Starting phenix.real_space_refine on Thu Jun 26 06:24:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a1x_15092/06_2025/8a1x_15092_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a1x_15092/06_2025/8a1x_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8a1x_15092/06_2025/8a1x_15092.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a1x_15092/06_2025/8a1x_15092.map" model { file = "/net/cci-nas-00/data/ceres_data/8a1x_15092/06_2025/8a1x_15092_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a1x_15092/06_2025/8a1x_15092_trim.cif" } resolution = 3.2 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= 0.008 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.74, per 1000 atoms: 0.60 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: 7.57 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 2.44 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: 11.42 Time building geometry restraints manager: 9.09 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: 11.400 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: 0.410 Extract box with map and model: 0.970 Check model and map are aligned: 0.190 Set scattering table: 0.280 Process input model: 79.180 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.100 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: 0.020 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.690 ------------------------------------------------------------------------------- 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 : 5.80 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 (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: 1.53 (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 TRP 0.014 0.001 TRP B 103 HIS 0.005 0.001 HIS F 356 PHE 0.017 0.001 PHE F 162 TYR 0.015 0.001 TYR B 360 ARG 0.002 0.000 ARG F 104 Details of bonding type rmsd hydrogen bonds : bond 0.14158 ( 765) hydrogen bonds : angle 6.25474 ( 2148) metal coordination : bond 0.01367 ( 8) metal coordination : angle 11.61486 ( 12) covalent geometry : bond 0.00438 (15199) covalent geometry : angle 0.61314 (20607) 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 : 2.094 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: 0.6989 time to fit residues: 227.0672 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 : 2.344 ------------------------------------------------------------------------------- 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 157 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 168 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 HIS B 324 ASN C 68 ASN D 68 ASN F 175 HIS F 362 ASN F 400 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.172466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.117132 restraints weight = 50574.852| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.05 r_work: 0.3159 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.0684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.119 15209 Z= 0.222 Angle : 0.617 19.092 20619 Z= 0.293 Chirality : 0.043 0.308 2330 Planarity : 0.004 0.042 2571 Dihedral : 10.160 97.403 2348 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.10 % Allowed : 15.41 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.19 (0.20), residues: 1881 helix: 1.42 (0.17), residues: 896 sheet: -0.23 (0.38), residues: 195 loop : 0.50 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 103 HIS 0.005 0.001 HIS B 328 PHE 0.020 0.002 PHE E 28 TYR 0.017 0.001 TYR B 360 ARG 0.004 0.001 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.04608 ( 765) hydrogen bonds : angle 5.11498 ( 2148) metal coordination : bond 0.02141 ( 8) metal coordination : angle 10.38294 ( 12) covalent geometry : bond 0.00522 (15199) covalent geometry : angle 0.56377 (20607) Misc. bond : bond 0.00192 ( 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 232 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 215 time to evaluate : 2.151 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: F 289 ARG cc_start: 0.6807 (OUTLIER) cc_final: 0.6414 (tpt-90) REVERT: F 295 GLN cc_start: 0.7530 (mp10) cc_final: 0.7032 (mm-40) REVERT: F 377 MET cc_start: 0.5267 (tmm) cc_final: 0.4995 (tmm) outliers start: 17 outliers final: 10 residues processed: 227 average time/residue: 0.5754 time to fit residues: 195.1541 Evaluate side-chains 216 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 205 time to evaluate : 2.084 ------------------------------------------------------------------------------- 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 75 GLN Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 289 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 24 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 149 optimal weight: 0.9980 chunk 137 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 163 optimal weight: 20.0000 chunk 76 optimal weight: 3.9990 chunk 175 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 GLN 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 = 0.4021 r_free = 0.4021 target = 0.176877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.117107 restraints weight = 50884.963| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.71 r_work: 0.3175 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.119 15209 Z= 0.200 Angle : 0.600 21.190 20619 Z= 0.282 Chirality : 0.043 0.360 2330 Planarity : 0.004 0.044 2571 Dihedral : 8.745 83.958 2346 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.97 % Allowed : 15.35 % 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 (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: 0.94 (0.20), residues: 1881 helix: 1.21 (0.17), residues: 900 sheet: -0.48 (0.39), residues: 183 loop : 0.39 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 103 HIS 0.004 0.001 HIS E 3 PHE 0.018 0.001 PHE E 28 TYR 0.017 0.001 TYR D 93 ARG 0.005 0.000 ARG F 104 Details of bonding type rmsd hydrogen bonds : bond 0.04300 ( 765) hydrogen bonds : angle 4.89090 ( 2148) metal coordination : bond 0.01916 ( 8) metal coordination : angle 10.22227 ( 12) covalent geometry : bond 0.00475 (15199) covalent geometry : angle 0.54737 (20607) Misc. bond : bond 0.00098 ( 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 233 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 218 time to evaluate : 2.466 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: 0.8929 (mt) cc_final: 0.8695 (mt) REVERT: E 134 TYR cc_start: 0.8024 (m-80) cc_final: 0.7823 (m-80) REVERT: F 244 GLN cc_start: 0.5331 (mt0) cc_final: 0.5052 (mt0) REVERT: F 285 MET cc_start: 0.6262 (tpp) cc_final: 0.6035 (tpp) REVERT: F 289 ARG cc_start: 0.6648 (OUTLIER) cc_final: 0.6277 (tpt-90) REVERT: F 295 GLN cc_start: 0.7563 (mp10) cc_final: 0.7079 (mm-40) REVERT: F 377 MET cc_start: 0.5136 (tmm) cc_final: 0.4782 (tmm) outliers start: 15 outliers final: 9 residues processed: 228 average time/residue: 0.5926 time to fit residues: 201.7790 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 : 2.093 ------------------------------------------------------------------------------- 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 186 ARG Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 289 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 137 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 19 optimal weight: 0.0000 chunk 100 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.9590 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.174949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.116729 restraints weight = 50874.281| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.70 r_work: 0.3189 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 15209 Z= 0.157 Angle : 0.571 20.836 20619 Z= 0.267 Chirality : 0.042 0.432 2330 Planarity : 0.004 0.046 2571 Dihedral : 8.082 69.355 2346 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.36 % Allowed : 15.48 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.98 (0.20), residues: 1881 helix: 1.31 (0.17), residues: 898 sheet: -0.52 (0.39), residues: 183 loop : 0.35 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 103 HIS 0.004 0.001 HIS F 356 PHE 0.016 0.001 PHE E 28 TYR 0.015 0.001 TYR B 360 ARG 0.003 0.000 ARG F 104 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 765) hydrogen bonds : angle 4.78500 ( 2148) metal coordination : bond 0.01727 ( 8) metal coordination : angle 9.99803 ( 12) covalent geometry : bond 0.00374 (15199) covalent geometry : angle 0.51806 (20607) Misc. bond : bond 0.00087 ( 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 227 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 206 time to evaluate : 2.155 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: 0.7612 (mmm) cc_final: 0.7265 (mmm) REVERT: F 199 ARG cc_start: 0.2121 (ptm160) cc_final: 0.1848 (ttp80) REVERT: F 244 GLN cc_start: 0.5154 (mt0) cc_final: 0.4922 (mt0) REVERT: F 295 GLN cc_start: 0.7395 (mp10) cc_final: 0.6897 (mm-40) REVERT: F 305 MET cc_start: 0.8520 (mtp) cc_final: 0.8298 (mtp) REVERT: F 377 MET cc_start: 0.5187 (tmm) cc_final: 0.4851 (tmm) outliers start: 21 outliers final: 14 residues processed: 224 average time/residue: 0.6113 time to fit residues: 202.7619 Evaluate side-chains 213 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 199 time to evaluate : 2.373 ------------------------------------------------------------------------------- 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 274 GLU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 153 VAL 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 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 39 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 154 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.4024 r_free = 0.4024 target = 0.177065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.117483 restraints weight = 50738.149| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.73 r_work: 0.3185 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1429 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= 0.157 Angle : 0.563 20.604 20619 Z= 0.263 Chirality : 0.042 0.423 2330 Planarity : 0.004 0.047 2571 Dihedral : 7.660 63.310 2346 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.30 % Allowed : 15.61 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.97 (0.20), residues: 1881 helix: 1.29 (0.17), residues: 901 sheet: -0.56 (0.39), residues: 185 loop : 0.36 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 103 HIS 0.004 0.001 HIS F 356 PHE 0.016 0.001 PHE E 28 TYR 0.015 0.001 TYR B 360 ARG 0.004 0.000 ARG F 104 Details of bonding type rmsd hydrogen bonds : bond 0.03895 ( 765) hydrogen bonds : angle 4.70201 ( 2148) metal coordination : bond 0.01673 ( 8) metal coordination : angle 9.88889 ( 12) covalent geometry : bond 0.00374 (15199) covalent geometry : angle 0.51056 (20607) Misc. bond : bond 0.00095 ( 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 224 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 204 time to evaluate : 2.123 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: F 199 ARG cc_start: 0.1953 (ptm160) cc_final: 0.1635 (ttp80) REVERT: F 244 GLN cc_start: 0.5361 (mt0) cc_final: 0.5048 (mt0) REVERT: F 285 MET cc_start: 0.5955 (tpp) cc_final: 0.5740 (tpp) REVERT: F 295 GLN cc_start: 0.7417 (mp10) cc_final: 0.6987 (mm-40) outliers start: 20 outliers final: 17 residues processed: 221 average time/residue: 0.6043 time to fit residues: 198.3682 Evaluate side-chains 214 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 197 time to evaluate : 2.336 ------------------------------------------------------------------------------- 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 136 VAL 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 C residue 186 ARG 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 90 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 378 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 156 optimal weight: 20.0000 chunk 146 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 177 optimal weight: 10.0000 chunk 170 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 166 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN C 68 ASN ** 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 = 0.3971 r_free = 0.3971 target = 0.171698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.117492 restraints weight = 51110.518| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.85 r_work: 0.3182 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 15209 Z= 0.223 Angle : 0.608 19.698 20619 Z= 0.289 Chirality : 0.043 0.358 2330 Planarity : 0.004 0.049 2571 Dihedral : 7.728 59.002 2346 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.55 % Allowed : 16.26 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.70 (0.19), residues: 1881 helix: 1.08 (0.17), residues: 903 sheet: -0.64 (0.38), residues: 185 loop : 0.18 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 103 HIS 0.005 0.001 HIS E 3 PHE 0.021 0.002 PHE E 28 TYR 0.017 0.002 TYR D 93 ARG 0.005 0.001 ARG F 104 Details of bonding type rmsd hydrogen bonds : bond 0.04134 ( 765) hydrogen bonds : angle 4.73641 ( 2148) metal coordination : bond 0.01829 ( 8) metal coordination : angle 10.18820 ( 12) covalent geometry : bond 0.00525 (15199) covalent geometry : angle 0.55587 (20607) Misc. bond : bond 0.00152 ( 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 237 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 time to evaluate : 2.177 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: 0.8144 (OUTLIER) cc_final: 0.7087 (tpp-160) REVERT: A 415 GLU cc_start: 0.8169 (mp0) cc_final: 0.7878 (mp0) REVERT: B 250 ILE cc_start: 0.8898 (mt) cc_final: 0.8617 (mt) REVERT: E 7 LEU cc_start: 0.7283 (tp) cc_final: 0.6926 (tp) REVERT: F 244 GLN cc_start: 0.5110 (mt0) cc_final: 0.4785 (mt0) REVERT: F 295 GLN cc_start: 0.7349 (mp10) cc_final: 0.6974 (mm-40) outliers start: 24 outliers final: 18 residues processed: 231 average time/residue: 0.6249 time to fit residues: 212.7826 Evaluate side-chains 219 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 200 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN 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 186 ARG Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain E residue 6 SER 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 F residue 99 SER Chi-restraints excluded: chain F residue 378 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 77 optimal weight: 2.9990 chunk 160 optimal weight: 20.0000 chunk 163 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN ** F 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.169558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.113727 restraints weight = 49373.475| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.54 r_work: 0.3034 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1805 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= 0.177 Angle : 0.582 19.442 20619 Z= 0.273 Chirality : 0.042 0.319 2330 Planarity : 0.004 0.049 2571 Dihedral : 7.565 57.697 2346 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.75 % Allowed : 16.58 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.77 (0.19), residues: 1881 helix: 1.16 (0.17), residues: 899 sheet: -0.65 (0.39), residues: 185 loop : 0.20 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 103 HIS 0.004 0.001 HIS F 356 PHE 0.017 0.001 PHE E 28 TYR 0.016 0.001 TYR B 360 ARG 0.004 0.000 ARG F 104 Details of bonding type rmsd hydrogen bonds : bond 0.03928 ( 765) hydrogen bonds : angle 4.67177 ( 2148) metal coordination : bond 0.01659 ( 8) metal coordination : angle 10.28947 ( 12) covalent geometry : bond 0.00421 (15199) covalent geometry : angle 0.52682 (20607) Misc. bond : bond 0.00123 ( 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 240 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 213 time to evaluate : 2.343 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: 0.8102 (OUTLIER) cc_final: 0.7094 (tpp-160) REVERT: B 250 ILE cc_start: 0.8919 (mt) cc_final: 0.8606 (mt) REVERT: C 36 LYS cc_start: 0.7343 (tttt) cc_final: 0.7101 (tptt) REVERT: C 110 GLN cc_start: 0.6968 (mt0) cc_final: 0.6452 (mp10) REVERT: E 7 LEU cc_start: 0.7205 (tp) cc_final: 0.6909 (tp) REVERT: F 31 PRO cc_start: 0.5716 (Cg_endo) cc_final: 0.5267 (Cg_exo) REVERT: F 244 GLN cc_start: 0.5108 (mt0) cc_final: 0.4779 (mt0) REVERT: F 295 GLN cc_start: 0.7421 (mp10) cc_final: 0.7051 (mm-40) outliers start: 27 outliers final: 23 residues processed: 232 average time/residue: 0.6245 time to fit residues: 214.2156 Evaluate side-chains 221 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 2.095 ------------------------------------------------------------------------------- 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 62 GLN Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 186 ARG 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 90 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 378 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 136 optimal weight: 8.9990 chunk 135 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.168622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.119649 restraints weight = 49471.149| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.85 r_work: 0.3007 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 15209 Z= 0.212 Angle : 0.605 18.610 20619 Z= 0.287 Chirality : 0.043 0.316 2330 Planarity : 0.004 0.050 2571 Dihedral : 7.601 58.500 2346 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.75 % Allowed : 17.10 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.67 (0.19), residues: 1881 helix: 1.08 (0.17), residues: 898 sheet: -0.72 (0.39), residues: 185 loop : 0.16 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 103 HIS 0.004 0.001 HIS B 328 PHE 0.018 0.001 PHE E 28 TYR 0.016 0.001 TYR B 360 ARG 0.005 0.000 ARG F 104 Details of bonding type rmsd hydrogen bonds : bond 0.04022 ( 765) hydrogen bonds : angle 4.70172 ( 2148) metal coordination : bond 0.01766 ( 8) metal coordination : angle 10.31785 ( 12) covalent geometry : bond 0.00505 (15199) covalent geometry : angle 0.55136 (20607) Misc. bond : bond 0.00122 ( 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 228 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 201 time to evaluate : 2.311 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: 0.8132 (OUTLIER) cc_final: 0.6979 (tpp-160) REVERT: A 253 THR cc_start: 0.8581 (p) cc_final: 0.8332 (t) REVERT: B 250 ILE cc_start: 0.8931 (mt) cc_final: 0.8603 (mt) REVERT: C 110 GLN cc_start: 0.6956 (mt0) cc_final: 0.6451 (mp10) REVERT: E 7 LEU cc_start: 0.7309 (tp) cc_final: 0.6975 (tp) REVERT: F 31 PRO cc_start: 0.5597 (Cg_endo) cc_final: 0.5141 (Cg_exo) REVERT: F 244 GLN cc_start: 0.4991 (mt0) cc_final: 0.4662 (mt0) REVERT: F 295 GLN cc_start: 0.7440 (mp10) cc_final: 0.7126 (mm-40) REVERT: F 377 MET cc_start: 0.5252 (tmm) cc_final: 0.4950 (tpt) outliers start: 27 outliers final: 23 residues processed: 221 average time/residue: 0.8714 time to fit residues: 291.1556 Evaluate side-chains 223 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 199 time to evaluate : 3.935 ------------------------------------------------------------------------------- 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 62 GLN Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 46 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 378 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 160 optimal weight: 20.0000 chunk 29 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 169 optimal weight: 0.0170 chunk 144 optimal weight: 0.8980 overall best weight: 1.5422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN D 137 ASN F 295 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.170306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.121428 restraints weight = 49391.482| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.76 r_work: 0.3023 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 15209 Z= 0.135 Angle : 0.561 19.236 20619 Z= 0.262 Chirality : 0.041 0.297 2330 Planarity : 0.004 0.049 2571 Dihedral : 7.298 57.711 2346 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.62 % Allowed : 17.42 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 1881 helix: 1.26 (0.17), residues: 898 sheet: -0.68 (0.39), residues: 185 loop : 0.22 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 103 HIS 0.005 0.001 HIS F 356 PHE 0.013 0.001 PHE F 267 TYR 0.016 0.001 TYR B 360 ARG 0.005 0.000 ARG F 104 Details of bonding type rmsd hydrogen bonds : bond 0.03736 ( 765) hydrogen bonds : angle 4.60810 ( 2148) metal coordination : bond 0.01473 ( 8) metal coordination : angle 9.82936 ( 12) covalent geometry : bond 0.00324 (15199) covalent geometry : angle 0.50807 (20607) Misc. bond : bond 0.00093 ( 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 237 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 212 time to evaluate : 2.345 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: 0.8034 (OUTLIER) cc_final: 0.7051 (tpp-160) REVERT: B 250 ILE cc_start: 0.8904 (mt) cc_final: 0.8656 (mt) REVERT: C 110 GLN cc_start: 0.6983 (mt0) cc_final: 0.6462 (mp10) REVERT: E 7 LEU cc_start: 0.7284 (tp) cc_final: 0.6949 (tp) REVERT: F 31 PRO cc_start: 0.5594 (Cg_endo) cc_final: 0.5136 (Cg_exo) REVERT: F 244 GLN cc_start: 0.4986 (mt0) cc_final: 0.4641 (mt0) REVERT: F 295 GLN cc_start: 0.7650 (mp-120) cc_final: 0.7320 (mm-40) outliers start: 25 outliers final: 23 residues processed: 231 average time/residue: 0.6256 time to fit residues: 212.0063 Evaluate side-chains 224 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 2.176 ------------------------------------------------------------------------------- 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 62 GLN Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 186 ARG 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 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 378 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 142 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 171 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 ASN 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 = 0.169954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.122082 restraints weight = 49308.892| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.78 r_work: 0.3034 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 15209 Z= 0.188 Angle : 0.774 59.184 20619 Z= 0.430 Chirality : 0.042 0.299 2330 Planarity : 0.005 0.135 2571 Dihedral : 7.297 57.639 2346 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.62 % Allowed : 17.49 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.84 (0.19), residues: 1881 helix: 1.24 (0.17), residues: 900 sheet: -0.68 (0.39), residues: 185 loop : 0.24 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 103 HIS 0.005 0.001 HIS F 356 PHE 0.013 0.001 PHE E 28 TYR 0.016 0.001 TYR B 360 ARG 0.004 0.000 ARG F 104 Details of bonding type rmsd hydrogen bonds : bond 0.03775 ( 765) hydrogen bonds : angle 4.61168 ( 2148) metal coordination : bond 0.01492 ( 8) metal coordination : angle 9.81560 ( 12) covalent geometry : bond 0.00417 (15199) covalent geometry : angle 0.73754 (20607) Misc. bond : bond 0.00089 ( 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 226 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 201 time to evaluate : 2.084 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: 0.8036 (OUTLIER) cc_final: 0.7054 (tpp-160) REVERT: A 253 THR cc_start: 0.8566 (p) cc_final: 0.8289 (t) REVERT: B 250 ILE cc_start: 0.8916 (mt) cc_final: 0.8669 (mt) REVERT: C 110 GLN cc_start: 0.6993 (mt0) cc_final: 0.6457 (mp10) REVERT: E 7 LEU cc_start: 0.7279 (tp) cc_final: 0.6947 (tp) REVERT: F 31 PRO cc_start: 0.5603 (Cg_endo) cc_final: 0.5153 (Cg_exo) REVERT: F 244 GLN cc_start: 0.4981 (mt0) cc_final: 0.4636 (mt0) REVERT: F 295 GLN cc_start: 0.7642 (mp-120) cc_final: 0.7306 (mm-40) outliers start: 25 outliers final: 22 residues processed: 218 average time/residue: 0.5882 time to fit residues: 188.5516 Evaluate side-chains 223 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 200 time to evaluate : 2.071 ------------------------------------------------------------------------------- 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 186 ARG 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 378 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 170 optimal weight: 9.9990 chunk 152 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 119 optimal weight: 0.6980 chunk 44 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 ASN 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 = 0.169923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.122057 restraints weight = 49216.670| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.77 r_work: 0.3032 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 15209 Z= 0.188 Angle : 0.774 59.200 20619 Z= 0.430 Chirality : 0.042 0.299 2330 Planarity : 0.005 0.135 2571 Dihedral : 7.297 57.639 2346 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.55 % Allowed : 17.55 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.84 (0.19), residues: 1881 helix: 1.24 (0.17), residues: 900 sheet: -0.68 (0.39), residues: 185 loop : 0.24 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 103 HIS 0.005 0.001 HIS F 356 PHE 0.013 0.001 PHE E 28 TYR 0.016 0.001 TYR B 360 ARG 0.004 0.000 ARG F 104 Details of bonding type rmsd hydrogen bonds : bond 0.03775 ( 765) hydrogen bonds : angle 4.61163 ( 2148) metal coordination : bond 0.01492 ( 8) metal coordination : angle 9.81560 ( 12) covalent geometry : bond 0.00417 (15199) covalent geometry : angle 0.73744 (20607) Misc. bond : bond 0.00089 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16335.47 seconds wall clock time: 280 minutes 39.81 seconds (16839.81 seconds total)