Starting phenix.real_space_refine on Wed Jul 30 09:06:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ew3_28641/07_2025/8ew3_28641.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ew3_28641/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ew3_28641/07_2025/8ew3_28641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ew3_28641/07_2025/8ew3_28641.map" model { file = "/net/cci-nas-00/data/ceres_data/8ew3_28641/07_2025/8ew3_28641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ew3_28641/07_2025/8ew3_28641.cif" } resolution = 2.65159 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 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: 8.18, per 1000 atoms: 0.69 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: 3.25 Conformation dependent library (CDL) restraints added in 1.7 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: 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: 1.43 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: 3.57 Time building geometry restraints manager: 3.81 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.570 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: 0.000 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 34.170 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.270 ------------------------------------------------------------------------------- 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 : 2.58 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 (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: 1.12 (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 TRP 0.014 0.001 TRP B 103 HIS 0.003 0.001 HIS B 330 PHE 0.013 0.001 PHE D 104 TYR 0.006 0.001 TYR A 429 ARG 0.003 0.000 ARG A 395 Details of bonding type rmsd hydrogen bonds : bond 0.21848 ( 662) hydrogen bonds : angle 6.85361 ( 1881) metal coordination : bond 0.00478 ( 4) metal coordination : angle 2.04330 ( 6) covalent geometry : bond 0.00321 (12170) covalent geometry : angle 0.44180 (16517) 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 : 1.465 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: 1.5421 time to fit residues: 280.3315 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 : 1.305 ------------------------------------------------------------------------------- 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: 3.9990 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3111 r_free = 0.3111 target = 0.063085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.046514 restraints weight = 31159.718| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 2.43 r_work: 0.2579 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2463 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 12176 Z= 0.319 Angle : 0.649 9.021 16523 Z= 0.338 Chirality : 0.047 0.187 1899 Planarity : 0.005 0.061 2062 Dihedral : 5.613 59.575 1663 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.19 % Allowed : 6.53 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.42 (0.21), residues: 1528 helix: 1.79 (0.18), residues: 786 sheet: -0.10 (0.53), residues: 90 loop : 0.15 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 103 HIS 0.005 0.001 HIS C 199 PHE 0.027 0.002 PHE E 22 TYR 0.014 0.002 TYR D 141 ARG 0.006 0.001 ARG B 43 Details of bonding type rmsd hydrogen bonds : bond 0.06151 ( 662) hydrogen bonds : angle 5.00501 ( 1881) metal coordination : bond 0.02088 ( 4) metal coordination : angle 3.49764 ( 6) covalent geometry : bond 0.00738 (12170) covalent geometry : angle 0.64536 (16517) Misc. bond : bond 0.00198 ( 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 129 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 1.368 Fit side-chains revert: symmetry clash REVERT: B 72 MET cc_start: 0.9510 (mtm) cc_final: 0.9295 (mtm) REVERT: D 87 ASP cc_start: 0.9150 (t70) cc_final: 0.8839 (t0) REVERT: D 115 MET cc_start: 0.8622 (tpt) cc_final: 0.8089 (tpp) REVERT: D 202 LYS cc_start: 0.7023 (mmtt) cc_final: 0.6613 (mttp) REVERT: E 17 MET cc_start: 0.8753 (mmm) cc_final: 0.8324 (mtt) REVERT: E 71 GLU cc_start: 0.8899 (mp0) cc_final: 0.8547 (tt0) REVERT: E 82 THR cc_start: 0.9354 (m) cc_final: 0.9133 (m) REVERT: E 132 ARG cc_start: 0.8944 (mtt180) cc_final: 0.8731 (mtt-85) REVERT: F 6 PHE cc_start: 0.8627 (OUTLIER) cc_final: 0.8216 (t80) REVERT: F 16 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7894 (mm) REVERT: F 28 LYS cc_start: 0.5128 (mmmt) cc_final: 0.4409 (tttm) outliers start: 15 outliers final: 3 residues processed: 119 average time/residue: 1.5172 time to fit residues: 194.0610 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 : 1.341 ------------------------------------------------------------------------------- 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 6 PHE 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 7 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.064442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.047950 restraints weight = 31148.670| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 2.44 r_work: 0.2621 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2505 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12176 Z= 0.142 Angle : 0.513 9.098 16523 Z= 0.269 Chirality : 0.041 0.160 1899 Planarity : 0.004 0.038 2062 Dihedral : 5.289 59.774 1663 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.04 % Allowed : 7.56 % 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 (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 (0.21), residues: 1528 helix: 1.95 (0.18), residues: 789 sheet: 0.36 (0.60), residues: 76 loop : 0.06 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 103 HIS 0.002 0.001 HIS B 101 PHE 0.018 0.001 PHE D 188 TYR 0.016 0.001 TYR D 141 ARG 0.006 0.000 ARG B 43 Details of bonding type rmsd hydrogen bonds : bond 0.05019 ( 662) hydrogen bonds : angle 4.66188 ( 1881) metal coordination : bond 0.01040 ( 4) metal coordination : angle 2.98820 ( 6) covalent geometry : bond 0.00311 (12170) covalent geometry : angle 0.51043 (16517) Misc. bond : bond 0.00091 ( 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 126 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 1.451 Fit side-chains revert: symmetry clash REVERT: B 72 MET cc_start: 0.9479 (mtm) cc_final: 0.9253 (mtm) REVERT: D 87 ASP cc_start: 0.9127 (t70) cc_final: 0.8831 (t0) REVERT: D 115 MET cc_start: 0.8539 (tpt) cc_final: 0.8155 (mmm) REVERT: D 202 LYS cc_start: 0.6969 (mmtt) cc_final: 0.6622 (mttp) REVERT: E 17 MET cc_start: 0.8750 (mmm) cc_final: 0.8345 (mtt) REVERT: E 82 THR cc_start: 0.9330 (m) cc_final: 0.9111 (m) REVERT: E 151 MET cc_start: 0.8892 (ttp) cc_final: 0.8358 (tpp) REVERT: F 6 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.8225 (t80) REVERT: F 16 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7909 (tm) REVERT: F 28 LYS cc_start: 0.5143 (mmmt) cc_final: 0.4449 (tttm) outliers start: 13 outliers final: 3 residues processed: 118 average time/residue: 1.5339 time to fit residues: 194.4787 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 : 1.296 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 5.9990 chunk 129 optimal weight: 0.5980 chunk 111 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 142 optimal weight: 0.7980 chunk 144 optimal weight: 8.9990 chunk 105 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 141 optimal weight: 0.0570 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 = 0.3160 r_free = 0.3160 target = 0.065314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.048947 restraints weight = 30859.957| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 2.44 r_work: 0.2648 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12176 Z= 0.112 Angle : 0.487 8.182 16523 Z= 0.254 Chirality : 0.040 0.158 1899 Planarity : 0.004 0.033 2062 Dihedral : 5.005 59.969 1663 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.11 % Allowed : 8.60 % 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 (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: 1.71 (0.22), residues: 1528 helix: 2.14 (0.19), residues: 781 sheet: 0.49 (0.62), residues: 74 loop : 0.06 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 103 HIS 0.002 0.001 HIS B 330 PHE 0.014 0.001 PHE E 22 TYR 0.014 0.001 TYR B 360 ARG 0.007 0.000 ARG B 43 Details of bonding type rmsd hydrogen bonds : bond 0.04337 ( 662) hydrogen bonds : angle 4.47123 ( 1881) metal coordination : bond 0.01014 ( 4) metal coordination : angle 2.42258 ( 6) covalent geometry : bond 0.00236 (12170) covalent geometry : angle 0.48468 (16517) Misc. bond : bond 0.00043 ( 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: 14 poor density : 114 time to evaluate : 1.357 Fit side-chains revert: symmetry clash REVERT: B 43 ARG cc_start: 0.8791 (mtm-85) cc_final: 0.8349 (mtm180) REVERT: B 72 MET cc_start: 0.9469 (mtm) cc_final: 0.9215 (mtm) REVERT: D 87 ASP cc_start: 0.9121 (t70) cc_final: 0.8845 (t0) REVERT: D 115 MET cc_start: 0.8458 (tpt) cc_final: 0.8144 (mmm) REVERT: D 153 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8655 (tt0) REVERT: D 202 LYS cc_start: 0.6877 (mmtt) cc_final: 0.6599 (mttp) REVERT: E 17 MET cc_start: 0.8724 (mmm) cc_final: 0.8320 (mtt) REVERT: E 71 GLU cc_start: 0.8946 (mp0) cc_final: 0.8584 (tt0) REVERT: E 82 THR cc_start: 0.9297 (m) cc_final: 0.9066 (m) REVERT: E 119 ASN cc_start: 0.8685 (t0) cc_final: 0.8475 (t0) REVERT: E 133 ASP cc_start: 0.8795 (t0) cc_final: 0.8384 (t0) REVERT: E 151 MET cc_start: 0.8870 (ttp) cc_final: 0.8380 (tpp) REVERT: F 6 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.8188 (t80) REVERT: F 16 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7910 (tm) REVERT: F 28 LYS cc_start: 0.5283 (mmmt) cc_final: 0.4664 (tttm) outliers start: 14 outliers final: 2 residues processed: 122 average time/residue: 1.4798 time to fit residues: 194.1536 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 : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 16 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 120 optimal weight: 0.0980 chunk 111 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 100 optimal weight: 0.0010 chunk 96 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 66 optimal weight: 0.1980 overall best weight: 0.4186 ------------------------------------------------------------------------------- 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 = 0.3179 r_free = 0.3179 target = 0.066136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.049961 restraints weight = 30792.183| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 2.43 r_work: 0.2675 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12176 Z= 0.098 Angle : 0.471 9.779 16523 Z= 0.244 Chirality : 0.039 0.155 1899 Planarity : 0.003 0.033 2062 Dihedral : 4.760 59.743 1663 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.96 % Allowed : 9.08 % 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 (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: 1.78 (0.22), residues: 1528 helix: 2.22 (0.18), residues: 785 sheet: 0.48 (0.63), residues: 74 loop : 0.05 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 103 HIS 0.002 0.001 HIS B 330 PHE 0.018 0.001 PHE E 22 TYR 0.015 0.001 TYR E 106 ARG 0.006 0.000 ARG B 43 Details of bonding type rmsd hydrogen bonds : bond 0.03949 ( 662) hydrogen bonds : angle 4.32449 ( 1881) metal coordination : bond 0.00912 ( 4) metal coordination : angle 2.17434 ( 6) covalent geometry : bond 0.00202 (12170) covalent geometry : angle 0.46937 (16517) Misc. bond : bond 0.00031 ( 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 128 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 1.290 Fit side-chains revert: symmetry clash REVERT: B 43 ARG cc_start: 0.8841 (mtm-85) cc_final: 0.8480 (mtm180) REVERT: B 72 MET cc_start: 0.9471 (mtm) cc_final: 0.9214 (mtm) REVERT: D 87 ASP cc_start: 0.9125 (t70) cc_final: 0.8868 (t0) REVERT: D 99 LYS cc_start: 0.9476 (mtpp) cc_final: 0.9162 (mtpp) REVERT: D 153 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8599 (tt0) REVERT: D 164 GLU cc_start: 0.8998 (tt0) cc_final: 0.8502 (tm-30) REVERT: D 202 LYS cc_start: 0.6794 (mmtt) cc_final: 0.6560 (mttp) REVERT: E 17 MET cc_start: 0.8715 (mmm) cc_final: 0.8307 (mtt) REVERT: E 82 THR cc_start: 0.9300 (m) cc_final: 0.9070 (m) REVERT: E 119 ASN cc_start: 0.8593 (t0) cc_final: 0.8317 (t0) REVERT: E 133 ASP cc_start: 0.8716 (t0) cc_final: 0.8376 (t0) REVERT: E 151 MET cc_start: 0.8880 (ttp) cc_final: 0.8309 (tpp) REVERT: F 6 PHE cc_start: 0.8592 (OUTLIER) cc_final: 0.8211 (t80) REVERT: F 10 MET cc_start: 0.8988 (tpt) cc_final: 0.8398 (tpp) REVERT: F 16 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7881 (tm) REVERT: F 28 LYS cc_start: 0.5162 (mmmt) cc_final: 0.4722 (tttm) outliers start: 12 outliers final: 3 residues processed: 122 average time/residue: 1.5336 time to fit residues: 200.7127 Evaluate side-chains 119 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 153 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 0.2980 chunk 9 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 138 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 GLN D 19 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.063609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.047242 restraints weight = 31314.713| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 2.44 r_work: 0.2607 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2491 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12176 Z= 0.204 Angle : 0.538 10.595 16523 Z= 0.278 Chirality : 0.042 0.164 1899 Planarity : 0.004 0.036 2062 Dihedral : 4.989 59.309 1663 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.04 % Allowed : 10.03 % 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: 1.67 (0.21), residues: 1528 helix: 2.12 (0.18), residues: 783 sheet: 0.33 (0.63), residues: 76 loop : 0.04 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 103 HIS 0.004 0.001 HIS B 330 PHE 0.027 0.002 PHE E 22 TYR 0.017 0.001 TYR D 141 ARG 0.005 0.000 ARG B 43 Details of bonding type rmsd hydrogen bonds : bond 0.04761 ( 662) hydrogen bonds : angle 4.49964 ( 1881) metal coordination : bond 0.01363 ( 4) metal coordination : angle 2.81009 ( 6) covalent geometry : bond 0.00472 (12170) covalent geometry : angle 0.53541 (16517) Misc. bond : bond 0.00140 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 1.308 Fit side-chains revert: symmetry clash REVERT: A 430 GLU cc_start: 0.9252 (OUTLIER) cc_final: 0.8860 (mt-10) REVERT: B 43 ARG cc_start: 0.8933 (mtm-85) cc_final: 0.8712 (mtm-85) REVERT: B 72 MET cc_start: 0.9510 (mtm) cc_final: 0.9299 (mtm) REVERT: D 87 ASP cc_start: 0.9131 (t70) cc_final: 0.8915 (t0) REVERT: D 99 LYS cc_start: 0.9493 (mtpp) cc_final: 0.9170 (mtpp) REVERT: D 164 GLU cc_start: 0.9011 (tt0) cc_final: 0.8567 (tm-30) REVERT: D 202 LYS cc_start: 0.6934 (mmtt) cc_final: 0.6672 (mttp) REVERT: E 17 MET cc_start: 0.8728 (mmm) cc_final: 0.8338 (mtt) REVERT: E 71 GLU cc_start: 0.8987 (mp0) cc_final: 0.8671 (tt0) REVERT: E 82 THR cc_start: 0.9313 (m) cc_final: 0.9081 (m) REVERT: E 133 ASP cc_start: 0.8760 (t0) cc_final: 0.8458 (t0) REVERT: E 151 MET cc_start: 0.9001 (ttp) cc_final: 0.8403 (ttm) REVERT: F 6 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.8240 (t80) REVERT: F 16 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7982 (tm) REVERT: F 28 LYS cc_start: 0.5304 (mmmt) cc_final: 0.4764 (tttm) outliers start: 13 outliers final: 4 residues processed: 116 average time/residue: 1.8176 time to fit residues: 226.0772 Evaluate side-chains 117 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 2.068 ------------------------------------------------------------------------------- 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 37 THR 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 73 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 119 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 90 optimal weight: 0.1980 chunk 77 optimal weight: 0.5980 chunk 149 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3159 r_free = 0.3159 target = 0.065119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.048916 restraints weight = 31347.363| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 2.46 r_work: 0.2650 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2535 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12176 Z= 0.104 Angle : 0.487 11.387 16523 Z= 0.250 Chirality : 0.040 0.151 1899 Planarity : 0.003 0.033 2062 Dihedral : 4.814 59.867 1663 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.80 % Allowed : 10.27 % 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: 1.77 (0.22), residues: 1528 helix: 2.25 (0.18), residues: 786 sheet: 0.42 (0.62), residues: 74 loop : -0.00 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 103 HIS 0.002 0.000 HIS B 101 PHE 0.024 0.001 PHE E 22 TYR 0.015 0.001 TYR D 141 ARG 0.005 0.000 ARG B 43 Details of bonding type rmsd hydrogen bonds : bond 0.04035 ( 662) hydrogen bonds : angle 4.32264 ( 1881) metal coordination : bond 0.00760 ( 4) metal coordination : angle 2.47162 ( 6) covalent geometry : bond 0.00219 (12170) covalent geometry : angle 0.48434 (16517) Misc. bond : bond 0.00042 ( 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 123 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 1.343 Fit side-chains revert: symmetry clash REVERT: A 430 GLU cc_start: 0.9216 (OUTLIER) cc_final: 0.8828 (mt-10) REVERT: B 72 MET cc_start: 0.9512 (mtm) cc_final: 0.9263 (mtm) REVERT: D 87 ASP cc_start: 0.9103 (t70) cc_final: 0.8877 (t0) REVERT: D 164 GLU cc_start: 0.8993 (tt0) cc_final: 0.8540 (tm-30) REVERT: D 202 LYS cc_start: 0.6868 (mmtt) cc_final: 0.6659 (mttp) REVERT: E 17 MET cc_start: 0.8651 (mmm) cc_final: 0.8319 (mtt) REVERT: E 22 PHE cc_start: 0.8340 (m-10) cc_final: 0.7845 (m-10) REVERT: E 71 GLU cc_start: 0.8919 (mp0) cc_final: 0.8612 (tt0) REVERT: E 82 THR cc_start: 0.9308 (m) cc_final: 0.9077 (m) REVERT: E 133 ASP cc_start: 0.8665 (t0) cc_final: 0.8340 (t0) REVERT: E 151 MET cc_start: 0.8932 (ttp) cc_final: 0.8432 (tpp) REVERT: F 10 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8401 (tpp) REVERT: F 16 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7982 (tm) REVERT: F 28 LYS cc_start: 0.5292 (mmmt) cc_final: 0.4829 (tttm) outliers start: 10 outliers final: 4 residues processed: 117 average time/residue: 1.8550 time to fit residues: 233.0274 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 : 1.717 ------------------------------------------------------------------------------- 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 10 MET 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 137 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3135 r_free = 0.3135 target = 0.063960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.047716 restraints weight = 31642.417| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 2.45 r_work: 0.2620 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2505 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12176 Z= 0.155 Angle : 0.518 11.640 16523 Z= 0.265 Chirality : 0.041 0.159 1899 Planarity : 0.004 0.034 2062 Dihedral : 4.886 59.526 1663 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.96 % Allowed : 10.99 % 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 (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: 1.73 (0.21), residues: 1528 helix: 2.19 (0.18), residues: 787 sheet: 0.40 (0.63), residues: 74 loop : 0.00 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 103 HIS 0.003 0.001 HIS A 225 PHE 0.026 0.001 PHE E 22 TYR 0.017 0.001 TYR D 141 ARG 0.008 0.000 ARG B 43 Details of bonding type rmsd hydrogen bonds : bond 0.04395 ( 662) hydrogen bonds : angle 4.39276 ( 1881) metal coordination : bond 0.01061 ( 4) metal coordination : angle 2.62862 ( 6) covalent geometry : bond 0.00353 (12170) covalent geometry : angle 0.51565 (16517) Misc. bond : bond 0.00094 ( 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: 12 poor density : 110 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 430 GLU cc_start: 0.9249 (OUTLIER) cc_final: 0.8841 (mt-10) REVERT: D 87 ASP cc_start: 0.9118 (t70) cc_final: 0.8893 (t0) REVERT: D 99 LYS cc_start: 0.9448 (mtpp) cc_final: 0.9145 (mtpp) REVERT: D 164 GLU cc_start: 0.9003 (tt0) cc_final: 0.8562 (tm-30) REVERT: E 17 MET cc_start: 0.8676 (mmm) cc_final: 0.8339 (mtt) REVERT: E 22 PHE cc_start: 0.8433 (m-10) cc_final: 0.7898 (m-10) REVERT: E 71 GLU cc_start: 0.8888 (mp0) cc_final: 0.8599 (tt0) REVERT: E 82 THR cc_start: 0.9324 (m) cc_final: 0.9093 (m) REVERT: E 133 ASP cc_start: 0.8679 (t0) cc_final: 0.8372 (t0) REVERT: F 6 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.8267 (t80) REVERT: F 10 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8414 (tpp) REVERT: F 16 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8032 (tm) REVERT: F 28 LYS cc_start: 0.5270 (mmmt) cc_final: 0.4762 (tttm) outliers start: 12 outliers final: 5 residues processed: 115 average time/residue: 1.9205 time to fit residues: 238.1223 Evaluate side-chains 117 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 16 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 87 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 0.0070 chunk 76 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 28 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 116 optimal weight: 0.3980 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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 = 0.3162 r_free = 0.3162 target = 0.065218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.049051 restraints weight = 31282.645| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 2.46 r_work: 0.2655 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12176 Z= 0.106 Angle : 0.493 12.251 16523 Z= 0.252 Chirality : 0.040 0.151 1899 Planarity : 0.003 0.033 2062 Dihedral : 4.750 59.818 1663 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.88 % Allowed : 11.15 % Favored : 87.98 % 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: 1.80 (0.22), residues: 1528 helix: 2.28 (0.18), residues: 787 sheet: 0.37 (0.62), residues: 74 loop : 0.02 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 103 HIS 0.002 0.001 HIS B 330 PHE 0.022 0.001 PHE E 22 TYR 0.015 0.001 TYR D 141 ARG 0.008 0.000 ARG B 43 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 662) hydrogen bonds : angle 4.28341 ( 1881) metal coordination : bond 0.00841 ( 4) metal coordination : angle 2.41020 ( 6) covalent geometry : bond 0.00228 (12170) covalent geometry : angle 0.49105 (16517) Misc. bond : bond 0.00048 ( 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 129 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 2.415 Fit side-chains revert: symmetry clash REVERT: A 430 GLU cc_start: 0.9220 (OUTLIER) cc_final: 0.8780 (mt-10) REVERT: D 37 LYS cc_start: 0.8691 (mtmm) cc_final: 0.8444 (mtpt) REVERT: D 87 ASP cc_start: 0.9139 (t70) cc_final: 0.8922 (t0) REVERT: D 99 LYS cc_start: 0.9457 (mtpp) cc_final: 0.9161 (mtpp) REVERT: D 164 GLU cc_start: 0.8998 (tt0) cc_final: 0.8533 (tm-30) REVERT: E 17 MET cc_start: 0.8647 (mmm) cc_final: 0.8330 (mtt) REVERT: E 22 PHE cc_start: 0.8391 (m-10) cc_final: 0.7968 (m-10) REVERT: E 82 THR cc_start: 0.9301 (m) cc_final: 0.9071 (m) REVERT: E 119 ASN cc_start: 0.8295 (t0) cc_final: 0.7893 (t0) REVERT: E 133 ASP cc_start: 0.8678 (t0) cc_final: 0.8365 (t0) REVERT: E 151 MET cc_start: 0.8921 (ttp) cc_final: 0.8374 (tpp) REVERT: F 6 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.8262 (t80) REVERT: F 10 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8429 (tpp) REVERT: F 16 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8009 (tm) REVERT: F 28 LYS cc_start: 0.4862 (mmmt) cc_final: 0.4409 (tttm) outliers start: 11 outliers final: 5 residues processed: 122 average time/residue: 2.1828 time to fit residues: 287.9643 Evaluate side-chains 120 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 16 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 124 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 HIS D 19 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.062839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.046506 restraints weight = 31174.450| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 2.44 r_work: 0.2588 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2473 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 12176 Z= 0.257 Angle : 0.597 12.576 16523 Z= 0.306 Chirality : 0.044 0.165 1899 Planarity : 0.004 0.047 2062 Dihedral : 5.132 59.338 1663 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.04 % Allowed : 11.31 % Favored : 87.66 % 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: 1.57 (0.21), residues: 1528 helix: 2.06 (0.18), residues: 783 sheet: 0.17 (0.62), residues: 78 loop : -0.03 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 103 HIS 0.005 0.001 HIS B 46 PHE 0.031 0.002 PHE E 22 TYR 0.028 0.002 TYR E 106 ARG 0.004 0.001 ARG A 260 Details of bonding type rmsd hydrogen bonds : bond 0.05035 ( 662) hydrogen bonds : angle 4.55130 ( 1881) metal coordination : bond 0.01527 ( 4) metal coordination : angle 3.33418 ( 6) covalent geometry : bond 0.00589 (12170) covalent geometry : angle 0.59392 (16517) Misc. bond : bond 0.00155 ( 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 122 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 1.392 Fit side-chains revert: symmetry clash REVERT: A 396 ASP cc_start: 0.8661 (m-30) cc_final: 0.8313 (m-30) REVERT: A 430 GLU cc_start: 0.9350 (OUTLIER) cc_final: 0.8824 (mt-10) REVERT: B 43 ARG cc_start: 0.8930 (mtm-85) cc_final: 0.8648 (mtm-85) REVERT: D 87 ASP cc_start: 0.9136 (t70) cc_final: 0.8933 (t0) REVERT: D 99 LYS cc_start: 0.9454 (mtpp) cc_final: 0.9160 (mtpp) REVERT: D 164 GLU cc_start: 0.9013 (tt0) cc_final: 0.8590 (tm-30) REVERT: D 204 GLU cc_start: 0.7250 (pm20) cc_final: 0.6970 (pm20) REVERT: E 2 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6834 (tp30) REVERT: E 17 MET cc_start: 0.8670 (mmm) cc_final: 0.8319 (mtt) REVERT: E 22 PHE cc_start: 0.8414 (m-10) cc_final: 0.7951 (m-10) REVERT: E 25 MET cc_start: 0.9132 (mmp) cc_final: 0.8728 (mmm) REVERT: E 71 GLU cc_start: 0.9023 (mp0) cc_final: 0.8705 (tt0) REVERT: E 82 THR cc_start: 0.9315 (m) cc_final: 0.9086 (m) REVERT: E 133 ASP cc_start: 0.8749 (t0) cc_final: 0.8496 (t0) REVERT: E 151 MET cc_start: 0.9010 (ttp) cc_final: 0.8406 (ttm) REVERT: F 6 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.8300 (t80) REVERT: F 10 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8467 (tpp) REVERT: F 16 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8082 (tm) REVERT: F 28 LYS cc_start: 0.5021 (mmmt) cc_final: 0.4467 (tttm) outliers start: 13 outliers final: 5 residues processed: 113 average time/residue: 1.4837 time to fit residues: 180.1590 Evaluate side-chains 117 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 1.276 ------------------------------------------------------------------------------- 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 E residue 2 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 16 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 140 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 132 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 110 optimal weight: 0.2980 chunk 124 optimal weight: 4.9990 chunk 146 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3131 r_free = 0.3131 target = 0.063754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.047523 restraints weight = 31315.435| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 2.44 r_work: 0.2615 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2500 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 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 0.040 12176 Z= 0.145 Angle : 0.532 12.237 16523 Z= 0.274 Chirality : 0.041 0.161 1899 Planarity : 0.004 0.035 2062 Dihedral : 4.988 59.738 1663 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.88 % Allowed : 11.39 % Favored : 87.74 % 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: 1.66 (0.21), residues: 1528 helix: 2.15 (0.18), residues: 786 sheet: 0.35 (0.63), residues: 74 loop : -0.04 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 103 HIS 0.002 0.001 HIS B 330 PHE 0.026 0.001 PHE E 22 TYR 0.016 0.001 TYR E 106 ARG 0.006 0.000 ARG B 43 Details of bonding type rmsd hydrogen bonds : bond 0.04404 ( 662) hydrogen bonds : angle 4.41167 ( 1881) metal coordination : bond 0.00887 ( 4) metal coordination : angle 2.64132 ( 6) covalent geometry : bond 0.00326 (12170) covalent geometry : angle 0.52949 (16517) Misc. bond : bond 0.00081 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9029.91 seconds wall clock time: 162 minutes 4.81 seconds (9724.81 seconds total)