Starting phenix.real_space_refine on Fri Mar 6 12:10:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a1v_15090/03_2026/8a1v_15090_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a1v_15090/03_2026/8a1v_15090.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a1v_15090/03_2026/8a1v_15090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a1v_15090/03_2026/8a1v_15090.map" model { file = "/net/cci-nas-00/data/ceres_data/8a1v_15090/03_2026/8a1v_15090_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a1v_15090/03_2026/8a1v_15090_trim.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 P 6 5.49 5 S 90 5.16 5 Na 2 4.78 5 C 9637 2.51 5 N 2413 2.21 5 O 3110 1.98 5 H 14644 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29906 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 6877 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 422} Chain: "B" Number of atoms: 6063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 6063 Classifications: {'peptide': 395} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 379} Chain: "C" Number of atoms: 3774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 3774 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain: "D" Number of atoms: 3154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3154 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 9, 'TRANS': 191} Chain: "E" Number of atoms: 3058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3058 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain: "F" Number of atoms: 6239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 6239 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 24, 'TRANS': 381} Chain: "B" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 194 Unusual residues: {' NA': 2, '3PE': 2, 'FMN': 1, 'LMT': 1, 'RBF': 1, 'UQ2': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 26 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: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FES': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'FAD': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 186 Classifications: {'water': 186} Link IDs: {None: 185} Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 140 Classifications: {'water': 140} Link IDs: {None: 139} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18378 SG CYS D 112 67.218 81.729 58.586 1.00 17.12 S ATOM 20270 SG CYS E 26 64.479 81.955 61.129 1.00 4.66 S ATOM 17045 SG CYS D 29 67.525 83.498 64.844 1.00 12.46 S ATOM 21775 SG CYS E 120 70.553 83.794 62.634 1.00 26.39 S ATOM 23956 SG CYS F 70 53.270 67.208 37.380 1.00 37.47 S ATOM 24005 SG CYS F 76 51.681 63.791 37.086 1.00 43.20 S ATOM 24039 SG CYS F 79 56.014 61.536 39.069 1.00 39.85 S ATOM 24523 SG CYS F 111 57.653 64.918 39.445 1.00 32.48 S Time building chain proxies: 5.40, per 1000 atoms: 0.18 Number of scatterers: 29906 At special positions: 0 Unit cell: (113.15, 134.137, 131.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 4 26.01 S 90 16.00 P 6 15.00 Na 2 11.00 O 3110 8.00 N 2413 7.00 C 9637 6.00 H 14644 1.00 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: 2.74 Conformation dependent library (CDL) restraints added in 937.3 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 202 " pdb="FE1 FES E 202 " - pdb=" SG CYS E 26 " pdb="FE2 FES E 202 " - pdb=" SG CYS D 29 " pdb="FE1 FES E 202 " - pdb=" SG CYS D 112 " pdb="FE2 FES E 202 " - pdb=" SG CYS E 120 " pdb=" FES F1502 " pdb="FE1 FES F1502 " - pdb=" SG CYS F 76 " pdb="FE2 FES F1502 " - pdb=" SG CYS F 79 " pdb="FE2 FES F1502 " - pdb=" SG CYS F 111 " pdb="FE1 FES F1502 " - pdb=" SG CYS F 70 " Number of angles added : 12 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3420 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 12 sheets defined 53.9% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' 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 106 through 113 removed outlier: 4.356A pdb=" N ALA A 111 " --> pdb=" O ASN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 125 Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 162 through 170 removed outlier: 3.920A pdb=" N GLU A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN A 170 " --> pdb=" O VAL A 166 " (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: 3.619A pdb=" N HIS A 354 " --> pdb=" O PHE A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 384 removed outlier: 3.519A pdb=" N LYS A 382 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 3.621A 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 414 through 417 Processing helix chain 'A' and resid 418 through 425 Processing helix chain 'A' and resid 430 through 446 removed outlier: 3.604A pdb=" N LEU A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 35 removed outlier: 3.665A pdb=" N ALA B 25 " --> pdb=" O GLU B 21 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU B 26 " --> pdb=" O LYS B 22 " (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 109 removed outlier: 3.555A pdb=" N THR B 105 " --> pdb=" O HIS B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 152 removed outlier: 3.709A pdb=" N TYR B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Proline residue: B 131 - end of helix removed outlier: 3.552A pdb=" N TRP B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 169 removed outlier: 4.291A pdb=" N VAL B 161 " --> pdb=" O GLU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 191 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 removed outlier: 3.567A pdb=" N ILE B 298 " --> pdb=" O SER B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 325 removed outlier: 3.534A pdb=" N PHE B 323 " --> pdb=" O ASN B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 333 removed outlier: 3.754A 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 391 Processing helix chain 'B' and resid 392 through 410 Processing helix chain 'B' and resid 411 through 414 Processing helix chain 'C' and resid 8 through 54 removed outlier: 4.826A pdb=" N ASP C 35 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LYS C 36 " --> pdb=" O GLY C 32 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN C 46 " --> pdb=" O ALA C 42 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 71 Processing helix chain 'C' and resid 92 through 99 Processing helix chain 'C' and resid 100 through 103 removed outlier: 3.657A pdb=" N SER C 103 " --> pdb=" O ALA C 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 100 through 103' Processing helix chain 'C' and resid 177 through 181 removed outlier: 3.580A pdb=" N VAL C 180 " --> pdb=" O GLY C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 188 Processing helix chain 'C' and resid 224 through 239 Processing helix chain 'C' and resid 244 through 253 removed outlier: 3.576A pdb=" N ASP C 253 " --> pdb=" O THR C 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 13 Processing helix chain 'D' and resid 27 through 34 removed outlier: 3.522A pdb=" N ALA D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 62 Processing helix chain 'D' and resid 63 through 66 Processing helix chain 'D' and resid 70 through 93 Processing helix chain 'D' and resid 94 through 102 Processing helix chain 'D' and resid 103 through 109 removed outlier: 3.581A pdb=" N GLY D 106 " --> pdb=" O VAL D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 121 Processing helix chain 'D' and resid 126 through 158 Processing helix chain 'D' and resid 178 through 182 Processing helix chain 'D' and resid 183 through 202 removed outlier: 4.178A pdb=" N ALA D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 3.671A 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 3 through 13 Processing helix chain 'E' and resid 24 through 31 Processing helix chain 'E' and resid 34 through 63 removed outlier: 3.528A pdb=" N ILE E 43 " --> pdb=" O PHE E 39 " (cutoff:3.500A) Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 78 through 102 removed outlier: 3.682A pdb=" N ASP E 99 " --> pdb=" O GLU E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 109 Processing helix chain 'E' and resid 112 through 117 Processing helix chain 'E' and resid 119 through 132 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 190 Processing helix chain 'E' and resid 191 through 194 Processing helix chain 'F' and resid 3 through 30 removed outlier: 3.654A pdb=" N LYS F 28 " --> pdb=" O PHE F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 62 removed outlier: 3.889A pdb=" N ALA F 58 " --> pdb=" O LYS F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 98 removed outlier: 4.169A pdb=" N HIS F 97 " --> pdb=" O THR F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 105 removed outlier: 3.692A pdb=" N GLU F 105 " --> pdb=" O GLY F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 129 Processing helix chain 'F' and resid 180 through 182 No H-bonds generated for 'chain 'F' and resid 180 through 182' Processing helix chain 'F' and resid 185 through 196 removed outlier: 4.638A pdb=" N ASP F 191 " --> pdb=" O LYS F 187 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS F 194 " --> pdb=" O GLY F 190 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE F 195 " --> pdb=" O ASP F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 199 No H-bonds generated for 'chain 'F' and resid 197 through 199' Processing helix chain 'F' and resid 244 through 252 Processing helix chain 'F' and resid 284 through 297 removed outlier: 3.694A pdb=" N MET F 288 " --> pdb=" O GLY F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 330 Processing helix chain 'F' and resid 354 through 363 removed outlier: 4.684A pdb=" N TYR F 360 " --> pdb=" O HIS F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 394 Processing helix chain 'F' and resid 397 through 399 No H-bonds generated for 'chain 'F' and resid 397 through 399' Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 6.644A pdb=" N ILE A 2 " --> pdb=" O ASP A 212 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 22 removed outlier: 7.398A pdb=" N SER A 21 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 9.749A pdb=" N VAL A 278 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL A 323 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N SER A 263 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N VAL A 325 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA A 265 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N ARG A 327 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 5.332A 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: 6.884A pdb=" N LEU A 87 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ARG A 81 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N SER A 89 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ILE A 79 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.934A 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: 7.085A pdb=" N PHE A 68 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 82 through 84 removed outlier: 3.588A pdb=" N ASP C 82 " --> pdb=" O ASP C 77 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU C 75 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 14.384A pdb=" N VAL C 121 " --> pdb=" O HIS C 141 " (cutoff:3.500A) removed outlier: 11.963A pdb=" N HIS C 141 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL C 123 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS C 135 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ASP C 129 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N THR C 133 " --> pdb=" O ASP C 129 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N MET C 148 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLU C 169 " --> pdb=" O MET C 148 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N TYR C 150 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N TYR C 167 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 6.682A 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: 6.684A pdb=" N ALA C 154 " --> pdb=" O SER C 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 204 through 206 removed outlier: 6.210A pdb=" N LYS C 204 " --> pdb=" O VAL C 218 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AA8, first strand: chain 'F' and resid 47 through 49 removed outlier: 6.504A pdb=" N THR F 36 " --> pdb=" O MET F 119 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LEU F 121 " --> pdb=" O THR F 36 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N SER F 38 " --> pdb=" O LEU F 121 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 226 through 229 removed outlier: 6.819A pdb=" N ILE F 147 " --> pdb=" O ASN F 142 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASN F 142 " --> pdb=" O ILE F 147 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N GLU F 149 " --> pdb=" O ASN F 140 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASN F 140 " --> pdb=" O GLU F 149 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LYS F 151 " --> pdb=" O ILE F 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 208 through 213 Processing sheet with id=AB2, first strand: chain 'F' and resid 175 through 178 Processing sheet with id=AB3, first strand: chain 'F' and resid 333 through 339 removed outlier: 6.767A pdb=" N MET F 305 " --> pdb=" O VAL F 334 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N HIS F 336 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TYR F 307 " --> pdb=" O HIS F 336 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ALA F 338 " --> pdb=" O TYR F 307 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N TYR F 309 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N MET F 276 " --> pdb=" O SER F 306 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N TRP F 308 " --> pdb=" O MET F 276 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N PHE F 278 " --> pdb=" O TRP F 308 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N GLY F 310 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N GLY F 280 " --> pdb=" O GLY F 310 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N LEU F 402 " --> pdb=" O CYS F 373 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N TYR F 375 " --> pdb=" O LEU F 402 " (cutoff:3.500A) 748 hydrogen bonds defined for protein. 2118 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: 7.24 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.10: 14631 1.10 - 1.37: 4891 1.37 - 1.65: 10179 1.65 - 1.93: 153 1.93 - 2.20: 8 Bond restraints: 29862 Sorted by residual: bond pdb=" ND2 ASN B 375 " pdb="HD21 ASN B 375 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" ND2 ASN B 375 " pdb="HD22 ASN B 375 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.57e+01 bond pdb=" C4 FMN C1000 " pdb=" C4A FMN C1000 " ideal model delta sigma weight residual 1.485 1.390 0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" C4 FMN B 606 " pdb=" C4A FMN B 606 " ideal model delta sigma weight residual 1.485 1.390 0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" O3P FAD F1501 " pdb=" P FAD F1501 " ideal model delta sigma weight residual 1.660 1.584 0.076 2.00e-02 2.50e+03 1.46e+01 ... (remaining 29857 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 53598 1.88 - 3.76: 292 3.76 - 5.64: 53 5.64 - 7.52: 11 7.52 - 9.40: 10 Bond angle restraints: 53964 Sorted by residual: angle pdb=" C SER B 44 " pdb=" N SER B 45 " pdb=" CA SER B 45 " ideal model delta sigma weight residual 121.70 128.09 -6.39 1.80e+00 3.09e-01 1.26e+01 angle pdb=" C2 LMT D 301 " pdb=" C3 LMT D 301 " pdb=" C4 LMT D 301 " ideal model delta sigma weight residual 117.09 107.69 9.40 3.00e+00 1.11e-01 9.81e+00 angle pdb=" C2 LMT E 201 " pdb=" C3 LMT E 201 " pdb=" C4 LMT E 201 " ideal model delta sigma weight residual 117.09 107.76 9.33 3.00e+00 1.11e-01 9.68e+00 angle pdb=" C2 LMT B 603 " pdb=" C3 LMT B 603 " pdb=" C4 LMT B 603 " ideal model delta sigma weight residual 117.09 107.93 9.16 3.00e+00 1.11e-01 9.32e+00 angle pdb=" C VAL B 373 " pdb=" CA VAL B 373 " pdb=" CB VAL B 373 " ideal model delta sigma weight residual 111.65 107.55 4.10 1.41e+00 5.03e-01 8.47e+00 ... (remaining 53959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.21: 13336 25.21 - 50.43: 678 50.43 - 75.64: 160 75.64 - 100.86: 19 100.86 - 126.07: 6 Dihedral angle restraints: 14199 sinusoidal: 7805 harmonic: 6394 Sorted by residual: dihedral pdb=" C2B LMT E 201 " pdb=" C1B LMT E 201 " pdb=" O5B LMT E 201 " pdb=" C5B LMT E 201 " ideal model delta sinusoidal sigma weight residual -57.12 68.95 -126.07 1 3.00e+01 1.11e-03 1.69e+01 dihedral pdb=" C5B LMT E 201 " pdb=" C1B LMT E 201 " pdb=" O5B LMT E 201 " pdb=" O1B LMT E 201 " ideal model delta sinusoidal sigma weight residual 295.61 169.89 125.72 1 3.00e+01 1.11e-03 1.69e+01 dihedral pdb=" O1B LMT B 603 " pdb=" C1B LMT B 603 " pdb=" C2B LMT B 603 " pdb=" O2B LMT B 603 " ideal model delta sinusoidal sigma weight residual 53.26 -65.60 118.86 1 3.00e+01 1.11e-03 1.58e+01 ... (remaining 14196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1914 0.048 - 0.095: 298 0.095 - 0.143: 108 0.143 - 0.191: 2 0.191 - 0.238: 8 Chirality restraints: 2330 Sorted by residual: chirality pdb=" C4' LMT B 603 " pdb=" C3' LMT B 603 " pdb=" C5' LMT B 603 " pdb=" O1B LMT B 603 " both_signs ideal model delta sigma weight residual False -2.55 -2.79 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C4' LMT D 301 " pdb=" C3' LMT D 301 " pdb=" C5' LMT D 301 " pdb=" O1B LMT D 301 " both_signs ideal model delta sigma weight residual False -2.55 -2.77 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C5' LMT B 603 " pdb=" C4' LMT B 603 " pdb=" C6' LMT B 603 " pdb=" O5' LMT B 603 " both_signs ideal model delta sigma weight residual False -2.51 -2.30 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 2327 not shown) Planarity restraints: 4375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 375 " -0.031 2.00e-02 2.50e+03 2.99e-02 1.34e+01 pdb=" CG ASN B 375 " 0.003 2.00e-02 2.50e+03 pdb=" OD1 ASN B 375 " 0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN B 375 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN B 375 " -0.044 2.00e-02 2.50e+03 pdb="HD22 ASN B 375 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 375 " -0.031 5.00e-02 4.00e+02 4.63e-02 3.42e+00 pdb=" N PRO B 376 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 376 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 376 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 70 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.45e+00 pdb=" N PRO A 71 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 71 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 71 " 0.022 5.00e-02 4.00e+02 ... (remaining 4372 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1820 2.20 - 2.80: 62568 2.80 - 3.40: 86230 3.40 - 4.00: 117497 4.00 - 4.60: 177307 Nonbonded interactions: 445422 Sorted by model distance: nonbonded pdb="HH21 ARG B 372 " pdb=" OE1 GLU B 380 " model vdw 1.604 2.450 nonbonded pdb=" O GLY E 175 " pdb=" HG1 THR E 179 " model vdw 1.609 2.450 nonbonded pdb=" O PRO E 114 " pdb=" HG1 THR E 117 " model vdw 1.613 2.450 nonbonded pdb="HH22 ARG A 273 " pdb=" OE2 GLU A 290 " model vdw 1.633 2.450 nonbonded pdb=" HH TYR B 87 " pdb=" O ASP B 230 " model vdw 1.633 2.450 ... (remaining 445417 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: 2.890 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: 0.220 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 35.670 Find NCS groups from input model: 0.130 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:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 15228 Z= 0.204 Angle : 0.566 9.397 20646 Z= 0.257 Chirality : 0.041 0.238 2330 Planarity : 0.003 0.046 2574 Dihedral : 15.450 126.069 5671 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.78 % Allowed : 8.35 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.20), residues: 1880 helix: 1.48 (0.18), residues: 858 sheet: -0.34 (0.42), residues: 162 loop : 0.17 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 407 TYR 0.009 0.001 TYR E 134 PHE 0.012 0.001 PHE B 213 TRP 0.012 0.001 TRP B 103 HIS 0.003 0.001 HIS F 356 Details of bonding type rmsd covalent geometry : bond 0.00403 (15218) covalent geometry : angle 0.56407 (20634) hydrogen bonds : bond 0.22825 ( 748) hydrogen bonds : angle 7.68148 ( 2118) metal coordination : bond 0.00818 ( 8) metal coordination : angle 2.04016 ( 12) Misc. bond : bond 0.04219 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 302 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 290 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.7784 (mtt-85) REVERT: B 28 GLU cc_start: 0.5007 (tp30) cc_final: 0.4578 (mt-10) REVERT: B 261 MET cc_start: 0.8197 (tpp) cc_final: 0.7926 (tpp) REVERT: F 126 GLU cc_start: 0.3264 (tp30) cc_final: 0.2814 (mt-10) REVERT: F 200 TYR cc_start: 0.3025 (m-80) cc_final: 0.2770 (m-80) outliers start: 12 outliers final: 8 residues processed: 301 average time/residue: 1.2703 time to fit residues: 423.6390 Evaluate side-chains 167 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 158 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 401 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 8.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 252 ASN B 324 ASN D 64 ASN D 176 GLN E 61 ASN F 244 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.139763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.094162 restraints weight = 59818.994| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.30 r_work: 0.2966 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15228 Z= 0.177 Angle : 0.590 7.787 20646 Z= 0.310 Chirality : 0.043 0.313 2330 Planarity : 0.004 0.065 2574 Dihedral : 11.406 96.701 2370 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.88 % Allowed : 13.86 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.19), residues: 1880 helix: 1.33 (0.18), residues: 889 sheet: -0.85 (0.38), residues: 174 loop : -0.13 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 252 TYR 0.017 0.002 TYR D 141 PHE 0.021 0.002 PHE D 50 TRP 0.014 0.001 TRP B 103 HIS 0.006 0.001 HIS F 356 Details of bonding type rmsd covalent geometry : bond 0.00379 (15218) covalent geometry : angle 0.58297 (20634) hydrogen bonds : bond 0.06316 ( 748) hydrogen bonds : angle 5.57266 ( 2118) metal coordination : bond 0.00647 ( 8) metal coordination : angle 3.81629 ( 12) Misc. bond : bond 0.01259 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 198 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.7928 (mtt-85) REVERT: A 444 LYS cc_start: 0.7958 (tttm) cc_final: 0.7611 (ttmm) REVERT: B 33 LEU cc_start: 0.6119 (tp) cc_final: 0.5801 (mt) REVERT: B 34 PHE cc_start: 0.7088 (m-10) cc_final: 0.6694 (m-80) REVERT: B 261 MET cc_start: 0.8547 (tpp) cc_final: 0.8307 (tpp) REVERT: C 198 ASN cc_start: 0.6345 (t0) cc_final: 0.5758 (p0) REVERT: C 253 ASP cc_start: 0.6359 (OUTLIER) cc_final: 0.5971 (p0) REVERT: F 126 GLU cc_start: 0.3371 (tp30) cc_final: 0.2892 (mt-10) REVERT: F 275 GLU cc_start: 0.6317 (tt0) cc_final: 0.5855 (mt-10) REVERT: F 288 MET cc_start: 0.5847 (mmt) cc_final: 0.5607 (mmm) outliers start: 29 outliers final: 14 residues processed: 192 average time/residue: 1.2505 time to fit residues: 268.1091 Evaluate side-chains 162 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 356 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 118 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 169 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 chunk 130 optimal weight: 0.7980 chunk 166 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 chunk 170 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.140155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.093832 restraints weight = 59920.224| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.19 r_work: 0.2975 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15228 Z= 0.127 Angle : 0.524 7.372 20646 Z= 0.270 Chirality : 0.042 0.377 2330 Planarity : 0.004 0.051 2574 Dihedral : 10.326 83.770 2364 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.23 % Allowed : 15.61 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.19), residues: 1880 helix: 1.32 (0.17), residues: 895 sheet: -1.05 (0.37), residues: 179 loop : -0.21 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 252 TYR 0.016 0.001 TYR B 360 PHE 0.014 0.001 PHE B 213 TRP 0.018 0.001 TRP B 103 HIS 0.007 0.001 HIS F 356 Details of bonding type rmsd covalent geometry : bond 0.00273 (15218) covalent geometry : angle 0.51645 (20634) hydrogen bonds : bond 0.05390 ( 748) hydrogen bonds : angle 5.20341 ( 2118) metal coordination : bond 0.00515 ( 8) metal coordination : angle 3.63243 ( 12) Misc. bond : bond 0.00048 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.7868 (mtt-85) REVERT: A 444 LYS cc_start: 0.7982 (tttm) cc_final: 0.7596 (ttmm) REVERT: B 34 PHE cc_start: 0.6973 (m-10) cc_final: 0.6684 (m-80) REVERT: B 154 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7389 (mm-30) REVERT: B 261 MET cc_start: 0.8572 (tpp) cc_final: 0.8346 (tpp) REVERT: C 253 ASP cc_start: 0.6310 (OUTLIER) cc_final: 0.5651 (p0) REVERT: F 126 GLU cc_start: 0.3315 (tp30) cc_final: 0.2970 (mt-10) REVERT: F 275 GLU cc_start: 0.6326 (tt0) cc_final: 0.5815 (mt-10) REVERT: F 276 MET cc_start: 0.6454 (mtp) cc_final: 0.6174 (mtp) outliers start: 19 outliers final: 8 residues processed: 176 average time/residue: 1.2498 time to fit residues: 246.7096 Evaluate side-chains 161 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 48 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 131 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 161 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 198 ASN F 244 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.138265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.092506 restraints weight = 59783.863| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.94 r_work: 0.2960 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15228 Z= 0.194 Angle : 0.586 11.787 20646 Z= 0.300 Chirality : 0.044 0.416 2330 Planarity : 0.004 0.052 2574 Dihedral : 10.049 73.768 2360 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.20 % Allowed : 15.03 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.19), residues: 1880 helix: 1.19 (0.17), residues: 894 sheet: -1.14 (0.37), residues: 173 loop : -0.47 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 407 TYR 0.017 0.002 TYR B 360 PHE 0.021 0.002 PHE B 213 TRP 0.018 0.002 TRP B 103 HIS 0.012 0.001 HIS F 356 Details of bonding type rmsd covalent geometry : bond 0.00443 (15218) covalent geometry : angle 0.57353 (20634) hydrogen bonds : bond 0.05519 ( 748) hydrogen bonds : angle 5.18395 ( 2118) metal coordination : bond 0.00669 ( 8) metal coordination : angle 4.93968 ( 12) Misc. bond : bond 0.00229 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 160 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8178 (mtt-85) REVERT: A 444 LYS cc_start: 0.7997 (tttm) cc_final: 0.7639 (ttmm) REVERT: B 34 PHE cc_start: 0.6991 (m-10) cc_final: 0.6684 (m-80) REVERT: B 261 MET cc_start: 0.8545 (tpp) cc_final: 0.8299 (tpp) REVERT: C 198 ASN cc_start: 0.6334 (t160) cc_final: 0.5665 (p0) REVERT: C 253 ASP cc_start: 0.6386 (OUTLIER) cc_final: 0.5921 (p0) REVERT: F 14 ILE cc_start: 0.7798 (OUTLIER) cc_final: 0.7577 (mt) REVERT: F 126 GLU cc_start: 0.3385 (tp30) cc_final: 0.2983 (mt-10) REVERT: F 275 GLU cc_start: 0.6410 (tt0) cc_final: 0.5976 (mt-10) REVERT: F 276 MET cc_start: 0.6419 (mtp) cc_final: 0.6020 (mtp) outliers start: 34 outliers final: 18 residues processed: 187 average time/residue: 1.2032 time to fit residues: 253.5332 Evaluate side-chains 163 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 245 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 177 optimal weight: 9.9990 chunk 172 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 181 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 198 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.137631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.092551 restraints weight = 60625.477| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.94 r_work: 0.2956 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15228 Z= 0.199 Angle : 0.588 11.516 20646 Z= 0.302 Chirality : 0.044 0.394 2330 Planarity : 0.004 0.050 2574 Dihedral : 9.750 68.237 2360 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.53 % Allowed : 15.22 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.19), residues: 1880 helix: 1.11 (0.17), residues: 895 sheet: -1.18 (0.37), residues: 172 loop : -0.57 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 407 TYR 0.018 0.002 TYR B 360 PHE 0.021 0.002 PHE B 213 TRP 0.019 0.002 TRP B 103 HIS 0.011 0.001 HIS F 356 Details of bonding type rmsd covalent geometry : bond 0.00459 (15218) covalent geometry : angle 0.57571 (20634) hydrogen bonds : bond 0.05469 ( 748) hydrogen bonds : angle 5.10949 ( 2118) metal coordination : bond 0.00722 ( 8) metal coordination : angle 4.98064 ( 12) Misc. bond : bond 0.00179 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8274 (mtt-85) REVERT: A 444 LYS cc_start: 0.7967 (tttm) cc_final: 0.7573 (ttmm) REVERT: B 34 PHE cc_start: 0.7013 (m-10) cc_final: 0.6703 (m-80) REVERT: B 154 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7354 (mm-30) REVERT: C 198 ASN cc_start: 0.6212 (t0) cc_final: 0.5538 (p0) REVERT: C 253 ASP cc_start: 0.6323 (OUTLIER) cc_final: 0.5811 (p0) REVERT: E 118 VAL cc_start: 0.7765 (m) cc_final: 0.7559 (p) REVERT: F 14 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7570 (mt) REVERT: F 126 GLU cc_start: 0.3307 (tp30) cc_final: 0.2957 (mt-10) REVERT: F 275 GLU cc_start: 0.6353 (tt0) cc_final: 0.5852 (mt-10) REVERT: F 276 MET cc_start: 0.6349 (mtp) cc_final: 0.6020 (mtp) outliers start: 39 outliers final: 22 residues processed: 180 average time/residue: 1.0873 time to fit residues: 221.8509 Evaluate side-chains 168 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 356 HIS Chi-restraints excluded: chain F residue 377 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 3.9990 chunk 178 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 144 optimal weight: 0.0370 chunk 150 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.139521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.093498 restraints weight = 59826.953| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.10 r_work: 0.2976 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15228 Z= 0.109 Angle : 0.513 8.056 20646 Z= 0.262 Chirality : 0.041 0.409 2330 Planarity : 0.004 0.045 2574 Dihedral : 9.047 65.464 2360 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.49 % Allowed : 16.39 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.19), residues: 1880 helix: 1.35 (0.17), residues: 896 sheet: -1.02 (0.38), residues: 172 loop : -0.40 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 104 TYR 0.016 0.001 TYR B 360 PHE 0.014 0.001 PHE B 213 TRP 0.018 0.001 TRP B 103 HIS 0.010 0.001 HIS F 356 Details of bonding type rmsd covalent geometry : bond 0.00238 (15218) covalent geometry : angle 0.50285 (20634) hydrogen bonds : bond 0.04454 ( 748) hydrogen bonds : angle 4.86924 ( 2118) metal coordination : bond 0.00583 ( 8) metal coordination : angle 4.29611 ( 12) Misc. bond : bond 0.00069 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8119 (mp0) REVERT: A 395 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.7973 (mtt-85) REVERT: A 444 LYS cc_start: 0.7940 (tttm) cc_final: 0.7556 (ttmm) REVERT: B 34 PHE cc_start: 0.7002 (m-10) cc_final: 0.6697 (m-80) REVERT: B 154 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7297 (mm-30) REVERT: C 44 ASP cc_start: 0.7172 (t0) cc_final: 0.6728 (OUTLIER) REVERT: C 198 ASN cc_start: 0.6305 (t0) cc_final: 0.5640 (p0) REVERT: D 119 GLU cc_start: 0.5580 (tp30) cc_final: 0.5377 (tp30) REVERT: E 134 TYR cc_start: 0.6630 (m-10) cc_final: 0.6346 (m-10) REVERT: F 126 GLU cc_start: 0.3332 (tp30) cc_final: 0.3004 (mt-10) REVERT: F 275 GLU cc_start: 0.6298 (tt0) cc_final: 0.5889 (mt-10) REVERT: F 276 MET cc_start: 0.6264 (mtp) cc_final: 0.5801 (mtp) outliers start: 23 outliers final: 14 residues processed: 173 average time/residue: 1.1909 time to fit residues: 231.8117 Evaluate side-chains 156 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 377 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 34 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 159 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.138203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.093090 restraints weight = 60283.948| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.86 r_work: 0.2988 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15228 Z= 0.161 Angle : 0.553 11.389 20646 Z= 0.282 Chirality : 0.042 0.339 2330 Planarity : 0.004 0.045 2574 Dihedral : 9.005 59.292 2360 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.62 % Allowed : 16.71 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.19), residues: 1880 helix: 1.30 (0.17), residues: 895 sheet: -1.06 (0.37), residues: 172 loop : -0.48 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 407 TYR 0.018 0.001 TYR B 360 PHE 0.019 0.001 PHE B 213 TRP 0.020 0.001 TRP B 103 HIS 0.009 0.001 HIS F 356 Details of bonding type rmsd covalent geometry : bond 0.00369 (15218) covalent geometry : angle 0.54028 (20634) hydrogen bonds : bond 0.04917 ( 748) hydrogen bonds : angle 4.90584 ( 2118) metal coordination : bond 0.00642 ( 8) metal coordination : angle 4.90644 ( 12) Misc. bond : bond 0.00133 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 166 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8173 (mtt-85) REVERT: A 444 LYS cc_start: 0.7945 (tttm) cc_final: 0.7571 (ttmm) REVERT: B 34 PHE cc_start: 0.6956 (m-10) cc_final: 0.6645 (m-80) REVERT: B 154 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7261 (mm-30) REVERT: C 44 ASP cc_start: 0.7232 (t0) cc_final: 0.6798 (OUTLIER) REVERT: C 198 ASN cc_start: 0.6372 (t0) cc_final: 0.5764 (p0) REVERT: C 253 ASP cc_start: 0.6396 (OUTLIER) cc_final: 0.5943 (p0) REVERT: D 133 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.6893 (t0) REVERT: E 134 TYR cc_start: 0.6628 (m-10) cc_final: 0.6327 (m-10) REVERT: F 14 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7510 (mt) REVERT: F 126 GLU cc_start: 0.3333 (tp30) cc_final: 0.2956 (tt0) REVERT: F 275 GLU cc_start: 0.6348 (tt0) cc_final: 0.5892 (mt-10) REVERT: F 276 MET cc_start: 0.6241 (mtp) cc_final: 0.5845 (mtp) outliers start: 25 outliers final: 18 residues processed: 161 average time/residue: 1.1120 time to fit residues: 203.0162 Evaluate side-chains 157 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 377 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 129 optimal weight: 6.9990 chunk 174 optimal weight: 8.9990 chunk 164 optimal weight: 9.9990 chunk 159 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 154 optimal weight: 8.9990 chunk 138 optimal weight: 0.7980 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.136896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.091106 restraints weight = 60481.307| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.21 r_work: 0.2936 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15228 Z= 0.230 Angle : 0.624 13.268 20646 Z= 0.319 Chirality : 0.045 0.348 2330 Planarity : 0.005 0.053 2574 Dihedral : 9.286 59.624 2360 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.40 % Allowed : 15.93 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.19), residues: 1880 helix: 1.05 (0.17), residues: 893 sheet: -1.22 (0.37), residues: 170 loop : -0.73 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 252 TYR 0.018 0.002 TYR D 141 PHE 0.024 0.002 PHE B 213 TRP 0.021 0.002 TRP B 103 HIS 0.008 0.002 HIS B 20 Details of bonding type rmsd covalent geometry : bond 0.00538 (15218) covalent geometry : angle 0.60915 (20634) hydrogen bonds : bond 0.05601 ( 748) hydrogen bonds : angle 5.09890 ( 2118) metal coordination : bond 0.00816 ( 8) metal coordination : angle 5.70511 ( 12) Misc. bond : bond 0.00196 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8479 (mtt-85) REVERT: A 444 LYS cc_start: 0.7928 (tttm) cc_final: 0.7566 (ttmm) REVERT: B 34 PHE cc_start: 0.7051 (m-10) cc_final: 0.6752 (m-80) REVERT: B 154 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7393 (mm-30) REVERT: C 198 ASN cc_start: 0.6421 (t0) cc_final: 0.5774 (p0) REVERT: C 253 ASP cc_start: 0.6332 (OUTLIER) cc_final: 0.5865 (p0) REVERT: D 8 LYS cc_start: 0.2848 (tttt) cc_final: 0.2302 (tptp) REVERT: D 133 ASP cc_start: 0.7294 (OUTLIER) cc_final: 0.6955 (t0) REVERT: E 118 VAL cc_start: 0.8007 (m) cc_final: 0.7747 (p) REVERT: F 14 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7512 (mt) REVERT: F 126 GLU cc_start: 0.3511 (tp30) cc_final: 0.3118 (tt0) REVERT: F 275 GLU cc_start: 0.6379 (tt0) cc_final: 0.5972 (mt-10) REVERT: F 276 MET cc_start: 0.6276 (mtp) cc_final: 0.5856 (mtp) outliers start: 37 outliers final: 23 residues processed: 166 average time/residue: 1.1323 time to fit residues: 212.3744 Evaluate side-chains 157 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 22 PHE Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 292 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 183 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 184 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 182 optimal weight: 0.3980 chunk 178 optimal weight: 20.0000 chunk 143 optimal weight: 0.5980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.138710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.093948 restraints weight = 60095.714| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.86 r_work: 0.2991 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15228 Z= 0.137 Angle : 0.551 10.126 20646 Z= 0.281 Chirality : 0.042 0.326 2330 Planarity : 0.004 0.044 2574 Dihedral : 8.919 59.322 2360 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.07 % Allowed : 16.32 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.19), residues: 1880 helix: 1.20 (0.17), residues: 894 sheet: -1.19 (0.37), residues: 174 loop : -0.61 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 117 TYR 0.017 0.001 TYR B 360 PHE 0.022 0.001 PHE D 50 TRP 0.019 0.001 TRP B 103 HIS 0.011 0.001 HIS F 356 Details of bonding type rmsd covalent geometry : bond 0.00306 (15218) covalent geometry : angle 0.53848 (20634) hydrogen bonds : bond 0.04849 ( 748) hydrogen bonds : angle 4.93363 ( 2118) metal coordination : bond 0.00588 ( 8) metal coordination : angle 4.96615 ( 12) Misc. bond : bond 0.00095 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 167 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8050 (mp0) REVERT: A 395 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8296 (mtt-85) REVERT: A 444 LYS cc_start: 0.7890 (tttm) cc_final: 0.7551 (ttmm) REVERT: B 34 PHE cc_start: 0.7027 (m-10) cc_final: 0.6700 (m-80) REVERT: B 154 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7319 (mm-30) REVERT: C 44 ASP cc_start: 0.6891 (t0) cc_final: 0.6473 (t70) REVERT: C 198 ASN cc_start: 0.6441 (t0) cc_final: 0.5806 (p0) REVERT: C 253 ASP cc_start: 0.6370 (OUTLIER) cc_final: 0.5893 (p0) REVERT: D 8 LYS cc_start: 0.2811 (tttt) cc_final: 0.2235 (tptp) REVERT: D 133 ASP cc_start: 0.7236 (OUTLIER) cc_final: 0.6875 (t0) REVERT: E 118 VAL cc_start: 0.7912 (m) cc_final: 0.7670 (p) REVERT: F 14 ILE cc_start: 0.7735 (OUTLIER) cc_final: 0.7512 (mt) REVERT: F 126 GLU cc_start: 0.3570 (tp30) cc_final: 0.3122 (tt0) REVERT: F 275 GLU cc_start: 0.6351 (tt0) cc_final: 0.5974 (mt-10) REVERT: F 276 MET cc_start: 0.6285 (mtp) cc_final: 0.5705 (mtp) outliers start: 32 outliers final: 23 residues processed: 161 average time/residue: 1.2312 time to fit residues: 222.9612 Evaluate side-chains 161 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 22 PHE Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 292 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 87 optimal weight: 4.9990 chunk 177 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 156 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 161 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.137969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.093340 restraints weight = 60084.244| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.85 r_work: 0.2975 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15228 Z= 0.192 Angle : 0.589 12.435 20646 Z= 0.299 Chirality : 0.043 0.313 2330 Planarity : 0.004 0.043 2574 Dihedral : 8.961 58.874 2360 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.14 % Allowed : 16.32 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.19), residues: 1880 helix: 1.14 (0.17), residues: 894 sheet: -1.22 (0.37), residues: 172 loop : -0.67 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 407 TYR 0.017 0.002 TYR B 360 PHE 0.024 0.002 PHE D 50 TRP 0.020 0.002 TRP B 103 HIS 0.010 0.001 HIS F 356 Details of bonding type rmsd covalent geometry : bond 0.00443 (15218) covalent geometry : angle 0.57460 (20634) hydrogen bonds : bond 0.05188 ( 748) hydrogen bonds : angle 4.99993 ( 2118) metal coordination : bond 0.00765 ( 8) metal coordination : angle 5.46774 ( 12) Misc. bond : bond 0.00157 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.7907 (tttm) cc_final: 0.7549 (ttmm) REVERT: B 34 PHE cc_start: 0.7002 (m-10) cc_final: 0.6663 (m-80) REVERT: B 154 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7284 (mm-30) REVERT: C 44 ASP cc_start: 0.7060 (t0) cc_final: 0.6626 (OUTLIER) REVERT: C 198 ASN cc_start: 0.6435 (t0) cc_final: 0.5794 (p0) REVERT: C 253 ASP cc_start: 0.6346 (OUTLIER) cc_final: 0.5820 (p0) REVERT: D 8 LYS cc_start: 0.2840 (tttt) cc_final: 0.2311 (tptp) REVERT: D 133 ASP cc_start: 0.7256 (OUTLIER) cc_final: 0.6910 (t0) REVERT: E 118 VAL cc_start: 0.7948 (m) cc_final: 0.7694 (p) REVERT: F 14 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7503 (mt) REVERT: F 119 MET cc_start: 0.3004 (ptt) cc_final: 0.2803 (ptt) REVERT: F 126 GLU cc_start: 0.3571 (tp30) cc_final: 0.3104 (tt0) REVERT: F 275 GLU cc_start: 0.6321 (tt0) cc_final: 0.5965 (mt-10) REVERT: F 276 MET cc_start: 0.6357 (mtp) cc_final: 0.5730 (mtp) REVERT: F 305 MET cc_start: 0.6044 (mmt) cc_final: 0.5637 (mmt) outliers start: 33 outliers final: 25 residues processed: 159 average time/residue: 1.1730 time to fit residues: 209.6098 Evaluate side-chains 156 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 22 PHE Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 292 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 49 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 67 optimal weight: 0.0070 chunk 47 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.139524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.095094 restraints weight = 60029.988| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.87 r_work: 0.3003 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15228 Z= 0.112 Angle : 0.523 8.695 20646 Z= 0.266 Chirality : 0.041 0.298 2330 Planarity : 0.004 0.046 2574 Dihedral : 8.380 57.683 2356 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.30 % Allowed : 17.23 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.19), residues: 1880 helix: 1.35 (0.18), residues: 897 sheet: -1.15 (0.38), residues: 174 loop : -0.49 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 252 TYR 0.017 0.001 TYR B 360 PHE 0.024 0.001 PHE D 50 TRP 0.018 0.001 TRP B 103 HIS 0.011 0.001 HIS F 356 Details of bonding type rmsd covalent geometry : bond 0.00246 (15218) covalent geometry : angle 0.51184 (20634) hydrogen bonds : bond 0.04447 ( 748) hydrogen bonds : angle 4.81408 ( 2118) metal coordination : bond 0.00604 ( 8) metal coordination : angle 4.54454 ( 12) Misc. bond : bond 0.00064 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10886.94 seconds wall clock time: 184 minutes 44.08 seconds (11084.08 seconds total)