Starting phenix.real_space_refine on Thu Jun 26 10:16:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a1t_15088/06_2025/8a1t_15088_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a1t_15088/06_2025/8a1t_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_15088/06_2025/8a1t_15088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a1t_15088/06_2025/8a1t_15088.map" model { file = "/net/cci-nas-00/data/ceres_data/8a1t_15088/06_2025/8a1t_15088_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a1t_15088/06_2025/8a1t_15088_trim.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29507 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 6880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 6880 Classifications: {'peptide': 446} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 23, 'TRANS': 422} Chain: "B" Number of atoms: 6011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 6011 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 14, 'TRANS': 377} Chain: "C" Number of atoms: 3774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 3774 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain: "D" Number of atoms: 3147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3147 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 9, 'TRANS': 191} Chain: "E" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 3078 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "F" Number of atoms: 6234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 6234 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 24, 'TRANS': 380} Chain: "B" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 213 Unusual residues: {' K': 1, ' NA': 1, '3PE': 2, 'FMN': 1, 'LMT': 2, 'RBF': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'3PE': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'FAD': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18322 SG CYS D 112 66.864 83.803 58.614 1.00 80.66 S ATOM 20214 SG CYS E 26 64.411 83.907 61.435 1.00 74.26 S ATOM 16996 SG CYS D 29 67.273 85.465 64.840 1.00 62.78 S ATOM 21719 SG CYS E 120 70.352 85.885 62.729 1.00 64.82 S ATOM 23920 SG CYS F 70 53.305 69.159 38.939 1.00213.23 S ATOM 23969 SG CYS F 76 51.317 66.358 37.391 1.00210.35 S ATOM 24004 SG CYS F 79 56.224 63.469 37.898 1.00199.79 S ATOM 24488 SG CYS F 111 57.448 66.701 39.384 1.00205.71 S Time building chain proxies: 13.90, per 1000 atoms: 0.47 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: 8.39 Conformation dependent library (CDL) restraints added in 2.5 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: 2.78 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: 11.26 Time building geometry restraints manager: 9.73 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: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.470 Extract box with map and model: 1.110 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 76.270 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 15231 Z= 0.207 Angle : 0.554 9.599 20640 Z= 0.246 Chirality : 0.041 0.231 2330 Planarity : 0.003 0.029 2569 Dihedral : 16.931 120.599 5702 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.51 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (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 TRP 0.011 0.001 TRP B 103 HIS 0.002 0.001 HIS F 356 PHE 0.010 0.001 PHE E 28 TYR 0.008 0.001 TYR F 167 ARG 0.002 0.000 ARG A 318 Details of bonding type rmsd hydrogen bonds : bond 0.20500 ( 756) hydrogen bonds : angle 7.50335 ( 2130) metal coordination : bond 0.02401 ( 8) metal coordination : angle 1.89977 ( 12) covalent geometry : bond 0.00412 (15221) covalent geometry : angle 0.55196 (20628) Misc. bond : bond 0.04867 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 2.268 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: 0.7444 (mmp) REVERT: B 154 GLU cc_start: 0.6927 (tt0) cc_final: 0.6617 (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: 0.3968 (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: 0.5653 time to fit residues: 184.3943 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 : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 0.0170 chunk 140 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 95 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 overall best weight: 2.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN C 199 HIS F 227 ASN F 400 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.151363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.103418 restraints weight = 63333.289| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.84 r_work: 0.3121 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 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= 0.176 Angle : 0.564 12.829 20640 Z= 0.287 Chirality : 0.042 0.336 2330 Planarity : 0.004 0.041 2569 Dihedral : 11.557 89.749 2392 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.04 % Allowed : 14.14 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.19), residues: 1877 helix: 1.52 (0.17), residues: 895 sheet: -0.33 (0.38), residues: 184 loop : 0.29 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 103 HIS 0.003 0.001 HIS B 328 PHE 0.015 0.001 PHE F 128 TYR 0.022 0.001 TYR F 217 ARG 0.004 0.000 ARG F 303 Details of bonding type rmsd hydrogen bonds : bond 0.05524 ( 756) hydrogen bonds : angle 5.54439 ( 2130) metal coordination : bond 0.01572 ( 8) metal coordination : angle 6.57955 ( 12) covalent geometry : bond 0.00380 (15221) covalent geometry : angle 0.54141 (20628) Misc. bond : bond 0.00062 ( 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 195 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 2.459 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: 0.7998 (m-30) cc_final: 0.7468 (m-30) REVERT: B 69 PHE cc_start: 0.8649 (m-10) cc_final: 0.8326 (m-80) REVERT: B 112 MET cc_start: 0.7923 (mmp) cc_final: 0.7201 (mmp) REVERT: D 87 ASP cc_start: 0.8056 (t70) cc_final: 0.7650 (t0) REVERT: D 115 MET cc_start: 0.7310 (mtm) cc_final: 0.6647 (mtm) REVERT: D 146 MET cc_start: 0.8672 (mmp) cc_final: 0.8323 (mmp) REVERT: E 197 GLN cc_start: 0.3910 (pm20) cc_final: 0.3653 (pm20) REVERT: F 54 LYS cc_start: 0.4591 (mmtm) cc_final: 0.3921 (mttt) REVERT: F 217 TYR cc_start: 0.4869 (p90) cc_final: 0.4548 (p90) REVERT: F 406 PHE cc_start: 0.2829 (p90) cc_final: 0.2585 (p90) outliers start: 16 outliers final: 13 residues processed: 185 average time/residue: 0.5542 time to fit residues: 158.1694 Evaluate side-chains 178 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 2.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU 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 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 114 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 137 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 163 optimal weight: 20.0000 chunk 76 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN C 110 GLN E 61 ASN F 400 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.149053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.101256 restraints weight = 64126.715| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.84 r_work: 0.3083 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 15231 Z= 0.247 Angle : 0.616 16.678 20640 Z= 0.303 Chirality : 0.044 0.459 2330 Planarity : 0.004 0.045 2569 Dihedral : 10.619 84.752 2392 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.36 % Allowed : 15.56 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.19), residues: 1877 helix: 1.06 (0.17), residues: 893 sheet: -0.81 (0.38), residues: 177 loop : 0.03 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 103 HIS 0.015 0.002 HIS C 199 PHE 0.016 0.002 PHE E 28 TYR 0.015 0.002 TYR B 360 ARG 0.004 0.001 ARG A 372 Details of bonding type rmsd hydrogen bonds : bond 0.05239 ( 756) hydrogen bonds : angle 5.28854 ( 2130) metal coordination : bond 0.02200 ( 8) metal coordination : angle 8.22978 ( 12) covalent geometry : bond 0.00560 (15221) covalent geometry : angle 0.58377 (20628) Misc. bond : bond 0.00036 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 2.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.6297 (tpp-160) REVERT: A 342 LYS cc_start: 0.7813 (tttm) cc_final: 0.7044 (ttpt) REVERT: A 403 ASP cc_start: 0.8077 (m-30) cc_final: 0.7463 (m-30) REVERT: D 87 ASP cc_start: 0.8066 (t70) cc_final: 0.7674 (t0) REVERT: D 115 MET cc_start: 0.7348 (mtm) cc_final: 0.6923 (mtm) REVERT: F 54 LYS cc_start: 0.4651 (mmtm) cc_final: 0.3825 (mttt) REVERT: F 217 TYR cc_start: 0.5110 (p90) cc_final: 0.4699 (p90) outliers start: 21 outliers final: 16 residues processed: 189 average time/residue: 0.5432 time to fit residues: 162.0277 Evaluate side-chains 176 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 2.328 ------------------------------------------------------------------------------- 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 31 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 192 TRP Chi-restraints excluded: chain F residue 204 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 123 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 74 optimal weight: 0.5980 chunk 64 optimal weight: 5.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN F 400 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.150076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.102670 restraints weight = 64226.019| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.86 r_work: 0.3104 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15231 Z= 0.156 Angle : 0.547 13.883 20640 Z= 0.267 Chirality : 0.042 0.438 2330 Planarity : 0.004 0.043 2569 Dihedral : 9.997 84.080 2392 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.30 % Allowed : 15.89 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.19), residues: 1877 helix: 1.15 (0.17), residues: 895 sheet: -0.62 (0.40), residues: 165 loop : -0.01 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.003 0.001 HIS B 328 PHE 0.014 0.001 PHE E 28 TYR 0.016 0.001 TYR B 360 ARG 0.002 0.000 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.04471 ( 756) hydrogen bonds : angle 5.04030 ( 2130) metal coordination : bond 0.01522 ( 8) metal coordination : angle 7.14590 ( 12) covalent geometry : bond 0.00350 (15221) covalent geometry : angle 0.51961 (20628) Misc. bond : bond 0.00019 ( 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 183 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 3.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.6355 (tpp-160) REVERT: A 342 LYS cc_start: 0.7819 (tttm) cc_final: 0.6993 (ttpt) REVERT: A 403 ASP cc_start: 0.8077 (m-30) cc_final: 0.7421 (m-30) REVERT: C 131 ASP cc_start: 0.5700 (t0) cc_final: 0.5176 (m-30) REVERT: D 87 ASP cc_start: 0.8100 (t70) cc_final: 0.7691 (t0) REVERT: D 141 TYR cc_start: 0.8489 (t80) cc_final: 0.8230 (t80) REVERT: F 50 GLN cc_start: 0.3768 (mm110) cc_final: 0.3420 (tt0) REVERT: F 54 LYS cc_start: 0.4648 (mmtm) cc_final: 0.3809 (mttt) REVERT: F 217 TYR cc_start: 0.5089 (p90) cc_final: 0.4730 (p90) outliers start: 20 outliers final: 17 residues processed: 176 average time/residue: 0.5442 time to fit residues: 153.5086 Evaluate side-chains 175 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 2.195 ------------------------------------------------------------------------------- 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 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 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 49 LEU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 192 TRP Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 383 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 40 optimal weight: 5.9990 chunk 172 optimal weight: 20.0000 chunk 64 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 173 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN F 400 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.150408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.103296 restraints weight = 63399.447| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.83 r_work: 0.3116 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15231 Z= 0.136 Angle : 0.521 13.340 20640 Z= 0.255 Chirality : 0.041 0.435 2330 Planarity : 0.004 0.041 2569 Dihedral : 9.455 80.106 2392 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.49 % Allowed : 15.95 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.19), residues: 1877 helix: 1.30 (0.17), residues: 895 sheet: -0.53 (0.40), residues: 165 loop : 0.04 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.003 0.001 HIS B 328 PHE 0.014 0.001 PHE E 28 TYR 0.016 0.001 TYR B 360 ARG 0.002 0.000 ARG F 303 Details of bonding type rmsd hydrogen bonds : bond 0.04182 ( 756) hydrogen bonds : angle 4.85484 ( 2130) metal coordination : bond 0.01480 ( 8) metal coordination : angle 6.34783 ( 12) covalent geometry : bond 0.00306 (15221) covalent geometry : angle 0.49840 (20628) Misc. bond : bond 0.00010 ( 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 190 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 3.194 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: 0.7799 (tttm) cc_final: 0.7018 (ttpt) REVERT: A 403 ASP cc_start: 0.8072 (m-30) cc_final: 0.7411 (m-30) REVERT: C 131 ASP cc_start: 0.5697 (t0) cc_final: 0.5178 (m-30) REVERT: D 87 ASP cc_start: 0.8107 (t70) cc_final: 0.7689 (t0) REVERT: E 67 ASP cc_start: 0.7433 (m-30) cc_final: 0.7148 (m-30) REVERT: F 50 GLN cc_start: 0.3886 (mm110) cc_final: 0.3460 (tt0) REVERT: F 54 LYS cc_start: 0.4657 (mmtm) cc_final: 0.3816 (mttt) REVERT: F 119 MET cc_start: 0.3919 (OUTLIER) cc_final: 0.2767 (mtm) REVERT: F 217 TYR cc_start: 0.4980 (p90) cc_final: 0.4630 (p90) outliers start: 23 outliers final: 19 residues processed: 183 average time/residue: 0.7904 time to fit residues: 234.5387 Evaluate side-chains 176 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 192 TRP Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 377 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 22 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.150484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.103407 restraints weight = 63656.798| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.85 r_work: 0.3103 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1844 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 : 0.513 13.593 20640 Z= 0.251 Chirality : 0.041 0.432 2330 Planarity : 0.004 0.040 2569 Dihedral : 9.191 76.220 2392 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.69 % Allowed : 15.89 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.19), residues: 1877 helix: 1.35 (0.17), residues: 899 sheet: -0.57 (0.40), residues: 165 loop : 0.07 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.003 0.001 HIS B 328 PHE 0.013 0.001 PHE E 28 TYR 0.016 0.001 TYR B 360 ARG 0.002 0.000 ARG F 303 Details of bonding type rmsd hydrogen bonds : bond 0.04012 ( 756) hydrogen bonds : angle 4.78848 ( 2130) metal coordination : bond 0.01303 ( 8) metal coordination : angle 6.35362 ( 12) covalent geometry : bond 0.00294 (15221) covalent geometry : angle 0.48981 (20628) Misc. bond : bond 0.00012 ( 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 194 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 2.156 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: 0.7558 (OUTLIER) cc_final: 0.6358 (tpp-160) REVERT: A 342 LYS cc_start: 0.7791 (tttm) cc_final: 0.7011 (ttpt) REVERT: A 403 ASP cc_start: 0.8091 (m-30) cc_final: 0.7636 (m-30) REVERT: C 131 ASP cc_start: 0.5708 (t0) cc_final: 0.5163 (m-30) REVERT: C 229 ASN cc_start: 0.8157 (m-40) cc_final: 0.7781 (m110) REVERT: D 87 ASP cc_start: 0.8027 (t70) cc_final: 0.7586 (t0) REVERT: D 115 MET cc_start: 0.7452 (mtm) cc_final: 0.7043 (mtm) REVERT: E 67 ASP cc_start: 0.7463 (m-30) cc_final: 0.7172 (m-30) REVERT: F 50 GLN cc_start: 0.3949 (mm110) cc_final: 0.3524 (tt0) REVERT: F 54 LYS cc_start: 0.4655 (mmtm) cc_final: 0.3824 (mttt) outliers start: 26 outliers final: 20 residues processed: 186 average time/residue: 0.5470 time to fit residues: 162.1590 Evaluate side-chains 182 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 2.113 ------------------------------------------------------------------------------- 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 C residue 26 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 192 TRP Chi-restraints excluded: chain F residue 401 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 12 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 177 optimal weight: 20.0000 chunk 72 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 175 optimal weight: 4.9990 chunk 173 optimal weight: 9.9990 chunk 135 optimal weight: 7.9990 chunk 153 optimal weight: 0.0070 chunk 58 optimal weight: 2.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** F 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.150267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.103000 restraints weight = 63459.549| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.85 r_work: 0.3120 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15231 Z= 0.143 Angle : 0.518 13.033 20640 Z= 0.254 Chirality : 0.041 0.426 2330 Planarity : 0.004 0.040 2569 Dihedral : 9.054 71.820 2392 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.62 % Allowed : 16.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.19), residues: 1877 helix: 1.36 (0.17), residues: 899 sheet: -0.80 (0.39), residues: 177 loop : 0.11 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.003 0.001 HIS B 328 PHE 0.014 0.001 PHE E 28 TYR 0.016 0.001 TYR B 360 ARG 0.003 0.000 ARG F 289 Details of bonding type rmsd hydrogen bonds : bond 0.03984 ( 756) hydrogen bonds : angle 4.76235 ( 2130) metal coordination : bond 0.01325 ( 8) metal coordination : angle 6.29242 ( 12) covalent geometry : bond 0.00324 (15221) covalent geometry : angle 0.49513 (20628) Misc. bond : bond 0.00014 ( 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 191 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 2.215 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: 0.7574 (OUTLIER) cc_final: 0.6234 (tpp-160) REVERT: A 342 LYS cc_start: 0.7841 (tttm) cc_final: 0.7050 (ttpt) REVERT: A 403 ASP cc_start: 0.8138 (m-30) cc_final: 0.7683 (m-30) REVERT: C 131 ASP cc_start: 0.5809 (t0) cc_final: 0.5173 (m-30) REVERT: C 229 ASN cc_start: 0.8143 (m-40) cc_final: 0.7811 (m110) REVERT: D 87 ASP cc_start: 0.8021 (t70) cc_final: 0.7579 (t0) REVERT: E 67 ASP cc_start: 0.7588 (m-30) cc_final: 0.7312 (m-30) REVERT: F 54 LYS cc_start: 0.4642 (mmtm) cc_final: 0.3825 (mttt) REVERT: F 119 MET cc_start: 0.3904 (ptp) cc_final: 0.3126 (ptp) outliers start: 25 outliers final: 22 residues processed: 184 average time/residue: 0.5200 time to fit residues: 152.2660 Evaluate side-chains 183 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 2.273 ------------------------------------------------------------------------------- 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 65 PHE Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain 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 F residue 192 TRP Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 384 ASN Chi-restraints excluded: chain F residue 401 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 129 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 115 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 143 optimal weight: 0.0980 chunk 101 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** F 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.150540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.103792 restraints weight = 63516.244| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.82 r_work: 0.3126 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15231 Z= 0.124 Angle : 0.508 12.700 20640 Z= 0.249 Chirality : 0.041 0.417 2330 Planarity : 0.004 0.040 2569 Dihedral : 8.802 68.477 2392 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.49 % Allowed : 16.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.19), residues: 1877 helix: 1.42 (0.17), residues: 899 sheet: -0.77 (0.39), residues: 177 loop : 0.15 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 103 HIS 0.003 0.001 HIS B 328 PHE 0.014 0.001 PHE E 28 TYR 0.016 0.001 TYR B 360 ARG 0.002 0.000 ARG B 209 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 756) hydrogen bonds : angle 4.70839 ( 2130) metal coordination : bond 0.01284 ( 8) metal coordination : angle 6.10507 ( 12) covalent geometry : bond 0.00280 (15221) covalent geometry : angle 0.48678 (20628) Misc. bond : bond 0.00010 ( 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 192 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 2.224 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: 0.7534 (OUTLIER) cc_final: 0.6339 (tpp-160) REVERT: A 342 LYS cc_start: 0.7854 (tttm) cc_final: 0.7090 (ttpt) REVERT: A 403 ASP cc_start: 0.8110 (m-30) cc_final: 0.7649 (m-30) REVERT: B 69 PHE cc_start: 0.8525 (m-10) cc_final: 0.8277 (m-80) REVERT: C 131 ASP cc_start: 0.5751 (t0) cc_final: 0.5170 (m-30) REVERT: C 215 GLU cc_start: 0.5836 (mt-10) cc_final: 0.5577 (mm-30) REVERT: C 229 ASN cc_start: 0.8148 (m-40) cc_final: 0.7831 (m110) REVERT: D 87 ASP cc_start: 0.8028 (t70) cc_final: 0.7581 (t0) REVERT: E 67 ASP cc_start: 0.7574 (m-30) cc_final: 0.7298 (m-30) REVERT: F 50 GLN cc_start: 0.3551 (tp40) cc_final: 0.3283 (tt0) REVERT: F 54 LYS cc_start: 0.4652 (mmtm) cc_final: 0.3793 (mttt) REVERT: F 119 MET cc_start: 0.3914 (ptp) cc_final: 0.3078 (ptp) REVERT: F 372 ASP cc_start: 0.6869 (m-30) cc_final: 0.6408 (t0) outliers start: 23 outliers final: 19 residues processed: 186 average time/residue: 0.7400 time to fit residues: 220.8476 Evaluate side-chains 183 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 4.154 ------------------------------------------------------------------------------- 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 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 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 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 F residue 192 TRP Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 384 ASN Chi-restraints excluded: chain F residue 401 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 136 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 98 optimal weight: 8.9990 chunk 138 optimal weight: 0.5980 chunk 172 optimal weight: 30.0000 chunk 88 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 176 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** F 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.149801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.102885 restraints weight = 63499.904| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.82 r_work: 0.3121 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15231 Z= 0.156 Angle : 0.528 13.186 20640 Z= 0.259 Chirality : 0.041 0.412 2330 Planarity : 0.004 0.041 2569 Dihedral : 8.731 80.690 2392 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.62 % Allowed : 16.60 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.19), residues: 1877 helix: 1.37 (0.17), residues: 896 sheet: -0.85 (0.39), residues: 179 loop : 0.09 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.003 0.001 HIS B 328 PHE 0.014 0.001 PHE E 28 TYR 0.016 0.001 TYR B 360 ARG 0.002 0.000 ARG F 80 Details of bonding type rmsd hydrogen bonds : bond 0.03945 ( 756) hydrogen bonds : angle 4.72352 ( 2130) metal coordination : bond 0.01375 ( 8) metal coordination : angle 6.49324 ( 12) covalent geometry : bond 0.00354 (15221) covalent geometry : angle 0.50492 (20628) Misc. bond : bond 0.00017 ( 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 193 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 3.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.6226 (tpp-160) REVERT: A 342 LYS cc_start: 0.7857 (tttm) cc_final: 0.7098 (ttpt) REVERT: A 403 ASP cc_start: 0.8114 (m-30) cc_final: 0.7641 (m-30) REVERT: B 54 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8556 (mttp) REVERT: B 69 PHE cc_start: 0.8534 (m-10) cc_final: 0.8285 (m-80) REVERT: C 131 ASP cc_start: 0.5759 (t0) cc_final: 0.5138 (m-30) REVERT: C 229 ASN cc_start: 0.8174 (m-40) cc_final: 0.7854 (m110) REVERT: D 87 ASP cc_start: 0.7999 (t70) cc_final: 0.7554 (t0) REVERT: E 67 ASP cc_start: 0.7598 (m-30) cc_final: 0.7332 (m-30) REVERT: F 50 GLN cc_start: 0.3560 (tp40) cc_final: 0.3324 (tt0) REVERT: F 54 LYS cc_start: 0.4664 (mmtm) cc_final: 0.3803 (mttt) REVERT: F 119 MET cc_start: 0.3693 (ptp) cc_final: 0.2669 (ptp) REVERT: F 133 TRP cc_start: 0.5828 (m-90) cc_final: 0.5613 (m-90) REVERT: F 264 PHE cc_start: 0.3504 (m-80) cc_final: 0.3274 (m-80) outliers start: 25 outliers final: 22 residues processed: 186 average time/residue: 0.8857 time to fit residues: 270.8179 Evaluate side-chains 188 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 6.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain B residue 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 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 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 204 VAL 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 113 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.150485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.103705 restraints weight = 63382.485| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.83 r_work: 0.3130 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15231 Z= 0.123 Angle : 0.508 12.550 20640 Z= 0.249 Chirality : 0.041 0.402 2330 Planarity : 0.004 0.041 2569 Dihedral : 8.510 89.790 2392 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.43 % Allowed : 16.93 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.19), residues: 1877 helix: 1.43 (0.17), residues: 897 sheet: -0.80 (0.39), residues: 179 loop : 0.14 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 103 HIS 0.003 0.001 HIS B 101 PHE 0.014 0.001 PHE E 28 TYR 0.016 0.001 TYR B 360 ARG 0.002 0.000 ARG B 209 Details of bonding type rmsd hydrogen bonds : bond 0.03808 ( 756) hydrogen bonds : angle 4.66146 ( 2130) metal coordination : bond 0.01249 ( 8) metal coordination : angle 6.17326 ( 12) covalent geometry : bond 0.00277 (15221) covalent geometry : angle 0.48591 (20628) Misc. bond : bond 0.00010 ( 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 190 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 2.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.6330 (tpp-160) REVERT: A 342 LYS cc_start: 0.7833 (tttm) cc_final: 0.7078 (ttpt) REVERT: A 403 ASP cc_start: 0.8110 (m-30) cc_final: 0.7631 (m-30) REVERT: B 69 PHE cc_start: 0.8512 (m-10) cc_final: 0.8278 (m-80) REVERT: C 131 ASP cc_start: 0.5842 (t0) cc_final: 0.5142 (m-30) REVERT: C 215 GLU cc_start: 0.5854 (mt-10) cc_final: 0.5562 (mm-30) REVERT: C 229 ASN cc_start: 0.8131 (m-40) cc_final: 0.7814 (m110) REVERT: E 67 ASP cc_start: 0.7535 (m-30) cc_final: 0.7226 (m-30) REVERT: F 50 GLN cc_start: 0.3589 (tp40) cc_final: 0.3349 (tt0) REVERT: F 54 LYS cc_start: 0.4641 (mmtm) cc_final: 0.3757 (mttt) REVERT: F 119 MET cc_start: 0.3465 (ptp) cc_final: 0.2490 (ptp) REVERT: F 133 TRP cc_start: 0.5843 (m-90) cc_final: 0.5585 (m-90) REVERT: F 295 GLN cc_start: 0.5916 (mp10) cc_final: 0.5685 (mp10) REVERT: F 372 ASP cc_start: 0.6525 (m-30) cc_final: 0.6218 (t0) outliers start: 22 outliers final: 20 residues processed: 184 average time/residue: 0.5106 time to fit residues: 147.9229 Evaluate side-chains 184 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain B residue 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 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 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 F residue 192 TRP Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 401 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 43 optimal weight: 2.9990 chunk 164 optimal weight: 8.9990 chunk 154 optimal weight: 20.0000 chunk 57 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 183 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.151127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.104478 restraints weight = 63167.136| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.82 r_work: 0.3130 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15231 Z= 0.109 Angle : 0.496 12.267 20640 Z= 0.243 Chirality : 0.040 0.386 2330 Planarity : 0.004 0.040 2569 Dihedral : 8.186 81.808 2392 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.77 % Favored : 97.18 % Rotamer: Outliers : 1.30 % Allowed : 16.99 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.20), residues: 1877 helix: 1.49 (0.18), residues: 897 sheet: -0.75 (0.41), residues: 169 loop : 0.23 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 103 HIS 0.003 0.001 HIS B 101 PHE 0.013 0.001 PHE E 28 TYR 0.016 0.001 TYR B 360 ARG 0.002 0.000 ARG B 209 Details of bonding type rmsd hydrogen bonds : bond 0.03687 ( 756) hydrogen bonds : angle 4.59438 ( 2130) metal coordination : bond 0.01074 ( 8) metal coordination : angle 6.12589 ( 12) covalent geometry : bond 0.00245 (15221) covalent geometry : angle 0.47389 (20628) Misc. bond : bond 0.00007 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16472.05 seconds wall clock time: 294 minutes 32.20 seconds (17672.20 seconds total)