Starting phenix.real_space_refine on Sat Aug 23 12:57:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ew3_28641/08_2025/8ew3_28641.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ew3_28641/08_2025/8ew3_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ew3_28641/08_2025/8ew3_28641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ew3_28641/08_2025/8ew3_28641.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ew3_28641/08_2025/8ew3_28641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ew3_28641/08_2025/8ew3_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-2.0-5787/lib/python3.9/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 Unresolved non-hydrogen dihedrals: 1 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 Unresolved non-hydrogen dihedrals: 1 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: 3.02, per 1000 atoms: 0.25 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: 1.16 Conformation dependent library (CDL) restraints added in 552.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.41 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: 2.03 Time building geometry restraints manager: 1.45 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 FMN C 301 " pdb=" C4A FMN C 301 " ideal model delta sigma weight residual 1.485 1.403 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C4 FMN B 600 " pdb=" C4A FMN B 600 " ideal model delta sigma weight residual 1.485 1.405 0.080 2.00e-02 2.50e+03 1.60e+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=" 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: 16308 1.50 - 3.00: 150 3.00 - 4.51: 41 4.51 - 6.01: 15 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 - 15.73: 6819 15.73 - 31.45: 240 31.45 - 47.18: 40 47.18 - 62.90: 9 62.90 - 78.63: 4 Dihedral angle restraints: 7112 sinusoidal: 2755 harmonic: 4357 Sorted by residual: dihedral pdb=" CA SER B 44 " pdb=" C SER B 44 " pdb=" N SER B 45 " pdb=" CA SER B 45 " ideal model delta harmonic sigma weight residual -180.00 -161.83 -18.17 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA GLU B 274 " pdb=" C GLU B 274 " pdb=" N VAL B 275 " pdb=" CA VAL B 275 " ideal model delta harmonic sigma weight residual 180.00 -163.50 -16.50 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA GLU A 430 " pdb=" CB GLU A 430 " pdb=" CG GLU A 430 " pdb=" CD GLU A 430 " ideal model delta sinusoidal sigma weight residual 60.00 113.54 -53.54 3 1.50e+01 4.44e-03 9.21e+00 ... (remaining 7109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1326 0.036 - 0.072: 430 0.072 - 0.108: 116 0.108 - 0.144: 25 0.144 - 0.180: 2 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=" C3' FMN B 600 " pdb=" C2' FMN B 600 " pdb=" C4' FMN B 600 " pdb=" O3' FMN B 600 " both_signs ideal model delta sigma weight residual False -2.38 -2.55 0.17 2.00e-01 2.50e+01 7.40e-01 chirality pdb=" C3' FMN C 301 " pdb=" C2' FMN C 301 " pdb=" C4' FMN C 301 " pdb=" O3' FMN C 301 " both_signs ideal model delta sigma weight residual False -2.38 -2.51 0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 1896 not shown) Planarity restraints: 2062 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 " 0.011 2.00e-02 2.50e+03 7.58e-03 2.58e+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 " 0.005 2.00e-02 2.50e+03 pdb=" C6 FMN C 301 " 0.003 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 " 0.007 2.00e-02 2.50e+03 pdb=" N3 FMN C 301 " -0.004 2.00e-02 2.50e+03 pdb=" N5 FMN C 301 " 0.009 2.00e-02 2.50e+03 pdb=" O2 FMN C 301 " -0.019 2.00e-02 2.50e+03 ... (remaining 2059 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.180 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 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 : 0.003 0.108 12176 Z= 0.204 Angle : 0.443 7.509 16523 Z= 0.216 Chirality : 0.039 0.180 1899 Planarity : 0.004 0.121 2062 Dihedral : 8.866 78.626 4328 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 aren 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 covalent geometry : bond 0.00321 (12170) covalent geometry : angle 0.44180 (16517) hydrogen bonds : bond 0.21848 ( 662) hydrogen bonds : angle 6.85361 ( 1881) metal coordination : bond 0.00478 ( 4) metal coordination : angle 2.04330 ( 6) Misc. bond : bond 0.10732 ( 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 : 0.562 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: 0.7566 time to fit residues: 137.4407 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 : 0.467 ------------------------------------------------------------------------------- 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: 4.9990 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: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3146 r_free = 0.3146 target = 0.064683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.048026 restraints weight = 31292.818| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 2.45 r_work: 0.2622 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2509 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12176 Z= 0.186 Angle : 0.562 8.544 16523 Z= 0.297 Chirality : 0.043 0.167 1899 Planarity : 0.004 0.059 2062 Dihedral : 5.432 59.985 1663 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.19 % Allowed : 6.45 % Favored : 92.36 % 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 aren not related in a simple way. whole: 1.61 (0.22), residues: 1528 helix: 1.98 (0.18), residues: 786 sheet: 0.04 (0.54), residues: 88 loop : 0.18 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 46 TYR 0.013 0.001 TYR E 106 PHE 0.025 0.002 PHE E 22 TRP 0.018 0.001 TRP B 103 HIS 0.004 0.001 HIS C 199 Details of bonding type rmsd covalent geometry : bond 0.00418 (12170) covalent geometry : angle 0.55915 (16517) hydrogen bonds : bond 0.05784 ( 662) hydrogen bonds : angle 4.94240 ( 1881) metal coordination : bond 0.01304 ( 4) metal coordination : angle 2.79716 ( 6) Misc. bond : bond 0.00181 ( 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: 15 poor density : 116 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: B 72 MET cc_start: 0.9474 (mtm) cc_final: 0.9267 (mtm) REVERT: D 87 ASP cc_start: 0.9119 (t70) cc_final: 0.8807 (t0) REVERT: D 115 MET cc_start: 0.8580 (tpt) cc_final: 0.8119 (tmm) REVERT: D 202 LYS cc_start: 0.6782 (mmtt) cc_final: 0.6365 (mttp) REVERT: E 17 MET cc_start: 0.8744 (mmm) cc_final: 0.8288 (mtt) REVERT: E 71 GLU cc_start: 0.8898 (mp0) cc_final: 0.8514 (tt0) REVERT: E 82 THR cc_start: 0.9362 (m) cc_final: 0.9142 (m) REVERT: E 151 MET cc_start: 0.8931 (ttp) cc_final: 0.8404 (tpp) REVERT: F 16 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7789 (tm) REVERT: F 28 LYS cc_start: 0.5002 (mmmt) cc_final: 0.4361 (tttm) outliers start: 15 outliers final: 3 residues processed: 120 average time/residue: 0.7495 time to fit residues: 96.3895 Evaluate side-chains 114 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 110 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain C residue 14 VAL 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: 8.9990 chunk 29 optimal weight: 0.0980 chunk 1 optimal weight: 0.8980 chunk 130 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.063056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.046547 restraints weight = 31462.158| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 2.44 r_work: 0.2582 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2466 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 12176 Z= 0.264 Angle : 0.590 9.463 16523 Z= 0.306 Chirality : 0.044 0.172 1899 Planarity : 0.004 0.040 2062 Dihedral : 5.402 59.162 1663 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.27 % Allowed : 7.32 % Favored : 91.40 % 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 aren not related in a simple way. whole: 1.46 (0.21), residues: 1528 helix: 1.86 (0.18), residues: 788 sheet: -0.14 (0.55), residues: 88 loop : 0.11 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 43 TYR 0.017 0.001 TYR D 141 PHE 0.022 0.002 PHE E 28 TRP 0.020 0.002 TRP B 103 HIS 0.004 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00611 (12170) covalent geometry : angle 0.58646 (16517) hydrogen bonds : bond 0.05615 ( 662) hydrogen bonds : angle 4.78303 ( 1881) metal coordination : bond 0.02141 ( 4) metal coordination : angle 3.56458 ( 6) Misc. bond : bond 0.00199 ( 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 128 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: B 72 MET cc_start: 0.9512 (mtm) cc_final: 0.9276 (mtm) REVERT: D 87 ASP cc_start: 0.9154 (t70) cc_final: 0.8861 (t0) REVERT: D 115 MET cc_start: 0.8581 (tpt) cc_final: 0.8206 (mmm) REVERT: D 164 GLU cc_start: 0.8708 (tt0) cc_final: 0.8332 (tm-30) REVERT: D 202 LYS cc_start: 0.7031 (mmtt) cc_final: 0.6685 (mttp) REVERT: E 10 LYS cc_start: 0.8334 (ttpp) cc_final: 0.8059 (ttpt) REVERT: E 17 MET cc_start: 0.8767 (mmm) cc_final: 0.8368 (mtt) REVERT: E 82 THR cc_start: 0.9333 (m) cc_final: 0.9111 (m) REVERT: E 151 MET cc_start: 0.8976 (ttp) cc_final: 0.8392 (ttm) REVERT: F 6 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.8252 (t80) REVERT: F 16 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7861 (tm) REVERT: F 28 LYS cc_start: 0.5084 (mmmt) cc_final: 0.4443 (tttm) outliers start: 16 outliers final: 3 residues processed: 119 average time/residue: 0.7383 time to fit residues: 94.4931 Evaluate side-chains 112 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 16 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 21 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 147 optimal weight: 0.0570 chunk 106 optimal weight: 2.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.064819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.048408 restraints weight = 30984.901| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 2.44 r_work: 0.2635 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2520 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12176 Z= 0.115 Angle : 0.494 8.317 16523 Z= 0.259 Chirality : 0.040 0.155 1899 Planarity : 0.004 0.036 2062 Dihedral : 5.052 59.972 1663 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.04 % Allowed : 8.68 % Favored : 90.29 % 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 aren not related in a simple way. whole: 1.64 (0.22), residues: 1528 helix: 2.06 (0.19), residues: 788 sheet: 0.48 (0.61), residues: 74 loop : 0.04 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 43 TYR 0.014 0.001 TYR D 141 PHE 0.013 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 covalent geometry : bond 0.00241 (12170) covalent geometry : angle 0.49194 (16517) hydrogen bonds : bond 0.04494 ( 662) hydrogen bonds : angle 4.51921 ( 1881) metal coordination : bond 0.00871 ( 4) metal coordination : angle 2.32491 ( 6) Misc. bond : bond 0.00071 ( 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 128 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: B 43 ARG cc_start: 0.8775 (mtm-85) cc_final: 0.8342 (mtm180) REVERT: B 72 MET cc_start: 0.9466 (mtm) cc_final: 0.9230 (mtm) REVERT: D 87 ASP cc_start: 0.9120 (t70) cc_final: 0.8840 (t0) REVERT: D 99 LYS cc_start: 0.9494 (mtpp) cc_final: 0.9151 (mtpp) REVERT: D 115 MET cc_start: 0.8451 (tpt) cc_final: 0.8126 (tmm) REVERT: D 202 LYS cc_start: 0.6922 (mmtt) cc_final: 0.6626 (mttp) REVERT: E 10 LYS cc_start: 0.8233 (ttpp) cc_final: 0.7945 (ttpt) REVERT: E 17 MET cc_start: 0.8733 (mmm) cc_final: 0.8332 (mtt) REVERT: E 71 GLU cc_start: 0.8983 (mp0) cc_final: 0.8619 (tt0) REVERT: E 82 THR cc_start: 0.9297 (m) cc_final: 0.9068 (m) REVERT: E 151 MET cc_start: 0.8867 (ttp) cc_final: 0.8351 (tpp) REVERT: F 6 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.8241 (t80) REVERT: F 16 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7952 (tm) REVERT: F 28 LYS cc_start: 0.5310 (mmmt) cc_final: 0.4793 (tttm) outliers start: 13 outliers final: 3 residues processed: 120 average time/residue: 0.7048 time to fit residues: 90.8937 Evaluate side-chains 114 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 109 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 92 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 39 optimal weight: 0.0970 chunk 84 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 134 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN E 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.063681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.047280 restraints weight = 31256.548| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 2.44 r_work: 0.2606 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2491 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12176 Z= 0.181 Angle : 0.524 9.960 16523 Z= 0.272 Chirality : 0.042 0.164 1899 Planarity : 0.004 0.036 2062 Dihedral : 5.073 59.452 1663 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.19 % Allowed : 8.84 % Favored : 89.97 % 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 aren not related in a simple way. whole: 1.63 (0.21), residues: 1528 helix: 2.11 (0.18), residues: 782 sheet: 0.38 (0.62), residues: 76 loop : -0.02 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 43 TYR 0.015 0.001 TYR B 360 PHE 0.014 0.001 PHE B 213 TRP 0.022 0.001 TRP B 103 HIS 0.003 0.001 HIS B 46 Details of bonding type rmsd covalent geometry : bond 0.00417 (12170) covalent geometry : angle 0.52190 (16517) hydrogen bonds : bond 0.04764 ( 662) hydrogen bonds : angle 4.53563 ( 1881) metal coordination : bond 0.01270 ( 4) metal coordination : angle 2.63252 ( 6) Misc. bond : bond 0.00125 ( 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 127 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 43 ARG cc_start: 0.8902 (mtm-85) cc_final: 0.8538 (mtm180) REVERT: B 72 MET cc_start: 0.9496 (mtm) cc_final: 0.9276 (mtm) REVERT: D 87 ASP cc_start: 0.9134 (t70) cc_final: 0.8863 (t0) REVERT: D 202 LYS cc_start: 0.6978 (mmtt) cc_final: 0.6703 (mttp) REVERT: E 10 LYS cc_start: 0.8207 (ttpp) cc_final: 0.7962 (ttpt) REVERT: E 17 MET cc_start: 0.8721 (mmm) cc_final: 0.8304 (mtt) REVERT: E 82 THR cc_start: 0.9305 (m) cc_final: 0.9075 (m) REVERT: E 133 ASP cc_start: 0.8735 (t0) cc_final: 0.8434 (t0) REVERT: F 6 PHE cc_start: 0.8637 (OUTLIER) cc_final: 0.8244 (t80) REVERT: F 16 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.7987 (tm) REVERT: F 28 LYS cc_start: 0.5324 (mmmt) cc_final: 0.4817 (tttm) outliers start: 15 outliers final: 6 residues processed: 117 average time/residue: 0.7410 time to fit residues: 93.1523 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 : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 E residue 162 GLU 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=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: 4.9990 chunk 143 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.062118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.045752 restraints weight = 31525.969| |-----------------------------------------------------------------------------| r_work (start): 0.2677 rms_B_bonded: 2.42 r_work: 0.2565 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2449 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 12176 Z= 0.296 Angle : 0.608 10.688 16523 Z= 0.314 Chirality : 0.045 0.171 1899 Planarity : 0.004 0.040 2062 Dihedral : 5.362 59.730 1663 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.27 % Allowed : 9.08 % Favored : 89.65 % 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 aren not related in a simple way. whole: 1.39 (0.21), residues: 1528 helix: 1.90 (0.18), residues: 785 sheet: -0.26 (0.58), residues: 88 loop : -0.06 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 43 TYR 0.015 0.002 TYR E 106 PHE 0.018 0.002 PHE D 104 TRP 0.023 0.002 TRP B 103 HIS 0.004 0.001 HIS B 46 Details of bonding type rmsd covalent geometry : bond 0.00687 (12170) covalent geometry : angle 0.60489 (16517) hydrogen bonds : bond 0.05435 ( 662) hydrogen bonds : angle 4.70110 ( 1881) metal coordination : bond 0.01564 ( 4) metal coordination : angle 3.50368 ( 6) Misc. bond : bond 0.00204 ( 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 125 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 430 GLU cc_start: 0.9310 (OUTLIER) cc_final: 0.8855 (mt-10) REVERT: B 43 ARG cc_start: 0.8961 (mtm-85) cc_final: 0.8661 (mtm-85) REVERT: B 72 MET cc_start: 0.9529 (mtm) cc_final: 0.9314 (mtm) REVERT: D 87 ASP cc_start: 0.9145 (t70) cc_final: 0.8898 (t0) REVERT: D 99 LYS cc_start: 0.9471 (mtpp) cc_final: 0.9194 (mtpp) REVERT: D 164 GLU cc_start: 0.8853 (tt0) cc_final: 0.8521 (tm-30) REVERT: D 202 LYS cc_start: 0.7287 (mmtt) cc_final: 0.7044 (mttp) REVERT: E 17 MET cc_start: 0.8766 (mmm) cc_final: 0.8379 (mtt) REVERT: E 71 GLU cc_start: 0.8970 (mp0) cc_final: 0.8676 (tt0) REVERT: E 82 THR cc_start: 0.9313 (m) cc_final: 0.9080 (m) REVERT: E 133 ASP cc_start: 0.8758 (t0) cc_final: 0.8495 (t0) REVERT: F 6 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.8261 (t80) REVERT: F 16 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8080 (tm) REVERT: F 28 LYS cc_start: 0.5451 (mmmt) cc_final: 0.4822 (tttm) outliers start: 16 outliers final: 7 residues processed: 116 average time/residue: 0.7297 time to fit residues: 91.0772 Evaluate side-chains 119 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 D residue 11 VAL Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 162 GLU 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: 0.7980 chunk 135 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 137 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.063743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.047440 restraints weight = 31139.612| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 2.44 r_work: 0.2610 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2494 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12176 Z= 0.135 Angle : 0.518 11.286 16523 Z= 0.268 Chirality : 0.041 0.153 1899 Planarity : 0.004 0.037 2062 Dihedral : 5.094 59.769 1663 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % 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 aren not related in a simple way. whole: 1.61 (0.21), residues: 1528 helix: 2.15 (0.19), residues: 781 sheet: 0.44 (0.63), residues: 74 loop : -0.11 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 43 TYR 0.015 0.001 TYR E 106 PHE 0.013 0.001 PHE D 188 TRP 0.023 0.001 TRP B 103 HIS 0.002 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00299 (12170) covalent geometry : angle 0.51547 (16517) hydrogen bonds : bond 0.04532 ( 662) hydrogen bonds : angle 4.49068 ( 1881) metal coordination : bond 0.00826 ( 4) metal coordination : angle 2.50127 ( 6) Misc. bond : bond 0.00071 ( 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 122 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 430 GLU cc_start: 0.9295 (OUTLIER) cc_final: 0.8846 (mt-10) REVERT: B 42 LYS cc_start: 0.9457 (mttt) cc_final: 0.9240 (mmpt) REVERT: B 43 ARG cc_start: 0.8861 (mtm-85) cc_final: 0.8592 (mtm-85) REVERT: B 72 MET cc_start: 0.9483 (mtm) cc_final: 0.9251 (mtm) REVERT: D 87 ASP cc_start: 0.9109 (t70) cc_final: 0.8854 (t0) REVERT: D 99 LYS cc_start: 0.9502 (mtpp) cc_final: 0.9195 (mtpp) REVERT: D 164 GLU cc_start: 0.8842 (tt0) cc_final: 0.8476 (tm-30) REVERT: E 17 MET cc_start: 0.8733 (mmm) cc_final: 0.8372 (mtt) REVERT: E 71 GLU cc_start: 0.8932 (mp0) cc_final: 0.8611 (tt0) REVERT: E 82 THR cc_start: 0.9292 (m) cc_final: 0.9062 (m) REVERT: E 133 ASP cc_start: 0.8706 (t0) cc_final: 0.8428 (t0) REVERT: F 6 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.8241 (t80) REVERT: F 16 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8103 (tm) REVERT: F 28 LYS cc_start: 0.5283 (mmmt) cc_final: 0.4745 (tttm) outliers start: 11 outliers final: 4 residues processed: 114 average time/residue: 0.7575 time to fit residues: 92.7519 Evaluate side-chains 115 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 147 optimal weight: 0.3980 chunk 66 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 19 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.063357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.047138 restraints weight = 31240.568| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 2.43 r_work: 0.2606 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2491 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2314 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= 0.154 Angle : 0.528 11.436 16523 Z= 0.272 Chirality : 0.041 0.163 1899 Planarity : 0.004 0.037 2062 Dihedral : 5.025 59.471 1663 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.96 % Allowed : 10.75 % 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 aren not related in a simple way. whole: 1.56 (0.21), residues: 1528 helix: 2.08 (0.18), residues: 790 sheet: 0.38 (0.63), residues: 74 loop : -0.13 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 43 TYR 0.017 0.001 TYR E 106 PHE 0.046 0.001 PHE E 22 TRP 0.021 0.001 TRP B 103 HIS 0.003 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00347 (12170) covalent geometry : angle 0.52588 (16517) hydrogen bonds : bond 0.04512 ( 662) hydrogen bonds : angle 4.46551 ( 1881) metal coordination : bond 0.00921 ( 4) metal coordination : angle 2.54591 ( 6) Misc. bond : bond 0.00082 ( 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 124 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 430 GLU cc_start: 0.9283 (OUTLIER) cc_final: 0.8866 (mt-10) REVERT: B 72 MET cc_start: 0.9520 (mtm) cc_final: 0.9294 (mtm) REVERT: D 87 ASP cc_start: 0.9127 (t70) cc_final: 0.8886 (t0) REVERT: D 99 LYS cc_start: 0.9476 (mtpp) cc_final: 0.9087 (mtpp) REVERT: D 164 GLU cc_start: 0.8880 (tt0) cc_final: 0.8533 (tm-30) REVERT: E 17 MET cc_start: 0.8679 (mmm) cc_final: 0.8333 (mtt) REVERT: E 71 GLU cc_start: 0.8863 (mp0) cc_final: 0.8575 (tt0) REVERT: E 82 THR cc_start: 0.9310 (m) cc_final: 0.9081 (m) REVERT: E 133 ASP cc_start: 0.8688 (t0) cc_final: 0.8415 (OUTLIER) REVERT: F 6 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.8246 (t80) REVERT: F 16 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8127 (tm) REVERT: F 28 LYS cc_start: 0.4912 (mmmt) cc_final: 0.4381 (tttm) outliers start: 12 outliers final: 6 residues processed: 116 average time/residue: 0.7292 time to fit residues: 91.0963 Evaluate side-chains 117 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 E residue 22 PHE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 139 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 142 optimal weight: 0.7980 chunk 111 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 119 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.064306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.048130 restraints weight = 31025.821| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 2.43 r_work: 0.2632 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2517 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12176 Z= 0.120 Angle : 0.515 12.398 16523 Z= 0.264 Chirality : 0.040 0.155 1899 Planarity : 0.004 0.036 2062 Dihedral : 4.892 59.955 1663 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.80 % Allowed : 10.99 % 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 aren not related in a simple way. whole: 1.59 (0.21), residues: 1528 helix: 2.11 (0.18), residues: 791 sheet: 0.33 (0.62), residues: 74 loop : -0.11 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 43 TYR 0.015 0.001 TYR E 106 PHE 0.036 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 covalent geometry : bond 0.00263 (12170) covalent geometry : angle 0.51279 (16517) hydrogen bonds : bond 0.04172 ( 662) hydrogen bonds : angle 4.38467 ( 1881) metal coordination : bond 0.00698 ( 4) metal coordination : angle 2.52652 ( 6) Misc. bond : bond 0.00046 ( 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 124 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 430 GLU cc_start: 0.9291 (OUTLIER) cc_final: 0.8812 (mt-10) REVERT: B 72 MET cc_start: 0.9503 (mtm) cc_final: 0.9295 (mtm) REVERT: D 8 LYS cc_start: 0.2110 (tttt) cc_final: 0.0932 (mmtt) REVERT: D 87 ASP cc_start: 0.9106 (t70) cc_final: 0.8867 (t0) REVERT: D 99 LYS cc_start: 0.9434 (mtpp) cc_final: 0.9183 (mtpp) REVERT: D 164 GLU cc_start: 0.8855 (tt0) cc_final: 0.8525 (tm-30) REVERT: E 17 MET cc_start: 0.8661 (mmm) cc_final: 0.8338 (mtt) REVERT: E 71 GLU cc_start: 0.8866 (mp0) cc_final: 0.8565 (tt0) REVERT: E 82 THR cc_start: 0.9310 (m) cc_final: 0.9082 (m) REVERT: E 119 ASN cc_start: 0.8643 (t0) cc_final: 0.8403 (t0) REVERT: F 6 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.8251 (t80) REVERT: F 10 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8407 (tpp) REVERT: F 16 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8125 (tm) REVERT: F 28 LYS cc_start: 0.4902 (mmmt) cc_final: 0.4389 (ttpp) outliers start: 10 outliers final: 3 residues processed: 118 average time/residue: 0.7178 time to fit residues: 90.8800 Evaluate side-chains 119 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 10 MET 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: 1.9990 chunk 126 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.062505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.046240 restraints weight = 31255.586| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 2.42 r_work: 0.2580 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2465 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 12176 Z= 0.259 Angle : 0.604 12.740 16523 Z= 0.309 Chirality : 0.044 0.165 1899 Planarity : 0.004 0.038 2062 Dihedral : 5.198 59.278 1663 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.72 % Allowed : 11.23 % Favored : 88.06 % 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 aren not related in a simple way. whole: 1.37 (0.21), residues: 1528 helix: 1.91 (0.18), residues: 793 sheet: -0.23 (0.57), residues: 88 loop : -0.13 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 174 TYR 0.018 0.002 TYR D 141 PHE 0.045 0.002 PHE E 22 TRP 0.024 0.002 TRP B 103 HIS 0.004 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00598 (12170) covalent geometry : angle 0.60160 (16517) hydrogen bonds : bond 0.05116 ( 662) hydrogen bonds : angle 4.60621 ( 1881) metal coordination : bond 0.01298 ( 4) metal coordination : angle 3.13454 ( 6) Misc. bond : bond 0.00165 ( 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 116 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 430 GLU cc_start: 0.9380 (OUTLIER) cc_final: 0.8844 (mt-10) REVERT: B 43 ARG cc_start: 0.8982 (mtm-85) cc_final: 0.8702 (mtm-85) REVERT: B 72 MET cc_start: 0.9508 (mtm) cc_final: 0.9306 (mtm) REVERT: D 87 ASP cc_start: 0.9137 (t70) cc_final: 0.8892 (t0) REVERT: D 99 LYS cc_start: 0.9443 (mtpp) cc_final: 0.9170 (mtpp) REVERT: D 164 GLU cc_start: 0.8889 (tt0) cc_final: 0.8526 (tm-30) REVERT: D 204 GLU cc_start: 0.7366 (pm20) cc_final: 0.6956 (pm20) REVERT: E 17 MET cc_start: 0.8679 (mmm) cc_final: 0.8362 (mtt) REVERT: E 82 THR cc_start: 0.9303 (m) cc_final: 0.9072 (m) REVERT: E 151 MET cc_start: 0.9006 (ttp) cc_final: 0.8383 (ttm) REVERT: F 6 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.8320 (t80) REVERT: F 16 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8119 (tm) REVERT: F 28 LYS cc_start: 0.4958 (mmmt) cc_final: 0.4406 (tttm) outliers start: 9 outliers final: 4 residues processed: 110 average time/residue: 0.7732 time to fit residues: 91.6505 Evaluate side-chains 112 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 105 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 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: 0.6980 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: 1.9990 chunk 83 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 90 optimal weight: 0.0670 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.063386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.047190 restraints weight = 31343.825| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 2.45 r_work: 0.2606 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2491 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12176 Z= 0.153 Angle : 0.545 12.705 16523 Z= 0.280 Chirality : 0.041 0.155 1899 Planarity : 0.004 0.037 2062 Dihedral : 5.048 59.694 1663 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.72 % Allowed : 11.39 % Favored : 87.90 % 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 aren not related in a simple way. whole: 1.46 (0.21), residues: 1528 helix: 2.01 (0.18), residues: 792 sheet: -0.12 (0.58), residues: 84 loop : -0.13 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 43 TYR 0.016 0.001 TYR E 106 PHE 0.041 0.001 PHE E 22 TRP 0.024 0.001 TRP B 103 HIS 0.003 0.001 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.00345 (12170) covalent geometry : angle 0.54238 (16517) hydrogen bonds : bond 0.04523 ( 662) hydrogen bonds : angle 4.47172 ( 1881) metal coordination : bond 0.00719 ( 4) metal coordination : angle 2.65446 ( 6) Misc. bond : bond 0.00080 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4457.25 seconds wall clock time: 76 minutes 51.02 seconds (4611.02 seconds total)