Starting phenix.real_space_refine on Thu Sep 18 07:37:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ud8_64064/09_2025/9ud8_64064.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ud8_64064/09_2025/9ud8_64064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ud8_64064/09_2025/9ud8_64064.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ud8_64064/09_2025/9ud8_64064.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ud8_64064/09_2025/9ud8_64064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ud8_64064/09_2025/9ud8_64064.map" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.020 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 Ca 1 9.91 5 Fe 4 7.16 5 P 4 5.49 5 S 92 5.16 5 C 9508 2.51 5 N 2409 2.21 5 O 2688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14706 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3416 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 422} Chain: "B" Number of atoms: 2964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2964 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 14, 'TRANS': 372} Chain: "C" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1902 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 7, 'TRANS': 243} Chain: "D" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1562 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "E" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1511 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "F" Number of atoms: 3165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3165 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 24, 'TRANS': 383} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'FMN': 1, 'RBF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 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 9088 SG CYS D 112 41.935 75.030 66.587 1.00 34.32 S ATOM 8449 SG CYS D 29 42.726 68.879 63.212 1.00 21.11 S ATOM 10776 SG CYS E 120 41.144 71.913 62.747 1.00 21.26 S ATOM 11902 SG CYS F 79 38.041 86.777 90.549 1.00110.23 S ATOM 12141 SG CYS F 111 37.940 86.504 87.322 1.00113.01 S ATOM 11855 SG CYS F 70 43.772 87.993 88.216 1.00108.59 S ATOM 11883 SG CYS F 76 43.010 87.992 91.765 1.00115.42 S Time building chain proxies: 3.84, per 1000 atoms: 0.26 Number of scatterers: 14706 At special positions: 0 Unit cell: (89.76, 126.72, 154.88, 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 Ca 1 19.99 S 92 16.00 P 4 15.00 O 2688 8.00 N 2409 7.00 C 9508 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 717.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE2 FES E 301 " - pdb=" SG CYS D 29 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 120 " pdb="FE1 FES E 301 " - pdb=" SG CYS D 112 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 26 " pdb=" FES F 501 " pdb="FE1 FES F 501 " - pdb=" SG CYS F 79 " pdb="FE1 FES F 501 " - pdb=" SG CYS F 111 " pdb="FE2 FES F 501 " - pdb=" SG CYS F 76 " pdb="FE2 FES F 501 " - pdb=" SG CYS F 70 " Number of angles added : 14 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3420 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 16 sheets defined 53.4% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 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 113 removed outlier: 3.831A pdb=" N ALA A 111 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 113 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 126 Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.534A pdb=" N PHE A 131 " --> pdb=" O TRP A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 168 removed outlier: 3.701A pdb=" N VAL A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 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 351 through 356 removed outlier: 3.612A pdb=" N HIS A 354 " --> pdb=" O PHE A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 389 through 399 Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 418 through 425 Processing helix chain 'A' and resid 430 through 446 removed outlier: 4.153A pdb=" N LEU A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY A 446 " --> pdb=" O ILE A 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.952A pdb=" N LEU B 33 " --> pdb=" O ALA B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 62 Processing helix chain 'B' and resid 64 through 87 removed outlier: 3.933A pdb=" N TYR B 73 " --> pdb=" O PHE B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 99 removed outlier: 3.769A pdb=" N ALA B 93 " --> pdb=" O GLY B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 109 removed outlier: 4.200A pdb=" N TRP B 103 " --> pdb=" O ASN B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 151 removed outlier: 3.594A pdb=" N TYR B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Proline residue: B 131 - end of helix Processing helix chain 'B' and resid 158 through 169 Processing helix chain 'B' and resid 175 through 189 removed outlier: 3.518A pdb=" N ALA B 179 " --> pdb=" O PRO B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 236 through 245 removed outlier: 3.647A pdb=" N TRP B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 249 Processing helix chain 'B' and resid 259 through 266 Processing helix chain 'B' and resid 276 through 290 removed outlier: 3.952A pdb=" N PHE B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE B 287 " --> pdb=" O GLY B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 316 removed outlier: 3.924A pdb=" N ILE B 298 " --> pdb=" O SER B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 325 removed outlier: 3.509A pdb=" N ASN B 324 " --> pdb=" O ALA B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 333 removed outlier: 4.299A pdb=" N VAL B 332 " --> pdb=" O HIS B 328 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU B 333 " --> pdb=" O TRP B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 353 through 375 removed outlier: 3.686A pdb=" N ASN B 375 " --> pdb=" O ILE B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 410 removed outlier: 4.047A pdb=" N LEU B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Proline residue: B 394 - end of helix Processing helix chain 'C' and resid 7 through 33 removed outlier: 3.965A pdb=" N LEU C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 54 Processing helix chain 'C' and resid 59 through 70 Processing helix chain 'C' and resid 92 through 99 Processing helix chain 'C' and resid 177 through 181 removed outlier: 4.113A pdb=" N VAL C 180 " --> pdb=" O GLY C 177 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU C 181 " --> pdb=" O GLY C 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 177 through 181' Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 188 through 190 No H-bonds generated for 'chain 'C' and resid 188 through 190' Processing helix chain 'C' and resid 224 through 239 Processing helix chain 'C' and resid 244 through 254 Processing helix chain 'D' and resid 8 through 13 removed outlier: 3.824A pdb=" N LEU D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) 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 28 through 34 removed outlier: 3.965A pdb=" N ALA D 33 " --> pdb=" O CYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 63 removed outlier: 3.561A pdb=" N ALA D 41 " --> pdb=" O LYS D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 69 No H-bonds generated for 'chain 'D' and resid 67 through 69' Processing helix chain 'D' and resid 70 through 94 removed outlier: 3.712A pdb=" N VAL D 85 " --> pdb=" O SER D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 102 removed outlier: 3.668A pdb=" N GLN D 100 " --> pdb=" O ASP D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 107 removed outlier: 4.133A pdb=" N GLY D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 111 through 121 removed outlier: 3.524A pdb=" N PHE D 121 " --> pdb=" O ARG D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 125 removed outlier: 3.694A pdb=" N SER D 125 " --> pdb=" O ALA D 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 122 through 125' Processing helix chain 'D' and resid 126 through 158 removed outlier: 3.805A pdb=" N VAL D 144 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE D 151 " --> pdb=" O THR D 147 " (cutoff:3.500A) 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: 3.842A pdb=" N ALA D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 206 Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 24 through 32 removed outlier: 3.806A pdb=" N SER E 32 " --> pdb=" O PHE E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 64 removed outlier: 4.160A pdb=" N ILE E 51 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Proline residue: E 54 - end of helix removed outlier: 3.592A pdb=" N LEU E 64 " --> pdb=" O TYR E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 102 removed outlier: 3.637A pdb=" N LEU E 94 " --> pdb=" O LEU E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 107 Processing helix chain 'E' and resid 112 through 117 Processing helix chain 'E' and resid 119 through 133 removed outlier: 3.832A pdb=" N PHE E 123 " --> pdb=" O ASN E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 164 removed outlier: 3.890A pdb=" N VAL E 148 " --> pdb=" O PHE E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 167 No H-bonds generated for 'chain 'E' and resid 165 through 167' Processing helix chain 'E' and resid 175 through 191 Processing helix chain 'E' and resid 192 through 196 removed outlier: 4.492A pdb=" N GLY E 195 " --> pdb=" O SER E 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 29 removed outlier: 3.695A pdb=" N LEU F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 63 Processing helix chain 'F' and resid 91 through 98 removed outlier: 3.810A pdb=" N HIS F 97 " --> pdb=" O THR F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 104 removed outlier: 3.580A pdb=" N ARG F 104 " --> pdb=" O LYS F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 113 No H-bonds generated for 'chain 'F' and resid 111 through 113' Processing helix chain 'F' and resid 124 through 129 Processing helix chain 'F' and resid 154 through 158 removed outlier: 3.566A pdb=" N GLU F 158 " --> pdb=" O PRO F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 182 removed outlier: 4.157A pdb=" N ASP F 181 " --> pdb=" O LYS F 178 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE F 182 " --> pdb=" O TYR F 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 178 through 182' Processing helix chain 'F' and resid 188 through 196 removed outlier: 4.302A pdb=" N TRP F 192 " --> pdb=" O TYR F 188 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS F 194 " --> pdb=" O GLY F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 200 Processing helix chain 'F' and resid 243 through 252 Processing helix chain 'F' and resid 284 through 298 removed outlier: 3.755A pdb=" N MET F 288 " --> pdb=" O GLY F 284 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER F 290 " --> pdb=" O ALA F 286 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N HIS F 291 " --> pdb=" O PRO F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 317 removed outlier: 3.721A pdb=" N MET F 317 " --> pdb=" O LYS F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 330 Processing helix chain 'F' and resid 354 through 363 Processing helix chain 'F' and resid 380 through 394 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 6.253A pdb=" N VAL A 189 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N HIS A 209 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N VAL A 191 " --> pdb=" O HIS A 209 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N PHE A 211 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS A 193 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 236 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 20 removed outlier: 4.190A pdb=" N LEU A 274 " --> pdb=" O SER A 17 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL A 19 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ARG A 276 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 326 " --> pdb=" O ARG A 297 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 297 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 32 removed outlier: 3.919A pdb=" N SER A 89 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU A 78 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU A 93 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N VAL A 76 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 43 removed outlier: 3.563A pdb=" N GLU A 59 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N PHE A 68 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 366 through 367 removed outlier: 4.702A pdb=" N LEU B 39 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.656A pdb=" N ASP C 82 " --> pdb=" O ASP C 77 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 126 " --> pdb=" O GLU C 72 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG C 74 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL C 124 " --> pdb=" O ARG C 74 " (cutoff:3.500A) removed outlier: 14.455A pdb=" N VAL C 121 " --> pdb=" O HIS C 141 " (cutoff:3.500A) removed outlier: 11.996A pdb=" N HIS C 141 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL C 123 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS C 135 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N MET C 148 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLU C 169 " --> pdb=" O MET C 148 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TYR C 150 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TYR C 167 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE C 152 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU C 165 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ALA C 154 " --> pdb=" O SER C 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 103 through 104 removed outlier: 3.521A pdb=" N ARG C 118 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 204 through 206 removed outlier: 3.615A pdb=" N VAL C 218 " --> pdb=" O LYS C 204 " (cutoff:3.500A) 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 35 through 38 Processing sheet with id=AB2, first strand: chain 'F' and resid 80 through 81 Processing sheet with id=AB3, first strand: chain 'F' and resid 83 through 85 removed outlier: 3.952A pdb=" N SER F 85 " --> pdb=" O ASP F 120 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP F 120 " --> pdb=" O SER F 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'F' and resid 224 through 225 removed outlier: 7.068A pdb=" N LYS F 151 " --> pdb=" O ILE F 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 147 through 148 Processing sheet with id=AB6, first strand: chain 'F' and resid 167 through 172 removed outlier: 3.651A pdb=" N ARG F 210 " --> pdb=" O ILE F 170 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 351 through 352 removed outlier: 4.331A pdb=" N TYR F 351 " --> pdb=" O CYS F 337 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU F 339 " --> pdb=" O TYR F 351 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N MET F 305 " --> pdb=" O VAL F 334 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N HIS F 336 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N TYR F 307 " --> pdb=" O HIS F 336 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ALA F 338 " --> pdb=" O TYR F 307 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR F 309 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N CYS F 378 " --> pdb=" O ILE F 279 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY F 281 " --> pdb=" O CYS F 378 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N TYR F 375 " --> pdb=" O LEU F 402 " (cutoff:3.500A) 706 hydrogen bonds defined for protein. 2007 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: 2.59 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.41: 6071 1.41 - 1.61: 8806 1.61 - 1.81: 131 1.81 - 2.01: 29 2.01 - 2.20: 8 Bond restraints: 15045 Sorted by residual: bond pdb=" C4 FMN C 301 " pdb=" C4A FMN C 301 " ideal model delta sigma weight residual 1.485 1.381 0.104 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C4 FMN B 501 " pdb=" C4A FMN B 501 " ideal model delta sigma weight residual 1.485 1.386 0.099 2.00e-02 2.50e+03 2.43e+01 bond pdb=" C4A FMN B 501 " pdb=" N5 FMN B 501 " ideal model delta sigma weight residual 1.300 1.378 -0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C4A FMN C 301 " pdb=" N5 FMN C 301 " ideal model delta sigma weight residual 1.300 1.374 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" O5' FMN B 501 " pdb=" P FMN B 501 " ideal model delta sigma weight residual 1.676 1.602 0.074 2.00e-02 2.50e+03 1.36e+01 ... (remaining 15040 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 20167 2.59 - 5.18: 223 5.18 - 7.77: 24 7.77 - 10.36: 3 10.36 - 12.95: 4 Bond angle restraints: 20421 Sorted by residual: angle pdb=" CB MET F 382 " pdb=" CG MET F 382 " pdb=" SD MET F 382 " ideal model delta sigma weight residual 112.70 125.65 -12.95 3.00e+00 1.11e-01 1.86e+01 angle pdb=" CB MET A 43 " pdb=" CG MET A 43 " pdb=" SD MET A 43 " ideal model delta sigma weight residual 112.70 124.59 -11.89 3.00e+00 1.11e-01 1.57e+01 angle pdb=" C PRO E 66 " pdb=" N ASP E 67 " pdb=" CA ASP E 67 " ideal model delta sigma weight residual 121.54 129.01 -7.47 1.91e+00 2.74e-01 1.53e+01 angle pdb=" CB MET F 317 " pdb=" CG MET F 317 " pdb=" SD MET F 317 " ideal model delta sigma weight residual 112.70 123.93 -11.23 3.00e+00 1.11e-01 1.40e+01 angle pdb=" CA GLY A 294 " pdb=" C GLY A 294 " pdb=" N GLU A 295 " ideal model delta sigma weight residual 114.23 117.43 -3.20 8.80e-01 1.29e+00 1.32e+01 ... (remaining 20416 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 7764 17.66 - 35.31: 863 35.31 - 52.97: 211 52.97 - 70.62: 36 70.62 - 88.28: 19 Dihedral angle restraints: 8893 sinusoidal: 3531 harmonic: 5362 Sorted by residual: dihedral pdb=" CA THR D 147 " pdb=" C THR D 147 " pdb=" N VAL D 148 " pdb=" CA VAL D 148 " ideal model delta harmonic sigma weight residual 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA PHE B 342 " pdb=" C PHE B 342 " pdb=" N MET B 343 " pdb=" CA MET B 343 " ideal model delta harmonic sigma weight residual -180.00 -160.69 -19.31 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ILE D 66 " pdb=" C ILE D 66 " pdb=" N PRO D 67 " pdb=" CA PRO D 67 " ideal model delta harmonic sigma weight residual 180.00 161.56 18.44 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 8890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1664 0.043 - 0.086: 471 0.086 - 0.129: 158 0.129 - 0.172: 11 0.172 - 0.215: 6 Chirality restraints: 2310 Sorted by residual: chirality pdb=" CA ILE F 127 " pdb=" N ILE F 127 " pdb=" C ILE F 127 " pdb=" CB ILE F 127 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ASP E 67 " pdb=" N ASP E 67 " pdb=" C ASP E 67 " pdb=" CB ASP E 67 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.59e-01 chirality pdb=" CB THR E 50 " pdb=" CA THR E 50 " pdb=" OG1 THR E 50 " pdb=" CG2 THR E 50 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.35e-01 ... (remaining 2307 not shown) Planarity restraints: 2567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 126 " -0.041 5.00e-02 4.00e+02 6.24e-02 6.24e+00 pdb=" N PRO D 127 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 127 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 127 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY F 262 " 0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO F 263 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO F 263 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 263 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 182 " 0.013 2.00e-02 2.50e+03 1.46e-02 3.73e+00 pdb=" CG PHE F 182 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE F 182 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE F 182 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE F 182 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE F 182 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE F 182 " -0.002 2.00e-02 2.50e+03 ... (remaining 2564 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1277 2.74 - 3.28: 14955 3.28 - 3.82: 24328 3.82 - 4.36: 27186 4.36 - 4.90: 47688 Nonbonded interactions: 115434 Sorted by model distance: nonbonded pdb=" O ALA B 377 " pdb=" O2' FMN C 301 " model vdw 2.199 3.040 nonbonded pdb=" NZ LYS F 304 " pdb=" O MET F 305 " model vdw 2.238 3.120 nonbonded pdb=" O VAL D 51 " pdb=" OG SER D 55 " model vdw 2.256 3.040 nonbonded pdb=" NZ LYS F 178 " pdb=" O PHE F 198 " model vdw 2.259 3.120 nonbonded pdb=" OG SER F 67 " pdb=" O GLN F 78 " model vdw 2.270 3.040 ... (remaining 115429 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.510 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 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 : 0.008 0.850 15053 Z= 0.257 Angle : 0.886 57.677 20435 Z= 0.360 Chirality : 0.044 0.215 2310 Planarity : 0.004 0.062 2567 Dihedral : 16.089 88.279 5473 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.50 % Allowed : 18.77 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.20), residues: 1882 helix: 0.95 (0.18), residues: 872 sheet: -0.76 (0.39), residues: 175 loop : -1.09 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 94 TYR 0.019 0.001 TYR F 319 PHE 0.034 0.001 PHE F 182 TRP 0.025 0.001 TRP F 250 HIS 0.010 0.001 HIS F 291 Details of bonding type rmsd covalent geometry : bond 0.00405 (15045) covalent geometry : angle 0.68762 (20421) hydrogen bonds : bond 0.14586 ( 706) hydrogen bonds : angle 5.87917 ( 2007) metal coordination : bond 0.30086 ( 8) metal coordination : angle 21.34228 ( 14) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 187 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 363 MET cc_start: 0.7959 (mtt) cc_final: 0.7747 (mtt) REVERT: D 137 ASN cc_start: 0.7253 (p0) cc_final: 0.7014 (m-40) REVERT: D 139 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8207 (mt) REVERT: E 43 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8043 (tp) REVERT: E 90 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7164 (tp) REVERT: F 16 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8233 (tt) REVERT: F 126 GLU cc_start: 0.2855 (OUTLIER) cc_final: 0.2616 (tm-30) REVERT: F 127 ILE cc_start: -0.1193 (OUTLIER) cc_final: -0.1446 (mm) REVERT: F 128 PHE cc_start: 0.3288 (OUTLIER) cc_final: 0.2837 (p90) REVERT: F 214 MET cc_start: 0.1789 (mpp) cc_final: 0.1028 (mmm) REVERT: F 225 MET cc_start: 0.1733 (ptm) cc_final: 0.1298 (ttp) REVERT: F 291 HIS cc_start: 0.7175 (m-70) cc_final: 0.6508 (m-70) REVERT: F 359 LEU cc_start: 0.8622 (pp) cc_final: 0.8308 (tp) REVERT: F 382 MET cc_start: 0.5986 (tmm) cc_final: 0.5238 (tmm) outliers start: 54 outliers final: 39 residues processed: 227 average time/residue: 0.1177 time to fit residues: 40.9225 Evaluate side-chains 214 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 168 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 126 GLU Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 128 PHE Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 240 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 50.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 HIS F 295 GLN F 330 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.181009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.143195 restraints weight = 19981.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.139205 restraints weight = 40970.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.140874 restraints weight = 38228.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.140545 restraints weight = 24567.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.140865 restraints weight = 24216.120| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.0789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15053 Z= 0.139 Angle : 0.709 38.911 20435 Z= 0.303 Chirality : 0.043 0.177 2310 Planarity : 0.004 0.055 2567 Dihedral : 8.576 97.849 2233 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.27 % Allowed : 18.06 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.20), residues: 1882 helix: 1.20 (0.18), residues: 866 sheet: -0.96 (0.37), residues: 191 loop : -0.92 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 94 TYR 0.013 0.001 TYR F 217 PHE 0.019 0.001 PHE F 198 TRP 0.014 0.001 TRP F 192 HIS 0.009 0.001 HIS F 291 Details of bonding type rmsd covalent geometry : bond 0.00320 (15045) covalent geometry : angle 0.57885 (20421) hydrogen bonds : bond 0.04396 ( 706) hydrogen bonds : angle 4.79371 ( 2007) metal coordination : bond 0.01412 ( 8) metal coordination : angle 15.67324 ( 14) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 189 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 363 MET cc_start: 0.8088 (mtt) cc_final: 0.7882 (mtt) REVERT: A 394 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8604 (mm) REVERT: B 262 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7518 (t0) REVERT: C 51 GLN cc_start: 0.7249 (tm-30) cc_final: 0.7036 (tm-30) REVERT: C 116 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7589 (pt0) REVERT: D 139 LEU cc_start: 0.8487 (tm) cc_final: 0.8213 (mt) REVERT: E 90 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7210 (tp) REVERT: F 16 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8563 (tp) REVERT: F 128 PHE cc_start: 0.3324 (OUTLIER) cc_final: 0.2321 (p90) REVERT: F 288 MET cc_start: 0.6513 (ptm) cc_final: 0.6276 (ptp) REVERT: F 291 HIS cc_start: 0.5992 (m-70) cc_final: 0.5611 (m90) outliers start: 66 outliers final: 43 residues processed: 233 average time/residue: 0.1162 time to fit residues: 41.8583 Evaluate side-chains 221 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 172 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain D residue 29 CYS Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 101 PHE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 128 PHE Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 277 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 99 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 107 optimal weight: 0.1980 chunk 185 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 165 optimal weight: 30.0000 chunk 166 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN E 16 ASN F 295 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.180771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.143138 restraints weight = 20203.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.138797 restraints weight = 41454.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.140564 restraints weight = 38264.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.140443 restraints weight = 23601.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.140756 restraints weight = 23906.760| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15053 Z= 0.136 Angle : 0.640 28.187 20435 Z= 0.286 Chirality : 0.042 0.176 2310 Planarity : 0.004 0.056 2567 Dihedral : 7.666 81.079 2195 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.47 % Allowed : 18.77 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.20), residues: 1882 helix: 1.29 (0.18), residues: 864 sheet: -0.91 (0.37), residues: 181 loop : -0.83 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 407 TYR 0.019 0.001 TYR F 179 PHE 0.015 0.001 PHE B 213 TRP 0.012 0.001 TRP B 103 HIS 0.008 0.001 HIS F 291 Details of bonding type rmsd covalent geometry : bond 0.00316 (15045) covalent geometry : angle 0.55162 (20421) hydrogen bonds : bond 0.04151 ( 706) hydrogen bonds : angle 4.60160 ( 2007) metal coordination : bond 0.01411 ( 8) metal coordination : angle 12.41193 ( 14) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 187 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8616 (mm) REVERT: B 262 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7463 (t0) REVERT: D 100 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7745 (mp10) REVERT: D 139 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8269 (mt) REVERT: E 90 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7220 (tp) REVERT: F 16 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8505 (tp) REVERT: F 291 HIS cc_start: 0.6192 (m-70) cc_final: 0.5861 (m90) outliers start: 69 outliers final: 46 residues processed: 231 average time/residue: 0.1133 time to fit residues: 40.5789 Evaluate side-chains 222 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 170 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain D residue 29 CYS Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 100 GLN Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 101 PHE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 128 PHE Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 277 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 117 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 157 optimal weight: 50.0000 chunk 161 optimal weight: 0.0980 chunk 81 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN ** F 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.180218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.144299 restraints weight = 20102.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.140718 restraints weight = 37653.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.142145 restraints weight = 38313.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.141342 restraints weight = 24239.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.141889 restraints weight = 21266.796| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15053 Z= 0.156 Angle : 0.649 26.528 20435 Z= 0.294 Chirality : 0.042 0.178 2310 Planarity : 0.004 0.058 2567 Dihedral : 7.659 83.866 2192 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 5.11 % Allowed : 19.09 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.20), residues: 1882 helix: 1.30 (0.18), residues: 857 sheet: -0.83 (0.38), residues: 179 loop : -0.78 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 94 TYR 0.015 0.001 TYR D 141 PHE 0.017 0.001 PHE B 213 TRP 0.013 0.001 TRP B 103 HIS 0.008 0.001 HIS F 291 Details of bonding type rmsd covalent geometry : bond 0.00372 (15045) covalent geometry : angle 0.57482 (20421) hydrogen bonds : bond 0.04253 ( 706) hydrogen bonds : angle 4.55085 ( 2007) metal coordination : bond 0.01224 ( 8) metal coordination : angle 11.51346 ( 14) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 179 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 ASN cc_start: 0.8428 (OUTLIER) cc_final: 0.8126 (m-40) REVERT: A 394 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8626 (mm) REVERT: B 262 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.7754 (t0) REVERT: D 100 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7709 (mp10) REVERT: D 139 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8243 (mt) REVERT: E 43 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.8011 (tp) REVERT: E 90 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7262 (tp) REVERT: F 16 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8315 (tt) REVERT: F 288 MET cc_start: 0.6656 (ptp) cc_final: 0.6426 (ptm) REVERT: F 291 HIS cc_start: 0.6135 (m-70) cc_final: 0.5804 (m90) REVERT: F 382 MET cc_start: 0.5522 (tmm) cc_final: 0.5254 (tmm) outliers start: 79 outliers final: 53 residues processed: 234 average time/residue: 0.1090 time to fit residues: 39.9692 Evaluate side-chains 232 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 171 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 29 CYS Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 100 GLN Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 101 PHE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 128 PHE Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 307 TYR Chi-restraints excluded: chain F residue 375 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 50 optimal weight: 5.9990 chunk 160 optimal weight: 30.0000 chunk 67 optimal weight: 0.2980 chunk 154 optimal weight: 50.0000 chunk 157 optimal weight: 20.0000 chunk 129 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 121 optimal weight: 0.6980 chunk 114 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 177 optimal weight: 20.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.180597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.143650 restraints weight = 20104.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.139476 restraints weight = 41906.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.141623 restraints weight = 38858.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.141271 restraints weight = 23625.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.141706 restraints weight = 21182.148| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15053 Z= 0.144 Angle : 0.636 24.274 20435 Z= 0.290 Chirality : 0.042 0.181 2310 Planarity : 0.004 0.058 2567 Dihedral : 7.535 87.331 2191 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 5.70 % Allowed : 19.42 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.20), residues: 1882 helix: 1.30 (0.18), residues: 859 sheet: -0.75 (0.38), residues: 179 loop : -0.73 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 94 TYR 0.014 0.001 TYR B 360 PHE 0.016 0.001 PHE B 213 TRP 0.013 0.001 TRP B 103 HIS 0.007 0.001 HIS F 291 Details of bonding type rmsd covalent geometry : bond 0.00343 (15045) covalent geometry : angle 0.56770 (20421) hydrogen bonds : bond 0.04082 ( 706) hydrogen bonds : angle 4.45168 ( 2007) metal coordination : bond 0.01075 ( 8) metal coordination : angle 10.95156 ( 14) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 183 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 ASN cc_start: 0.8431 (OUTLIER) cc_final: 0.8137 (m-40) REVERT: A 394 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8618 (mm) REVERT: B 262 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7694 (t0) REVERT: D 100 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7664 (mp10) REVERT: D 139 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8210 (mt) REVERT: E 43 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.7995 (tp) REVERT: E 90 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7264 (tp) REVERT: F 16 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8268 (tt) REVERT: F 288 MET cc_start: 0.6715 (ptp) cc_final: 0.6457 (ptm) REVERT: F 291 HIS cc_start: 0.6237 (m-70) cc_final: 0.5986 (m90) outliers start: 88 outliers final: 63 residues processed: 244 average time/residue: 0.1117 time to fit residues: 42.4863 Evaluate side-chains 248 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 177 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 29 CYS Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 100 GLN Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 101 PHE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 128 PHE Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 307 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 55 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 172 optimal weight: 20.0000 chunk 85 optimal weight: 8.9990 chunk 90 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN ** F 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.176355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.139250 restraints weight = 20131.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.135940 restraints weight = 44130.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.136923 restraints weight = 39509.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.136004 restraints weight = 25270.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.136537 restraints weight = 23430.687| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 15053 Z= 0.265 Angle : 0.732 22.429 20435 Z= 0.345 Chirality : 0.045 0.191 2310 Planarity : 0.005 0.060 2567 Dihedral : 7.798 88.796 2190 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 5.89 % Allowed : 20.06 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.20), residues: 1882 helix: 1.07 (0.18), residues: 851 sheet: -0.76 (0.38), residues: 179 loop : -0.87 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 94 TYR 0.020 0.002 TYR B 360 PHE 0.027 0.002 PHE E 28 TRP 0.014 0.002 TRP B 103 HIS 0.005 0.001 HIS C 199 Details of bonding type rmsd covalent geometry : bond 0.00647 (15045) covalent geometry : angle 0.67184 (20421) hydrogen bonds : bond 0.04960 ( 706) hydrogen bonds : angle 4.63348 ( 2007) metal coordination : bond 0.01336 ( 8) metal coordination : angle 11.16453 ( 14) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 173 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8578 (mm) REVERT: B 52 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7356 (p0) REVERT: B 103 TRP cc_start: 0.7309 (p-90) cc_final: 0.7089 (p-90) REVERT: B 262 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.7751 (t0) REVERT: B 402 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7534 (tm-30) REVERT: D 137 ASN cc_start: 0.7391 (OUTLIER) cc_final: 0.7181 (t0) REVERT: D 139 LEU cc_start: 0.8550 (tm) cc_final: 0.8207 (mt) REVERT: D 194 MET cc_start: 0.7615 (ttm) cc_final: 0.7375 (ttm) REVERT: E 43 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7909 (tp) REVERT: F 16 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8165 (tt) REVERT: F 291 HIS cc_start: 0.6191 (m-70) cc_final: 0.5801 (m-70) outliers start: 91 outliers final: 70 residues processed: 241 average time/residue: 0.1081 time to fit residues: 40.7855 Evaluate side-chains 240 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 164 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 100 TRP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 29 CYS Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 101 PHE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 128 PHE Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 278 PHE Chi-restraints excluded: chain F residue 307 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 174 optimal weight: 40.0000 chunk 102 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 124 optimal weight: 0.0570 chunk 60 optimal weight: 0.9980 chunk 178 optimal weight: 30.0000 chunk 138 optimal weight: 10.0000 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.179134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.142891 restraints weight = 19959.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.139135 restraints weight = 41348.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.141068 restraints weight = 38639.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.140588 restraints weight = 24082.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.141109 restraints weight = 22175.906| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15053 Z= 0.149 Angle : 0.657 21.331 20435 Z= 0.306 Chirality : 0.043 0.190 2310 Planarity : 0.004 0.060 2567 Dihedral : 7.579 89.122 2188 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.98 % Allowed : 21.62 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.20), residues: 1882 helix: 1.20 (0.18), residues: 856 sheet: -0.64 (0.38), residues: 183 loop : -0.78 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 94 TYR 0.016 0.001 TYR B 360 PHE 0.021 0.001 PHE F 267 TRP 0.014 0.001 TRP B 260 HIS 0.006 0.001 HIS F 291 Details of bonding type rmsd covalent geometry : bond 0.00354 (15045) covalent geometry : angle 0.59705 (20421) hydrogen bonds : bond 0.04251 ( 706) hydrogen bonds : angle 4.49564 ( 2007) metal coordination : bond 0.00993 ( 8) metal coordination : angle 10.53359 ( 14) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 178 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8598 (mm) REVERT: B 103 TRP cc_start: 0.7254 (p-90) cc_final: 0.6984 (p-90) REVERT: B 262 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.7753 (t0) REVERT: D 76 MET cc_start: 0.8750 (mmm) cc_final: 0.8520 (tpp) REVERT: D 139 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8160 (mt) REVERT: E 43 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7937 (tp) REVERT: E 90 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7221 (tp) REVERT: F 1 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.6763 (ppp) REVERT: F 16 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8141 (tt) REVERT: F 291 HIS cc_start: 0.6077 (m-70) cc_final: 0.5868 (m90) outliers start: 77 outliers final: 59 residues processed: 233 average time/residue: 0.1064 time to fit residues: 38.7864 Evaluate side-chains 236 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 170 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 100 TRP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 29 CYS Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 101 PHE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 128 PHE Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 278 PHE Chi-restraints excluded: chain F residue 307 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 19 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 137 optimal weight: 0.0270 chunk 120 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 163 optimal weight: 0.7980 chunk 108 optimal weight: 7.9990 chunk 164 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 ASN ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN ** F 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.180299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.144194 restraints weight = 20095.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.140842 restraints weight = 40820.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.142169 restraints weight = 37902.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.142387 restraints weight = 23981.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.142441 restraints weight = 21568.136| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15053 Z= 0.134 Angle : 0.647 20.070 20435 Z= 0.301 Chirality : 0.042 0.183 2310 Planarity : 0.004 0.062 2567 Dihedral : 7.488 86.591 2188 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.92 % Allowed : 22.07 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.20), residues: 1882 helix: 1.31 (0.18), residues: 854 sheet: -0.55 (0.38), residues: 183 loop : -0.75 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 94 TYR 0.013 0.001 TYR B 360 PHE 0.018 0.001 PHE F 267 TRP 0.013 0.001 TRP B 103 HIS 0.006 0.001 HIS F 291 Details of bonding type rmsd covalent geometry : bond 0.00316 (15045) covalent geometry : angle 0.59180 (20421) hydrogen bonds : bond 0.04042 ( 706) hydrogen bonds : angle 4.41266 ( 2007) metal coordination : bond 0.00906 ( 8) metal coordination : angle 10.04083 ( 14) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 179 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8605 (mm) REVERT: B 103 TRP cc_start: 0.7253 (p-90) cc_final: 0.7001 (p-90) REVERT: B 262 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.7731 (t0) REVERT: D 139 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8133 (mt) REVERT: E 43 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7931 (tp) REVERT: E 90 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7177 (tp) REVERT: F 1 MET cc_start: 0.7596 (OUTLIER) cc_final: 0.6762 (ppp) REVERT: F 16 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8105 (tt) REVERT: F 382 MET cc_start: 0.5285 (tmm) cc_final: 0.5003 (tmm) outliers start: 76 outliers final: 60 residues processed: 236 average time/residue: 0.1045 time to fit residues: 38.3528 Evaluate side-chains 240 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 173 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 100 TRP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 29 CYS Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 101 PHE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 128 PHE Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 278 PHE Chi-restraints excluded: chain F residue 307 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 161 optimal weight: 20.0000 chunk 29 optimal weight: 0.0040 chunk 31 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 150 optimal weight: 30.0000 chunk 78 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.178960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.143151 restraints weight = 20184.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.139574 restraints weight = 39826.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.141341 restraints weight = 37941.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.140881 restraints weight = 23258.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.141608 restraints weight = 21239.960| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15053 Z= 0.177 Angle : 0.686 19.791 20435 Z= 0.320 Chirality : 0.043 0.185 2310 Planarity : 0.005 0.061 2567 Dihedral : 7.559 85.385 2188 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 5.05 % Allowed : 21.88 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.20), residues: 1882 helix: 1.19 (0.18), residues: 856 sheet: -0.51 (0.38), residues: 183 loop : -0.77 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 94 TYR 0.016 0.001 TYR B 360 PHE 0.017 0.001 PHE E 28 TRP 0.013 0.001 TRP B 103 HIS 0.005 0.001 HIS C 199 Details of bonding type rmsd covalent geometry : bond 0.00428 (15045) covalent geometry : angle 0.63329 (20421) hydrogen bonds : bond 0.04332 ( 706) hydrogen bonds : angle 4.46109 ( 2007) metal coordination : bond 0.01012 ( 8) metal coordination : angle 10.06205 ( 14) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 175 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8628 (mm) REVERT: B 103 TRP cc_start: 0.7279 (p-90) cc_final: 0.7017 (p-90) REVERT: B 262 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7514 (t0) REVERT: B 402 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7414 (tm-30) REVERT: D 126 GLU cc_start: 0.6293 (tm-30) cc_final: 0.5757 (tp30) REVERT: D 139 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8146 (mt) REVERT: E 43 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7938 (tp) REVERT: E 90 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7250 (tp) REVERT: F 1 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.6804 (ppp) REVERT: F 16 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8152 (tt) REVERT: F 382 MET cc_start: 0.5488 (tmm) cc_final: 0.5242 (tmm) outliers start: 78 outliers final: 66 residues processed: 231 average time/residue: 0.1074 time to fit residues: 38.6738 Evaluate side-chains 243 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 170 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 100 TRP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 29 CYS Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 101 PHE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 128 PHE Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 278 PHE Chi-restraints excluded: chain F residue 307 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 177 optimal weight: 6.9990 chunk 172 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 154 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 148 optimal weight: 7.9990 chunk 143 optimal weight: 0.0870 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 ASN ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.179811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.142324 restraints weight = 19948.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.137597 restraints weight = 42702.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.139401 restraints weight = 39780.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.139745 restraints weight = 24457.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.139885 restraints weight = 23448.342| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15053 Z= 0.149 Angle : 0.668 19.280 20435 Z= 0.312 Chirality : 0.043 0.186 2310 Planarity : 0.004 0.061 2567 Dihedral : 7.518 83.787 2188 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 5.05 % Allowed : 22.27 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.20), residues: 1882 helix: 1.22 (0.18), residues: 855 sheet: -0.49 (0.38), residues: 183 loop : -0.75 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 94 TYR 0.015 0.001 TYR B 360 PHE 0.017 0.001 PHE F 267 TRP 0.014 0.001 TRP B 103 HIS 0.008 0.001 HIS F 291 Details of bonding type rmsd covalent geometry : bond 0.00355 (15045) covalent geometry : angle 0.61737 (20421) hydrogen bonds : bond 0.04152 ( 706) hydrogen bonds : angle 4.43137 ( 2007) metal coordination : bond 0.00901 ( 8) metal coordination : angle 9.78204 ( 14) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 173 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8618 (mm) REVERT: B 250 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8794 (pt) REVERT: B 262 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7440 (t0) REVERT: B 402 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7396 (tm-30) REVERT: D 126 GLU cc_start: 0.6328 (tm-30) cc_final: 0.5808 (tp30) REVERT: D 139 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8202 (mt) REVERT: E 43 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7936 (tp) REVERT: E 90 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7226 (tp) REVERT: F 1 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.6773 (ppp) REVERT: F 16 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8149 (tt) outliers start: 78 outliers final: 66 residues processed: 230 average time/residue: 0.1103 time to fit residues: 39.5692 Evaluate side-chains 247 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 173 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 100 TRP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 29 CYS Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 101 PHE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 128 PHE Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 278 PHE Chi-restraints excluded: chain F residue 307 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 174 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 159 optimal weight: 20.0000 chunk 58 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.175384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.138644 restraints weight = 20145.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.135112 restraints weight = 44057.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.136626 restraints weight = 41444.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.135986 restraints weight = 26298.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.136214 restraints weight = 23192.013| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 15053 Z= 0.269 Angle : 0.766 19.238 20435 Z= 0.365 Chirality : 0.046 0.193 2310 Planarity : 0.005 0.060 2567 Dihedral : 7.662 80.175 2188 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 5.18 % Allowed : 21.68 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.19), residues: 1882 helix: 0.93 (0.18), residues: 853 sheet: -0.55 (0.38), residues: 183 loop : -0.94 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 94 TYR 0.022 0.002 TYR B 360 PHE 0.027 0.002 PHE E 28 TRP 0.013 0.002 TRP B 103 HIS 0.005 0.001 HIS C 199 Details of bonding type rmsd covalent geometry : bond 0.00656 (15045) covalent geometry : angle 0.71519 (20421) hydrogen bonds : bond 0.05081 ( 706) hydrogen bonds : angle 4.64880 ( 2007) metal coordination : bond 0.01241 ( 8) metal coordination : angle 10.54786 ( 14) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2092.95 seconds wall clock time: 37 minutes 16.98 seconds (2236.98 seconds total)