Starting phenix.real_space_refine on Fri Mar 6 10:47:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a1x_15092/03_2026/8a1x_15092_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a1x_15092/03_2026/8a1x_15092.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8a1x_15092/03_2026/8a1x_15092_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a1x_15092/03_2026/8a1x_15092_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8a1x_15092/03_2026/8a1x_15092.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a1x_15092/03_2026/8a1x_15092.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 6 5.49 5 S 90 5.16 5 C 9621 2.51 5 N 2414 2.21 5 O 2720 1.98 5 H 14655 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29510 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 6879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 6879 Classifications: {'peptide': 446} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 23, 'TRANS': 422} Chain: "B" Number of atoms: 6086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 6086 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 14, 'TRANS': 381} 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: 3154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3154 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 9, 'TRANS': 191} Chain: "E" Number of atoms: 3041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 3041 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain: "F" Number of atoms: 6246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 6246 Classifications: {'peptide': 407} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 382} Chain: "B" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 160 Unusual residues: {'3PE': 1, 'FMN': 1, 'LMT': 2, 'RBF': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'3PE': 1, 'LMT': 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'FAD': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18403 SG CYS D 112 65.875 82.945 59.148 1.00 59.70 S ATOM 20295 SG CYS E 26 63.347 83.271 61.745 1.00 71.64 S ATOM 17070 SG CYS D 29 65.762 83.991 65.280 1.00 73.51 S ATOM 21800 SG CYS E 120 69.101 85.136 64.226 1.00 76.26 S ATOM 23964 SG CYS F 70 52.567 68.460 38.977 1.00 74.33 S ATOM 24013 SG CYS F 76 50.482 65.790 37.319 1.00 72.64 S ATOM 24047 SG CYS F 79 55.306 62.683 38.007 1.00 68.99 S ATOM 24531 SG CYS F 111 56.531 65.890 39.571 1.00 54.96 S Time building chain proxies: 5.07, per 1000 atoms: 0.17 Number of scatterers: 29510 At special positions: 0 Unit cell: (110.94, 135.871, 130.885, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 S 90 16.00 P 6 15.00 O 2720 8.00 N 2414 7.00 C 9621 6.00 H 14655 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 728.5 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E1001 " pdb="FE1 FES E1001 " - pdb=" SG CYS E 26 " pdb="FE2 FES E1001 " - pdb=" SG CYS D 29 " pdb="FE1 FES E1001 " - pdb=" SG CYS D 112 " pdb="FE2 FES E1001 " - pdb=" SG CYS E 120 " pdb=" FES F1502 " pdb="FE1 FES F1502 " - pdb=" SG CYS F 76 " pdb="FE2 FES F1502 " - pdb=" SG CYS F 79 " pdb="FE2 FES F1502 " - pdb=" SG CYS F 111 " pdb="FE1 FES F1502 " - pdb=" SG CYS F 70 " Number of angles added : 12 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3420 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 13 sheets defined 54.6% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.774A pdb=" N LEU A 113 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 125 Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 162 through 170 removed outlier: 3.557A pdb=" N VAL A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 3.559A 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: 3.692A pdb=" N HIS A 354 " --> pdb=" O PHE A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 384 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 418 through 424 Processing helix chain 'A' and resid 430 through 446 Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 23 through 35 Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.531A pdb=" N VAL B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 87 Processing helix chain 'B' and resid 89 through 99 Processing helix chain 'B' and resid 99 through 108 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: 4.213A pdb=" N VAL B 161 " --> pdb=" O GLU B 157 " (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 221 removed outlier: 3.968A pdb=" N SER B 221 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 245 Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 259 through 266 Processing helix chain 'B' and resid 276 through 290 removed outlier: 3.552A pdb=" N LEU B 280 " --> pdb=" O SER B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 316 removed outlier: 3.519A pdb=" N ILE B 298 " --> pdb=" O SER B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 325 Processing helix chain 'B' and resid 326 through 333 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 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: 3.660A pdb=" N SER C 23 " --> pdb=" O SER C 19 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASP C 35 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS C 36 " --> pdb=" O GLY C 32 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU C 39 " --> pdb=" O ASP C 35 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP C 44 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYS C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 70 Processing helix chain 'C' and resid 92 through 98 removed outlier: 3.535A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 181 removed outlier: 3.924A pdb=" N VAL C 180 " --> pdb=" O GLY C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 188 Processing helix chain 'C' and resid 224 through 239 Processing helix chain 'C' and resid 244 through 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 35 removed outlier: 3.544A pdb=" N ALA D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA D 33 " --> pdb=" O CYS D 29 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR D 35 " --> pdb=" O ALA D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 62 Processing helix chain 'D' and resid 70 through 93 removed outlier: 3.640A pdb=" N ILE D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE D 79 " --> pdb=" O GLN D 75 " (cutoff:3.500A) 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 120 removed outlier: 3.837A pdb=" N MET D 115 " --> pdb=" O ASN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 125 removed outlier: 4.172A pdb=" N SER D 125 " --> pdb=" O ALA D 122 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 183 through 202 removed outlier: 4.289A pdb=" N ALA D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 206 Processing helix chain 'E' and resid 3 through 13 Processing helix chain 'E' and resid 24 through 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: 3.655A pdb=" N VAL E 86 " --> pdb=" O THR E 82 " (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 165 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: 3.536A pdb=" N ALA F 58 " --> pdb=" O LYS F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 98 removed outlier: 3.602A pdb=" N LEU F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP F 96 " --> pdb=" O PRO F 92 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N HIS F 97 " --> pdb=" O THR F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 106 Processing helix chain 'F' and resid 124 through 129 Processing helix chain 'F' and resid 155 through 158 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 188 Processing helix chain 'F' and resid 189 through 196 Processing helix chain 'F' and resid 197 through 199 No H-bonds generated for 'chain 'F' and resid 197 through 199' Processing helix chain 'F' and resid 243 through 252 Processing helix chain 'F' and resid 284 through 297 Processing helix chain 'F' and resid 313 through 317 Processing helix chain 'F' and resid 319 through 330 Processing helix chain 'F' and resid 343 through 347 Processing helix chain 'F' and resid 354 through 363 Processing helix chain 'F' and resid 369 through 373 Processing helix chain 'F' and resid 380 through 394 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 6.177A pdb=" N VAL A 189 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N HIS A 209 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL A 191 " --> pdb=" O HIS A 209 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N PHE A 211 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LYS A 193 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE A 149 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N CYS A 192 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL A 151 " --> pdb=" O CYS A 192 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 22 removed outlier: 5.712A 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 32 removed outlier: 6.721A pdb=" N LEU A 87 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ARG A 81 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N SER A 89 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ILE A 79 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.981A 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: 7.325A pdb=" N PHE A 68 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 250 through 251 Processing sheet with id=AA6, first strand: chain 'C' and resid 82 through 84 removed outlier: 4.197A pdb=" N LEU C 75 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 15.138A pdb=" N VAL C 121 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 11.564A pdb=" N VAL C 140 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N VAL C 123 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU C 138 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TYR C 125 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL C 136 " --> pdb=" O TYR C 125 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL C 127 " --> pdb=" O SER C 134 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE C 152 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N TYR C 167 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ALA C 154 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU C 165 " --> pdb=" O ALA C 154 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N GLU C 156 " --> pdb=" O SER C 163 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N SER C 163 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 103 through 105 Processing sheet with id=AA8, first strand: chain 'C' and resid 204 through 206 removed outlier: 6.494A pdb=" N LYS C 204 " --> pdb=" O VAL C 218 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AB1, first strand: chain 'F' and resid 47 through 49 removed outlier: 6.729A pdb=" N THR F 36 " --> pdb=" O MET F 119 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N LEU F 121 " --> pdb=" O THR F 36 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N SER F 38 " --> pdb=" O LEU F 121 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER F 85 " --> pdb=" O ASP F 120 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 208 through 213 removed outlier: 7.554A pdb=" N GLN F 169 " --> pdb=" O GLY F 262 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N GLY F 262 " --> pdb=" O GLN F 169 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLU F 171 " --> pdb=" O ILE F 260 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ILE F 260 " --> pdb=" O GLU F 171 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LYS F 151 " --> pdb=" O ILE F 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 175 through 178 Processing sheet with id=AB4, first strand: chain 'F' and resid 333 through 339 removed outlier: 6.476A pdb=" N MET F 305 " --> pdb=" O VAL F 334 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N HIS F 336 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N TYR F 307 " --> pdb=" O HIS F 336 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ALA F 338 " --> pdb=" O TYR F 307 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TYR F 309 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TYR F 375 " --> pdb=" O LEU F 402 " (cutoff:3.500A) 765 hydrogen bonds defined for protein. 2148 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.80 Time building geometry restraints manager: 3.63 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: 14642 1.11 - 1.38: 5850 1.38 - 1.66: 9203 1.66 - 1.93: 151 1.93 - 2.21: 8 Bond restraints: 29854 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 2.34e+01 bond pdb=" C4 FMN B 501 " pdb=" C4A FMN B 501 " ideal model delta sigma weight residual 1.485 1.389 0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" O3P FAD F1501 " pdb=" P FAD F1501 " ideal model delta sigma weight residual 1.660 1.584 0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C4 RBF B 502 " pdb=" C4A RBF B 502 " ideal model delta sigma weight residual 1.481 1.405 0.076 2.00e-02 2.50e+03 1.43e+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 ... (remaining 29849 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.69: 53942 6.69 - 13.39: 16 13.39 - 20.08: 1 20.08 - 26.77: 2 26.77 - 33.46: 3 Bond angle restraints: 53964 Sorted by residual: angle pdb=" HG2 PRO F 92 " pdb=" CG PRO F 92 " pdb=" HG3 PRO F 92 " ideal model delta sigma weight residual 110.00 76.54 33.46 3.00e+00 1.11e-01 1.24e+02 angle pdb=" CD PRO F 92 " pdb=" CG PRO F 92 " pdb=" HG2 PRO F 92 " ideal model delta sigma weight residual 110.00 79.87 30.13 3.00e+00 1.11e-01 1.01e+02 angle pdb=" CB PRO F 92 " pdb=" CG PRO F 92 " pdb=" HG3 PRO F 92 " ideal model delta sigma weight residual 109.00 78.90 30.10 3.00e+00 1.11e-01 1.01e+02 angle pdb=" CD PRO F 92 " pdb=" CG PRO F 92 " pdb=" HG3 PRO F 92 " ideal model delta sigma weight residual 110.00 133.74 -23.74 3.00e+00 1.11e-01 6.26e+01 angle pdb=" CB PRO F 92 " pdb=" CG PRO F 92 " pdb=" HG2 PRO F 92 " ideal model delta sigma weight residual 109.00 131.01 -22.01 3.00e+00 1.11e-01 5.38e+01 ... (remaining 53959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.90: 13176 24.90 - 49.80: 785 49.80 - 74.69: 201 74.69 - 99.59: 26 99.59 - 124.49: 6 Dihedral angle restraints: 14194 sinusoidal: 7799 harmonic: 6395 Sorted by residual: dihedral pdb=" C2B LMT B 503 " pdb=" C1B LMT B 503 " pdb=" O5B LMT B 503 " pdb=" C5B LMT B 503 " ideal model delta sinusoidal sigma weight residual -57.12 67.37 -124.49 1 3.00e+01 1.11e-03 1.67e+01 dihedral pdb=" C5B LMT B 503 " pdb=" C1B LMT B 503 " pdb=" O5B LMT B 503 " pdb=" O1B LMT B 503 " ideal model delta sinusoidal sigma weight residual 295.61 171.51 124.10 1 3.00e+01 1.11e-03 1.66e+01 dihedral pdb=" O1B LMT B 504 " pdb=" C1B LMT B 504 " pdb=" C2B LMT B 504 " pdb=" O2B LMT B 504 " ideal model delta sinusoidal sigma weight residual 53.26 -70.44 123.70 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 14191 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1873 0.044 - 0.089: 310 0.089 - 0.133: 131 0.133 - 0.178: 6 0.178 - 0.222: 10 Chirality restraints: 2330 Sorted by residual: chirality pdb=" C4' LMT B 504 " pdb=" C3' LMT B 504 " pdb=" C5' LMT B 504 " pdb=" O1B LMT B 504 " both_signs ideal model delta sigma weight residual False -2.55 -2.78 0.22 2.00e-01 2.50e+01 1.23e+00 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 -2.77 0.22 2.00e-01 2.50e+01 1.21e+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 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 2327 not shown) Planarity restraints: 4374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 113 " 0.062 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO E 114 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO E 114 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO E 114 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 74 " 0.008 2.00e-02 2.50e+03 1.55e-02 2.40e+00 pdb=" C ASP E 74 " -0.027 2.00e-02 2.50e+03 pdb=" O ASP E 74 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU E 75 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 70 " 0.025 5.00e-02 4.00e+02 3.82e-02 2.34e+00 pdb=" N PRO A 71 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 71 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 71 " 0.021 5.00e-02 4.00e+02 ... (remaining 4371 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 759 2.13 - 2.75: 54305 2.75 - 3.37: 88126 3.37 - 3.98: 113799 3.98 - 4.60: 178383 Nonbonded interactions: 435372 Sorted by model distance: nonbonded pdb=" H ALA F 215 " pdb=" O MET F 225 " model vdw 1.513 2.450 nonbonded pdb=" OE1 GLU C 197 " pdb=" H GLU C 197 " model vdw 1.540 2.450 nonbonded pdb=" OD1 ASP A 414 " pdb=" H GLU A 415 " model vdw 1.571 2.450 nonbonded pdb=" O PRO E 114 " pdb=" HG1 THR E 117 " model vdw 1.582 2.450 nonbonded pdb=" OE1 GLU C 56 " pdb=" H GLU C 56 " model vdw 1.602 2.450 ... (remaining 435367 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: 0.510 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: 0.160 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 34.320 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 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 0.130 15209 Z= 0.213 Angle : 0.674 28.132 20619 Z= 0.287 Chirality : 0.042 0.222 2330 Planarity : 0.003 0.091 2571 Dihedral : 16.734 124.488 5664 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.06 % Allowed : 15.48 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.20), residues: 1881 helix: 1.81 (0.18), residues: 863 sheet: 0.09 (0.40), residues: 169 loop : 0.52 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 104 TYR 0.015 0.001 TYR B 360 PHE 0.017 0.001 PHE F 162 TRP 0.014 0.001 TRP B 103 HIS 0.005 0.001 HIS F 356 Details of bonding type rmsd covalent geometry : bond 0.00438 (15199) covalent geometry : angle 0.61314 (20607) hydrogen bonds : bond 0.14158 ( 765) hydrogen bonds : angle 6.25474 ( 2148) metal coordination : bond 0.01367 ( 8) metal coordination : angle 11.61486 ( 12) Misc. bond : bond 0.04626 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 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. Evaluate side-chains 222 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 221 time to evaluate : 0.733 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 289 SER cc_start: 0.8560 (t) cc_final: 0.8349 (t) REVERT: B 406 LYS cc_start: 0.8002 (mttp) cc_final: 0.7722 (mtmt) REVERT: C 110 GLN cc_start: 0.7328 (mt0) cc_final: 0.7112 (mt0) outliers start: 1 outliers final: 1 residues processed: 221 average time/residue: 0.2993 time to fit residues: 96.4045 Evaluate side-chains 211 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 210 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 267 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 GLN C 68 ASN D 68 ASN F 175 HIS F 362 ASN F 400 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.174358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.119086 restraints weight = 50544.234| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.06 r_work: 0.3205 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.0604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 15209 Z= 0.161 Angle : 0.582 18.809 20619 Z= 0.274 Chirality : 0.042 0.323 2330 Planarity : 0.004 0.041 2571 Dihedral : 9.915 96.145 2348 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.84 % Allowed : 15.35 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.20), residues: 1881 helix: 1.58 (0.18), residues: 894 sheet: -0.23 (0.40), residues: 181 loop : 0.59 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 63 TYR 0.015 0.001 TYR B 360 PHE 0.017 0.001 PHE E 28 TRP 0.016 0.001 TRP B 103 HIS 0.004 0.001 HIS F 356 Details of bonding type rmsd covalent geometry : bond 0.00373 (15199) covalent geometry : angle 0.53177 (20607) hydrogen bonds : bond 0.04432 ( 765) hydrogen bonds : angle 5.05835 ( 2148) metal coordination : bond 0.01756 ( 8) metal coordination : angle 9.79098 ( 12) Misc. bond : bond 0.00088 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 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. Evaluate side-chains 225 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 212 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 244 GLN cc_start: 0.5327 (mt0) cc_final: 0.5086 (mt0) REVERT: F 289 ARG cc_start: 0.6793 (OUTLIER) cc_final: 0.6387 (tpt-90) REVERT: F 295 GLN cc_start: 0.7528 (mp10) cc_final: 0.7029 (mm-40) REVERT: F 377 MET cc_start: 0.5225 (tmm) cc_final: 0.4955 (tmm) outliers start: 13 outliers final: 6 residues processed: 220 average time/residue: 0.2787 time to fit residues: 91.8106 Evaluate side-chains 211 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 204 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 289 ARG Chi-restraints excluded: chain F residue 335 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 95 optimal weight: 6.9990 chunk 161 optimal weight: 20.0000 chunk 167 optimal weight: 20.0000 chunk 99 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 156 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 132 optimal weight: 0.8980 chunk 157 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 ASN D 68 ASN F 343 GLN F 362 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.176056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.117731 restraints weight = 50635.427| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.69 r_work: 0.3181 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 15209 Z= 0.172 Angle : 0.578 20.901 20619 Z= 0.270 Chirality : 0.042 0.369 2330 Planarity : 0.004 0.043 2571 Dihedral : 8.559 84.818 2346 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.04 % Allowed : 15.03 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.20), residues: 1881 helix: 1.42 (0.17), residues: 897 sheet: -0.39 (0.39), residues: 183 loop : 0.49 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 134 TYR 0.015 0.001 TYR B 360 PHE 0.016 0.001 PHE E 28 TRP 0.018 0.001 TRP B 103 HIS 0.004 0.001 HIS F 291 Details of bonding type rmsd covalent geometry : bond 0.00406 (15199) covalent geometry : angle 0.52714 (20607) hydrogen bonds : bond 0.04196 ( 765) hydrogen bonds : angle 4.84515 ( 2148) metal coordination : bond 0.01783 ( 8) metal coordination : angle 9.87003 ( 12) Misc. bond : bond 0.00095 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 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. Evaluate side-chains 235 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 219 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 250 ILE cc_start: 0.8951 (mt) cc_final: 0.8724 (mt) REVERT: F 295 GLN cc_start: 0.7527 (mp10) cc_final: 0.7036 (mm-40) REVERT: F 377 MET cc_start: 0.5178 (tmm) cc_final: 0.4888 (tmm) outliers start: 16 outliers final: 10 residues processed: 230 average time/residue: 0.2897 time to fit residues: 98.4838 Evaluate side-chains 216 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 206 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain F residue 335 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 138 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 162 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 156 optimal weight: 20.0000 chunk 154 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 ASN D 68 ASN F 343 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.174913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.116844 restraints weight = 50320.361| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.67 r_work: 0.3190 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 15209 Z= 0.181 Angle : 0.581 20.856 20619 Z= 0.272 Chirality : 0.043 0.435 2330 Planarity : 0.004 0.058 2571 Dihedral : 7.939 67.711 2346 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.36 % Allowed : 14.96 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.20), residues: 1881 helix: 1.36 (0.17), residues: 895 sheet: -0.48 (0.39), residues: 183 loop : 0.34 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 199 TYR 0.016 0.001 TYR B 360 PHE 0.018 0.001 PHE E 28 TRP 0.017 0.001 TRP B 103 HIS 0.003 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00427 (15199) covalent geometry : angle 0.52728 (20607) hydrogen bonds : bond 0.04013 ( 765) hydrogen bonds : angle 4.76724 ( 2148) metal coordination : bond 0.01855 ( 8) metal coordination : angle 10.15421 ( 12) Misc. bond : bond 0.00093 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 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. Evaluate side-chains 230 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 209 time to evaluate : 0.798 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: D 115 MET cc_start: 0.7537 (mmm) cc_final: 0.7198 (mmm) REVERT: F 295 GLN cc_start: 0.7400 (mp10) cc_final: 0.6900 (mm-40) REVERT: F 377 MET cc_start: 0.5152 (tmm) cc_final: 0.4832 (tmm) outliers start: 21 outliers final: 15 residues processed: 225 average time/residue: 0.2800 time to fit residues: 94.0049 Evaluate side-chains 218 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 203 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 23 LEU 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 130 VAL Chi-restraints excluded: chain E residue 190 PHE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 335 TRP Chi-restraints excluded: chain F residue 362 ASN Chi-restraints excluded: chain F residue 378 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 78 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 151 optimal weight: 9.9990 chunk 94 optimal weight: 10.9990 chunk 137 optimal weight: 0.4980 chunk 95 optimal weight: 5.9990 chunk 169 optimal weight: 9.9990 chunk 164 optimal weight: 30.0000 chunk 7 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.173692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.115558 restraints weight = 50786.038| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.68 r_work: 0.3157 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 15209 Z= 0.196 Angle : 0.587 20.749 20619 Z= 0.277 Chirality : 0.043 0.401 2330 Planarity : 0.004 0.047 2571 Dihedral : 7.671 62.035 2346 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.42 % Allowed : 15.67 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.19), residues: 1881 helix: 1.24 (0.17), residues: 899 sheet: -0.64 (0.38), residues: 185 loop : 0.31 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 48 TYR 0.016 0.001 TYR B 360 PHE 0.018 0.001 PHE E 28 TRP 0.018 0.001 TRP B 103 HIS 0.008 0.001 HIS F 175 Details of bonding type rmsd covalent geometry : bond 0.00464 (15199) covalent geometry : angle 0.53369 (20607) hydrogen bonds : bond 0.04036 ( 765) hydrogen bonds : angle 4.73635 ( 2148) metal coordination : bond 0.01801 ( 8) metal coordination : angle 10.17224 ( 12) Misc. bond : bond 0.00127 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 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. Evaluate side-chains 230 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 208 time to evaluate : 0.768 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: 0.8077 (OUTLIER) cc_final: 0.7264 (tpp-160) REVERT: F 295 GLN cc_start: 0.7207 (mp10) cc_final: 0.6879 (mm-40) outliers start: 22 outliers final: 17 residues processed: 224 average time/residue: 0.2743 time to fit residues: 91.7899 Evaluate side-chains 215 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 190 PHE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 335 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 41 optimal weight: 0.9980 chunk 166 optimal weight: 20.0000 chunk 83 optimal weight: 8.9990 chunk 43 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 chunk 179 optimal weight: 20.0000 chunk 183 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 ASN F 169 GLN ** F 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.173127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.115159 restraints weight = 50663.336| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.68 r_work: 0.3206 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 15209 Z= 0.185 Angle : 0.578 20.408 20619 Z= 0.272 Chirality : 0.042 0.350 2330 Planarity : 0.004 0.048 2571 Dihedral : 7.542 59.234 2346 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.49 % Allowed : 15.80 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.19), residues: 1881 helix: 1.20 (0.17), residues: 904 sheet: -0.66 (0.38), residues: 185 loop : 0.26 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 104 TYR 0.016 0.001 TYR B 360 PHE 0.017 0.001 PHE E 28 TRP 0.018 0.001 TRP B 103 HIS 0.004 0.001 HIS E 3 Details of bonding type rmsd covalent geometry : bond 0.00440 (15199) covalent geometry : angle 0.52484 (20607) hydrogen bonds : bond 0.03945 ( 765) hydrogen bonds : angle 4.69993 ( 2148) metal coordination : bond 0.01695 ( 8) metal coordination : angle 10.04800 ( 12) Misc. bond : bond 0.00142 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 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. Evaluate side-chains 229 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.728 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: 0.8064 (OUTLIER) cc_final: 0.7272 (tpp-160) REVERT: A 415 GLU cc_start: 0.8153 (mp0) cc_final: 0.7893 (mp0) REVERT: B 250 ILE cc_start: 0.8921 (mt) cc_final: 0.8607 (mt) REVERT: E 7 LEU cc_start: 0.7190 (tp) cc_final: 0.6812 (tp) REVERT: F 295 GLN cc_start: 0.7303 (mp10) cc_final: 0.6952 (mm-40) outliers start: 23 outliers final: 20 residues processed: 223 average time/residue: 0.2844 time to fit residues: 93.9563 Evaluate side-chains 220 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 132 ILE 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 130 VAL Chi-restraints excluded: chain E residue 190 PHE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 335 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 156 optimal weight: 20.0000 chunk 150 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 343 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.170224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.121234 restraints weight = 49423.563| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.68 r_work: 0.3017 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 15209 Z= 0.168 Angle : 0.571 19.071 20619 Z= 0.267 Chirality : 0.042 0.311 2330 Planarity : 0.004 0.048 2571 Dihedral : 7.392 57.797 2346 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.49 % Allowed : 16.39 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.19), residues: 1881 helix: 1.26 (0.17), residues: 900 sheet: -0.62 (0.39), residues: 185 loop : 0.27 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 104 TYR 0.015 0.001 TYR B 360 PHE 0.016 0.001 PHE E 28 TRP 0.018 0.001 TRP B 103 HIS 0.004 0.001 HIS F 356 Details of bonding type rmsd covalent geometry : bond 0.00402 (15199) covalent geometry : angle 0.51615 (20607) hydrogen bonds : bond 0.03851 ( 765) hydrogen bonds : angle 4.63871 ( 2148) metal coordination : bond 0.01633 ( 8) metal coordination : angle 10.14804 ( 12) Misc. bond : bond 0.00114 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 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. Evaluate side-chains 234 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 211 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7256 (tpp-160) REVERT: B 250 ILE cc_start: 0.8947 (mt) cc_final: 0.8700 (mt) REVERT: C 36 LYS cc_start: 0.7317 (tttt) cc_final: 0.7072 (tptt) REVERT: C 110 GLN cc_start: 0.6966 (mt0) cc_final: 0.6436 (mp10) REVERT: E 7 LEU cc_start: 0.7141 (tp) cc_final: 0.6843 (tp) REVERT: F 31 PRO cc_start: 0.5703 (Cg_endo) cc_final: 0.5250 (Cg_exo) REVERT: F 295 GLN cc_start: 0.7306 (mp10) cc_final: 0.6943 (mm-40) outliers start: 23 outliers final: 19 residues processed: 227 average time/residue: 0.3132 time to fit residues: 103.3590 Evaluate side-chains 219 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 199 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain E residue 22 PHE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 190 PHE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 335 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 14 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 33 optimal weight: 0.0670 chunk 20 optimal weight: 0.9980 chunk 99 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN D 137 ASN ** F 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 ASN F 343 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.170458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.122932 restraints weight = 49487.134| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.91 r_work: 0.3153 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 15209 Z= 0.149 Angle : 0.564 19.039 20619 Z= 0.263 Chirality : 0.041 0.301 2330 Planarity : 0.004 0.048 2571 Dihedral : 7.262 57.781 2346 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.42 % Allowed : 17.03 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.19), residues: 1881 helix: 1.29 (0.17), residues: 900 sheet: -0.62 (0.39), residues: 185 loop : 0.25 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 104 TYR 0.015 0.001 TYR B 360 PHE 0.015 0.001 PHE E 28 TRP 0.018 0.001 TRP B 103 HIS 0.007 0.001 HIS F 175 Details of bonding type rmsd covalent geometry : bond 0.00359 (15199) covalent geometry : angle 0.51042 (20607) hydrogen bonds : bond 0.03781 ( 765) hydrogen bonds : angle 4.59934 ( 2148) metal coordination : bond 0.01547 ( 8) metal coordination : angle 9.91114 ( 12) Misc. bond : bond 0.00108 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 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. Evaluate side-chains 226 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 0.853 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: 0.8065 (OUTLIER) cc_final: 0.7269 (tpp-160) REVERT: B 250 ILE cc_start: 0.8939 (mt) cc_final: 0.8693 (mt) REVERT: C 110 GLN cc_start: 0.6968 (mt0) cc_final: 0.6429 (mp10) REVERT: E 7 LEU cc_start: 0.7418 (tp) cc_final: 0.7077 (tp) REVERT: F 31 PRO cc_start: 0.5707 (Cg_endo) cc_final: 0.5244 (Cg_exo) REVERT: F 295 GLN cc_start: 0.7384 (mp10) cc_final: 0.7087 (mm-40) outliers start: 22 outliers final: 17 residues processed: 220 average time/residue: 0.2899 time to fit residues: 93.4263 Evaluate side-chains 218 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 200 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain E residue 22 PHE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 190 PHE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 335 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 31 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 160 optimal weight: 20.0000 chunk 79 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 182 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN ** F 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.169562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.121536 restraints weight = 49391.298| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.69 r_work: 0.2999 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 15209 Z= 0.186 Angle : 0.582 18.485 20619 Z= 0.274 Chirality : 0.042 0.297 2330 Planarity : 0.004 0.049 2571 Dihedral : 7.316 58.045 2346 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.42 % Allowed : 17.10 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.19), residues: 1881 helix: 1.23 (0.17), residues: 899 sheet: -0.68 (0.39), residues: 185 loop : 0.24 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 104 TYR 0.016 0.001 TYR B 360 PHE 0.017 0.001 PHE E 28 TRP 0.018 0.001 TRP B 103 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00445 (15199) covalent geometry : angle 0.52822 (20607) hydrogen bonds : bond 0.03867 ( 765) hydrogen bonds : angle 4.62640 ( 2148) metal coordination : bond 0.01662 ( 8) metal coordination : angle 10.12050 ( 12) Misc. bond : bond 0.00127 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 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. Evaluate side-chains 227 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 0.808 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: 0.8106 (OUTLIER) cc_final: 0.7172 (tpp-160) REVERT: A 253 THR cc_start: 0.8601 (p) cc_final: 0.8347 (t) REVERT: B 250 ILE cc_start: 0.8950 (mt) cc_final: 0.8704 (mt) REVERT: C 110 GLN cc_start: 0.6984 (mt0) cc_final: 0.6439 (mp10) REVERT: E 7 LEU cc_start: 0.7336 (tp) cc_final: 0.6989 (tp) REVERT: F 31 PRO cc_start: 0.5562 (Cg_endo) cc_final: 0.5112 (Cg_exo) REVERT: F 295 GLN cc_start: 0.7347 (mp10) cc_final: 0.7040 (mm-40) REVERT: F 377 MET cc_start: 0.5321 (tmm) cc_final: 0.5118 (tpt) outliers start: 22 outliers final: 20 residues processed: 220 average time/residue: 0.2851 time to fit residues: 92.3016 Evaluate side-chains 222 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 201 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain E residue 22 PHE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 190 PHE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 335 TRP 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 29 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 166 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 185 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN ** F 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.169775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.121043 restraints weight = 49097.868| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.80 r_work: 0.3058 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.152 15209 Z= 0.182 Angle : 0.776 59.194 20619 Z= 0.423 Chirality : 0.042 0.294 2330 Planarity : 0.004 0.049 2571 Dihedral : 7.314 58.030 2346 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.55 % Allowed : 17.23 % Favored : 81.22 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.19), residues: 1881 helix: 1.23 (0.17), residues: 899 sheet: -0.68 (0.39), residues: 185 loop : 0.24 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 104 TYR 0.017 0.001 TYR F 309 PHE 0.017 0.001 PHE E 28 TRP 0.018 0.001 TRP B 103 HIS 0.003 0.001 HIS F 356 Details of bonding type rmsd covalent geometry : bond 0.00429 (15199) covalent geometry : angle 0.73704 (20607) hydrogen bonds : bond 0.03849 ( 765) hydrogen bonds : angle 4.62671 ( 2148) metal coordination : bond 0.01621 ( 8) metal coordination : angle 10.12134 ( 12) Misc. bond : bond 0.00103 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 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. Evaluate side-chains 227 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 203 time to evaluate : 0.813 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: 0.8058 (OUTLIER) cc_final: 0.7174 (tpp-160) REVERT: A 253 THR cc_start: 0.8591 (p) cc_final: 0.8333 (t) REVERT: B 250 ILE cc_start: 0.8938 (mt) cc_final: 0.8691 (mt) REVERT: C 110 GLN cc_start: 0.6995 (mt0) cc_final: 0.6452 (mp10) REVERT: E 7 LEU cc_start: 0.7360 (tp) cc_final: 0.7013 (tp) REVERT: F 31 PRO cc_start: 0.5546 (Cg_endo) cc_final: 0.5093 (Cg_exo) REVERT: F 295 GLN cc_start: 0.7331 (mp10) cc_final: 0.7035 (mm-40) REVERT: F 377 MET cc_start: 0.5284 (tmm) cc_final: 0.5077 (tpt) outliers start: 24 outliers final: 22 residues processed: 219 average time/residue: 0.2806 time to fit residues: 90.7788 Evaluate side-chains 224 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain E residue 22 PHE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 190 PHE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain F residue 335 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 181 optimal weight: 10.0000 chunk 16 optimal weight: 0.6980 chunk 147 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 chunk 86 optimal weight: 9.9990 chunk 148 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 168 optimal weight: 7.9990 chunk 106 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN ** F 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.169717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.114085 restraints weight = 49321.258| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.53 r_work: 0.3011 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.152 15209 Z= 0.182 Angle : 0.776 59.200 20619 Z= 0.423 Chirality : 0.042 0.294 2330 Planarity : 0.004 0.049 2571 Dihedral : 7.314 58.030 2346 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.55 % Allowed : 17.16 % Favored : 81.28 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.19), residues: 1881 helix: 1.23 (0.17), residues: 899 sheet: -0.68 (0.39), residues: 185 loop : 0.24 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 104 TYR 0.017 0.001 TYR F 309 PHE 0.017 0.001 PHE E 28 TRP 0.018 0.001 TRP B 103 HIS 0.003 0.001 HIS F 356 Details of bonding type rmsd covalent geometry : bond 0.00429 (15199) covalent geometry : angle 0.73705 (20607) hydrogen bonds : bond 0.03849 ( 765) hydrogen bonds : angle 4.62671 ( 2148) metal coordination : bond 0.01621 ( 8) metal coordination : angle 10.12134 ( 12) Misc. bond : bond 0.00103 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7999.94 seconds wall clock time: 136 minutes 21.98 seconds (8181.98 seconds total)