Starting phenix.real_space_refine on Sat Feb 7 04:20:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a1t_15088/02_2026/8a1t_15088_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a1t_15088/02_2026/8a1t_15088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a1t_15088/02_2026/8a1t_15088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a1t_15088/02_2026/8a1t_15088.map" model { file = "/net/cci-nas-00/data/ceres_data/8a1t_15088/02_2026/8a1t_15088_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a1t_15088/02_2026/8a1t_15088_trim.cif" } resolution = 3.37 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= 0.007 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: 9 Type Number sf(0) Gaussians K 1 8.98 5 Fe 4 7.16 5 P 7 5.49 5 S 90 5.16 5 Na 1 4.78 5 C 9646 2.51 5 N 2408 2.21 5 O 2724 1.98 5 H 14626 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29507 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 6880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 6880 Classifications: {'peptide': 446} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 23, 'TRANS': 422} Chain: "B" Number of atoms: 6011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 6011 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 14, 'TRANS': 377} Chain: "C" Number of atoms: 3774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 3774 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain: "D" Number of atoms: 3147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3147 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 9, 'TRANS': 191} Chain: "E" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 3078 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "F" Number of atoms: 6234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 6234 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 24, 'TRANS': 380} Chain: "B" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 213 Unusual residues: {' K': 1, ' NA': 1, '3PE': 2, 'FMN': 1, 'LMT': 2, 'RBF': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'3PE': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'FAD': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18322 SG CYS D 112 66.864 83.803 58.614 1.00 80.66 S ATOM 20214 SG CYS E 26 64.411 83.907 61.435 1.00 74.26 S ATOM 16996 SG CYS D 29 67.273 85.465 64.840 1.00 62.78 S ATOM 21719 SG CYS E 120 70.352 85.885 62.729 1.00 64.82 S ATOM 23920 SG CYS F 70 53.305 69.159 38.939 1.00213.23 S ATOM 23969 SG CYS F 76 51.317 66.358 37.391 1.00210.35 S ATOM 24004 SG CYS F 79 56.224 63.469 37.898 1.00199.79 S ATOM 24488 SG CYS F 111 57.448 66.701 39.384 1.00205.71 S Time building chain proxies: 5.12, per 1000 atoms: 0.17 Number of scatterers: 29507 At special positions: 0 Unit cell: (113.433, 137.117, 130.885, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Fe 4 26.01 K 1 19.00 S 90 16.00 P 7 15.00 Na 1 11.00 O 2724 8.00 N 2408 7.00 C 9646 6.00 H 14626 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 756.8 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES D 302 " pdb="FE1 FES D 302 " - pdb=" SG CYS E 26 " pdb="FE2 FES D 302 " - pdb=" SG CYS E 120 " pdb="FE2 FES D 302 " - pdb=" SG CYS D 29 " pdb="FE1 FES D 302 " - pdb=" SG CYS D 112 " pdb=" FES F1502 " pdb="FE1 FES F1502 " - pdb=" SG CYS F 76 " pdb="FE2 FES F1502 " - pdb=" SG CYS F 111 " pdb="FE2 FES F1502 " - pdb=" SG CYS F 79 " pdb="FE1 FES F1502 " - pdb=" SG CYS F 70 " Number of angles added : 12 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3416 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 13 sheets defined 55.0% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 32 through 36 Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 106 through 113 removed outlier: 4.308A pdb=" N ALA A 111 " --> pdb=" O ASN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 126 Processing helix chain 'A' and resid 127 through 131 Processing helix chain 'A' and resid 162 through 170 removed outlier: 3.546A pdb=" N VAL A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN A 170 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 219 through 228 Processing helix chain 'A' and resid 241 through 254 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.650A 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 400 Processing helix chain 'A' and resid 401 through 408 Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 414 through 417 Processing helix chain 'A' and resid 418 through 424 Processing helix chain 'A' and resid 430 through 446 Processing helix chain 'B' and resid 24 through 35 Processing helix chain 'B' and resid 52 through 64 Processing helix chain 'B' and resid 64 through 87 Processing helix chain 'B' and resid 88 through 98 Processing helix chain 'B' and resid 99 through 108 removed outlier: 3.541A pdb=" N TRP B 103 " --> pdb=" O ASN B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 152 Proline residue: B 131 - end of helix Processing helix chain 'B' and resid 157 through 168 removed outlier: 4.385A pdb=" N VAL B 161 " --> pdb=" O GLU B 157 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE B 164 " --> pdb=" O PHE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 191 through 195 Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 236 through 245 Processing helix chain 'B' and resid 246 through 249 Processing helix chain 'B' and resid 259 through 266 Processing helix chain 'B' and resid 276 through 290 removed outlier: 3.531A pdb=" N ILE B 287 " --> pdb=" O GLY B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 316 Processing helix chain 'B' and resid 320 through 325 Processing helix chain 'B' and resid 326 through 333 removed outlier: 3.583A pdb=" N VAL B 332 " --> pdb=" O HIS B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 353 through 375 Processing helix chain 'B' and resid 381 through 410 removed outlier: 3.629A pdb=" N LEU B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Proline residue: B 394 - end of helix Processing helix chain 'B' and resid 411 through 414 Processing helix chain 'C' and resid 8 through 54 removed outlier: 4.803A pdb=" N ASP C 35 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N LYS C 36 " --> pdb=" O GLY C 32 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 70 Processing helix chain 'C' and resid 92 through 98 Processing helix chain 'C' and resid 99 through 101 No H-bonds generated for 'chain 'C' and resid 99 through 101' Processing helix chain 'C' and resid 177 through 181 removed outlier: 3.747A pdb=" N VAL C 180 " --> pdb=" O GLY C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 189 removed outlier: 3.846A pdb=" N TRP C 189 " --> pdb=" O TRP C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 239 Processing helix chain 'C' and resid 244 through 254 Processing helix chain 'D' and resid 9 through 17 Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.832A pdb=" N ALA D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 62 Processing helix chain 'D' and resid 70 through 93 Processing helix chain 'D' and resid 94 through 102 Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 111 through 121 removed outlier: 3.649A pdb=" N MET D 115 " --> pdb=" O ASN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 125 removed outlier: 3.538A pdb=" N SER D 125 " --> pdb=" O ALA D 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 122 through 125' Processing helix chain 'D' and resid 126 through 158 Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 178 through 182 removed outlier: 3.585A pdb=" N LEU D 182 " --> pdb=" O GLY D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 202 removed outlier: 4.196A pdb=" N ALA D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE D 201 " --> pdb=" O ALA D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 206 Processing helix chain 'E' and resid 3 through 13 Processing helix chain 'E' and resid 16 through 22 Processing helix chain 'E' and resid 24 through 29 Processing helix chain 'E' and resid 34 through 63 Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 75 through 77 No H-bonds generated for 'chain 'E' and resid 75 through 77' Processing helix chain 'E' and resid 78 through 102 removed outlier: 3.970A pdb=" N THR E 82 " --> pdb=" O LEU E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 109 Processing helix chain 'E' and resid 112 through 117 Processing helix chain 'E' and resid 119 through 132 Processing helix chain 'E' and resid 135 through 164 Processing helix chain 'E' and resid 165 through 167 No H-bonds generated for 'chain 'E' and resid 165 through 167' Processing helix chain 'E' and resid 175 through 191 Processing helix chain 'E' and resid 192 through 194 No H-bonds generated for 'chain 'E' and resid 192 through 194' Processing helix chain 'F' and resid 3 through 30 Processing helix chain 'F' and resid 54 through 62 removed outlier: 3.692A pdb=" N ALA F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 96 removed outlier: 3.777A pdb=" N ASP F 96 " --> pdb=" O PRO F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 106 Processing helix chain 'F' and resid 124 through 129 Processing helix chain 'F' and resid 180 through 182 No H-bonds generated for 'chain 'F' and resid 180 through 182' Processing helix chain 'F' and resid 185 through 196 removed outlier: 4.329A pdb=" N ASP F 191 " --> pdb=" O LYS F 187 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE F 195 " --> pdb=" O ASP F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 199 No H-bonds generated for 'chain 'F' and resid 197 through 199' Processing helix chain 'F' and resid 245 through 252 removed outlier: 3.589A pdb=" N LEU F 252 " --> pdb=" O TYR F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 283 No H-bonds generated for 'chain 'F' and resid 281 through 283' Processing helix chain 'F' and resid 284 through 297 removed outlier: 3.510A pdb=" N MET F 288 " --> pdb=" O GLY F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 317 Processing helix chain 'F' and resid 319 through 330 Processing helix chain 'F' and resid 354 through 363 removed outlier: 4.535A pdb=" N TYR F 360 " --> pdb=" O HIS F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 395 Processing helix chain 'F' and resid 397 through 399 No H-bonds generated for 'chain 'F' and resid 397 through 399' Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 22 removed outlier: 7.170A pdb=" N SER A 21 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 9.556A pdb=" N VAL A 278 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N GLN A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 31 removed outlier: 6.560A pdb=" N LEU A 87 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ARG A 81 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N SER A 89 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ILE A 79 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL A 91 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 43 removed outlier: 7.110A pdb=" N PHE A 68 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 82 through 84 removed outlier: 3.511A pdb=" N ASP C 82 " --> pdb=" O ASP C 77 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU C 75 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 15.256A pdb=" N VAL C 121 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 11.644A pdb=" N VAL C 140 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 8.968A pdb=" N VAL C 123 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU C 138 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TYR C 125 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N VAL C 136 " --> pdb=" O TYR C 125 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL C 127 " --> pdb=" O SER C 134 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N PHE C 152 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N TYR C 167 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ALA C 154 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU C 165 " --> pdb=" O ALA C 154 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N GLU C 156 " --> pdb=" O SER C 163 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N SER C 163 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 103 through 105 Processing sheet with id=AA7, first strand: chain 'C' and resid 204 through 206 removed outlier: 6.602A pdb=" N LYS C 204 " --> pdb=" O VAL C 218 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AA9, first strand: chain 'F' and resid 47 through 49 removed outlier: 8.137A pdb=" N LEU F 121 " --> pdb=" O THR F 36 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N SER F 38 " --> pdb=" O LEU F 121 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER F 85 " --> pdb=" O ASP F 120 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 223 through 229 removed outlier: 6.657A pdb=" N LYS F 151 " --> pdb=" O ILE F 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 208 through 213 Processing sheet with id=AB3, first strand: chain 'F' and resid 175 through 178 Processing sheet with id=AB4, first strand: chain 'F' and resid 333 through 339 removed outlier: 6.549A pdb=" N MET F 305 " --> pdb=" O VAL F 334 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N HIS F 336 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N TYR F 307 " --> pdb=" O HIS F 336 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ALA F 338 " --> pdb=" O TYR F 307 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TYR F 309 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLU F 275 " --> pdb=" O GLU F 374 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N TYR F 376 " --> pdb=" O GLU F 275 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL F 277 " --> pdb=" O TYR F 376 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LEU F 402 " --> pdb=" O CYS F 373 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N TYR F 375 " --> pdb=" O LEU F 402 " (cutoff:3.500A) 756 hydrogen bonds defined for protein. 2130 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: 6.68 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.11: 14611 1.11 - 1.38: 5845 1.38 - 1.66: 9232 1.66 - 1.93: 151 1.93 - 2.20: 8 Bond restraints: 29847 Sorted by residual: bond pdb=" C4 FMN C1000 " pdb=" C4A FMN C1000 " ideal model delta sigma weight residual 1.485 1.388 0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C4 FMN B 501 " pdb=" C4A FMN B 501 " ideal model delta sigma weight residual 1.485 1.388 0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" O3P FAD F1501 " pdb=" P FAD F1501 " ideal model delta sigma weight residual 1.660 1.583 0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C4A FMN C1000 " pdb=" N5 FMN C1000 " ideal model delta sigma weight residual 1.300 1.375 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C4A FMN B 501 " pdb=" N5 FMN B 501 " ideal model delta sigma weight residual 1.300 1.375 -0.075 2.00e-02 2.50e+03 1.39e+01 ... (remaining 29842 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 53615 1.92 - 3.84: 227 3.84 - 5.76: 52 5.76 - 7.68: 9 7.68 - 9.60: 9 Bond angle restraints: 53912 Sorted by residual: angle pdb=" C2 LMT B 506 " pdb=" C3 LMT B 506 " pdb=" C4 LMT B 506 " ideal model delta sigma weight residual 117.09 107.49 9.60 3.00e+00 1.11e-01 1.02e+01 angle pdb=" C2 LMT E 201 " pdb=" C3 LMT E 201 " pdb=" C4 LMT E 201 " ideal model delta sigma weight residual 117.09 107.69 9.40 3.00e+00 1.11e-01 9.82e+00 angle pdb=" C2 LMT B 503 " pdb=" C3 LMT B 503 " pdb=" C4 LMT B 503 " ideal model delta sigma weight residual 117.09 107.77 9.32 3.00e+00 1.11e-01 9.64e+00 angle pdb=" N VAL E 31 " pdb=" CA VAL E 31 " pdb=" C VAL E 31 " ideal model delta sigma weight residual 111.91 109.27 2.64 8.90e-01 1.26e+00 8.77e+00 angle pdb=" C10 LMT B 506 " pdb=" C9 LMT B 506 " pdb=" C8 LMT B 506 " ideal model delta sigma weight residual 116.03 107.53 8.50 3.00e+00 1.11e-01 8.03e+00 ... (remaining 53907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.12: 13156 24.12 - 48.24: 784 48.24 - 72.36: 247 72.36 - 96.48: 24 96.48 - 120.60: 11 Dihedral angle restraints: 14222 sinusoidal: 7837 harmonic: 6385 Sorted by residual: dihedral pdb=" O1B LMT B 503 " pdb=" C1B LMT B 503 " pdb=" C2B LMT B 503 " pdb=" O2B LMT B 503 " ideal model delta sinusoidal sigma weight residual 53.26 -67.34 120.60 1 3.00e+01 1.11e-03 1.61e+01 dihedral pdb=" O2B LMT B 503 " pdb=" C1B LMT B 503 " pdb=" C2B LMT B 503 " pdb=" O5B LMT B 503 " ideal model delta sinusoidal sigma weight residual -176.42 -57.01 -119.41 1 3.00e+01 1.11e-03 1.59e+01 dihedral pdb=" C2B LMT E 201 " pdb=" C1B LMT E 201 " pdb=" O5B LMT E 201 " pdb=" C5B LMT E 201 " ideal model delta sinusoidal sigma weight residual -57.12 61.40 -118.52 1 3.00e+01 1.11e-03 1.58e+01 ... (remaining 14219 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1902 0.046 - 0.093: 299 0.093 - 0.139: 118 0.139 - 0.185: 2 0.185 - 0.231: 9 Chirality restraints: 2330 Sorted by residual: chirality pdb=" C4' LMT B 503 " pdb=" C3' LMT B 503 " pdb=" C5' LMT B 503 " pdb=" O1B LMT B 503 " both_signs ideal model delta sigma weight residual False -2.55 -2.79 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C4' LMT E 201 " pdb=" C3' LMT E 201 " pdb=" C5' LMT E 201 " pdb=" O1B LMT E 201 " both_signs ideal model delta sigma weight residual False -2.55 -2.77 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C5' LMT B 503 " pdb=" C4' LMT B 503 " pdb=" C6' LMT B 503 " pdb=" O5' LMT B 503 " both_signs ideal model delta sigma weight residual False -2.51 -2.29 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 2327 not shown) Planarity restraints: 4368 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 134 " 0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO A 135 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 135 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 135 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 213 " 0.019 5.00e-02 4.00e+02 2.81e-02 1.27e+00 pdb=" N PRO A 214 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 214 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 214 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 375 " 0.017 5.00e-02 4.00e+02 2.61e-02 1.09e+00 pdb=" N PRO A 376 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 376 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 376 " 0.015 5.00e-02 4.00e+02 ... (remaining 4365 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.30: 6023 2.30 - 3.01: 82408 3.01 - 3.72: 112570 3.72 - 4.43: 173081 4.43 - 5.14: 268326 Nonbonded interactions: 642408 Sorted by model distance: nonbonded pdb=" O CYS F 373 " pdb="HD22 ASN F 400 " model vdw 1.584 2.450 nonbonded pdb="HH21 ARG B 372 " pdb=" OE2 GLU B 380 " model vdw 1.585 2.450 nonbonded pdb=" OE2 GLU B 144 " pdb=" HZ1 LYS B 191 " model vdw 1.588 2.450 nonbonded pdb=" O TRP C 238 " pdb=" H PHE C 244 " model vdw 1.616 2.450 nonbonded pdb=" OE2 GLU A 415 " pdb=" HE ARG A 436 " model vdw 1.623 2.450 ... (remaining 642403 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.190 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 33.900 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 15231 Z= 0.207 Angle : 0.554 9.599 20640 Z= 0.246 Chirality : 0.041 0.231 2330 Planarity : 0.003 0.029 2569 Dihedral : 16.931 120.599 5702 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 12.78 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.51 (0.20), residues: 1877 helix: 1.89 (0.18), residues: 879 sheet: -0.38 (0.37), residues: 198 loop : 0.51 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 318 TYR 0.008 0.001 TYR F 167 PHE 0.010 0.001 PHE E 28 TRP 0.011 0.001 TRP B 103 HIS 0.002 0.001 HIS F 356 Details of bonding type rmsd covalent geometry : bond 0.00412 (15221) covalent geometry : angle 0.55196 (20628) hydrogen bonds : bond 0.20500 ( 756) hydrogen bonds : angle 7.50335 ( 2130) metal coordination : bond 0.02401 ( 8) metal coordination : angle 1.89977 ( 12) Misc. bond : bond 0.04867 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 VAL cc_start: 0.9018 (t) cc_final: 0.8738 (m) REVERT: A 403 ASP cc_start: 0.7652 (m-30) cc_final: 0.7368 (m-30) REVERT: A 431 TYR cc_start: 0.8889 (m-80) cc_final: 0.8652 (m-80) REVERT: B 112 MET cc_start: 0.8053 (mmp) cc_final: 0.7439 (mmp) REVERT: B 154 GLU cc_start: 0.6927 (tt0) cc_final: 0.6618 (mt-10) REVERT: C 252 ARG cc_start: 0.6506 (ttm110) cc_final: 0.6172 (ttm-80) REVERT: D 87 ASP cc_start: 0.7900 (t70) cc_final: 0.7518 (t0) REVERT: F 54 LYS cc_start: 0.4630 (mmtm) cc_final: 0.3967 (mttt) REVERT: F 133 TRP cc_start: 0.5539 (m-10) cc_final: 0.5246 (m-10) REVERT: F 276 MET cc_start: 0.5820 (mtt) cc_final: 0.5422 (mtt) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.2378 time to fit residues: 77.0153 Evaluate side-chains 176 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN C 199 HIS D 68 ASN F 227 ASN F 400 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.151136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.103143 restraints weight = 63897.932| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.86 r_work: 0.3124 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15231 Z= 0.181 Angle : 0.565 13.003 20640 Z= 0.287 Chirality : 0.042 0.314 2330 Planarity : 0.004 0.041 2569 Dihedral : 11.607 89.612 2392 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.17 % Allowed : 14.01 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.13 (0.19), residues: 1877 helix: 1.51 (0.17), residues: 895 sheet: -0.34 (0.38), residues: 184 loop : 0.28 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 303 TYR 0.022 0.001 TYR F 217 PHE 0.014 0.001 PHE F 128 TRP 0.013 0.001 TRP B 103 HIS 0.003 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00389 (15221) covalent geometry : angle 0.54185 (20628) hydrogen bonds : bond 0.05793 ( 756) hydrogen bonds : angle 5.55467 ( 2130) metal coordination : bond 0.01646 ( 8) metal coordination : angle 6.72374 ( 12) Misc. bond : bond 0.00524 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 178 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 ASP cc_start: 0.8023 (m-30) cc_final: 0.7487 (m-30) REVERT: B 69 PHE cc_start: 0.8651 (m-10) cc_final: 0.8327 (m-80) REVERT: B 112 MET cc_start: 0.7921 (mmp) cc_final: 0.7206 (mmp) REVERT: D 87 ASP cc_start: 0.8065 (t70) cc_final: 0.7658 (t0) REVERT: D 115 MET cc_start: 0.7320 (mtm) cc_final: 0.6660 (mtm) REVERT: E 197 GLN cc_start: 0.3917 (pm20) cc_final: 0.3660 (pm20) REVERT: F 54 LYS cc_start: 0.4597 (mmtm) cc_final: 0.3926 (mttt) REVERT: F 217 TYR cc_start: 0.4853 (p90) cc_final: 0.4521 (p90) REVERT: F 406 PHE cc_start: 0.2833 (p90) cc_final: 0.2590 (p90) outliers start: 18 outliers final: 15 residues processed: 186 average time/residue: 0.2509 time to fit residues: 72.1976 Evaluate side-chains 177 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 383 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 176 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 161 optimal weight: 8.9990 chunk 167 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 156 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN E 61 ASN F 400 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.149529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.101695 restraints weight = 64469.011| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.86 r_work: 0.3090 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 15231 Z= 0.228 Angle : 0.600 16.951 20640 Z= 0.296 Chirality : 0.043 0.451 2330 Planarity : 0.004 0.041 2569 Dihedral : 10.546 85.839 2392 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.30 % Allowed : 15.69 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.63 (0.19), residues: 1877 helix: 1.10 (0.17), residues: 894 sheet: -0.74 (0.38), residues: 177 loop : 0.07 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 134 TYR 0.016 0.002 TYR B 360 PHE 0.015 0.002 PHE E 28 TRP 0.018 0.001 TRP B 103 HIS 0.016 0.001 HIS C 199 Details of bonding type rmsd covalent geometry : bond 0.00514 (15221) covalent geometry : angle 0.56835 (20628) hydrogen bonds : bond 0.05147 ( 756) hydrogen bonds : angle 5.27093 ( 2130) metal coordination : bond 0.02030 ( 8) metal coordination : angle 7.96540 ( 12) Misc. bond : bond 0.00030 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.6421 (tpp-160) REVERT: A 342 LYS cc_start: 0.7719 (tttm) cc_final: 0.6968 (ttpt) REVERT: A 403 ASP cc_start: 0.8103 (m-30) cc_final: 0.7500 (m-30) REVERT: D 87 ASP cc_start: 0.8048 (t70) cc_final: 0.7656 (t0) REVERT: D 115 MET cc_start: 0.7272 (mtm) cc_final: 0.6806 (mtm) REVERT: F 54 LYS cc_start: 0.4638 (mmtm) cc_final: 0.3819 (mttt) REVERT: F 217 TYR cc_start: 0.5142 (p90) cc_final: 0.4719 (p90) REVERT: F 378 CYS cc_start: 0.5668 (OUTLIER) cc_final: 0.5466 (m) outliers start: 20 outliers final: 15 residues processed: 189 average time/residue: 0.2293 time to fit residues: 67.9239 Evaluate side-chains 178 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 192 TRP Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 378 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 7 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 182 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 138 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 162 optimal weight: 8.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN F 400 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.150708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.103326 restraints weight = 63716.619| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.84 r_work: 0.3099 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15231 Z= 0.135 Angle : 0.531 13.547 20640 Z= 0.259 Chirality : 0.041 0.442 2330 Planarity : 0.004 0.063 2569 Dihedral : 9.815 85.596 2392 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.04 % Allowed : 15.82 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.77 (0.19), residues: 1877 helix: 1.22 (0.17), residues: 896 sheet: -0.57 (0.40), residues: 165 loop : 0.08 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 303 TYR 0.016 0.001 TYR B 360 PHE 0.013 0.001 PHE E 28 TRP 0.017 0.001 TRP B 103 HIS 0.003 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00302 (15221) covalent geometry : angle 0.50416 (20628) hydrogen bonds : bond 0.04411 ( 756) hydrogen bonds : angle 5.00390 ( 2130) metal coordination : bond 0.01351 ( 8) metal coordination : angle 6.88280 ( 12) Misc. bond : bond 0.00013 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.6389 (tpp-160) REVERT: A 342 LYS cc_start: 0.7755 (tttm) cc_final: 0.6989 (ttpt) REVERT: A 403 ASP cc_start: 0.8052 (m-30) cc_final: 0.7426 (m-30) REVERT: C 131 ASP cc_start: 0.5677 (t0) cc_final: 0.5165 (m-30) REVERT: D 87 ASP cc_start: 0.8089 (t70) cc_final: 0.7675 (t0) REVERT: F 50 GLN cc_start: 0.3899 (mm110) cc_final: 0.3440 (tt0) REVERT: F 54 LYS cc_start: 0.4645 (mmtm) cc_final: 0.3800 (mttt) REVERT: F 217 TYR cc_start: 0.5080 (p90) cc_final: 0.4717 (p90) outliers start: 16 outliers final: 14 residues processed: 181 average time/residue: 0.2430 time to fit residues: 69.2023 Evaluate side-chains 175 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 192 TRP Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 383 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 141 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 93 optimal weight: 0.0980 chunk 83 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 155 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN C 110 GLN F 400 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.150225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.102849 restraints weight = 63862.895| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.85 r_work: 0.3123 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15231 Z= 0.154 Angle : 0.529 13.139 20640 Z= 0.260 Chirality : 0.041 0.435 2330 Planarity : 0.004 0.056 2569 Dihedral : 9.593 81.607 2392 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.49 % Allowed : 16.08 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.79 (0.19), residues: 1877 helix: 1.27 (0.17), residues: 894 sheet: -0.55 (0.40), residues: 165 loop : 0.05 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 134 TYR 0.016 0.001 TYR B 360 PHE 0.014 0.001 PHE E 28 TRP 0.017 0.001 TRP B 103 HIS 0.003 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00349 (15221) covalent geometry : angle 0.50565 (20628) hydrogen bonds : bond 0.04270 ( 756) hydrogen bonds : angle 4.91144 ( 2130) metal coordination : bond 0.01503 ( 8) metal coordination : angle 6.53447 ( 12) Misc. bond : bond 0.00017 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 LYS cc_start: 0.7808 (tttm) cc_final: 0.7014 (ttpt) REVERT: A 403 ASP cc_start: 0.8068 (m-30) cc_final: 0.7408 (m-30) REVERT: B 274 GLU cc_start: 0.7706 (pt0) cc_final: 0.7457 (pt0) REVERT: B 382 MET cc_start: 0.8510 (tpt) cc_final: 0.7831 (tpt) REVERT: C 131 ASP cc_start: 0.5702 (t0) cc_final: 0.5172 (m-30) REVERT: D 87 ASP cc_start: 0.8104 (t70) cc_final: 0.7692 (t0) REVERT: E 67 ASP cc_start: 0.7360 (m-30) cc_final: 0.7057 (m-30) REVERT: F 50 GLN cc_start: 0.3912 (mm110) cc_final: 0.3453 (tt0) REVERT: F 54 LYS cc_start: 0.4645 (mmtm) cc_final: 0.3808 (mttt) REVERT: F 217 TYR cc_start: 0.5093 (p90) cc_final: 0.4710 (p90) REVERT: F 378 CYS cc_start: 0.5818 (OUTLIER) cc_final: 0.5558 (m) outliers start: 23 outliers final: 20 residues processed: 178 average time/residue: 0.2135 time to fit residues: 61.1846 Evaluate side-chains 180 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 192 TRP Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 383 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 47 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 167 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN B 324 ASN F 175 HIS F 400 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.148218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.100883 restraints weight = 63817.655| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.83 r_work: 0.3095 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 15231 Z= 0.241 Angle : 0.594 15.052 20640 Z= 0.294 Chirality : 0.044 0.441 2330 Planarity : 0.005 0.049 2569 Dihedral : 9.780 72.180 2392 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.14 % Allowed : 15.76 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.45 (0.19), residues: 1877 helix: 1.03 (0.17), residues: 894 sheet: -0.95 (0.38), residues: 177 loop : -0.11 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 134 TYR 0.017 0.002 TYR B 360 PHE 0.015 0.002 PHE E 28 TRP 0.019 0.002 TRP B 103 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00552 (15221) covalent geometry : angle 0.56686 (20628) hydrogen bonds : bond 0.04493 ( 756) hydrogen bonds : angle 5.01322 ( 2130) metal coordination : bond 0.01891 ( 8) metal coordination : angle 7.37331 ( 12) Misc. bond : bond 0.00054 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 163 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.6165 (tpp-160) REVERT: A 342 LYS cc_start: 0.7857 (tttm) cc_final: 0.7062 (ttpt) REVERT: B 54 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8618 (mttp) REVERT: B 324 ASN cc_start: 0.8208 (OUTLIER) cc_final: 0.7554 (p0) REVERT: C 131 ASP cc_start: 0.5746 (t0) cc_final: 0.5195 (m-30) REVERT: D 87 ASP cc_start: 0.8115 (t70) cc_final: 0.7766 (t0) REVERT: D 115 MET cc_start: 0.7558 (mtm) cc_final: 0.7193 (mtm) REVERT: D 141 TYR cc_start: 0.8562 (t80) cc_final: 0.8255 (t80) REVERT: E 67 ASP cc_start: 0.7400 (m-30) cc_final: 0.7106 (m-30) REVERT: F 50 GLN cc_start: 0.3738 (mm110) cc_final: 0.3369 (tt0) REVERT: F 54 LYS cc_start: 0.4611 (mmtm) cc_final: 0.3757 (mttt) REVERT: F 119 MET cc_start: 0.3513 (ptp) cc_final: 0.2975 (ptp) REVERT: F 217 TYR cc_start: 0.4999 (p90) cc_final: 0.4673 (p90) REVERT: F 264 PHE cc_start: 0.3589 (m-80) cc_final: 0.3315 (m-80) REVERT: F 378 CYS cc_start: 0.5844 (OUTLIER) cc_final: 0.5598 (m) outliers start: 33 outliers final: 23 residues processed: 188 average time/residue: 0.2362 time to fit residues: 70.2520 Evaluate side-chains 182 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain F residue 175 HIS Chi-restraints excluded: chain F residue 192 TRP Chi-restraints excluded: chain F residue 377 MET Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 402 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 178 optimal weight: 10.0000 chunk 133 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 174 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 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 80 ASN F 400 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.149020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.101880 restraints weight = 63580.731| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.82 r_work: 0.3100 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15231 Z= 0.178 Angle : 0.559 14.832 20640 Z= 0.277 Chirality : 0.042 0.435 2330 Planarity : 0.004 0.048 2569 Dihedral : 9.536 67.270 2392 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.14 % Allowed : 16.28 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.52 (0.19), residues: 1877 helix: 1.12 (0.17), residues: 893 sheet: -0.81 (0.38), residues: 177 loop : -0.14 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 296 TYR 0.016 0.001 TYR B 360 PHE 0.015 0.001 PHE E 28 TRP 0.018 0.001 TRP B 103 HIS 0.019 0.001 HIS F 175 Details of bonding type rmsd covalent geometry : bond 0.00404 (15221) covalent geometry : angle 0.53500 (20628) hydrogen bonds : bond 0.04312 ( 756) hydrogen bonds : angle 4.91394 ( 2130) metal coordination : bond 0.01622 ( 8) metal coordination : angle 6.81007 ( 12) Misc. bond : bond 0.00015 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 163 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.6196 (tpp-160) REVERT: A 342 LYS cc_start: 0.7871 (tttm) cc_final: 0.7083 (ttpt) REVERT: C 131 ASP cc_start: 0.5889 (t0) cc_final: 0.5315 (m-30) REVERT: D 87 ASP cc_start: 0.8107 (t70) cc_final: 0.7702 (t0) REVERT: D 141 TYR cc_start: 0.8514 (t80) cc_final: 0.8250 (t80) REVERT: E 67 ASP cc_start: 0.7592 (m-30) cc_final: 0.7316 (m-30) REVERT: F 50 GLN cc_start: 0.3793 (mm110) cc_final: 0.3300 (tt0) REVERT: F 54 LYS cc_start: 0.4630 (mmtm) cc_final: 0.3736 (mttt) REVERT: F 119 MET cc_start: 0.3480 (ptp) cc_final: 0.2951 (ptp) REVERT: F 217 TYR cc_start: 0.5014 (p90) cc_final: 0.4730 (p90) REVERT: F 264 PHE cc_start: 0.3609 (m-80) cc_final: 0.3327 (m-80) REVERT: F 378 CYS cc_start: 0.5818 (OUTLIER) cc_final: 0.5567 (m) outliers start: 33 outliers final: 25 residues processed: 187 average time/residue: 0.2302 time to fit residues: 68.5539 Evaluate side-chains 186 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain F residue 192 TRP Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 406 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 91 optimal weight: 9.9990 chunk 145 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 147 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 167 optimal weight: 20.0000 chunk 129 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.149471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.102434 restraints weight = 63743.016| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.83 r_work: 0.3083 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15231 Z= 0.152 Angle : 0.535 14.151 20640 Z= 0.264 Chirality : 0.041 0.428 2330 Planarity : 0.004 0.042 2569 Dihedral : 9.215 73.619 2392 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.75 % Allowed : 16.93 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.63 (0.19), residues: 1877 helix: 1.19 (0.17), residues: 893 sheet: -0.67 (0.40), residues: 165 loop : -0.09 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 80 TYR 0.017 0.001 TYR B 360 PHE 0.015 0.001 PHE E 28 TRP 0.018 0.001 TRP B 103 HIS 0.003 0.001 HIS F 176 Details of bonding type rmsd covalent geometry : bond 0.00345 (15221) covalent geometry : angle 0.51203 (20628) hydrogen bonds : bond 0.04117 ( 756) hydrogen bonds : angle 4.82138 ( 2130) metal coordination : bond 0.01445 ( 8) metal coordination : angle 6.48812 ( 12) Misc. bond : bond 0.00014 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.6206 (tpp-160) REVERT: A 342 LYS cc_start: 0.7870 (tttm) cc_final: 0.7098 (ttpt) REVERT: C 131 ASP cc_start: 0.5898 (t0) cc_final: 0.5303 (m-30) REVERT: D 87 ASP cc_start: 0.8003 (t70) cc_final: 0.7563 (t0) REVERT: E 67 ASP cc_start: 0.7590 (m-30) cc_final: 0.7311 (m-30) REVERT: F 50 GLN cc_start: 0.3866 (mm110) cc_final: 0.3348 (tt0) REVERT: F 54 LYS cc_start: 0.4635 (mmtm) cc_final: 0.3745 (mttt) REVERT: F 119 MET cc_start: 0.3490 (ptp) cc_final: 0.2962 (ptp) REVERT: F 225 MET cc_start: 0.3345 (mpp) cc_final: 0.3094 (mpp) REVERT: F 264 PHE cc_start: 0.3593 (m-80) cc_final: 0.3315 (m-80) REVERT: F 295 GLN cc_start: 0.5893 (mp10) cc_final: 0.5639 (mp10) outliers start: 27 outliers final: 25 residues processed: 185 average time/residue: 0.2229 time to fit residues: 65.8203 Evaluate side-chains 187 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain F residue 192 TRP Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 377 MET Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 402 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 174 optimal weight: 20.0000 chunk 115 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 185 optimal weight: 8.9990 chunk 146 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 chunk 184 optimal weight: 0.9980 chunk 180 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN B 324 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.149367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.102435 restraints weight = 63596.725| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.82 r_work: 0.3116 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15231 Z= 0.160 Angle : 0.545 13.978 20640 Z= 0.266 Chirality : 0.041 0.430 2330 Planarity : 0.004 0.041 2569 Dihedral : 9.066 87.147 2392 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.08 % Allowed : 16.73 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.64 (0.19), residues: 1877 helix: 1.24 (0.17), residues: 891 sheet: -0.88 (0.38), residues: 177 loop : -0.06 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 80 TYR 0.016 0.001 TYR B 360 PHE 0.015 0.001 PHE E 28 TRP 0.017 0.001 TRP B 103 HIS 0.003 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00366 (15221) covalent geometry : angle 0.51671 (20628) hydrogen bonds : bond 0.04086 ( 756) hydrogen bonds : angle 4.79024 ( 2130) metal coordination : bond 0.01387 ( 8) metal coordination : angle 7.17121 ( 12) Misc. bond : bond 0.00023 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.6213 (tpp-160) REVERT: A 342 LYS cc_start: 0.7867 (tttm) cc_final: 0.7109 (ttpt) REVERT: C 131 ASP cc_start: 0.5941 (t0) cc_final: 0.5317 (m-30) REVERT: E 67 ASP cc_start: 0.7618 (m-30) cc_final: 0.7345 (m-30) REVERT: E 132 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7206 (mtt-85) REVERT: E 134 TYR cc_start: 0.7336 (m-80) cc_final: 0.6989 (m-10) REVERT: F 50 GLN cc_start: 0.3851 (mm110) cc_final: 0.3323 (tt0) REVERT: F 54 LYS cc_start: 0.4667 (mmtm) cc_final: 0.3761 (mttt) REVERT: F 119 MET cc_start: 0.3538 (ptp) cc_final: 0.3006 (ptp) REVERT: F 225 MET cc_start: 0.3183 (mpp) cc_final: 0.2945 (mpp) REVERT: F 264 PHE cc_start: 0.3603 (m-80) cc_final: 0.3331 (m-80) REVERT: F 372 ASP cc_start: 0.6814 (m-30) cc_final: 0.6244 (t0) outliers start: 32 outliers final: 26 residues processed: 188 average time/residue: 0.2181 time to fit residues: 64.2801 Evaluate side-chains 187 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 132 ARG Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain F residue 192 TRP Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 406 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 72 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 181 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 chunk 135 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 101 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 0.1980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.150214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.103404 restraints weight = 63352.868| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.83 r_work: 0.3131 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15231 Z= 0.124 Angle : 0.520 13.121 20640 Z= 0.255 Chirality : 0.041 0.418 2330 Planarity : 0.004 0.041 2569 Dihedral : 8.715 84.765 2392 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.56 % Allowed : 17.06 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.80 (0.19), residues: 1877 helix: 1.34 (0.17), residues: 889 sheet: -0.60 (0.40), residues: 167 loop : 0.00 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 209 TYR 0.016 0.001 TYR B 360 PHE 0.014 0.001 PHE E 28 TRP 0.018 0.001 TRP B 103 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00278 (15221) covalent geometry : angle 0.49624 (20628) hydrogen bonds : bond 0.03907 ( 756) hydrogen bonds : angle 4.71430 ( 2130) metal coordination : bond 0.01224 ( 8) metal coordination : angle 6.52118 ( 12) Misc. bond : bond 0.00013 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.6297 (tpp-160) REVERT: A 342 LYS cc_start: 0.7866 (tttm) cc_final: 0.7102 (ttpt) REVERT: B 69 PHE cc_start: 0.8518 (m-10) cc_final: 0.8282 (m-80) REVERT: C 131 ASP cc_start: 0.5899 (t0) cc_final: 0.5285 (m-30) REVERT: E 67 ASP cc_start: 0.7545 (m-30) cc_final: 0.7243 (m-30) REVERT: F 50 GLN cc_start: 0.3852 (mm110) cc_final: 0.3326 (tt0) REVERT: F 54 LYS cc_start: 0.4647 (mmtm) cc_final: 0.3760 (mttt) REVERT: F 119 MET cc_start: 0.3262 (ptp) cc_final: 0.2757 (ptp) REVERT: F 264 PHE cc_start: 0.3533 (m-80) cc_final: 0.3279 (m-80) REVERT: F 295 GLN cc_start: 0.5914 (mp10) cc_final: 0.5664 (mp10) outliers start: 24 outliers final: 22 residues processed: 186 average time/residue: 0.2291 time to fit residues: 67.4405 Evaluate side-chains 187 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain F residue 192 TRP Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 401 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 43 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN D 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.150232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.103452 restraints weight = 63709.242| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.82 r_work: 0.3120 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15231 Z= 0.128 Angle : 0.519 12.986 20640 Z= 0.253 Chirality : 0.041 0.412 2330 Planarity : 0.004 0.041 2569 Dihedral : 8.482 77.755 2392 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.56 % Allowed : 17.19 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.86 (0.19), residues: 1877 helix: 1.39 (0.17), residues: 890 sheet: -0.75 (0.39), residues: 179 loop : 0.08 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 289 TYR 0.017 0.001 TYR B 360 PHE 0.014 0.001 PHE E 28 TRP 0.018 0.001 TRP B 103 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00289 (15221) covalent geometry : angle 0.49311 (20628) hydrogen bonds : bond 0.03850 ( 756) hydrogen bonds : angle 4.68571 ( 2130) metal coordination : bond 0.01242 ( 8) metal coordination : angle 6.70848 ( 12) Misc. bond : bond 0.00013 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7497.22 seconds wall clock time: 127 minutes 46.20 seconds (7666.20 seconds total)