Starting phenix.real_space_refine on Fri Jun 27 01:58:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a1y_15093/06_2025/8a1y_15093_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a1y_15093/06_2025/8a1y_15093.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a1y_15093/06_2025/8a1y_15093.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a1y_15093/06_2025/8a1y_15093.map" model { file = "/net/cci-nas-00/data/ceres_data/8a1y_15093/06_2025/8a1y_15093_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a1y_15093/06_2025/8a1y_15093_trim.cif" } resolution = 3.3 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= 0.011 sd= 0.130 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: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 7 5.49 5 S 91 5.16 5 C 9843 2.51 5 N 2454 2.21 5 O 2782 1.98 5 H 14864 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 30045 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 6910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 6910 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 424} Chain: "B" Number of atoms: 6347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 6347 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 15, 'TRANS': 396} Chain: "C" Number of atoms: 3840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 3840 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 7, 'TRANS': 245} Chain: "D" Number of atoms: 3166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3166 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 9, 'TRANS': 192} Chain: "E" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 3078 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "F" Number of atoms: 6269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 6269 Classifications: {'peptide': 408} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 383} Chain: "B" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 274 Unusual residues: {'3PE': 3, 'FMN': 1, 'HQO': 1, 'LMT': 2, 'RBF': 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: 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: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18773 SG CYS D 112 67.035 82.568 59.443 1.00121.94 S ATOM 20665 SG CYS E 26 64.349 82.937 62.001 1.00110.64 S ATOM 17447 SG CYS D 29 67.030 84.311 65.651 1.00 92.56 S ATOM 22170 SG CYS E 120 70.308 84.504 63.885 1.00117.42 S ATOM 24391 SG CYS F 70 52.091 66.625 37.855 1.00276.78 S ATOM 24440 SG CYS F 76 50.364 63.329 37.299 1.00271.01 S ATOM 24474 SG CYS F 79 55.179 60.974 38.770 1.00261.99 S ATOM 24959 SG CYS F 111 56.470 64.481 39.250 1.00255.78 S Time building chain proxies: 14.21, per 1000 atoms: 0.47 Number of scatterers: 30045 At special positions: 0 Unit cell: (111.739, 136.849, 131.827, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 S 91 16.00 P 7 15.00 O 2782 8.00 N 2454 7.00 C 9843 6.00 H 14864 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: 8.22 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES D1001 " pdb="FE2 FES D1001 " - pdb=" SG CYS D 29 " pdb="FE1 FES D1001 " - pdb=" SG CYS E 26 " pdb="FE1 FES D1001 " - pdb=" SG CYS D 112 " pdb="FE2 FES D1001 " - pdb=" SG CYS E 120 " pdb=" FES F1502 " pdb="FE2 FES F1502 " - pdb=" SG CYS F 79 " pdb="FE1 FES F1502 " - pdb=" SG CYS F 76 " pdb="FE1 FES F1502 " - pdb=" SG CYS F 70 " pdb="FE2 FES F1502 " - pdb=" SG CYS F 111 " Number of angles added : 12 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3468 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 13 sheets defined 53.9% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 107 through 111 Processing helix chain 'A' and resid 114 through 126 Processing helix chain 'A' and resid 127 through 131 Processing helix chain 'A' and resid 162 through 170 removed outlier: 3.712A pdb=" N VAL A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 3.627A 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 214 through 218 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 351 through 356 Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 401 through 409 removed outlier: 3.780A pdb=" N ARG A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 424 Processing helix chain 'A' and resid 430 through 446 removed outlier: 3.505A pdb=" N LEU A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 15 removed outlier: 4.529A pdb=" N HIS B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N HIS B 13 " --> pdb=" O ASP B 9 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B 14 " --> pdb=" O ILE B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 23 through 35 Processing helix chain 'B' and resid 52 through 55 Processing helix chain 'B' and resid 56 through 62 removed outlier: 3.589A pdb=" N VAL B 60 " --> pdb=" O ILE B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 87 Processing helix chain 'B' and resid 89 through 99 removed outlier: 3.699A pdb=" N ALA B 93 " --> pdb=" O GLY B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 109 removed outlier: 3.646A pdb=" N LEU B 104 " --> pdb=" O TRP B 100 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR B 105 " --> pdb=" O HIS B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 152 Proline residue: B 131 - end of helix Processing helix chain 'B' and resid 159 through 167 removed outlier: 3.560A pdb=" N ILE B 164 " --> pdb=" O PHE B 160 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 165 " --> pdb=" O VAL B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 217 through 221 removed outlier: 3.873A pdb=" N SER B 221 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 244 Processing helix chain 'B' and resid 245 through 248 Processing helix chain 'B' and resid 259 through 266 Processing helix chain 'B' and resid 277 through 290 removed outlier: 3.758A pdb=" N PHE B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE B 287 " --> pdb=" O GLY B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 316 removed outlier: 3.815A pdb=" N ILE B 298 " --> pdb=" O SER B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 325 Processing helix chain 'B' and resid 326 through 332 removed outlier: 3.763A 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 374 removed outlier: 3.572A pdb=" N TRP B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 410 Proline residue: B 394 - end of helix Processing helix chain 'B' and resid 411 through 414 Processing helix chain 'C' and resid 7 through 33 Processing helix chain 'C' and resid 33 through 54 removed outlier: 3.568A pdb=" N LYS C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 70 Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.709A pdb=" N TYR C 91 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 99 Processing helix chain 'C' and resid 177 through 181 removed outlier: 3.724A 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 Processing helix chain 'D' and resid 8 through 13 Processing helix chain 'D' and resid 14 through 16 No H-bonds generated for 'chain 'D' and resid 14 through 16' Processing helix chain 'D' and resid 27 through 35 removed outlier: 3.981A pdb=" N ALA D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR D 35 " --> pdb=" O ALA D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 62 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 108 Processing helix chain 'D' and resid 111 through 121 Processing helix chain 'D' and resid 126 through 157 Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 178 through 182 Processing helix chain 'D' and resid 183 through 202 removed outlier: 4.205A pdb=" N ALA D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP D 196 " --> pdb=" O GLY D 192 " (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 Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 75 through 77 No H-bonds generated for 'chain 'E' and resid 75 through 77' Processing helix chain 'E' and resid 78 through 102 removed outlier: 3.895A pdb=" N ASP E 99 " --> pdb=" O GLU E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 110 removed outlier: 3.523A pdb=" N ALA E 108 " --> pdb=" O PRO E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 117 removed outlier: 3.633A pdb=" N ILE E 116 " --> pdb=" O PHE E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 132 removed outlier: 3.543A pdb=" N PHE E 123 " --> pdb=" O ASN E 119 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL E 126 " --> pdb=" O ILE E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 164 Processing helix chain 'E' and resid 165 through 167 No H-bonds generated for 'chain 'E' and resid 165 through 167' Processing helix chain 'E' and resid 175 through 191 removed outlier: 3.547A pdb=" N THR E 179 " --> pdb=" O GLY E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 196 removed outlier: 4.303A pdb=" N GLY E 195 " --> pdb=" O SER E 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 28 removed outlier: 3.726A pdb=" N PHE F 6 " --> pdb=" O SER F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 63 removed outlier: 3.866A pdb=" N ALA F 58 " --> pdb=" O LYS F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 98 removed outlier: 4.136A pdb=" N HIS F 97 " --> pdb=" O THR F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 106 Processing helix chain 'F' and resid 124 through 130 Processing helix chain 'F' and resid 154 through 158 removed outlier: 3.702A pdb=" N GLU F 158 " --> pdb=" O PRO F 155 " (cutoff:3.500A) 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: 3.947A pdb=" N GLY F 190 " --> pdb=" O GLU F 186 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASP F 191 " --> pdb=" O LYS F 187 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TRP F 192 " --> pdb=" O TYR F 188 " (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 243 through 252 Processing helix chain 'F' and resid 284 through 297 removed outlier: 3.701A pdb=" N MET F 288 " --> pdb=" O GLY F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 330 removed outlier: 3.500A pdb=" N LEU F 326 " --> pdb=" O ASP F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 347 removed outlier: 3.726A pdb=" N ASN F 347 " --> pdb=" O PRO F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 363 removed outlier: 3.764A pdb=" N TYR F 360 " --> pdb=" O HIS F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 373 removed outlier: 3.775A pdb=" N ASP F 372 " --> pdb=" O ALA F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 394 Processing sheet with id=AA1, first strand: chain 'A' and resid 1 through 3 Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 21 removed outlier: 7.826A pdb=" N VAL A 323 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N SER A 263 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL A 325 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ALA A 265 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 9.709A pdb=" N ARG A 327 " --> pdb=" O ALA A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 32 removed outlier: 6.764A pdb=" N LEU A 87 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ARG A 81 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N SER A 89 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ILE A 79 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 7.103A 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: 7.138A pdb=" N PHE A 68 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 250 through 251 removed outlier: 3.560A pdb=" N GLN B 256 " --> pdb=" O ASN B 251 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 83 through 84 removed outlier: 4.158A pdb=" N LEU C 75 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 14.041A pdb=" N VAL C 121 " --> pdb=" O HIS C 141 " (cutoff:3.500A) removed outlier: 12.313A pdb=" N HIS C 141 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL C 123 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS C 135 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU C 169 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N PHE C 152 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N TYR C 167 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ALA C 154 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU C 165 " --> pdb=" O ALA C 154 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N GLU C 156 " --> pdb=" O SER C 163 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N SER C 163 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 103 through 105 Processing sheet with id=AA8, first strand: chain 'C' and resid 204 through 206 removed outlier: 6.322A pdb=" N LYS C 204 " --> pdb=" O VAL C 218 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AB1, first strand: chain 'F' and resid 42 through 49 removed outlier: 5.324A pdb=" N LYS F 45 " --> pdb=" O ILE F 39 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N THR F 36 " --> pdb=" O MET F 119 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU F 121 " --> pdb=" O THR F 36 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N SER F 38 " --> pdb=" O LEU F 121 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ASP F 120 " --> pdb=" O LYS F 84 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 208 through 213 removed outlier: 6.712A pdb=" N TYR F 167 " --> pdb=" O PRO F 263 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N THR F 259 " --> pdb=" O GLU F 171 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N VAL F 137 " --> pdb=" O ALA F 153 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ALA F 153 " --> pdb=" O VAL F 137 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 175 through 178 Processing sheet with id=AB4, first strand: chain 'F' and resid 334 through 339 removed outlier: 6.013A pdb=" N MET F 305 " --> pdb=" O VAL F 334 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N HIS F 336 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N TYR F 307 " --> pdb=" O HIS F 336 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ALA F 338 " --> pdb=" O TYR F 307 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TYR F 309 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N MET F 276 " --> pdb=" O SER F 306 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N TRP F 308 " --> pdb=" O MET F 276 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N PHE F 278 " --> pdb=" O TRP F 308 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N GLY F 310 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLY F 280 " --> pdb=" O GLY F 310 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TYR F 375 " --> pdb=" O LEU F 402 " (cutoff:3.500A) 748 hydrogen bonds defined for protein. 2106 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: 13.87 Time building geometry restraints manager: 9.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.11: 14851 1.11 - 1.39: 6010 1.39 - 1.66: 9375 1.66 - 1.93: 153 1.93 - 2.20: 8 Bond restraints: 30397 Sorted by residual: bond pdb=" C4 FMN C1000 " pdb=" C4A FMN C1000 " ideal model delta sigma weight residual 1.485 1.385 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" N1 HQO B 607 " pdb=" O4 HQO B 607 " ideal model delta sigma weight residual 1.285 1.383 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" C4 FMN B 600 " pdb=" C4A FMN B 600 " ideal model delta sigma weight residual 1.485 1.387 0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" C1 HQO B 607 " pdb=" O1 HQO B 607 " ideal model delta sigma weight residual 1.335 1.243 0.092 2.00e-02 2.50e+03 2.14e+01 bond pdb=" C4A FMN B 600 " pdb=" N5 FMN B 600 " ideal model delta sigma weight residual 1.300 1.376 -0.076 2.00e-02 2.50e+03 1.43e+01 ... (remaining 30392 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 54580 1.94 - 3.88: 233 3.88 - 5.83: 51 5.83 - 7.77: 10 7.77 - 9.71: 12 Bond angle restraints: 54886 Sorted by residual: angle pdb=" C2 LMT E 201 " pdb=" C3 LMT E 201 " pdb=" C4 LMT E 201 " ideal model delta sigma weight residual 117.09 107.38 9.71 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C2 LMT B 605 " pdb=" C3 LMT B 605 " pdb=" C4 LMT B 605 " ideal model delta sigma weight residual 117.09 107.61 9.48 3.00e+00 1.11e-01 9.98e+00 angle pdb=" C2 LMT D1002 " pdb=" C3 LMT D1002 " pdb=" C4 LMT D1002 " ideal model delta sigma weight residual 117.09 107.64 9.45 3.00e+00 1.11e-01 9.92e+00 angle pdb=" C2 LMT B 603 " pdb=" C3 LMT B 603 " pdb=" C4 LMT B 603 " ideal model delta sigma weight residual 117.09 107.69 9.40 3.00e+00 1.11e-01 9.81e+00 angle pdb=" C10 LMT B 603 " pdb=" C9 LMT B 603 " pdb=" C8 LMT B 603 " ideal model delta sigma weight residual 116.03 107.29 8.74 3.00e+00 1.11e-01 8.49e+00 ... (remaining 54881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.73: 13497 24.73 - 49.46: 751 49.46 - 74.20: 230 74.20 - 98.93: 30 98.93 - 123.66: 13 Dihedral angle restraints: 14521 sinusoidal: 8026 harmonic: 6495 Sorted by residual: dihedral pdb=" O5' FAD F1501 " pdb=" O3P FAD F1501 " pdb=" P FAD F1501 " pdb=" PA FAD F1501 " ideal model delta sinusoidal sigma weight residual 298.23 174.57 123.66 1 3.00e+01 1.11e-03 1.66e+01 dihedral pdb=" C3B LMT D1002 " pdb=" C4B LMT D1002 " pdb=" C5B LMT D1002 " pdb=" O5B LMT D1002 " ideal model delta sinusoidal sigma weight residual -57.62 62.01 -119.63 1 3.00e+01 1.11e-03 1.59e+01 dihedral pdb=" O2B LMT B 605 " pdb=" C1B LMT B 605 " pdb=" C2B LMT B 605 " pdb=" O5B LMT B 605 " ideal model delta sinusoidal sigma weight residual -176.42 -58.83 -117.59 1 3.00e+01 1.11e-03 1.56e+01 ... (remaining 14518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1897 0.044 - 0.088: 322 0.088 - 0.132: 135 0.132 - 0.176: 5 0.176 - 0.221: 12 Chirality restraints: 2371 Sorted by residual: chirality pdb=" C4' LMT B 605 " pdb=" C3' LMT B 605 " pdb=" C5' LMT B 605 " pdb=" O1B LMT B 605 " both_signs ideal model delta sigma weight residual False -2.55 -2.77 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C3B LMT D1002 " pdb=" C2B LMT D1002 " pdb=" C4B LMT D1002 " pdb=" O3B LMT D1002 " both_signs ideal model delta sigma weight residual False 2.50 2.28 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" C5' LMT B 605 " pdb=" C4' LMT B 605 " pdb=" C6' LMT B 605 " pdb=" O5' LMT B 605 " both_signs ideal model delta sigma weight residual False -2.51 -2.30 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 2368 not shown) Planarity restraints: 4445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 213 " 0.016 5.00e-02 4.00e+02 2.42e-02 9.37e-01 pdb=" N PRO A 214 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 214 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 214 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 160 " -0.015 5.00e-02 4.00e+02 2.31e-02 8.50e-01 pdb=" N PRO F 161 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO F 161 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO F 161 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 102 " -0.014 5.00e-02 4.00e+02 2.11e-02 7.12e-01 pdb=" N PRO E 103 " 0.036 5.00e-02 4.00e+02 pdb=" CA PRO E 103 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO E 103 " -0.012 5.00e-02 4.00e+02 ... (remaining 4442 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1269 2.18 - 2.79: 60128 2.79 - 3.39: 84224 3.39 - 4.00: 110268 4.00 - 4.60: 171290 Nonbonded interactions: 427179 Sorted by model distance: nonbonded pdb=" H LEU D 38 " pdb=" OE1 GLU D 153 " model vdw 1.577 2.450 nonbonded pdb=" O ASN F 140 " pdb=" HZ1 LYS F 148 " model vdw 1.597 2.450 nonbonded pdb=" OE1 GLU C 109 " pdb=" H GLU C 109 " model vdw 1.613 2.450 nonbonded pdb=" H GLY A 301 " pdb=" O GLN A 322 " model vdw 1.623 2.450 nonbonded pdb=" O VAL D 48 " pdb=" HG1 THR D 52 " model vdw 1.635 2.450 ... (remaining 427174 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=0.00 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: 0.490 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: 0.500 Extract box with map and model: 1.110 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 81.300 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.090 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:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 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 : 0.005 0.100 15543 Z= 0.227 Angle : 0.562 9.709 21054 Z= 0.246 Chirality : 0.041 0.221 2371 Planarity : 0.002 0.024 2616 Dihedral : 17.134 123.662 5867 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.06 % Allowed : 14.09 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.20), residues: 1908 helix: 1.95 (0.19), residues: 871 sheet: -0.26 (0.40), residues: 185 loop : 0.02 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 103 HIS 0.002 0.000 HIS B 328 PHE 0.006 0.001 PHE B 166 TYR 0.005 0.001 TYR B 27 ARG 0.001 0.000 ARG B 209 Details of bonding type rmsd hydrogen bonds : bond 0.24534 ( 748) hydrogen bonds : angle 7.60931 ( 2106) metal coordination : bond 0.01822 ( 8) metal coordination : angle 1.82242 ( 12) covalent geometry : bond 0.00455 (15533) covalent geometry : angle 0.56012 (21042) Misc. bond : bond 0.04353 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 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. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 293 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 292 time to evaluate : 2.513 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 THR cc_start: 0.9048 (m) cc_final: 0.8772 (p) REVERT: A 349 ARG cc_start: 0.8252 (mtm-85) cc_final: 0.7447 (mtp85) REVERT: A 445 GLU cc_start: 0.8283 (mt-10) cc_final: 0.8038 (mt-10) REVERT: B 57 MET cc_start: 0.8722 (mmt) cc_final: 0.8426 (mmt) REVERT: B 122 MET cc_start: 0.8742 (ttm) cc_final: 0.8515 (ttp) REVERT: B 382 MET cc_start: 0.8533 (tpt) cc_final: 0.7627 (tpt) REVERT: C 84 VAL cc_start: 0.6120 (t) cc_final: 0.5887 (t) REVERT: C 94 ARG cc_start: 0.7340 (mtt180) cc_final: 0.5932 (tpp80) REVERT: D 32 LEU cc_start: 0.9017 (mt) cc_final: 0.8788 (mt) REVERT: D 207 GLU cc_start: 0.7976 (tp30) cc_final: 0.7744 (tp30) REVERT: F 24 PHE cc_start: 0.6945 (t80) cc_final: 0.6737 (m-80) REVERT: F 210 ARG cc_start: 0.3751 (mmt-90) cc_final: 0.3416 (mmt90) REVERT: F 264 PHE cc_start: 0.5706 (m-80) cc_final: 0.5112 (m-80) REVERT: F 312 ARG cc_start: 0.4690 (ttp-170) cc_final: 0.3482 (mmm160) REVERT: F 375 TYR cc_start: 0.6595 (m-80) cc_final: 0.6265 (m-80) outliers start: 1 outliers final: 0 residues processed: 292 average time/residue: 0.7001 time to fit residues: 301.6584 Evaluate side-chains 212 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 171 optimal weight: 20.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN B 84 ASN C 143 ASN D 75 GLN E 79 ASN F 295 GLN F 330 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.153865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.109339 restraints weight = 67433.561| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.69 r_work: 0.3321 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 62 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15543 Z= 0.196 Angle : 0.572 8.234 21054 Z= 0.301 Chirality : 0.043 0.197 2371 Planarity : 0.004 0.032 2616 Dihedral : 11.999 118.879 2490 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.83 % Allowed : 16.45 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.19), residues: 1908 helix: 1.57 (0.18), residues: 876 sheet: -0.37 (0.38), residues: 188 loop : -0.17 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 308 HIS 0.003 0.001 HIS B 330 PHE 0.022 0.001 PHE F 11 TYR 0.014 0.001 TYR B 360 ARG 0.016 0.001 ARG F 298 Details of bonding type rmsd hydrogen bonds : bond 0.06239 ( 748) hydrogen bonds : angle 5.46365 ( 2106) metal coordination : bond 0.01050 ( 8) metal coordination : angle 4.27351 ( 12) covalent geometry : bond 0.00431 (15533) covalent geometry : angle 0.56263 (21042) Misc. bond : bond 0.00301 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 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. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 237 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 224 time to evaluate : 2.397 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: symmetry clash REVERT: A 46 ARG cc_start: 0.7965 (mtm-85) cc_final: 0.7603 (mtp85) REVERT: A 231 SER cc_start: 0.8770 (OUTLIER) cc_final: 0.8512 (p) REVERT: A 349 ARG cc_start: 0.8324 (mtm-85) cc_final: 0.7662 (mtp85) REVERT: A 415 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8314 (mt-10) REVERT: A 445 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7980 (mt-10) REVERT: B 57 MET cc_start: 0.9104 (mmt) cc_final: 0.8862 (mmt) REVERT: B 382 MET cc_start: 0.8334 (tpt) cc_final: 0.7713 (tpt) REVERT: C 170 GLN cc_start: 0.8351 (pp30) cc_final: 0.7527 (pp30) REVERT: D 207 GLU cc_start: 0.8388 (tp30) cc_final: 0.8159 (tp30) REVERT: E 120 CYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7327 (m) REVERT: F 292 ILE cc_start: 0.8395 (mt) cc_final: 0.7981 (tp) REVERT: F 308 TRP cc_start: 0.2503 (m100) cc_final: 0.2174 (m100) REVERT: F 312 ARG cc_start: 0.4319 (ttp-170) cc_final: 0.3551 (mmm160) REVERT: F 318 PHE cc_start: 0.5843 (OUTLIER) cc_final: 0.5534 (p90) REVERT: F 374 GLU cc_start: 0.6915 (tp30) cc_final: 0.6662 (mt-10) REVERT: F 375 TYR cc_start: 0.7166 (m-80) cc_final: 0.6308 (m-80) REVERT: F 397 GLU cc_start: 0.6275 (mp0) cc_final: 0.5990 (mp0) outliers start: 13 outliers final: 8 residues processed: 231 average time/residue: 0.6069 time to fit residues: 212.6366 Evaluate side-chains 207 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 196 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 120 CYS Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 318 PHE Chi-restraints excluded: chain F residue 336 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 135 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 136 optimal weight: 0.6980 chunk 131 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 85 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.154160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.108535 restraints weight = 67609.913| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.50 r_work: 0.3333 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 62 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 74 | |-----------------------------------------------------------------------------| r_final: 0.3224 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15543 Z= 0.134 Angle : 0.509 7.082 21054 Z= 0.257 Chirality : 0.041 0.322 2371 Planarity : 0.003 0.031 2616 Dihedral : 10.045 117.944 2490 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.08 % Allowed : 16.45 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.19), residues: 1908 helix: 1.58 (0.18), residues: 877 sheet: -0.52 (0.37), residues: 187 loop : -0.19 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 103 HIS 0.004 0.001 HIS B 330 PHE 0.028 0.001 PHE B 14 TYR 0.016 0.001 TYR B 27 ARG 0.002 0.000 ARG E 100 Details of bonding type rmsd hydrogen bonds : bond 0.05050 ( 748) hydrogen bonds : angle 4.90237 ( 2106) metal coordination : bond 0.01380 ( 8) metal coordination : angle 3.59093 ( 12) covalent geometry : bond 0.00301 (15533) covalent geometry : angle 0.50156 (21042) Misc. bond : bond 0.00158 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 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. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 226 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 209 time to evaluate : 2.233 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: A 46 ARG cc_start: 0.8011 (mtm-85) cc_final: 0.7605 (mtp85) REVERT: A 60 ASP cc_start: 0.7060 (t0) cc_final: 0.6758 (t0) REVERT: A 231 SER cc_start: 0.8705 (OUTLIER) cc_final: 0.8423 (p) REVERT: A 349 ARG cc_start: 0.8277 (mtm-85) cc_final: 0.7590 (mtp85) REVERT: A 415 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8302 (mt-10) REVERT: A 445 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7820 (mt-10) REVERT: B 382 MET cc_start: 0.8288 (tpt) cc_final: 0.7623 (tpt) REVERT: C 170 GLN cc_start: 0.8332 (pp30) cc_final: 0.7512 (pp30) REVERT: E 120 CYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7172 (m) REVERT: E 197 GLN cc_start: 0.5888 (OUTLIER) cc_final: 0.4847 (pm20) REVERT: F 276 MET cc_start: 0.8344 (mtm) cc_final: 0.7932 (mtm) REVERT: F 312 ARG cc_start: 0.4594 (ttp-170) cc_final: 0.3758 (mmm160) REVERT: F 375 TYR cc_start: 0.6947 (m-80) cc_final: 0.6149 (m-80) REVERT: F 377 MET cc_start: 0.5434 (tpt) cc_final: 0.5190 (tpt) REVERT: F 390 MET cc_start: -0.0136 (mtp) cc_final: -0.0389 (mtp) outliers start: 17 outliers final: 8 residues processed: 221 average time/residue: 0.5853 time to fit residues: 198.6057 Evaluate side-chains 203 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 192 time to evaluate : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain E residue 120 CYS Chi-restraints excluded: chain E residue 197 GLN Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 336 HIS Chi-restraints excluded: chain F residue 339 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 161 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 172 optimal weight: 0.4980 chunk 148 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 102 optimal weight: 0.2980 chunk 22 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 398 HIS E 61 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.153067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.107770 restraints weight = 67897.773| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.44 r_work: 0.3318 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 74 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15543 Z= 0.150 Angle : 0.506 6.932 21054 Z= 0.255 Chirality : 0.041 0.359 2371 Planarity : 0.003 0.033 2616 Dihedral : 9.436 117.058 2490 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.15 % Allowed : 16.96 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.19), residues: 1908 helix: 1.64 (0.18), residues: 874 sheet: -0.62 (0.37), residues: 189 loop : -0.22 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 308 HIS 0.002 0.001 HIS B 330 PHE 0.020 0.001 PHE F 11 TYR 0.015 0.001 TYR F 309 ARG 0.002 0.000 ARG D 117 Details of bonding type rmsd hydrogen bonds : bond 0.04519 ( 748) hydrogen bonds : angle 4.74554 ( 2106) metal coordination : bond 0.01132 ( 8) metal coordination : angle 4.02266 ( 12) covalent geometry : bond 0.00343 (15533) covalent geometry : angle 0.49718 (21042) Misc. bond : bond 0.00140 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 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. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 214 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 196 time to evaluate : 2.183 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: A 46 ARG cc_start: 0.8028 (mtm-85) cc_final: 0.7602 (mtp85) REVERT: A 60 ASP cc_start: 0.7136 (t0) cc_final: 0.6829 (t0) REVERT: A 349 ARG cc_start: 0.8290 (mtm-85) cc_final: 0.7611 (mtp85) REVERT: A 415 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8287 (mt-10) REVERT: B 382 MET cc_start: 0.8352 (tpt) cc_final: 0.7668 (tpt) REVERT: C 170 GLN cc_start: 0.8337 (pp30) cc_final: 0.7530 (pp30) REVERT: D 117 ARG cc_start: 0.8208 (mmm160) cc_final: 0.7984 (mmm160) REVERT: E 197 GLN cc_start: 0.5816 (OUTLIER) cc_final: 0.5612 (pm20) REVERT: F 312 ARG cc_start: 0.4406 (ttp-170) cc_final: 0.3662 (mmm160) REVERT: F 318 PHE cc_start: 0.5699 (OUTLIER) cc_final: 0.5278 (p90) REVERT: F 375 TYR cc_start: 0.6613 (m-80) cc_final: 0.6199 (m-80) REVERT: F 377 MET cc_start: 0.5525 (tpt) cc_final: 0.5304 (tpt) REVERT: F 390 MET cc_start: 0.0205 (mtp) cc_final: -0.0023 (mtp) outliers start: 18 outliers final: 10 residues processed: 207 average time/residue: 0.5599 time to fit residues: 175.6437 Evaluate side-chains 196 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 184 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain E residue 197 GLN Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 318 PHE Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 336 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 134 optimal weight: 0.6980 chunk 174 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.151763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.106940 restraints weight = 67953.515| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.61 r_work: 0.3296 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15543 Z= 0.171 Angle : 0.517 7.563 21054 Z= 0.259 Chirality : 0.041 0.372 2371 Planarity : 0.003 0.032 2616 Dihedral : 8.999 117.007 2490 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.53 % Allowed : 16.58 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.19), residues: 1908 helix: 1.63 (0.18), residues: 877 sheet: -0.71 (0.37), residues: 189 loop : -0.27 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 103 HIS 0.003 0.001 HIS B 330 PHE 0.021 0.001 PHE F 11 TYR 0.016 0.001 TYR B 27 ARG 0.002 0.000 ARG E 100 Details of bonding type rmsd hydrogen bonds : bond 0.04387 ( 748) hydrogen bonds : angle 4.64228 ( 2106) metal coordination : bond 0.01517 ( 8) metal coordination : angle 4.63145 ( 12) covalent geometry : bond 0.00393 (15533) covalent geometry : angle 0.50525 (21042) Misc. bond : bond 0.00082 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 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. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 215 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 191 time to evaluate : 2.380 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: symmetry clash REVERT: A 46 ARG cc_start: 0.7995 (mtm-85) cc_final: 0.7605 (mtp85) REVERT: A 231 SER cc_start: 0.8769 (OUTLIER) cc_final: 0.8492 (p) REVERT: B 382 MET cc_start: 0.8512 (tpt) cc_final: 0.7842 (tpt) REVERT: C 170 GLN cc_start: 0.8412 (pp30) cc_final: 0.7549 (pp30) REVERT: D 117 ARG cc_start: 0.8245 (mmm160) cc_final: 0.8004 (mmm160) REVERT: E 120 CYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7287 (m) REVERT: E 197 GLN cc_start: 0.5789 (OUTLIER) cc_final: 0.5554 (pm20) REVERT: F 312 ARG cc_start: 0.4474 (ttp-170) cc_final: 0.3628 (mmm160) REVERT: F 318 PHE cc_start: 0.5616 (OUTLIER) cc_final: 0.5020 (p90) REVERT: F 375 TYR cc_start: 0.6666 (m-80) cc_final: 0.6213 (m-80) REVERT: F 377 MET cc_start: 0.5573 (tpt) cc_final: 0.5355 (tpt) REVERT: F 390 MET cc_start: 0.0297 (mtp) cc_final: 0.0088 (mtp) outliers start: 24 outliers final: 17 residues processed: 207 average time/residue: 0.5565 time to fit residues: 177.2344 Evaluate side-chains 205 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 2.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain E residue 120 CYS Chi-restraints excluded: chain E residue 197 GLN Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 318 PHE Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 336 HIS Chi-restraints excluded: chain F residue 339 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 48 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 180 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.152157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.106991 restraints weight = 67929.452| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.62 r_work: 0.3299 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 83 | |-----------------------------------------------------------------------------| r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15543 Z= 0.136 Angle : 0.492 7.303 21054 Z= 0.247 Chirality : 0.041 0.350 2371 Planarity : 0.003 0.033 2616 Dihedral : 8.631 118.852 2490 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.15 % Allowed : 17.03 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.19), residues: 1908 helix: 1.69 (0.18), residues: 877 sheet: -0.42 (0.38), residues: 182 loop : -0.30 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 103 HIS 0.003 0.001 HIS B 330 PHE 0.020 0.001 PHE F 11 TYR 0.012 0.001 TYR B 27 ARG 0.002 0.000 ARG E 100 Details of bonding type rmsd hydrogen bonds : bond 0.04080 ( 748) hydrogen bonds : angle 4.49157 ( 2106) metal coordination : bond 0.01241 ( 8) metal coordination : angle 4.05762 ( 12) covalent geometry : bond 0.00311 (15533) covalent geometry : angle 0.48216 (21042) Misc. bond : bond 0.00064 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 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. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 2.612 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: symmetry clash revert: symmetry clash REVERT: A 231 SER cc_start: 0.8761 (OUTLIER) cc_final: 0.8485 (p) REVERT: A 415 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8282 (mt-10) REVERT: B 322 MET cc_start: 0.8825 (tpp) cc_final: 0.8599 (tpp) REVERT: B 325 MET cc_start: 0.8923 (ttp) cc_final: 0.8567 (ttp) REVERT: B 382 MET cc_start: 0.8472 (tpt) cc_final: 0.7792 (tpt) REVERT: C 170 GLN cc_start: 0.8405 (pp30) cc_final: 0.7558 (pp30) REVERT: D 52 THR cc_start: 0.9072 (OUTLIER) cc_final: 0.8867 (t) REVERT: E 120 CYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7327 (m) REVERT: E 197 GLN cc_start: 0.5806 (OUTLIER) cc_final: 0.5561 (pm20) REVERT: F 312 ARG cc_start: 0.4465 (ttp-170) cc_final: 0.3628 (mmm160) REVERT: F 375 TYR cc_start: 0.6765 (m-80) cc_final: 0.6404 (m-80) REVERT: F 390 MET cc_start: 0.0601 (mtp) cc_final: 0.0394 (mtp) outliers start: 18 outliers final: 10 residues processed: 203 average time/residue: 0.5661 time to fit residues: 176.9221 Evaluate side-chains 199 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 185 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain E residue 120 CYS Chi-restraints excluded: chain E residue 197 GLN Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 318 PHE Chi-restraints excluded: chain F residue 326 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 151 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 chunk 176 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.150983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.106089 restraints weight = 67852.464| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.57 r_work: 0.3274 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 83 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15543 Z= 0.199 Angle : 0.536 9.523 21054 Z= 0.270 Chirality : 0.042 0.327 2371 Planarity : 0.004 0.033 2616 Dihedral : 8.659 120.701 2490 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.85 % Allowed : 17.22 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.19), residues: 1908 helix: 1.65 (0.18), residues: 877 sheet: -0.40 (0.38), residues: 180 loop : -0.47 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 103 HIS 0.003 0.001 HIS A 225 PHE 0.023 0.001 PHE F 333 TYR 0.015 0.001 TYR B 27 ARG 0.002 0.000 ARG A 115 Details of bonding type rmsd hydrogen bonds : bond 0.04281 ( 748) hydrogen bonds : angle 4.53594 ( 2106) metal coordination : bond 0.01660 ( 8) metal coordination : angle 5.14948 ( 12) covalent geometry : bond 0.00457 (15533) covalent geometry : angle 0.52180 (21042) Misc. bond : bond 0.00092 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 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. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 214 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 2.190 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 231 SER cc_start: 0.8827 (OUTLIER) cc_final: 0.8556 (p) REVERT: B 187 VAL cc_start: 0.9080 (OUTLIER) cc_final: 0.8860 (t) REVERT: B 322 MET cc_start: 0.8834 (tpp) cc_final: 0.8575 (tpp) REVERT: B 382 MET cc_start: 0.8533 (tpt) cc_final: 0.7833 (tpt) REVERT: C 170 GLN cc_start: 0.8449 (pp30) cc_final: 0.7560 (pp30) REVERT: D 117 ARG cc_start: 0.8224 (mmm160) cc_final: 0.7968 (mmm160) REVERT: E 120 CYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7377 (m) REVERT: F 312 ARG cc_start: 0.4051 (ttp-170) cc_final: 0.3258 (mmm160) REVERT: F 375 TYR cc_start: 0.6994 (m-80) cc_final: 0.6614 (m-80) outliers start: 29 outliers final: 20 residues processed: 202 average time/residue: 0.5548 time to fit residues: 171.5264 Evaluate side-chains 205 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 182 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain E residue 120 CYS Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 318 PHE Chi-restraints excluded: chain F residue 326 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 158 optimal weight: 4.9990 chunk 160 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 156 optimal weight: 9.9990 chunk 171 optimal weight: 8.9990 chunk 177 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.151946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.106940 restraints weight = 67945.046| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.64 r_work: 0.3286 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15543 Z= 0.143 Angle : 0.501 7.568 21054 Z= 0.251 Chirality : 0.041 0.322 2371 Planarity : 0.003 0.033 2616 Dihedral : 8.443 123.182 2490 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.40 % Allowed : 17.67 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.19), residues: 1908 helix: 1.72 (0.18), residues: 877 sheet: -0.42 (0.38), residues: 180 loop : -0.41 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 103 HIS 0.003 0.001 HIS A 354 PHE 0.019 0.001 PHE F 11 TYR 0.012 0.001 TYR B 360 ARG 0.002 0.000 ARG F 303 Details of bonding type rmsd hydrogen bonds : bond 0.04013 ( 748) hydrogen bonds : angle 4.43109 ( 2106) metal coordination : bond 0.01196 ( 8) metal coordination : angle 4.39611 ( 12) covalent geometry : bond 0.00332 (15533) covalent geometry : angle 0.48956 (21042) Misc. bond : bond 0.00055 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 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. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 2.324 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: symmetry clash revert: symmetry clash REVERT: A 231 SER cc_start: 0.8825 (OUTLIER) cc_final: 0.8554 (p) REVERT: A 415 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8238 (mt-10) REVERT: B 187 VAL cc_start: 0.9130 (OUTLIER) cc_final: 0.8884 (t) REVERT: B 382 MET cc_start: 0.8483 (tpt) cc_final: 0.7790 (tpt) REVERT: C 170 GLN cc_start: 0.8443 (pp30) cc_final: 0.7571 (pp30) REVERT: E 120 CYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7377 (m) REVERT: F 312 ARG cc_start: 0.3941 (ttp-170) cc_final: 0.3259 (mmm160) REVERT: F 375 TYR cc_start: 0.7014 (m-80) cc_final: 0.6685 (m-80) outliers start: 22 outliers final: 18 residues processed: 201 average time/residue: 0.5624 time to fit residues: 173.5144 Evaluate side-chains 207 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 186 time to evaluate : 2.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 120 CYS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 318 PHE Chi-restraints excluded: chain F residue 326 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 43 optimal weight: 3.9990 chunk 27 optimal weight: 0.0870 chunk 105 optimal weight: 0.0770 chunk 21 optimal weight: 0.9990 chunk 183 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 160 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.151219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.106891 restraints weight = 68098.041| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.64 r_work: 0.3295 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 85 | |-----------------------------------------------------------------------------| r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15543 Z= 0.125 Angle : 0.485 7.656 21054 Z= 0.243 Chirality : 0.041 0.303 2371 Planarity : 0.003 0.033 2616 Dihedral : 8.269 125.858 2490 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.15 % Allowed : 17.73 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.19), residues: 1908 helix: 1.81 (0.18), residues: 877 sheet: -0.36 (0.38), residues: 182 loop : -0.34 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 103 HIS 0.003 0.001 HIS A 354 PHE 0.023 0.001 PHE F 333 TYR 0.017 0.001 TYR F 309 ARG 0.002 0.000 ARG F 303 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 748) hydrogen bonds : angle 4.36398 ( 2106) metal coordination : bond 0.00994 ( 8) metal coordination : angle 4.22761 ( 12) covalent geometry : bond 0.00287 (15533) covalent geometry : angle 0.47424 (21042) Misc. bond : bond 0.00053 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 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. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 193 time to evaluate : 2.250 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: symmetry clash revert: symmetry clash REVERT: A 231 SER cc_start: 0.8814 (OUTLIER) cc_final: 0.8529 (p) REVERT: A 415 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8235 (mt-10) REVERT: B 382 MET cc_start: 0.8426 (tpt) cc_final: 0.7711 (tpt) REVERT: C 170 GLN cc_start: 0.8428 (pp30) cc_final: 0.7551 (pp30) REVERT: D 117 ARG cc_start: 0.8221 (mmm160) cc_final: 0.8003 (mmm160) REVERT: E 120 CYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7318 (m) REVERT: F 194 LYS cc_start: 0.4424 (tttt) cc_final: 0.3932 (mtpt) REVERT: F 312 ARG cc_start: 0.4071 (ttp-170) cc_final: 0.3382 (mmm160) REVERT: F 375 TYR cc_start: 0.7018 (m-80) cc_final: 0.6639 (m-80) REVERT: F 397 GLU cc_start: 0.6564 (mm-30) cc_final: 0.5113 (pm20) outliers start: 18 outliers final: 14 residues processed: 204 average time/residue: 0.5662 time to fit residues: 176.7627 Evaluate side-chains 202 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 120 CYS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 318 PHE Chi-restraints excluded: chain F residue 326 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 6 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 182 optimal weight: 7.9990 chunk 37 optimal weight: 0.0770 chunk 170 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 overall best weight: 1.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.151466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.107174 restraints weight = 67883.701| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.47 r_work: 0.3285 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 85 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 85 | |-----------------------------------------------------------------------------| r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15543 Z= 0.152 Angle : 0.503 8.166 21054 Z= 0.252 Chirality : 0.041 0.293 2371 Planarity : 0.003 0.034 2616 Dihedral : 8.281 128.182 2490 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.02 % Allowed : 18.30 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.19), residues: 1908 helix: 1.81 (0.18), residues: 877 sheet: -0.52 (0.38), residues: 188 loop : -0.34 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 103 HIS 0.003 0.001 HIS A 215 PHE 0.019 0.001 PHE F 11 TYR 0.012 0.001 TYR B 360 ARG 0.002 0.000 ARG C 94 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 748) hydrogen bonds : angle 4.37040 ( 2106) metal coordination : bond 0.01186 ( 8) metal coordination : angle 4.59572 ( 12) covalent geometry : bond 0.00351 (15533) covalent geometry : angle 0.49099 (21042) Misc. bond : bond 0.00064 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 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. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 203 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 2.321 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 231 SER cc_start: 0.8830 (OUTLIER) cc_final: 0.8541 (p) REVERT: A 415 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8207 (mt-10) REVERT: B 382 MET cc_start: 0.8450 (tpt) cc_final: 0.7775 (tpt) REVERT: C 170 GLN cc_start: 0.8439 (pp30) cc_final: 0.7560 (pp30) REVERT: D 117 ARG cc_start: 0.8247 (mmm160) cc_final: 0.7996 (mmm160) REVERT: D 146 MET cc_start: 0.8416 (mmp) cc_final: 0.7963 (mmp) REVERT: E 120 CYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7379 (m) REVERT: F 133 TRP cc_start: 0.8089 (m100) cc_final: 0.7607 (m100) REVERT: F 194 LYS cc_start: 0.4425 (tttt) cc_final: 0.4029 (mttt) REVERT: F 285 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7959 (tpp) REVERT: F 312 ARG cc_start: 0.4081 (ttp-170) cc_final: 0.3446 (mmm160) REVERT: F 375 TYR cc_start: 0.7138 (m-80) cc_final: 0.6760 (m-80) REVERT: F 397 GLU cc_start: 0.6638 (mm-30) cc_final: 0.5215 (pm20) outliers start: 16 outliers final: 12 residues processed: 197 average time/residue: 0.5772 time to fit residues: 174.5270 Evaluate side-chains 199 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 184 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 120 CYS Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 318 PHE Chi-restraints excluded: chain F residue 326 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 9.9990 chunk 140 optimal weight: 2.9990 chunk 184 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.149629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.104848 restraints weight = 68115.713| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.39 r_work: 0.3278 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 85 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 85 | |-----------------------------------------------------------------------------| r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15543 Z= 0.168 Angle : 0.514 9.330 21054 Z= 0.258 Chirality : 0.041 0.290 2371 Planarity : 0.003 0.033 2616 Dihedral : 8.320 130.170 2490 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.02 % Allowed : 18.30 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.19), residues: 1908 helix: 1.78 (0.18), residues: 876 sheet: -0.61 (0.38), residues: 188 loop : -0.38 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 103 HIS 0.003 0.001 HIS A 354 PHE 0.021 0.001 PHE F 11 TYR 0.012 0.001 TYR B 360 ARG 0.005 0.000 ARG F 303 Details of bonding type rmsd hydrogen bonds : bond 0.03937 ( 748) hydrogen bonds : angle 4.38368 ( 2106) metal coordination : bond 0.01292 ( 8) metal coordination : angle 4.94551 ( 12) covalent geometry : bond 0.00388 (15533) covalent geometry : angle 0.50029 (21042) Misc. bond : bond 0.00090 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17166.27 seconds wall clock time: 294 minutes 26.79 seconds (17666.79 seconds total)