 Z= 0.136 Angle : 0.519 12.390 16523 Z= 0.266 Chirality : 0.041 0.157 1899 Planarity : 0.004 0.035 2060 Dihedral : 8.201 176.918 1646 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.19 % Allowed : 10.27 % 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: 1.66 (0.22), residues: 1528 helix: 2.16 (0.18), residues: 793 sheet: 0.42 (0.63), residues: 74 loop : -0.08 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 43 TYR 0.027 0.001 TYR E 106 PHE 0.027 0.001 PHE E 22 TRP 0.024 0.001 TRP B 103 HIS 0.002 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (12170) covalent geometry : angle 0.51717 / 0.27 (16517) hydrogen bonds : bond 0.04224 / 2.84 ( 662) hydrogen bonds : angle 4.36987 / 3.06 ( 1881) metal coordination : bond 0.00853 / 0.43 ( 4) metal coordination : angle 2.10975 / 0.94 ( 6) Misc. bond : bond 0.00053 / 0.03 ( 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 131 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 430 GLU cc_start: 0.9327 (OUTLIER) cc_final: 0.8826 (mt-10) REVERT: B 43 ARG cc_start: 0.8894 (mtm-85) cc_final: 0.8431 (mtm180) REVERT: B 72 MET cc_start: 0.9511 (mtm) cc_final: 0.9296 (mtm) REVERT: D 87 ASP cc_start: 0.9109 (t70) cc_final: 0.8883 (t0) REVERT: D 99 LYS cc_start: 0.9460 (mtpp) cc_final: 0.9120 (mtpp) REVERT: D 164 GLU cc_start: 0.8800 (tt0) cc_final: 0.8436 (tm-30) REVERT: E 17 MET cc_start: 0.8614 (mmm) cc_final: 0.8249 (mtt) REVERT: E 22 PHE cc_start: 0.8330 (m-10) cc_final: 0.7813 (m-10) REVERT: E 71 GLU cc_start: 0.8856 (mp0) cc_final: 0.8566 (tt0) REVERT: E 82 THR cc_start: 0.9321 (m) cc_final: 0.9093 (m) REVERT: E 119 ASN cc_start: 0.8602 (t0) cc_final: 0.8338 (t0) REVERT: F 6 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.8292 (t80) REVERT: F 10 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8407 (tpp) REVERT: F 16 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8114 (tm) REVERT: F 28 LYS cc_start: 0.4753 (mmmt) cc_final: 0.4277 (tttm) outliers start: 15 outliers final: 6 residues processed: 122 average time/residue: 0.6129 time to fit residues: 80.3474 Evaluate side-chains 123 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 16 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 63 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 19 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.062780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.046423 restraints weight = 31339.366| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 2.44 r_work: 0.2588 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2472 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 12176 Z= 0.256 Angle : 0.594 12.308 16523 Z= 0.303 Chirality : 0.044 0.166 1899 Planarity : 0.004 0.037 2060 Dihedral : 8.317 177.508 1646 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.88 % Allowed : 10.91 % Favored : 88.22 % 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 (0.21), residues: 1528 helix: 2.01 (0.18), residues: 787 sheet: -0.22 (0.58), residues: 88 loop : -0.10 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 174 TYR 0.018 0.002 TYR D 141 PHE 0.035 0.002 PHE E 22 TRP 0.024 0.002 TRP B 103 HIS 0.005 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.26 (12170) covalent geometry : angle 0.59174 / 0.30 (16517) hydrogen bonds : bond 0.05017 / 3.36 ( 662) hydrogen bonds : angle 4.56305 / 3.19 ( 1881) metal coordination : bond 0.01460 / 0.75 ( 4) metal coordination : angle 2.80989 / 1.18 ( 6) Misc. bond : bond 0.00147 / 0.07 ( 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 119 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 430 GLU cc_start: 0.9384 (OUTLIER) cc_final: 0.8857 (mt-10) REVERT: B 43 ARG cc_start: 0.8995 (mtm-85) cc_final: 0.8500 (mtm180) REVERT: B 72 MET cc_start: 0.9511 (mtm) cc_final: 0.9290 (mtm) REVERT: D 87 ASP cc_start: 0.9125 (t70) cc_final: 0.8913 (t0) REVERT: D 99 LYS cc_start: 0.9439 (mtpp) cc_final: 0.9158 (mtpp) REVERT: D 164 GLU cc_start: 0.8893 (tt0) cc_final: 0.8549 (tm-30) REVERT: E 17 MET cc_start: 0.8605 (mmm) cc_final: 0.8259 (mtt) REVERT: E 22 PHE cc_start: 0.8446 (m-10) cc_final: 0.7889 (m-10) REVERT: E 71 GLU cc_start: 0.8888 (mp0) cc_final: 0.8571 (tt0) REVERT: E 82 THR cc_start: 0.9308 (m) cc_final: 0.9076 (m) REVERT: E 151 MET cc_start: 0.9005 (ttp) cc_final: 0.8392 (ttm) REVERT: F 6 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.8328 (t80) REVERT: F 16 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8114 (tm) REVERT: F 28 LYS cc_start: 0.5122 (mmmt) cc_final: 0.4564 (tttm) outliers start: 11 outliers final: 3 residues processed: 113 average time/residue: 0.6150 time to fit residues: 74.7773 Evaluate side-chains 114 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 16 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.062766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.046518 restraints weight = 31608.777| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 2.44 r_work: 0.2591 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2476 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12176 Z= 0.219 Angle : 0.579 12.280 16523 Z= 0.295 Chirality : 0.043 0.160 1899 Planarity : 0.004 0.037 2060 Dihedral : 8.289 178.234 1646 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.72 % Allowed : 10.99 % 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: 1.41 (0.21), residues: 1528 helix: 1.97 (0.18), residues: 789 sheet: -0.26 (0.58), residues: 88 loop : -0.13 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 43 TYR 0.016 0.001 TYR E 106 PHE 0.034 0.002 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 0.00505 / 0.22 (12170) covalent geometry : angle 0.57741 / 0.29 (16517) hydrogen bonds : bond 0.04845 / 3.25 ( 662) hydrogen bonds : angle 4.54137 / 3.18 ( 1881) metal coordination : bond 0.01314 / 0.67 ( 4) metal coordination : angle 2.46530 / 1.03 ( 6) Misc. bond : bond 0.00124 / 0.06 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4050.55 seconds wall clock time: 69 minutes 56.43 seconds (4196.43 seconds total)