Starting phenix.real_space_refine on Thu Jun 26 19:22:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a1v_15090/06_2025/8a1v_15090_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a1v_15090/06_2025/8a1v_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_15090/06_2025/8a1v_15090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a1v_15090/06_2025/8a1v_15090.map" model { file = "/net/cci-nas-00/data/ceres_data/8a1v_15090/06_2025/8a1v_15090_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a1v_15090/06_2025/8a1v_15090_trim.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.38, per 1000 atoms: 0.48 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: 7.91 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 2.43 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: 11.48 Time building geometry restraints manager: 9.44 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: 0.000 Normalize map: mean=0, sd=1: 2.180 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: 0.560 Extract box with map and model: 1.090 Check model and map are aligned: 0.220 Set scattering table: 0.260 Process input model: 77.240 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.780 ------------------------------------------------------------------------------- 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 : 3.08 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (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 TRP 0.012 0.001 TRP B 103 HIS 0.003 0.001 HIS F 356 PHE 0.012 0.001 PHE B 213 TYR 0.009 0.001 TYR E 134 ARG 0.002 0.000 ARG B 407 Details of bonding type rmsd hydrogen bonds : bond 0.22825 ( 748) hydrogen bonds : angle 7.68148 ( 2118) metal coordination : bond 0.00818 ( 8) metal coordination : angle 2.04016 ( 12) covalent geometry : bond 0.00403 (15218) covalent geometry : angle 0.56407 (20634) 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 : 2.112 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: 0.7785 (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: 0.2771 (m-80) outliers start: 12 outliers final: 9 residues processed: 301 average time/residue: 2.5150 time to fit residues: 843.5823 Evaluate side-chains 168 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 158 time to evaluate : 2.205 ------------------------------------------------------------------------------- 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 79 ASN 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 157 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 168 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 = 0.3834 r_free = 0.3834 target = 0.139133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.092161 restraints weight = 59473.314| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.84 r_work: 0.2960 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15228 Z= 0.188 Angle : 0.597 7.784 20646 Z= 0.315 Chirality : 0.044 0.316 2330 Planarity : 0.004 0.062 2574 Dihedral : 11.681 98.847 2372 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.94 % Allowed : 13.99 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.19), residues: 1880 helix: 1.30 (0.18), residues: 888 sheet: -0.87 (0.38), residues: 174 loop : -0.17 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 103 HIS 0.005 0.001 HIS F 356 PHE 0.021 0.002 PHE D 50 TYR 0.018 0.002 TYR D 141 ARG 0.006 0.001 ARG C 252 Details of bonding type rmsd hydrogen bonds : bond 0.06730 ( 748) hydrogen bonds : angle 5.66926 ( 2118) metal coordination : bond 0.00653 ( 8) metal coordination : angle 3.81388 ( 12) covalent geometry : bond 0.00416 (15218) covalent geometry : angle 0.59036 (20634) Misc. bond : bond 0.00335 ( 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 195 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 2.320 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: 0.8791 (OUTLIER) cc_final: 0.8030 (mtt-85) REVERT: A 444 LYS cc_start: 0.7953 (tttm) cc_final: 0.7603 (ttmm) REVERT: B 34 PHE cc_start: 0.7128 (m-10) cc_final: 0.6746 (m-80) REVERT: B 261 MET cc_start: 0.8540 (tpp) cc_final: 0.8293 (tpp) REVERT: C 198 ASN cc_start: 0.6385 (t0) cc_final: 0.5781 (p0) REVERT: C 253 ASP cc_start: 0.6326 (OUTLIER) cc_final: 0.5932 (p0) REVERT: E 46 ILE cc_start: 0.7947 (mt) cc_final: 0.7728 (tp) REVERT: F 126 GLU cc_start: 0.3384 (tp30) cc_final: 0.2913 (mt-10) REVERT: F 275 GLU cc_start: 0.6365 (tt0) cc_final: 0.5839 (mt-10) REVERT: F 288 MET cc_start: 0.5874 (mmt) cc_final: 0.5581 (mmm) outliers start: 30 outliers final: 15 residues processed: 189 average time/residue: 2.2767 time to fit residues: 485.5264 Evaluate side-chains 165 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 2.107 ------------------------------------------------------------------------------- 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 292 ILE 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 47 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 157 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 182 optimal weight: 0.9980 chunk 160 optimal weight: 20.0000 chunk 1 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.139407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.094180 restraints weight = 60009.772| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.06 r_work: 0.2981 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15228 Z= 0.141 Angle : 0.538 7.469 20646 Z= 0.279 Chirality : 0.042 0.377 2330 Planarity : 0.004 0.052 2574 Dihedral : 10.443 85.377 2364 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.49 % Allowed : 15.28 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.19), residues: 1880 helix: 1.27 (0.17), residues: 896 sheet: -1.08 (0.37), residues: 179 loop : -0.24 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.007 0.001 HIS F 356 PHE 0.014 0.001 PHE D 50 TYR 0.016 0.001 TYR B 360 ARG 0.004 0.000 ARG C 252 Details of bonding type rmsd hydrogen bonds : bond 0.05462 ( 748) hydrogen bonds : angle 5.25167 ( 2118) metal coordination : bond 0.00465 ( 8) metal coordination : angle 3.79559 ( 12) covalent geometry : bond 0.00307 (15218) covalent geometry : angle 0.52994 (20634) Misc. bond : bond 0.00156 ( 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 181 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 2.383 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: A 395 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.7962 (mtt-85) REVERT: A 444 LYS cc_start: 0.7979 (tttm) cc_final: 0.7619 (ttmm) REVERT: B 34 PHE cc_start: 0.6935 (m-10) cc_final: 0.6619 (m-80) REVERT: B 154 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7368 (mm-30) REVERT: B 261 MET cc_start: 0.8529 (tpp) cc_final: 0.8295 (tpp) REVERT: C 253 ASP cc_start: 0.6329 (OUTLIER) cc_final: 0.5864 (p0) REVERT: E 46 ILE cc_start: 0.7949 (mt) cc_final: 0.7736 (tp) REVERT: F 126 GLU cc_start: 0.3347 (tp30) cc_final: 0.2995 (mt-10) REVERT: F 276 MET cc_start: 0.6506 (mtp) cc_final: 0.6153 (mtp) outliers start: 23 outliers final: 10 residues processed: 177 average time/residue: 2.3740 time to fit residues: 474.0048 Evaluate side-chains 160 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 2.232 ------------------------------------------------------------------------------- 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 20 SER Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 79 ASN 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 178 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 171 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 chunk 146 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 124 optimal weight: 0.5980 chunk 86 optimal weight: 10.0000 overall best weight: 3.5188 ------------------------------------------------------------------------------- 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 = 0.3820 r_free = 0.3820 target = 0.137786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.091664 restraints weight = 60359.911| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.91 r_work: 0.2953 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2622 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= 0.214 Angle : 0.602 12.601 20646 Z= 0.310 Chirality : 0.044 0.409 2330 Planarity : 0.004 0.049 2574 Dihedral : 10.162 71.458 2360 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.40 % Allowed : 14.31 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.19), residues: 1880 helix: 1.14 (0.17), residues: 888 sheet: -1.22 (0.37), residues: 173 loop : -0.52 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 103 HIS 0.011 0.002 HIS F 356 PHE 0.022 0.002 PHE B 213 TYR 0.018 0.002 TYR B 360 ARG 0.004 0.001 ARG B 407 Details of bonding type rmsd hydrogen bonds : bond 0.05710 ( 748) hydrogen bonds : angle 5.23495 ( 2118) metal coordination : bond 0.00739 ( 8) metal coordination : angle 5.17805 ( 12) covalent geometry : bond 0.00489 (15218) covalent geometry : angle 0.58930 (20634) Misc. bond : bond 0.00199 ( 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 190 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 153 time to evaluate : 2.841 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: 0.8807 (OUTLIER) cc_final: 0.8236 (mtt-85) REVERT: A 444 LYS cc_start: 0.7976 (tttm) cc_final: 0.7600 (ttmm) REVERT: B 34 PHE cc_start: 0.6960 (m-10) cc_final: 0.6661 (m-80) REVERT: C 198 ASN cc_start: 0.6336 (t0) cc_final: 0.5630 (p0) REVERT: C 253 ASP cc_start: 0.6357 (OUTLIER) cc_final: 0.5905 (p0) REVERT: F 14 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7537 (mt) REVERT: F 126 GLU cc_start: 0.3389 (tp30) cc_final: 0.2986 (mt-10) REVERT: F 275 GLU cc_start: 0.6382 (tt0) cc_final: 0.5896 (mt-10) REVERT: F 276 MET cc_start: 0.6395 (mtp) cc_final: 0.6011 (mtp) outliers start: 37 outliers final: 21 residues processed: 183 average time/residue: 2.2246 time to fit residues: 464.0278 Evaluate side-chains 167 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 2.384 ------------------------------------------------------------------------------- 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 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 61 LYS 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 76 MET 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 79 ASN 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 1 optimal weight: 0.1980 chunk 161 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- 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 = 0.3824 r_free = 0.3824 target = 0.137987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.091957 restraints weight = 60042.126| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.94 r_work: 0.2957 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15228 Z= 0.175 Angle : 0.572 10.786 20646 Z= 0.293 Chirality : 0.043 0.415 2330 Planarity : 0.004 0.049 2574 Dihedral : 9.742 67.587 2360 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.33 % Allowed : 15.22 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.19), residues: 1880 helix: 1.13 (0.17), residues: 895 sheet: -1.17 (0.37), residues: 172 loop : -0.55 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 103 HIS 0.010 0.001 HIS F 356 PHE 0.020 0.002 PHE B 213 TYR 0.017 0.002 TYR B 360 ARG 0.003 0.000 ARG B 407 Details of bonding type rmsd hydrogen bonds : bond 0.05297 ( 748) hydrogen bonds : angle 5.11712 ( 2118) metal coordination : bond 0.00701 ( 8) metal coordination : angle 4.75080 ( 12) covalent geometry : bond 0.00400 (15218) covalent geometry : angle 0.56011 (20634) Misc. bond : bond 0.00157 ( 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 185 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 2.502 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: A 395 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8216 (mtt-85) REVERT: A 444 LYS cc_start: 0.7997 (tttm) cc_final: 0.7619 (ttmm) REVERT: B 34 PHE cc_start: 0.7003 (m-10) cc_final: 0.6695 (m-80) REVERT: B 154 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7399 (mm-30) REVERT: C 44 ASP cc_start: 0.7280 (t0) cc_final: 0.6862 (t70) REVERT: C 198 ASN cc_start: 0.6425 (t0) cc_final: 0.5716 (p0) REVERT: C 253 ASP cc_start: 0.6349 (OUTLIER) cc_final: 0.5902 (p0) REVERT: F 14 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7575 (mt) REVERT: F 126 GLU cc_start: 0.3310 (tp30) cc_final: 0.2968 (mt-10) REVERT: F 275 GLU cc_start: 0.6341 (tt0) cc_final: 0.5900 (mt-10) REVERT: F 276 MET cc_start: 0.6436 (mtp) cc_final: 0.5659 (mtp) REVERT: F 305 MET cc_start: 0.5992 (mmt) cc_final: 0.5359 (mmt) REVERT: F 383 MET cc_start: 0.4028 (ttt) cc_final: 0.2429 (mmp) outliers start: 36 outliers final: 23 residues processed: 181 average time/residue: 2.4750 time to fit residues: 510.0489 Evaluate side-chains 172 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 2.248 ------------------------------------------------------------------------------- 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 349 SER 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 E residue 6 SER Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 79 ASN 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 245 MET Chi-restraints excluded: chain F residue 356 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 91 optimal weight: 9.9990 chunk 163 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 152 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 GLN B 324 ASN F 244 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.138769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.092599 restraints weight = 60235.908| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.01 r_work: 0.2960 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2886 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= 0.134 Angle : 0.533 9.681 20646 Z= 0.271 Chirality : 0.042 0.411 2330 Planarity : 0.004 0.045 2574 Dihedral : 9.192 62.919 2360 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.14 % Allowed : 15.35 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.19), residues: 1880 helix: 1.28 (0.17), residues: 896 sheet: -1.08 (0.37), residues: 172 loop : -0.48 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 103 HIS 0.010 0.001 HIS F 356 PHE 0.016 0.001 PHE B 213 TYR 0.017 0.001 TYR B 360 ARG 0.002 0.000 ARG B 372 Details of bonding type rmsd hydrogen bonds : bond 0.04763 ( 748) hydrogen bonds : angle 4.94870 ( 2118) metal coordination : bond 0.00576 ( 8) metal coordination : angle 4.79121 ( 12) covalent geometry : bond 0.00300 (15218) covalent geometry : angle 0.52051 (20634) Misc. bond : bond 0.00112 ( 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 183 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 2.315 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 124 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8072 (mp0) REVERT: A 395 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8110 (mtt-85) REVERT: A 444 LYS cc_start: 0.7979 (tttm) cc_final: 0.7591 (ttmm) REVERT: B 34 PHE cc_start: 0.6991 (m-10) cc_final: 0.6676 (m-80) REVERT: B 154 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7345 (mm-30) REVERT: C 44 ASP cc_start: 0.7383 (t0) cc_final: 0.6983 (t70) REVERT: C 198 ASN cc_start: 0.6425 (t0) cc_final: 0.5758 (p0) REVERT: C 253 ASP cc_start: 0.6377 (OUTLIER) cc_final: 0.5935 (p0) REVERT: D 119 GLU cc_start: 0.5594 (tp30) cc_final: 0.5369 (tp30) REVERT: F 126 GLU cc_start: 0.3329 (tp30) cc_final: 0.2995 (mt-10) REVERT: F 275 GLU cc_start: 0.6349 (tt0) cc_final: 0.5929 (mt-10) REVERT: F 276 MET cc_start: 0.6264 (mtp) cc_final: 0.5350 (mtp) REVERT: F 305 MET cc_start: 0.5967 (mmt) cc_final: 0.5337 (mmt) REVERT: F 387 VAL cc_start: 0.6783 (t) cc_final: 0.6572 (p) outliers start: 33 outliers final: 20 residues processed: 178 average time/residue: 2.2833 time to fit residues: 460.3230 Evaluate side-chains 166 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 2.323 ------------------------------------------------------------------------------- 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 216 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 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 79 ASN 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 137 VAL Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 245 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 3.9990 chunk 176 optimal weight: 9.9990 chunk 149 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 170 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 156 optimal weight: 20.0000 chunk 76 optimal weight: 4.9990 chunk 174 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.136798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.091273 restraints weight = 60207.205| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.21 r_work: 0.2926 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 15228 Z= 0.250 Angle : 0.635 13.993 20646 Z= 0.324 Chirality : 0.046 0.388 2330 Planarity : 0.005 0.052 2574 Dihedral : 9.590 62.034 2360 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.40 % Allowed : 16.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.19), residues: 1880 helix: 1.00 (0.17), residues: 893 sheet: -1.28 (0.36), residues: 170 loop : -0.74 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 103 HIS 0.009 0.002 HIS F 356 PHE 0.025 0.002 PHE B 213 TYR 0.018 0.002 TYR B 360 ARG 0.005 0.001 ARG B 407 Details of bonding type rmsd hydrogen bonds : bond 0.05729 ( 748) hydrogen bonds : angle 5.16356 ( 2118) metal coordination : bond 0.00847 ( 8) metal coordination : angle 5.93469 ( 12) covalent geometry : bond 0.00582 (15218) covalent geometry : angle 0.61901 (20634) Misc. bond : bond 0.00218 ( 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 180 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 2.319 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: 0.8805 (OUTLIER) cc_final: 0.8421 (mtt-85) REVERT: A 444 LYS cc_start: 0.7942 (tttm) cc_final: 0.7564 (ttmm) REVERT: B 34 PHE cc_start: 0.7053 (m-10) cc_final: 0.6741 (m-80) REVERT: C 44 ASP cc_start: 0.7370 (t0) cc_final: 0.6996 (OUTLIER) REVERT: C 198 ASN cc_start: 0.6423 (t0) cc_final: 0.5758 (p0) REVERT: C 253 ASP cc_start: 0.6365 (OUTLIER) cc_final: 0.5837 (p0) REVERT: D 8 LYS cc_start: 0.2738 (tttt) cc_final: 0.2298 (tptt) REVERT: D 133 ASP cc_start: 0.7296 (OUTLIER) cc_final: 0.6974 (t0) REVERT: E 118 VAL cc_start: 0.7985 (m) cc_final: 0.7721 (p) REVERT: F 14 ILE cc_start: 0.7698 (OUTLIER) cc_final: 0.7459 (mt) REVERT: F 126 GLU cc_start: 0.3302 (tp30) cc_final: 0.2957 (mt-10) REVERT: F 170 ILE cc_start: 0.2998 (tt) cc_final: 0.2797 (mp) REVERT: F 275 GLU cc_start: 0.6423 (tt0) cc_final: 0.6022 (mt-10) REVERT: F 276 MET cc_start: 0.6142 (mtp) cc_final: 0.5357 (mtp) REVERT: F 305 MET cc_start: 0.6001 (mmt) cc_final: 0.5476 (mmt) outliers start: 37 outliers final: 25 residues processed: 174 average time/residue: 2.2091 time to fit residues: 435.4574 Evaluate side-chains 164 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 2.099 ------------------------------------------------------------------------------- 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 281 MET 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 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 223 ILE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 356 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 40 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 174 optimal weight: 9.9990 chunk 68 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.138004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.092037 restraints weight = 60383.911| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.91 r_work: 0.2967 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15228 Z= 0.153 Angle : 0.558 10.615 20646 Z= 0.284 Chirality : 0.042 0.372 2330 Planarity : 0.004 0.046 2574 Dihedral : 9.141 58.896 2360 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 4.82 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.19), residues: 1880 helix: 1.14 (0.17), residues: 894 sheet: -1.24 (0.37), residues: 172 loop : -0.66 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 103 HIS 0.008 0.001 HIS F 356 PHE 0.022 0.001 PHE D 50 TYR 0.018 0.001 TYR B 360 ARG 0.004 0.000 ARG C 252 Details of bonding type rmsd hydrogen bonds : bond 0.04952 ( 748) hydrogen bonds : angle 5.00727 ( 2118) metal coordination : bond 0.00573 ( 8) metal coordination : angle 5.19739 ( 12) covalent geometry : bond 0.00347 (15218) covalent geometry : angle 0.54424 (20634) Misc. bond : bond 0.00125 ( 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 177 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 2.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8315 (mtt-85) REVERT: A 444 LYS cc_start: 0.7941 (tttm) cc_final: 0.7587 (ttmm) REVERT: B 34 PHE cc_start: 0.7029 (m-10) cc_final: 0.6713 (m-80) REVERT: B 154 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7367 (mm-30) REVERT: C 44 ASP cc_start: 0.7282 (t0) cc_final: 0.6922 (OUTLIER) REVERT: C 198 ASN cc_start: 0.6446 (t0) cc_final: 0.5789 (p0) REVERT: C 253 ASP cc_start: 0.6304 (OUTLIER) cc_final: 0.5801 (p0) REVERT: D 8 LYS cc_start: 0.2783 (tttt) cc_final: 0.2347 (tptt) REVERT: D 133 ASP cc_start: 0.7257 (OUTLIER) cc_final: 0.6900 (t0) REVERT: E 22 PHE cc_start: 0.7036 (OUTLIER) cc_final: 0.5888 (m-10) REVERT: F 14 ILE cc_start: 0.7736 (OUTLIER) cc_final: 0.7514 (mt) REVERT: F 126 GLU cc_start: 0.3313 (tp30) cc_final: 0.2932 (tt0) REVERT: F 275 GLU cc_start: 0.6370 (tt0) cc_final: 0.5992 (mt-10) REVERT: F 276 MET cc_start: 0.6147 (mtp) cc_final: 0.5100 (mtp) REVERT: F 305 MET cc_start: 0.5999 (mmt) cc_final: 0.5322 (mmt) outliers start: 32 outliers final: 22 residues processed: 173 average time/residue: 2.2851 time to fit residues: 448.7119 Evaluate side-chains 163 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 2.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 155 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 77 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 134 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 42 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.138212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.091567 restraints weight = 60043.840| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.94 r_work: 0.2976 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15228 Z= 0.147 Angle : 0.556 10.679 20646 Z= 0.283 Chirality : 0.042 0.335 2330 Planarity : 0.004 0.044 2574 Dihedral : 8.866 59.878 2360 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.94 % Allowed : 16.71 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.19), residues: 1880 helix: 1.21 (0.17), residues: 895 sheet: -1.15 (0.37), residues: 172 loop : -0.61 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 103 HIS 0.009 0.001 HIS F 356 PHE 0.023 0.001 PHE D 50 TYR 0.018 0.001 TYR B 360 ARG 0.003 0.000 ARG C 252 Details of bonding type rmsd hydrogen bonds : bond 0.04814 ( 748) hydrogen bonds : angle 4.94271 ( 2118) metal coordination : bond 0.00553 ( 8) metal coordination : angle 4.93716 ( 12) covalent geometry : bond 0.00334 (15218) covalent geometry : angle 0.54305 (20634) Misc. bond : bond 0.00111 ( 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 169 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 2.219 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: 0.8706 (OUTLIER) cc_final: 0.8218 (mtt-85) REVERT: A 444 LYS cc_start: 0.7911 (tttm) cc_final: 0.7540 (ttmm) REVERT: B 34 PHE cc_start: 0.6990 (m-10) cc_final: 0.6673 (m-80) REVERT: B 154 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7317 (mm-30) REVERT: C 44 ASP cc_start: 0.7299 (t0) cc_final: 0.6939 (t70) REVERT: C 198 ASN cc_start: 0.6446 (t0) cc_final: 0.5783 (p0) REVERT: C 253 ASP cc_start: 0.6289 (OUTLIER) cc_final: 0.5826 (p0) REVERT: D 8 LYS cc_start: 0.2731 (tttt) cc_final: 0.2167 (tptp) REVERT: D 133 ASP cc_start: 0.7246 (OUTLIER) cc_final: 0.6876 (t0) REVERT: E 22 PHE cc_start: 0.7045 (OUTLIER) cc_final: 0.5939 (m-10) REVERT: F 14 ILE cc_start: 0.7721 (OUTLIER) cc_final: 0.7497 (mt) REVERT: F 126 GLU cc_start: 0.3639 (tp30) cc_final: 0.3208 (tt0) REVERT: F 275 GLU cc_start: 0.6355 (tt0) cc_final: 0.5976 (mt-10) REVERT: F 276 MET cc_start: 0.6045 (mtp) cc_final: 0.5111 (mtp) REVERT: F 305 MET cc_start: 0.5986 (mmt) cc_final: 0.5424 (mmt) outliers start: 30 outliers final: 21 residues processed: 164 average time/residue: 2.3250 time to fit residues: 432.9249 Evaluate side-chains 162 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 155 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 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 6 SER 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 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 149 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3830 r_free = 0.3830 target = 0.138445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.092790 restraints weight = 60191.442| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.97 r_work: 0.2958 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15228 Z= 0.140 Angle : 0.544 10.241 20646 Z= 0.277 Chirality : 0.042 0.308 2330 Planarity : 0.004 0.044 2574 Dihedral : 8.605 58.686 2360 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.94 % Allowed : 16.65 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.19), residues: 1880 helix: 1.27 (0.17), residues: 895 sheet: -1.10 (0.37), residues: 172 loop : -0.58 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 103 HIS 0.008 0.001 HIS F 356 PHE 0.025 0.001 PHE D 50 TYR 0.018 0.001 TYR B 360 ARG 0.003 0.000 ARG C 252 Details of bonding type rmsd hydrogen bonds : bond 0.04686 ( 748) hydrogen bonds : angle 4.88218 ( 2118) metal coordination : bond 0.00599 ( 8) metal coordination : angle 4.83904 ( 12) covalent geometry : bond 0.00318 (15218) covalent geometry : angle 0.53100 (20634) Misc. bond : bond 0.00106 ( 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 167 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 2.137 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: 0.8764 (OUTLIER) cc_final: 0.8324 (mtt-85) REVERT: A 444 LYS cc_start: 0.7957 (tttm) cc_final: 0.7610 (ttmm) REVERT: B 34 PHE cc_start: 0.7033 (m-10) cc_final: 0.6721 (m-80) REVERT: B 154 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7397 (mm-30) REVERT: C 44 ASP cc_start: 0.7339 (t0) cc_final: 0.6981 (t70) REVERT: C 198 ASN cc_start: 0.6462 (t0) cc_final: 0.5788 (p0) REVERT: C 253 ASP cc_start: 0.6299 (OUTLIER) cc_final: 0.5823 (p0) REVERT: D 8 LYS cc_start: 0.2697 (tttt) cc_final: 0.2147 (tptp) REVERT: D 133 ASP cc_start: 0.7298 (OUTLIER) cc_final: 0.6933 (t0) REVERT: E 22 PHE cc_start: 0.7010 (OUTLIER) cc_final: 0.5930 (m-10) REVERT: F 14 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.7527 (mt) REVERT: F 126 GLU cc_start: 0.3562 (tp30) cc_final: 0.3107 (tt0) REVERT: F 245 MET cc_start: 0.1714 (ttt) cc_final: 0.1487 (ttp) REVERT: F 275 GLU cc_start: 0.6383 (tt0) cc_final: 0.6020 (mt-10) REVERT: F 276 MET cc_start: 0.6191 (mtp) cc_final: 0.4941 (mtp) REVERT: F 305 MET cc_start: 0.6059 (mmt) cc_final: 0.5328 (mmt) outliers start: 30 outliers final: 20 residues processed: 162 average time/residue: 2.2892 time to fit residues: 419.9182 Evaluate side-chains 158 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 2.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 155 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 253 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain E residue 6 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 22 PHE 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 183 ASP Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 306 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 61 optimal weight: 3.9990 chunk 140 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 156 optimal weight: 10.0000 chunk 4 optimal weight: 0.0030 chunk 130 optimal weight: 2.9990 chunk 181 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 119 optimal weight: 0.2980 overall best weight: 1.8596 ------------------------------------------------------------------------------- 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 = 0.3830 r_free = 0.3830 target = 0.138421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.092565 restraints weight = 60067.426| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.01 r_work: 0.2961 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3228 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= 0.135 Angle : 0.539 10.042 20646 Z= 0.274 Chirality : 0.041 0.289 2330 Planarity : 0.004 0.045 2574 Dihedral : 8.436 58.126 2360 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.49 % Allowed : 17.49 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.19), residues: 1880 helix: 1.32 (0.17), residues: 895 sheet: -1.05 (0.37), residues: 170 loop : -0.55 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 103 HIS 0.013 0.001 HIS F 356 PHE 0.024 0.001 PHE D 50 TYR 0.018 0.001 TYR B 360 ARG 0.003 0.000 ARG C 252 Details of bonding type rmsd hydrogen bonds : bond 0.04608 ( 748) hydrogen bonds : angle 4.83862 ( 2118) metal coordination : bond 0.00575 ( 8) metal coordination : angle 4.90719 ( 12) covalent geometry : bond 0.00307 (15218) covalent geometry : angle 0.52566 (20634) Misc. bond : bond 0.00096 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21789.24 seconds wall clock time: 370 minutes 43.33 seconds (22243.33 seconds total)