Starting phenix.real_space_refine on Sun Jul 5 21:20:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a1t_15088/07_2026/8a1t_15088_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a1t_15088/07_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_15088/07_2026/8a1t_15088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a1t_15088/07_2026/8a1t_15088.map" model { file = "/net/cci-nas-00/data/ceres_data/8a1t_15088/07_2026/8a1t_15088_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a1t_15088/07_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-dev-6108/lib/python3.11/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, 211 Ad-hoc single atom residues: {' NA': 1, ' K': 1} Unusual residues: {'3PE': 2, 'FMN': 1, 'LMT': 2, 'RBF': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain breaks: 2 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: 4.72, per 1000 atoms: 0.16 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: 2.52 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.74 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: 7.21 Time building geometry restraints manager: 3.57 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: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 37.110 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 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/Z covalent geometry : bond 0.00412 / 0.20 (15221) covalent geometry : angle 0.55196 / 0.25 (20628) hydrogen bonds : bond 0.20500 / 14.18 ( 756) hydrogen bonds : angle 7.50335 / 5.35 ( 2130) metal coordination : bond 0.02401 / 1.16 ( 8) metal coordination : angle 1.89977 / 0.98 ( 12) Misc. bond : bond 0.04867 / 2.32 ( 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 : 0.705 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: 0.2314 time to fit residues: 75.0067 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 : 0.700 ------------------------------------------------------------------------------- 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... 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 = 0.3883 r_free = 0.3883 target = 0.151188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.103444 restraints weight = 63648.670| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.84 r_work: 0.3114 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15231 Z= 0.182 Angle : 0.568 12.548 20640 Z= 0.290 Chirality : 0.042 0.311 2330 Planarity : 0.004 0.041 2569 Dihedral : 11.622 90.225 2392 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.17 % Allowed : 14.07 % Favored : 84.76 % 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: 1.14 (0.19), residues: 1877 helix: 1.53 (0.17), residues: 895 sheet: -0.34 (0.38), residues: 184 loop : 0.29 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 303 TYR 0.021 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 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (15221) covalent geometry : angle 0.54603 / 0.29 (20628) hydrogen bonds : bond 0.05646 / 3.91 ( 756) hydrogen bonds : angle 5.55707 / 3.95 ( 2130) metal coordination : bond 0.01630 / 0.81 ( 8) metal coordination : angle 6.50335 / 4.13 ( 12) Misc. bond : bond 0.00342 / 0.16 ( 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 194 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 0.671 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 403 ASP cc_start: 0.8003 (m-30) cc_final: 0.7478 (m-30) REVERT: B 69 PHE cc_start: 0.8653 (m-10) cc_final: 0.8328 (m-80) REVERT: B 112 MET cc_start: 0.7936 (mmp) cc_final: 0.7220 (mmp) REVERT: D 87 ASP cc_start: 0.8055 (t70) cc_final: 0.7653 (t0) REVERT: D 115 MET cc_start: 0.7314 (mtm) cc_final: 0.6643 (mtm) REVERT: D 146 MET cc_start: 0.8686 (mmp) cc_final: 0.8340 (mmp) REVERT: E 197 GLN cc_start: 0.3939 (pm20) cc_final: 0.3677 (pm20) REVERT: F 54 LYS cc_start: 0.4598 (mmtm) cc_final: 0.3927 (mttt) REVERT: F 217 TYR cc_start: 0.4856 (p90) cc_final: 0.4534 (p90) REVERT: F 406 PHE cc_start: 0.2834 (p90) cc_final: 0.2592 (p90) outliers start: 18 outliers final: 15 residues processed: 184 average time/residue: 0.2324 time to fit residues: 66.1021 Evaluate side-chains 178 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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: 4.9990 chunk 84 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 161 optimal weight: 9.9990 chunk 167 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3867 r_free = 0.3867 target = 0.149842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.101865 restraints weight = 64281.912| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.85 r_work: 0.3104 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15231 Z= 0.219 Angle : 0.589 16.573 20640 Z= 0.290 Chirality : 0.043 0.454 2330 Planarity : 0.004 0.041 2569 Dihedral : 10.556 86.431 2392 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.23 % Allowed : 15.30 % Favored : 83.46 % 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: 0.70 (0.19), residues: 1877 helix: 1.15 (0.17), residues: 894 sheet: -0.71 (0.38), residues: 177 loop : 0.11 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 303 TYR 0.015 0.002 TYR B 360 PHE 0.015 0.002 PHE E 28 TRP 0.017 0.001 TRP B 103 HIS 0.017 0.001 HIS C 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.22 (15221) covalent geometry : angle 0.55849 / 0.29 (20628) hydrogen bonds : bond 0.05200 / 3.61 ( 756) hydrogen bonds : angle 5.28217 / 3.75 ( 2130) metal coordination : bond 0.01900 / 0.97 ( 8) metal coordination : angle 7.80862 / 4.97 ( 12) Misc. bond : bond 0.00054 / 0.03 ( 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 192 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 0.666 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: 0.7858 (OUTLIER) cc_final: 0.6438 (tpp-160) REVERT: A 342 LYS cc_start: 0.7700 (tttm) cc_final: 0.6953 (ttpt) REVERT: A 403 ASP cc_start: 0.8040 (m-30) cc_final: 0.7443 (m-30) REVERT: D 87 ASP cc_start: 0.8048 (t70) cc_final: 0.7655 (t0) REVERT: D 115 MET cc_start: 0.7252 (mtm) cc_final: 0.6780 (mtm) REVERT: F 54 LYS cc_start: 0.4648 (mmtm) cc_final: 0.3817 (mttt) REVERT: F 217 TYR cc_start: 0.5099 (p90) cc_final: 0.4687 (p90) outliers start: 19 outliers final: 15 residues processed: 186 average time/residue: 0.2155 time to fit residues: 62.9438 Evaluate side-chains 173 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 36 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 182 optimal weight: 9.9990 chunk 3 optimal weight: 0.6980 chunk 138 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 162 optimal weight: 7.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN F 175 HIS 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 = 0.150422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.102705 restraints weight = 63786.579| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.84 r_work: 0.3118 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15231 Z= 0.158 Angle : 0.540 13.577 20640 Z= 0.265 Chirality : 0.042 0.446 2330 Planarity : 0.004 0.060 2569 Dihedral : 9.888 84.955 2392 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.23 % Allowed : 15.63 % 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: 0.74 (0.19), residues: 1877 helix: 1.21 (0.17), residues: 895 sheet: -0.58 (0.40), residues: 165 loop : 0.05 (0.22), residues: 817 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 0.013 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/Z covalent geometry : bond 0.00353 / 0.16 (15221) covalent geometry : angle 0.51403 / 0.26 (20628) hydrogen bonds : bond 0.04476 / 3.12 ( 756) hydrogen bonds : angle 5.03888 / 3.59 ( 2130) metal coordination : bond 0.01518 / 0.76 ( 8) metal coordination : angle 6.93967 / 4.32 ( 12) Misc. bond : bond 0.00022 / 0.01 ( 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 188 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.485 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: 0.7619 (OUTLIER) cc_final: 0.6425 (tpp-160) REVERT: A 342 LYS cc_start: 0.7752 (tttm) cc_final: 0.6971 (ttpt) REVERT: A 403 ASP cc_start: 0.8052 (m-30) cc_final: 0.7415 (m-30) REVERT: C 131 ASP cc_start: 0.5697 (t0) cc_final: 0.5177 (m-30) REVERT: D 87 ASP cc_start: 0.8087 (t70) cc_final: 0.7678 (t0) REVERT: D 141 TYR cc_start: 0.8491 (t80) cc_final: 0.8238 (t80) REVERT: F 50 GLN cc_start: 0.3767 (mm110) cc_final: 0.3420 (tt0) REVERT: F 54 LYS cc_start: 0.4662 (mmtm) cc_final: 0.3808 (mttt) REVERT: F 214 MET cc_start: 0.0563 (mtt) cc_final: 0.0333 (mtp) REVERT: F 217 TYR cc_start: 0.5096 (p90) cc_final: 0.4728 (p90) REVERT: F 378 CYS cc_start: 0.5632 (OUTLIER) cc_final: 0.5425 (m) outliers start: 19 outliers final: 16 residues processed: 181 average time/residue: 0.1988 time to fit residues: 56.8711 Evaluate side-chains 179 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU 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 175 HIS 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=3.50 ------------------------------------------------------------------------------- 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: 9.9990 chunk 83 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 146 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN B 324 ASN C 110 GLN F 400 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.148866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.101354 restraints weight = 64020.034| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.83 r_work: 0.3099 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15231 Z= 0.226 Angle : 0.579 14.377 20640 Z= 0.286 Chirality : 0.043 0.439 2330 Planarity : 0.004 0.056 2569 Dihedral : 9.945 78.366 2392 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.82 % Allowed : 16.15 % Favored : 82.04 % 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: 0.50 (0.19), residues: 1877 helix: 1.05 (0.17), residues: 901 sheet: -0.86 (0.38), residues: 177 loop : -0.06 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 134 TYR 0.017 0.002 TYR B 360 PHE 0.015 0.002 PHE E 28 TRP 0.018 0.001 TRP B 103 HIS 0.011 0.001 HIS F 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.23 (15221) covalent geometry : angle 0.55302 / 0.29 (20628) hydrogen bonds : bond 0.04550 / 3.16 ( 756) hydrogen bonds : angle 5.04068 / 3.59 ( 2130) metal coordination : bond 0.01934 / 0.97 ( 8) metal coordination : angle 7.19447 / 4.41 ( 12) Misc. bond : bond 0.00019 / 0.01 ( 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 191 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.665 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: 0.7707 (OUTLIER) cc_final: 0.6239 (tpp-160) REVERT: A 342 LYS cc_start: 0.7834 (tttm) cc_final: 0.7043 (ttpt) REVERT: B 324 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7528 (p0) REVERT: C 131 ASP cc_start: 0.5698 (t0) cc_final: 0.5186 (m-30) REVERT: D 87 ASP cc_start: 0.8094 (t70) cc_final: 0.7695 (t0) REVERT: D 141 TYR cc_start: 0.8506 (t80) cc_final: 0.8224 (t80) REVERT: E 67 ASP cc_start: 0.7386 (m-30) cc_final: 0.7087 (m-30) REVERT: F 50 GLN cc_start: 0.3808 (mm110) cc_final: 0.3455 (tt0) REVERT: F 54 LYS cc_start: 0.4603 (mmtm) cc_final: 0.3747 (mttt) REVERT: F 217 TYR cc_start: 0.5059 (p90) cc_final: 0.4688 (p90) REVERT: F 378 CYS cc_start: 0.5797 (OUTLIER) cc_final: 0.5473 (m) outliers start: 28 outliers final: 20 residues processed: 183 average time/residue: 0.1996 time to fit residues: 58.9150 Evaluate side-chains 178 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 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 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 F residue 168 ILE Chi-restraints excluded: chain F residue 192 TRP Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 401 ILE 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: 6.9990 chunk 66 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 167 optimal weight: 20.0000 chunk 110 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.148681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.101465 restraints weight = 63479.437| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.83 r_work: 0.3098 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15231 Z= 0.213 Angle : 0.577 15.272 20640 Z= 0.287 Chirality : 0.043 0.436 2330 Planarity : 0.004 0.053 2569 Dihedral : 9.800 73.497 2392 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.01 % Allowed : 16.08 % Favored : 81.91 % 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: 1.04 (0.17), residues: 894 sheet: -0.74 (0.39), residues: 167 loop : -0.17 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 134 TYR 0.017 0.002 TYR B 360 PHE 0.015 0.002 PHE E 28 TRP 0.019 0.001 TRP B 103 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.21 (15221) covalent geometry : angle 0.55124 / 0.29 (20628) hydrogen bonds : bond 0.04432 / 3.09 ( 756) hydrogen bonds : angle 5.00130 / 3.56 ( 2130) metal coordination : bond 0.01793 / 0.90 ( 8) metal coordination : angle 7.12494 / 4.37 ( 12) Misc. bond : bond 0.00028 / 0.01 ( 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 188 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.745 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: 0.7712 (OUTLIER) cc_final: 0.6224 (tpp-160) REVERT: A 342 LYS cc_start: 0.7830 (tttm) cc_final: 0.7038 (ttpt) REVERT: B 54 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8591 (mttp) REVERT: C 131 ASP cc_start: 0.5768 (t0) cc_final: 0.5183 (m-30) REVERT: D 87 ASP cc_start: 0.8107 (t70) cc_final: 0.7703 (t0) REVERT: D 115 MET cc_start: 0.7578 (mtm) cc_final: 0.7144 (mtm) REVERT: D 141 TYR cc_start: 0.8509 (t80) cc_final: 0.8237 (t80) REVERT: E 67 ASP cc_start: 0.7479 (m-30) cc_final: 0.7197 (m-30) REVERT: F 50 GLN cc_start: 0.3735 (mm110) cc_final: 0.3364 (tt0) REVERT: F 54 LYS cc_start: 0.4606 (mmtm) cc_final: 0.3750 (mttt) REVERT: F 217 TYR cc_start: 0.5022 (p90) cc_final: 0.4686 (p90) REVERT: F 264 PHE cc_start: 0.3577 (m-80) cc_final: 0.3332 (m-80) REVERT: F 378 CYS cc_start: 0.5787 (OUTLIER) cc_final: 0.5485 (m) outliers start: 31 outliers final: 24 residues processed: 179 average time/residue: 0.2064 time to fit residues: 58.8547 Evaluate side-chains 181 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 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 E residue 57 ASN Chi-restraints excluded: chain F residue 168 ILE 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: 9.9990 chunk 133 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 10 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 174 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.150157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.103214 restraints weight = 63125.941| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.82 r_work: 0.3098 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1954 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= 0.131 Angle : 0.520 14.438 20640 Z= 0.255 Chirality : 0.041 0.431 2330 Planarity : 0.004 0.046 2569 Dihedral : 9.266 70.224 2392 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.82 % Allowed : 16.34 % Favored : 81.84 % 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: 0.71 (0.19), residues: 1877 helix: 1.28 (0.17), residues: 893 sheet: -0.72 (0.39), residues: 177 loop : -0.04 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 273 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 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (15221) covalent geometry : angle 0.49756 / 0.25 (20628) hydrogen bonds : bond 0.04062 / 2.82 ( 756) hydrogen bonds : angle 4.81506 / 3.43 ( 2130) metal coordination : bond 0.01357 / 0.67 ( 8) metal coordination : angle 6.32904 / 3.85 ( 12) Misc. bond : bond 0.00011 / 0.01 ( 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 198 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 0.742 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: 0.7600 (OUTLIER) cc_final: 0.6308 (tpp-160) REVERT: A 342 LYS cc_start: 0.7850 (tttm) cc_final: 0.7073 (ttpt) REVERT: B 367 MET cc_start: 0.8185 (mmm) cc_final: 0.7974 (mmm) REVERT: C 131 ASP cc_start: 0.5756 (t0) cc_final: 0.5164 (m-30) REVERT: D 87 ASP cc_start: 0.8035 (t70) cc_final: 0.7585 (t0) REVERT: D 141 TYR cc_start: 0.8503 (t80) cc_final: 0.8240 (t80) REVERT: E 67 ASP cc_start: 0.7577 (m-30) cc_final: 0.7299 (m-30) REVERT: F 50 GLN cc_start: 0.3776 (mm110) cc_final: 0.3402 (tt0) REVERT: F 54 LYS cc_start: 0.4688 (mmtm) cc_final: 0.3795 (mttt) REVERT: F 119 MET cc_start: 0.3545 (ptp) cc_final: 0.2991 (ptp) REVERT: F 217 TYR cc_start: 0.4967 (p90) cc_final: 0.4690 (p90) REVERT: F 264 PHE cc_start: 0.3511 (m-80) cc_final: 0.3274 (m-80) REVERT: F 372 ASP cc_start: 0.6993 (m-30) cc_final: 0.6272 (t0) REVERT: F 378 CYS cc_start: 0.5805 (OUTLIER) cc_final: 0.5504 (m) outliers start: 28 outliers final: 20 residues processed: 193 average time/residue: 0.2111 time to fit residues: 65.2493 Evaluate side-chains 183 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 134 ARG 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 91 optimal weight: 9.9990 chunk 145 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 147 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 167 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN B 324 ASN F 384 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.149166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.101992 restraints weight = 63546.557| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.83 r_work: 0.3106 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2067 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= 0.181 Angle : 0.547 13.988 20640 Z= 0.270 Chirality : 0.042 0.435 2330 Planarity : 0.004 0.043 2569 Dihedral : 9.277 73.522 2392 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.14 % Allowed : 16.67 % 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: 0.60 (0.19), residues: 1877 helix: 1.20 (0.17), residues: 893 sheet: -0.88 (0.39), residues: 177 loop : -0.07 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 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 0.004 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (15221) covalent geometry : angle 0.52336 / 0.27 (20628) hydrogen bonds : bond 0.04153 / 2.89 ( 756) hydrogen bonds : angle 4.85294 / 3.46 ( 2130) metal coordination : bond 0.01580 / 0.79 ( 8) metal coordination : angle 6.65623 / 4.02 ( 12) Misc. bond : bond 0.00024 / 0.01 ( 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 194 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 0.824 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: 0.7645 (OUTLIER) cc_final: 0.6225 (tpp-160) REVERT: A 342 LYS cc_start: 0.7875 (tttm) cc_final: 0.7109 (ttpt) REVERT: B 54 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8575 (mttp) REVERT: C 131 ASP cc_start: 0.5816 (t0) cc_final: 0.5166 (m-30) REVERT: D 87 ASP cc_start: 0.8103 (t70) cc_final: 0.7700 (t0) REVERT: D 141 TYR cc_start: 0.8496 (t80) cc_final: 0.8234 (t80) REVERT: E 67 ASP cc_start: 0.7603 (m-30) cc_final: 0.7324 (m-30) REVERT: F 50 GLN cc_start: 0.3796 (mm110) cc_final: 0.3302 (tt0) REVERT: F 54 LYS cc_start: 0.4683 (mmtm) cc_final: 0.3803 (mttt) REVERT: F 119 MET cc_start: 0.3527 (ptp) cc_final: 0.2972 (ptp) REVERT: F 217 TYR cc_start: 0.4916 (p90) cc_final: 0.4708 (p90) REVERT: F 264 PHE cc_start: 0.3589 (m-80) cc_final: 0.3314 (m-80) REVERT: F 378 CYS cc_start: 0.5894 (OUTLIER) cc_final: 0.5616 (m) REVERT: F 384 ASN cc_start: 0.6583 (OUTLIER) cc_final: 0.6041 (t0) outliers start: 33 outliers final: 25 residues processed: 187 average time/residue: 0.2046 time to fit residues: 60.6085 Evaluate side-chains 189 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 208 ILE Chi-restraints excluded: chain F residue 377 MET Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 384 ASN 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: 6.9990 chunk 115 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 185 optimal weight: 7.9990 chunk 146 optimal weight: 10.0000 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 160 optimal weight: 10.0000 chunk 184 optimal weight: 1.9990 chunk 180 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN F 244 GLN ** F 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.149770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.102945 restraints weight = 63144.912| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.81 r_work: 0.3099 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2090 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= 0.134 Angle : 0.526 13.882 20640 Z= 0.258 Chirality : 0.041 0.430 2330 Planarity : 0.004 0.041 2569 Dihedral : 9.074 79.909 2392 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.75 % Allowed : 17.12 % Favored : 81.13 % 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: 0.73 (0.19), residues: 1877 helix: 1.31 (0.17), residues: 888 sheet: -0.65 (0.40), residues: 165 loop : -0.06 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 80 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 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (15221) covalent geometry : angle 0.50020 / 0.26 (20628) hydrogen bonds : bond 0.04047 / 2.81 ( 756) hydrogen bonds : angle 4.77349 / 3.40 ( 2130) metal coordination : bond 0.01278 / 0.64 ( 8) metal coordination : angle 6.81670 / 4.10 ( 12) Misc. bond : bond 0.00010 / 0.00 ( 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 194 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 LYS cc_start: 0.7849 (tttm) cc_final: 0.7090 (ttpt) REVERT: C 131 ASP cc_start: 0.5895 (t0) cc_final: 0.5287 (m-30) REVERT: D 87 ASP cc_start: 0.8001 (t70) cc_final: 0.7559 (t0) REVERT: D 115 MET cc_start: 0.7492 (mtm) cc_final: 0.7105 (mtm) REVERT: E 67 ASP cc_start: 0.7593 (m-30) cc_final: 0.7328 (m-30) REVERT: F 50 GLN cc_start: 0.3790 (mm110) cc_final: 0.3296 (tt0) REVERT: F 54 LYS cc_start: 0.4642 (mmtm) cc_final: 0.3752 (mttt) REVERT: F 119 MET cc_start: 0.3578 (ptp) cc_final: 0.3107 (ptp) REVERT: F 264 PHE cc_start: 0.3556 (m-80) cc_final: 0.3290 (m-80) REVERT: F 378 CYS cc_start: 0.5841 (OUTLIER) cc_final: 0.5610 (m) outliers start: 27 outliers final: 23 residues processed: 189 average time/residue: 0.2127 time to fit residues: 64.4119 Evaluate side-chains 187 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 325 VAL 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 D residue 145 LEU 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 378 CYS Chi-restraints excluded: chain F residue 383 MET 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 72 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 181 optimal weight: 9.9990 chunk 178 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN F 244 GLN ** F 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.148732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.101775 restraints weight = 63331.642| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.81 r_work: 0.3102 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15231 Z= 0.197 Angle : 0.566 14.269 20640 Z= 0.279 Chirality : 0.042 0.430 2330 Planarity : 0.004 0.042 2569 Dihedral : 9.146 85.757 2392 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.69 % Allowed : 17.12 % 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: 0.52 (0.19), residues: 1877 helix: 1.13 (0.17), residues: 891 sheet: -0.93 (0.39), residues: 177 loop : -0.12 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 289 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 0.004 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 (15221) covalent geometry : angle 0.53826 / 0.28 (20628) hydrogen bonds : bond 0.04182 / 2.91 ( 756) hydrogen bonds : angle 4.85168 / 3.46 ( 2130) metal coordination : bond 0.01577 / 0.79 ( 8) metal coordination : angle 7.29076 / 4.36 ( 12) Misc. bond : bond 0.00031 / 0.01 ( 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 188 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.772 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: 0.7675 (OUTLIER) cc_final: 0.6306 (tpp-160) REVERT: A 342 LYS cc_start: 0.7858 (tttm) cc_final: 0.7103 (ttpt) REVERT: C 131 ASP cc_start: 0.5923 (t0) cc_final: 0.5298 (m-30) REVERT: D 87 ASP cc_start: 0.8110 (t70) cc_final: 0.7686 (t0) REVERT: D 141 TYR cc_start: 0.8495 (t80) cc_final: 0.8238 (t80) REVERT: E 67 ASP cc_start: 0.7621 (m-30) cc_final: 0.7349 (m-30) REVERT: E 132 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7216 (mtt-85) REVERT: F 50 GLN cc_start: 0.3782 (mm110) cc_final: 0.3276 (tt0) REVERT: F 54 LYS cc_start: 0.4685 (mmtm) cc_final: 0.3772 (mttt) REVERT: F 119 MET cc_start: 0.3558 (ptp) cc_final: 0.2961 (ptp) REVERT: F 264 PHE cc_start: 0.3567 (m-80) cc_final: 0.3309 (m-80) REVERT: F 295 GLN cc_start: 0.5840 (mp10) cc_final: 0.5612 (mp10) REVERT: F 378 CYS cc_start: 0.5881 (OUTLIER) cc_final: 0.5629 (m) outliers start: 26 outliers final: 22 residues processed: 184 average time/residue: 0.2219 time to fit residues: 64.0276 Evaluate side-chains 185 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 378 CYS 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: 3.9990 chunk 175 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 150 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN F 244 GLN ** F 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.150533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.103848 restraints weight = 63256.778| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.81 r_work: 0.3132 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15231 Z= 0.109 Angle : 0.512 13.550 20640 Z= 0.249 Chirality : 0.041 0.417 2330 Planarity : 0.004 0.040 2569 Dihedral : 8.592 81.087 2392 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.56 % Allowed : 17.38 % Favored : 81.06 % 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: 0.81 (0.20), residues: 1877 helix: 1.34 (0.18), residues: 896 sheet: -0.58 (0.41), residues: 165 loop : -0.01 (0.22), residues: 816 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/Z covalent geometry : bond 0.00243 / 0.11 (15221) covalent geometry : angle 0.48613 / 0.25 (20628) hydrogen bonds : bond 0.03845 / 2.67 ( 756) hydrogen bonds : angle 4.69452 / 3.35 ( 2130) metal coordination : bond 0.01171 / 0.58 ( 8) metal coordination : angle 6.61917 / 3.91 ( 12) Misc. bond : bond 0.00010 / 0.00 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6702.57 seconds wall clock time: 114 minutes 17.45 seconds (6857.45 seconds total)