Starting phenix.real_space_refine on Wed Jul 30 08:49:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8evu_28637/07_2025/8evu_28637.cif Found real_map, /net/cci-nas-00/data/ceres_data/8evu_28637/07_2025/8evu_28637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5804 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8evu_28637/07_2025/8evu_28637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8evu_28637/07_2025/8evu_28637.map" model { file = "/net/cci-nas-00/data/ceres_data/8evu_28637/07_2025/8evu_28637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8evu_28637/07_2025/8evu_28637.cif" } resolution = 2.5804 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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 65.958 42.181 63.643 1.00 79.57 S ATOM 10247 SG CYS E 26 64.578 45.018 65.377 1.00 65.74 S ATOM 8651 SG CYS D 29 62.336 42.626 69.152 1.00 69.87 S ATOM 10969 SG CYS E 120 64.405 39.385 68.240 1.00 75.41 S Time building chain proxies: 7.90, per 1000 atoms: 0.66 Number of scatterers: 11902 At special positions: 0 Unit cell: (99.324, 110.004, 133.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 S 68 16.00 P 2 15.00 O 2135 8.00 N 1949 7.00 C 7746 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.40 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS D 112 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 26 " pdb="FE2 FES E 301 " - pdb=" SG CYS D 29 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 120 " Number of angles added : 6 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2784 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 8 sheets defined 60.7% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 109 through 113 Processing helix chain 'A' and resid 114 through 125 Processing helix chain 'A' and resid 126 through 131 removed outlier: 3.596A pdb=" N THR A 129 " --> pdb=" O GLY A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 170 removed outlier: 3.919A pdb=" N VAL A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 219 through 228 Processing helix chain 'A' and resid 241 through 254 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 335 through 339 Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.737A pdb=" N HIS A 354 " --> pdb=" O PHE A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 384 removed outlier: 3.866A pdb=" N LYS A 382 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 383 " --> pdb=" O ASN A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 401 through 408 Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 415 through 417 No H-bonds generated for 'chain 'A' and resid 415 through 417' Processing helix chain 'A' and resid 418 through 424 Processing helix chain 'A' and resid 430 through 446 removed outlier: 3.622A pdb=" N LEU A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 10 Processing helix chain 'B' and resid 10 through 15 removed outlier: 3.906A pdb=" N PHE B 14 " --> pdb=" O ILE B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 23 through 35 removed outlier: 3.694A pdb=" N LEU B 33 " --> pdb=" O ALA B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.569A pdb=" N VAL B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 87 Processing helix chain 'B' and resid 89 through 99 Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 117 through 152 Proline residue: B 131 - end of helix Processing helix chain 'B' and resid 158 through 169 Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 191 through 195 Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 236 through 245 Processing helix chain 'B' and resid 246 through 249 Processing helix chain 'B' and resid 259 through 266 Processing helix chain 'B' and resid 276 through 290 Processing helix chain 'B' and resid 294 through 316 Processing helix chain 'B' and resid 320 through 325 removed outlier: 3.542A pdb=" N MET B 325 " --> pdb=" O MET B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 333 removed outlier: 3.528A pdb=" N VAL B 332 " --> pdb=" O HIS B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 353 through 375 Processing helix chain 'B' and resid 381 through 410 removed outlier: 3.585A pdb=" N LEU B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Proline residue: B 394 - end of helix Processing helix chain 'B' and resid 411 through 414 Processing helix chain 'C' and resid 8 through 33 Processing helix chain 'C' and resid 33 through 54 removed outlier: 3.529A pdb=" N LYS C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 70 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 92 through 98 Processing helix chain 'C' and resid 99 through 101 No H-bonds generated for 'chain 'C' and resid 99 through 101' Processing helix chain 'C' and resid 177 through 181 Processing helix chain 'C' and resid 182 through 188 removed outlier: 3.777A pdb=" N GLN C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 239 Processing helix chain 'C' and resid 244 through 253 Processing helix chain 'D' and resid 9 through 17 Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 27 through 34 removed outlier: 3.652A pdb=" N ALA D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA D 33 " --> pdb=" O CYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 62 Processing helix chain 'D' and resid 70 through 94 Processing helix chain 'D' and resid 94 through 102 Processing helix chain 'D' and resid 103 through 109 Processing helix chain 'D' and resid 111 through 121 Processing helix chain 'D' and resid 122 through 125 removed outlier: 3.615A pdb=" N SER D 125 " --> pdb=" O ALA D 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 122 through 125' Processing helix chain 'D' and resid 126 through 158 Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 178 through 182 Processing helix chain 'D' and resid 183 through 202 removed outlier: 4.233A pdb=" N ALA D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 206 Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 24 through 31 Processing helix chain 'E' and resid 34 through 63 Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 75 through 77 No H-bonds generated for 'chain 'E' and resid 75 through 77' Processing helix chain 'E' and resid 78 through 102 removed outlier: 3.575A pdb=" N GLN E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG E 100 " --> pdb=" O MET E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 109 Processing helix chain 'E' and resid 110 through 113 Processing helix chain 'E' and resid 119 through 133 Processing helix chain 'E' and resid 135 through 164 Processing helix chain 'E' and resid 165 through 167 No H-bonds generated for 'chain 'E' and resid 165 through 167' Processing helix chain 'E' and resid 175 through 191 Processing helix chain 'E' and resid 192 through 194 No H-bonds generated for 'chain 'E' and resid 192 through 194' Processing helix chain 'F' and resid 2 through 30 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 6.245A pdb=" N ILE A 2 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL A 189 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N HIS A 209 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL A 191 " --> pdb=" O HIS A 209 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N PHE A 211 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LYS A 193 " --> pdb=" O PHE A 211 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 22 removed outlier: 3.519A pdb=" N LEU A 274 " --> pdb=" O SER A 17 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N VAL A 19 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ARG A 276 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N SER A 21 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 9.729A pdb=" N VAL A 278 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL A 323 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N SER A 263 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL A 325 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA A 265 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N ARG A 327 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N GLN A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 32 removed outlier: 6.962A pdb=" N LEU A 87 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ARG A 81 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N SER A 89 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ILE A 79 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL A 91 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 43 removed outlier: 7.130A pdb=" N PHE A 68 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 83 through 84 removed outlier: 3.959A pdb=" N LEU C 75 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 14.780A pdb=" N VAL C 121 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N VAL C 140 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N VAL C 123 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU C 138 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR C 125 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL C 136 " --> pdb=" O TYR C 125 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL C 127 " --> pdb=" O SER C 134 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS C 132 " --> pdb=" O ASP C 129 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N MET C 148 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLU C 169 " --> pdb=" O MET C 148 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TYR C 150 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR C 167 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE C 152 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU C 165 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA C 154 " --> pdb=" O SER C 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 103 through 105 Processing sheet with id=AA7, first strand: chain 'C' and resid 204 through 206 Processing sheet with id=AA8, first strand: chain 'D' and resid 159 through 160 668 hydrogen bonds defined for protein. 1890 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.35 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.42: 5002 1.42 - 1.61: 7044 1.61 - 1.81: 120 1.81 - 2.01: 0 2.01 - 2.20: 4 Bond restraints: 12170 Sorted by residual: bond pdb=" C2 UQ1 B 602 " pdb=" C3 UQ1 B 602 " ideal model delta sigma weight residual 1.339 1.425 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C4 FMN C 301 " pdb=" C4A FMN C 301 " ideal model delta sigma weight residual 1.485 1.405 0.080 2.00e-02 2.50e+03 1.59e+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 1.58e+01 bond pdb=" C1 UQ1 B 602 " pdb=" C2 UQ1 B 602 " ideal model delta sigma weight residual 1.485 1.408 0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C4 RBF B 601 " pdb=" C4A RBF B 601 " ideal model delta sigma weight residual 1.481 1.406 0.075 2.00e-02 2.50e+03 1.40e+01 ... (remaining 12165 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 16310 1.51 - 3.02: 151 3.02 - 4.54: 38 4.54 - 6.05: 17 6.05 - 7.56: 1 Bond angle restraints: 16517 Sorted by residual: angle pdb=" C3 UQ1 B 602 " pdb=" C2 UQ1 B 602 " pdb=" O2 UQ1 B 602 " ideal model delta sigma weight residual 122.52 130.08 -7.56 3.00e+00 1.11e-01 6.35e+00 angle pdb=" N VAL A 287 " pdb=" CA VAL A 287 " pdb=" CB VAL A 287 " ideal model delta sigma weight residual 111.81 107.07 4.74 2.24e+00 1.99e-01 4.47e+00 angle pdb=" C ILE C 115 " pdb=" N GLN C 116 " pdb=" CA GLN C 116 " ideal model delta sigma weight residual 121.54 125.54 -4.00 1.91e+00 2.74e-01 4.39e+00 angle pdb=" C1 UQ1 B 602 " pdb=" C2 UQ1 B 602 " pdb=" O2 UQ1 B 602 " ideal model delta sigma weight residual 117.10 111.14 5.96 3.00e+00 1.11e-01 3.95e+00 angle pdb=" CA TRP B 103 " pdb=" CB TRP B 103 " pdb=" CG TRP B 103 " ideal model delta sigma weight residual 113.60 117.23 -3.63 1.90e+00 2.77e-01 3.66e+00 ... (remaining 16512 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 6900 17.93 - 35.85: 176 35.85 - 53.78: 26 53.78 - 71.71: 7 71.71 - 89.63: 3 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 -161.92 -18.08 0 5.00e+00 4.00e-02 1.31e+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 -163.61 -16.39 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA VAL E 63 " pdb=" C VAL E 63 " pdb=" N LEU E 64 " pdb=" CA LEU E 64 " ideal model delta harmonic sigma weight residual -180.00 -164.43 -15.57 0 5.00e+00 4.00e-02 9.70e+00 ... (remaining 7109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1385 0.040 - 0.081: 398 0.081 - 0.121: 107 0.121 - 0.161: 7 0.161 - 0.201: 2 Chirality restraints: 1899 Sorted by residual: 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 -2.58 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" C4' RBF B 601 " pdb=" C3' RBF B 601 " pdb=" C5' RBF B 601 " pdb=" O4' RBF B 601 " both_signs ideal model delta sigma weight residual False -2.27 -2.47 0.19 2.00e-01 2.50e+01 9.41e-01 chirality pdb=" CA ILE C 205 " pdb=" N ILE C 205 " pdb=" C ILE C 205 " pdb=" CB ILE C 205 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 1896 not shown) Planarity restraints: 2062 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ1 B 602 " 0.028 2.00e-02 2.50e+03 6.15e-02 1.14e+02 pdb=" C2 UQ1 B 602 " 0.011 2.00e-02 2.50e+03 pdb=" C3 UQ1 B 602 " 0.012 2.00e-02 2.50e+03 pdb=" C4 UQ1 B 602 " 0.056 2.00e-02 2.50e+03 pdb=" C5 UQ1 B 602 " 0.004 2.00e-02 2.50e+03 pdb=" C6 UQ1 B 602 " -0.001 2.00e-02 2.50e+03 pdb=" C7 UQ1 B 602 " -0.070 2.00e-02 2.50e+03 pdb=" CM5 UQ1 B 602 " -0.064 2.00e-02 2.50e+03 pdb=" O1 UQ1 B 602 " 0.074 2.00e-02 2.50e+03 pdb=" O2 UQ1 B 602 " -0.031 2.00e-02 2.50e+03 pdb=" O3 UQ1 B 602 " -0.124 2.00e-02 2.50e+03 pdb=" O4 UQ1 B 602 " 0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ1 B 602 " 0.007 2.00e-02 2.50e+03 4.18e-02 2.18e+01 pdb=" C11 UQ1 B 602 " -0.042 2.00e-02 2.50e+03 pdb=" C7 UQ1 B 602 " -0.050 2.00e-02 2.50e+03 pdb=" C8 UQ1 B 602 " 0.062 2.00e-02 2.50e+03 pdb=" C9 UQ1 B 602 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FMN C 301 " 0.012 2.00e-02 2.50e+03 7.27e-03 2.38e+00 pdb=" C10 FMN C 301 " 0.004 2.00e-02 2.50e+03 pdb=" C2 FMN C 301 " -0.006 2.00e-02 2.50e+03 pdb=" C4 FMN C 301 " 0.003 2.00e-02 2.50e+03 pdb=" C4A FMN C 301 " 0.007 2.00e-02 2.50e+03 pdb=" C5A FMN C 301 " 0.004 2.00e-02 2.50e+03 pdb=" C6 FMN C 301 " 0.003 2.00e-02 2.50e+03 pdb=" C7 FMN C 301 " -0.004 2.00e-02 2.50e+03 pdb=" C7M FMN C 301 " -0.007 2.00e-02 2.50e+03 pdb=" C8 FMN C 301 " -0.006 2.00e-02 2.50e+03 pdb=" C8M FMN C 301 " -0.009 2.00e-02 2.50e+03 pdb=" C9 FMN C 301 " 0.003 2.00e-02 2.50e+03 pdb=" C9A FMN C 301 " 0.003 2.00e-02 2.50e+03 pdb=" N1 FMN C 301 " 0.002 2.00e-02 2.50e+03 pdb=" N10 FMN C 301 " 0.006 2.00e-02 2.50e+03 pdb=" N3 FMN C 301 " -0.004 2.00e-02 2.50e+03 pdb=" N5 FMN C 301 " 0.009 2.00e-02 2.50e+03 pdb=" O2 FMN C 301 " -0.018 2.00e-02 2.50e+03 ... (remaining 2059 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3125 2.80 - 3.33: 11271 3.33 - 3.85: 20185 3.85 - 4.38: 24700 4.38 - 4.90: 41563 Nonbonded interactions: 100844 Sorted by model distance: nonbonded pdb=" O GLU C 99 " pdb=" OG SER C 103 " model vdw 2.279 3.040 nonbonded pdb=" O GLU B 28 " pdb=" OG1 THR B 32 " model vdw 2.283 3.040 nonbonded pdb=" O ILE E 46 " pdb=" OG1 THR E 50 " model vdw 2.317 3.040 nonbonded pdb=" NH1 ARG B 199 " pdb=" O TYR E 166 " model vdw 2.329 3.120 nonbonded pdb=" O ASN E 57 " pdb=" ND2 ASN E 61 " model vdw 2.342 3.120 ... (remaining 100839 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 3.440 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.900 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:12.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9045 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 0.109 12176 Z= 0.204 Angle : 0.450 10.329 16523 Z= 0.215 Chirality : 0.040 0.201 1899 Planarity : 0.004 0.062 2062 Dihedral : 8.857 89.635 4328 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.08 % Allowed : 1.35 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.21), residues: 1528 helix: 1.47 (0.18), residues: 786 sheet: 0.62 (0.58), residues: 74 loop : 0.05 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 103 HIS 0.003 0.001 HIS B 328 PHE 0.020 0.001 PHE E 22 TYR 0.010 0.001 TYR D 141 ARG 0.003 0.000 ARG E 174 Details of bonding type rmsd hydrogen bonds : bond 0.21006 ( 668) hydrogen bonds : angle 6.70307 ( 1890) metal coordination : bond 0.00700 ( 4) metal coordination : angle 4.93056 ( 6) covalent geometry : bond 0.00320 (12170) covalent geometry : angle 0.44036 (16517) Misc. bond : bond 0.10783 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.9352 (mmm) cc_final: 0.9126 (tpp) REVERT: E 138 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8523 (mt-10) REVERT: F 26 LYS cc_start: 0.9033 (tttt) cc_final: 0.8630 (tmmt) outliers start: 1 outliers final: 0 residues processed: 159 average time/residue: 1.6451 time to fit residues: 278.4212 Evaluate side-chains 119 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN E 79 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.057939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.043567 restraints weight = 30632.640| |-----------------------------------------------------------------------------| r_work (start): 0.2594 rms_B_bonded: 2.25 r_work: 0.2484 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2371 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 12176 Z= 0.212 Angle : 0.557 9.586 16523 Z= 0.295 Chirality : 0.043 0.162 1899 Planarity : 0.004 0.039 2062 Dihedral : 5.634 63.999 1663 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.88 % Allowed : 6.53 % Favored : 92.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.22), residues: 1528 helix: 1.88 (0.19), residues: 789 sheet: -0.03 (0.53), residues: 89 loop : 0.07 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 103 HIS 0.005 0.001 HIS B 330 PHE 0.022 0.002 PHE E 22 TYR 0.013 0.001 TYR B 360 ARG 0.005 0.001 ARG D 71 Details of bonding type rmsd hydrogen bonds : bond 0.05886 ( 668) hydrogen bonds : angle 4.86427 ( 1890) metal coordination : bond 0.01739 ( 4) metal coordination : angle 4.40933 ( 6) covalent geometry : bond 0.00481 (12170) covalent geometry : angle 0.55081 (16517) Misc. bond : bond 0.00138 ( 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 127 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.9491 (mmm) cc_final: 0.9234 (tpp) REVERT: B 13 HIS cc_start: 0.7439 (m-70) cc_final: 0.6786 (m-70) REVERT: D 9 LYS cc_start: 0.8925 (pptt) cc_final: 0.8144 (mppt) REVERT: D 96 ASP cc_start: 0.8493 (p0) cc_final: 0.8133 (p0) REVERT: E 117 THR cc_start: 0.8876 (m) cc_final: 0.8663 (m) REVERT: E 138 GLU cc_start: 0.9322 (mt-10) cc_final: 0.9051 (mt-10) REVERT: E 186 MET cc_start: 0.9411 (mtp) cc_final: 0.9183 (mtp) REVERT: F 26 LYS cc_start: 0.9336 (tttt) cc_final: 0.8655 (tmmt) outliers start: 11 outliers final: 4 residues processed: 122 average time/residue: 1.4936 time to fit residues: 195.8408 Evaluate side-chains 116 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain E residue 1 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 7 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 chunk 42 optimal weight: 0.0870 chunk 116 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 34 optimal weight: 0.0870 overall best weight: 0.9538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.058738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.044434 restraints weight = 30930.244| |-----------------------------------------------------------------------------| r_work (start): 0.2619 rms_B_bonded: 2.28 r_work: 0.2508 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2396 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12176 Z= 0.137 Angle : 0.491 10.083 16523 Z= 0.258 Chirality : 0.041 0.161 1899 Planarity : 0.004 0.036 2062 Dihedral : 5.195 59.977 1663 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.88 % Allowed : 7.09 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.22), residues: 1528 helix: 1.93 (0.18), residues: 797 sheet: -0.07 (0.53), residues: 91 loop : 0.05 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 103 HIS 0.004 0.001 HIS B 330 PHE 0.017 0.001 PHE E 22 TYR 0.015 0.001 TYR B 360 ARG 0.003 0.000 ARG D 71 Details of bonding type rmsd hydrogen bonds : bond 0.04911 ( 668) hydrogen bonds : angle 4.54706 ( 1890) metal coordination : bond 0.01106 ( 4) metal coordination : angle 4.54886 ( 6) covalent geometry : bond 0.00300 (12170) covalent geometry : angle 0.48370 (16517) Misc. bond : bond 0.00099 ( 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 127 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 1.376 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.9511 (mmm) cc_final: 0.9245 (tpp) REVERT: B 34 PHE cc_start: 0.9019 (m-80) cc_final: 0.8657 (m-80) REVERT: D 9 LYS cc_start: 0.8891 (pptt) cc_final: 0.8166 (mppt) REVERT: D 96 ASP cc_start: 0.8530 (p0) cc_final: 0.8133 (p0) REVERT: E 17 MET cc_start: 0.9239 (mmm) cc_final: 0.8818 (tpp) REVERT: E 138 GLU cc_start: 0.9297 (mt-10) cc_final: 0.9079 (mt-10) REVERT: F 26 LYS cc_start: 0.9345 (tttt) cc_final: 0.8651 (tmmt) outliers start: 11 outliers final: 3 residues processed: 121 average time/residue: 1.5461 time to fit residues: 200.9286 Evaluate side-chains 119 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 116 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain E residue 1 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 105 optimal weight: 0.3980 chunk 103 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.058188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.043884 restraints weight = 30887.182| |-----------------------------------------------------------------------------| r_work (start): 0.2605 rms_B_bonded: 2.27 r_work: 0.2494 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2381 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12176 Z= 0.179 Angle : 0.516 8.508 16523 Z= 0.272 Chirality : 0.042 0.168 1899 Planarity : 0.004 0.054 2062 Dihedral : 5.046 59.828 1663 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.04 % Allowed : 8.12 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.22), residues: 1528 helix: 1.93 (0.18), residues: 797 sheet: -0.26 (0.52), residues: 99 loop : 0.06 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 103 HIS 0.005 0.001 HIS B 330 PHE 0.019 0.001 PHE E 22 TYR 0.016 0.001 TYR D 141 ARG 0.002 0.000 ARG A 318 Details of bonding type rmsd hydrogen bonds : bond 0.04956 ( 668) hydrogen bonds : angle 4.50980 ( 1890) metal coordination : bond 0.01375 ( 4) metal coordination : angle 3.89015 ( 6) covalent geometry : bond 0.00410 (12170) covalent geometry : angle 0.51091 (16517) Misc. bond : bond 0.00132 ( 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: 13 poor density : 114 time to evaluate : 1.428 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.9502 (mmm) cc_final: 0.9233 (tpp) REVERT: D 9 LYS cc_start: 0.8900 (pptt) cc_final: 0.8187 (mppt) REVERT: D 96 ASP cc_start: 0.8559 (p0) cc_final: 0.8205 (p0) REVERT: E 138 GLU cc_start: 0.9284 (mt-10) cc_final: 0.9056 (mt-10) REVERT: F 26 LYS cc_start: 0.9359 (tttt) cc_final: 0.8666 (tmmt) outliers start: 13 outliers final: 5 residues processed: 118 average time/residue: 1.5101 time to fit residues: 191.8991 Evaluate side-chains 116 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain E residue 1 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 120 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 108 optimal weight: 0.5980 chunk 100 optimal weight: 0.2980 chunk 96 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.058206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.043921 restraints weight = 30819.017| |-----------------------------------------------------------------------------| r_work (start): 0.2607 rms_B_bonded: 2.27 r_work: 0.2496 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2383 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12176 Z= 0.169 Angle : 0.512 8.635 16523 Z= 0.269 Chirality : 0.041 0.166 1899 Planarity : 0.004 0.045 2062 Dihedral : 4.978 59.887 1663 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.35 % Allowed : 8.04 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.22), residues: 1528 helix: 1.93 (0.18), residues: 798 sheet: -0.31 (0.52), residues: 99 loop : 0.02 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 103 HIS 0.003 0.001 HIS B 330 PHE 0.019 0.001 PHE E 22 TYR 0.020 0.001 TYR D 141 ARG 0.003 0.000 ARG D 71 Details of bonding type rmsd hydrogen bonds : bond 0.04799 ( 668) hydrogen bonds : angle 4.45042 ( 1890) metal coordination : bond 0.01143 ( 4) metal coordination : angle 3.90685 ( 6) covalent geometry : bond 0.00384 (12170) covalent geometry : angle 0.50645 (16517) Misc. bond : bond 0.00128 ( 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 131 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.9502 (mmm) cc_final: 0.9230 (tpp) REVERT: B 34 PHE cc_start: 0.8864 (m-80) cc_final: 0.8659 (m-80) REVERT: B 68 MET cc_start: 0.9509 (ttp) cc_final: 0.9241 (ttp) REVERT: D 9 LYS cc_start: 0.8896 (pptt) cc_final: 0.8198 (mppt) REVERT: D 96 ASP cc_start: 0.8580 (p0) cc_final: 0.8287 (p0) REVERT: E 17 MET cc_start: 0.9229 (mmm) cc_final: 0.8793 (tpp) REVERT: E 138 GLU cc_start: 0.9280 (mt-10) cc_final: 0.9043 (mt-10) REVERT: F 26 LYS cc_start: 0.9369 (tttt) cc_final: 0.8688 (tmmt) outliers start: 17 outliers final: 7 residues processed: 121 average time/residue: 1.5965 time to fit residues: 207.5792 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 : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain E residue 1 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN E 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.058829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.044572 restraints weight = 31116.799| |-----------------------------------------------------------------------------| r_work (start): 0.2624 rms_B_bonded: 2.28 r_work: 0.2514 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2401 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12176 Z= 0.130 Angle : 0.490 8.211 16523 Z= 0.257 Chirality : 0.040 0.161 1899 Planarity : 0.004 0.040 2062 Dihedral : 4.858 59.891 1663 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.11 % Allowed : 8.84 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.22), residues: 1528 helix: 2.01 (0.19), residues: 798 sheet: -0.17 (0.54), residues: 95 loop : -0.00 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 103 HIS 0.003 0.001 HIS B 330 PHE 0.017 0.001 PHE E 22 TYR 0.017 0.001 TYR D 141 ARG 0.004 0.000 ARG D 71 Details of bonding type rmsd hydrogen bonds : bond 0.04468 ( 668) hydrogen bonds : angle 4.35851 ( 1890) metal coordination : bond 0.00790 ( 4) metal coordination : angle 3.69229 ( 6) covalent geometry : bond 0.00290 (12170) covalent geometry : angle 0.48494 (16517) Misc. bond : bond 0.00077 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 1.402 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.9521 (mmm) cc_final: 0.9256 (tpp) REVERT: B 15 GLU cc_start: 0.8865 (tp30) cc_final: 0.8046 (pp20) REVERT: B 34 PHE cc_start: 0.8879 (m-80) cc_final: 0.8646 (m-80) REVERT: D 9 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8222 (mppt) REVERT: D 96 ASP cc_start: 0.8562 (p0) cc_final: 0.8278 (p0) REVERT: E 17 MET cc_start: 0.9218 (mmm) cc_final: 0.8763 (tpp) REVERT: E 138 GLU cc_start: 0.9291 (mt-10) cc_final: 0.9034 (mt-10) REVERT: F 26 LYS cc_start: 0.9370 (tttt) cc_final: 0.8668 (tmmt) outliers start: 14 outliers final: 4 residues processed: 118 average time/residue: 1.5922 time to fit residues: 201.5212 Evaluate side-chains 117 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 112 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 9 LYS Chi-restraints excluded: chain D residue 133 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 73 optimal weight: 2.9990 chunk 135 optimal weight: 0.0770 chunk 124 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 140 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 149 optimal weight: 5.9990 overall best weight: 0.8742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.058932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.044662 restraints weight = 31008.888| |-----------------------------------------------------------------------------| r_work (start): 0.2628 rms_B_bonded: 2.28 r_work: 0.2518 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2405 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12176 Z= 0.131 Angle : 0.496 8.751 16523 Z= 0.258 Chirality : 0.040 0.161 1899 Planarity : 0.004 0.038 2062 Dihedral : 4.797 59.915 1663 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.88 % Allowed : 9.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.22), residues: 1528 helix: 2.05 (0.19), residues: 798 sheet: -0.18 (0.54), residues: 95 loop : -0.01 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 103 HIS 0.003 0.001 HIS B 330 PHE 0.017 0.001 PHE E 22 TYR 0.019 0.001 TYR D 141 ARG 0.004 0.000 ARG D 71 Details of bonding type rmsd hydrogen bonds : bond 0.04409 ( 668) hydrogen bonds : angle 4.32886 ( 1890) metal coordination : bond 0.00785 ( 4) metal coordination : angle 3.69341 ( 6) covalent geometry : bond 0.00291 (12170) covalent geometry : angle 0.49116 (16517) Misc. bond : bond 0.00073 ( 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 124 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 2.993 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.9518 (mmm) cc_final: 0.9257 (tpp) REVERT: B 15 GLU cc_start: 0.8815 (tp30) cc_final: 0.7974 (pp20) REVERT: B 34 PHE cc_start: 0.8910 (m-80) cc_final: 0.8639 (m-80) REVERT: D 9 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8231 (mppt) REVERT: D 96 ASP cc_start: 0.8610 (p0) cc_final: 0.8384 (p0) REVERT: E 17 MET cc_start: 0.9210 (mmm) cc_final: 0.8755 (tpp) REVERT: E 138 GLU cc_start: 0.9287 (mt-10) cc_final: 0.9059 (mt-10) REVERT: F 26 LYS cc_start: 0.9367 (tttt) cc_final: 0.8669 (tmmt) outliers start: 11 outliers final: 4 residues processed: 115 average time/residue: 1.9563 time to fit residues: 240.6709 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 : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 9 LYS Chi-restraints excluded: chain E residue 1 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 137 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.057352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.043101 restraints weight = 31373.687| |-----------------------------------------------------------------------------| r_work (start): 0.2585 rms_B_bonded: 2.27 r_work: 0.2473 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2360 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12176 Z= 0.231 Angle : 0.558 8.384 16523 Z= 0.290 Chirality : 0.043 0.168 1899 Planarity : 0.004 0.038 2062 Dihedral : 4.962 59.977 1663 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.88 % Allowed : 9.63 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.22), residues: 1528 helix: 1.88 (0.18), residues: 804 sheet: -0.32 (0.53), residues: 99 loop : -0.03 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 103 HIS 0.004 0.001 HIS A 225 PHE 0.022 0.002 PHE E 22 TYR 0.023 0.001 TYR D 141 ARG 0.005 0.000 ARG D 71 Details of bonding type rmsd hydrogen bonds : bond 0.05109 ( 668) hydrogen bonds : angle 4.47483 ( 1890) metal coordination : bond 0.01609 ( 4) metal coordination : angle 3.69631 ( 6) covalent geometry : bond 0.00536 (12170) covalent geometry : angle 0.55404 (16517) Misc. bond : bond 0.00152 ( 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 122 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 1.368 Fit side-chains REVERT: A 43 MET cc_start: 0.9490 (mmm) cc_final: 0.9214 (tpp) REVERT: B 8 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6907 (pm20) REVERT: D 9 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8213 (mppt) REVERT: D 96 ASP cc_start: 0.8629 (p0) cc_final: 0.8422 (p0) REVERT: D 119 GLU cc_start: 0.8740 (tp30) cc_final: 0.8381 (tp30) REVERT: E 17 MET cc_start: 0.9178 (mmm) cc_final: 0.8723 (tpp) REVERT: E 138 GLU cc_start: 0.9300 (mt-10) cc_final: 0.9100 (mt-10) REVERT: F 26 LYS cc_start: 0.9399 (tttt) cc_final: 0.8688 (tmmt) outliers start: 11 outliers final: 3 residues processed: 115 average time/residue: 1.6159 time to fit residues: 199.5605 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 : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 9 LYS Chi-restraints excluded: chain E residue 1 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 87 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 116 optimal weight: 0.3980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.058502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.044222 restraints weight = 30971.866| |-----------------------------------------------------------------------------| r_work (start): 0.2618 rms_B_bonded: 2.28 r_work: 0.2507 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2394 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12176 Z= 0.141 Angle : 0.517 9.514 16523 Z= 0.269 Chirality : 0.041 0.161 1899 Planarity : 0.004 0.036 2062 Dihedral : 4.851 59.997 1663 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.72 % Allowed : 10.35 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.22), residues: 1528 helix: 1.95 (0.18), residues: 804 sheet: -0.24 (0.53), residues: 97 loop : -0.04 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 103 HIS 0.003 0.001 HIS B 330 PHE 0.018 0.001 PHE E 22 TYR 0.020 0.001 TYR D 141 ARG 0.004 0.000 ARG D 71 Details of bonding type rmsd hydrogen bonds : bond 0.04507 ( 668) hydrogen bonds : angle 4.37187 ( 1890) metal coordination : bond 0.00871 ( 4) metal coordination : angle 3.87775 ( 6) covalent geometry : bond 0.00319 (12170) covalent geometry : angle 0.51184 (16517) Misc. bond : bond 0.00078 ( 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: 9 poor density : 115 time to evaluate : 1.650 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.9518 (mmm) cc_final: 0.9246 (tpp) REVERT: B 8 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6888 (pm20) REVERT: B 15 GLU cc_start: 0.8862 (tp30) cc_final: 0.8128 (pp20) REVERT: D 9 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8208 (mppt) REVERT: D 96 ASP cc_start: 0.8606 (p0) cc_final: 0.8389 (p0) REVERT: D 119 GLU cc_start: 0.8739 (tp30) cc_final: 0.8387 (tp30) REVERT: E 17 MET cc_start: 0.9167 (mmm) cc_final: 0.8697 (tpp) REVERT: E 138 GLU cc_start: 0.9286 (mt-10) cc_final: 0.9061 (mt-10) REVERT: F 26 LYS cc_start: 0.9393 (tttt) cc_final: 0.8681 (tmmt) outliers start: 9 outliers final: 3 residues processed: 121 average time/residue: 1.9322 time to fit residues: 250.9579 Evaluate side-chains 116 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 9 LYS Chi-restraints excluded: chain E residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 124 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.057796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.043593 restraints weight = 31047.562| |-----------------------------------------------------------------------------| r_work (start): 0.2599 rms_B_bonded: 2.26 r_work: 0.2487 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2374 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12176 Z= 0.193 Angle : 0.550 9.981 16523 Z= 0.286 Chirality : 0.042 0.164 1899 Planarity : 0.004 0.036 2062 Dihedral : 4.893 59.961 1663 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.56 % Allowed : 10.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.22), residues: 1528 helix: 1.89 (0.18), residues: 805 sheet: -0.33 (0.53), residues: 99 loop : -0.03 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 103 HIS 0.003 0.001 HIS A 225 PHE 0.035 0.001 PHE E 22 TYR 0.024 0.001 TYR D 141 ARG 0.005 0.000 ARG D 71 Details of bonding type rmsd hydrogen bonds : bond 0.04805 ( 668) hydrogen bonds : angle 4.42942 ( 1890) metal coordination : bond 0.01226 ( 4) metal coordination : angle 3.84302 ( 6) covalent geometry : bond 0.00445 (12170) covalent geometry : angle 0.54539 (16517) Misc. bond : bond 0.00110 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 1.233 Fit side-chains REVERT: A 43 MET cc_start: 0.9503 (mmm) cc_final: 0.9220 (tpp) REVERT: B 8 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6906 (pm20) REVERT: B 15 GLU cc_start: 0.8913 (tp30) cc_final: 0.8207 (pp20) REVERT: D 9 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8214 (mppt) REVERT: D 119 GLU cc_start: 0.8747 (tp30) cc_final: 0.8279 (tp30) REVERT: E 2 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7456 (tm-30) REVERT: E 17 MET cc_start: 0.9157 (mmm) cc_final: 0.8704 (tpp) REVERT: E 138 GLU cc_start: 0.9289 (mt-10) cc_final: 0.9076 (mt-10) REVERT: F 26 LYS cc_start: 0.9392 (tttt) cc_final: 0.8678 (tmmt) outliers start: 7 outliers final: 3 residues processed: 113 average time/residue: 1.5628 time to fit residues: 189.4694 Evaluate side-chains 116 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 9 LYS Chi-restraints excluded: chain E residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 140 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 115 optimal weight: 0.1980 chunk 132 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 110 optimal weight: 0.0570 chunk 124 optimal weight: 4.9990 chunk 146 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 overall best weight: 1.0502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.058487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.044239 restraints weight = 30929.912| |-----------------------------------------------------------------------------| r_work (start): 0.2616 rms_B_bonded: 2.27 r_work: 0.2506 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2392 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12176 Z= 0.147 Angle : 0.523 8.920 16523 Z= 0.273 Chirality : 0.041 0.159 1899 Planarity : 0.004 0.036 2062 Dihedral : 4.822 59.949 1663 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.48 % Allowed : 10.67 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.22), residues: 1528 helix: 1.93 (0.18), residues: 805 sheet: 0.06 (0.57), residues: 87 loop : -0.06 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 103 HIS 0.003 0.001 HIS B 330 PHE 0.032 0.001 PHE E 22 TYR 0.023 0.001 TYR D 141 ARG 0.003 0.000 ARG D 199 Details of bonding type rmsd hydrogen bonds : bond 0.04532 ( 668) hydrogen bonds : angle 4.37187 ( 1890) metal coordination : bond 0.00888 ( 4) metal coordination : angle 3.78536 ( 6) covalent geometry : bond 0.00335 (12170) covalent geometry : angle 0.51827 (16517) Misc. bond : bond 0.00064 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9467.24 seconds wall clock time: 167 minutes 53.22 seconds (10073.22 seconds total)