Starting phenix.real_space_refine on Sat Aug 23 22:33:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9udf_64068/08_2025/9udf_64068.cif Found real_map, /net/cci-nas-00/data/ceres_data/9udf_64068/08_2025/9udf_64068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9udf_64068/08_2025/9udf_64068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9udf_64068/08_2025/9udf_64068.map" model { file = "/net/cci-nas-00/data/ceres_data/9udf_64068/08_2025/9udf_64068.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9udf_64068/08_2025/9udf_64068.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.102 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 Ca 1 9.91 5 Fe 4 7.16 5 P 6 5.49 5 S 92 5.16 5 C 9791 2.51 5 N 2451 2.21 5 O 2779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15124 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3416 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 422} Chain: "B" Number of atoms: 3178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3178 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 15, 'TRANS': 396} Chain: "C" Number of atoms: 1911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1911 Classifications: {'peptide': 252} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 244} Chain: "D" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1581 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "E" Number of atoms: 1512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1512 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "F" Number of atoms: 3157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3157 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 383} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 225 Unusual residues: {'FMN': 1, 'IQT': 1, 'LMT': 1, 'PEE': 2, 'RBF': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' CA': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FES': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9329 SG CYS D 112 45.174 73.509 65.685 1.00 75.27 S ATOM 10296 SG CYS E 26 47.030 70.558 66.892 1.00 74.20 S ATOM 8690 SG CYS D 29 45.754 67.696 63.023 1.00 67.63 S ATOM 11018 SG CYS E 120 44.072 70.350 60.967 1.00 74.22 S ATOM 12122 SG CYS F 76 44.868 88.218 96.640 1.00184.95 S ATOM 12141 SG CYS F 79 40.711 88.303 96.117 1.00174.50 S ATOM 12141 SG CYS F 79 40.711 88.303 96.117 1.00174.50 S ATOM 12380 SG CYS F 111 41.843 89.354 93.386 1.00186.85 S Time building chain proxies: 4.07, per 1000 atoms: 0.27 Number of scatterers: 15124 At special positions: 0 Unit cell: (90.64, 124.08, 153.12, 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 Ca 1 19.99 S 92 16.00 P 6 15.00 O 2779 8.00 N 2451 7.00 C 9791 6.00 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=0, symmetry=0 Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 777.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES D 302 " pdb="FE1 FES D 302 " - pdb=" SG CYS E 26 " pdb="FE2 FES D 302 " - pdb=" SG CYS D 29 " pdb="FE1 FES D 302 " - pdb=" SG CYS D 112 " pdb="FE2 FES D 302 " - pdb=" SG CYS E 120 " pdb=" FES F 501 " pdb="FE2 FES F 501 " - pdb=" SG CYS F 79 " pdb="FE2 FES F 501 " - pdb=" SG CYS F 111 " pdb="FE1 FES F 501 " - pdb=" SG CYS F 76 " Number of angles added : 14 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3472 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 12 sheets defined 51.9% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 106 through 113 removed outlier: 3.960A pdb=" N LEU A 110 " --> pdb=" O ALA A 107 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ALA A 111 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A 112 " --> pdb=" O GLN A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 126 Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.523A pdb=" N PHE A 131 " --> pdb=" O TRP A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 168 removed outlier: 3.775A pdb=" N VAL A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 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 335 through 339 Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.868A pdb=" N HIS A 354 " --> pdb=" O PHE A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 401 through 409 removed outlier: 3.549A pdb=" N ARG A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 413 Processing helix chain 'A' and resid 414 through 417 Processing helix chain 'A' and resid 418 through 424 Processing helix chain 'A' and resid 430 through 446 removed outlier: 3.909A pdb=" N LEU A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 10 Processing helix chain 'B' and resid 11 through 15 Processing helix chain 'B' and resid 23 through 35 Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.609A pdb=" N VAL B 60 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 3.800A 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 98 Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 117 through 152 removed outlier: 3.589A pdb=" N TYR B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Proline residue: B 131 - end of helix removed outlier: 3.611A pdb=" N TRP B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 168 removed outlier: 4.134A pdb=" N ILE B 164 " --> pdb=" O PHE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 191 through 195 Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.701A pdb=" N ARG B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 236 through 245 removed outlier: 3.619A pdb=" N ALA B 242 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) 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: 3.830A pdb=" N PHE B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE B 287 " --> pdb=" O GLY B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 316 Processing helix chain 'B' and resid 326 through 332 removed outlier: 3.976A pdb=" N VAL B 332 " --> pdb=" O HIS B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 353 through 375 removed outlier: 3.857A pdb=" N TRP B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN B 375 " --> pdb=" O ILE B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 410 removed outlier: 4.048A pdb=" N LEU B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Proline residue: B 394 - end of helix Processing helix chain 'C' and resid 7 through 32 removed outlier: 3.630A pdb=" N ILE C 25 " --> pdb=" O VAL C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 53 removed outlier: 3.634A pdb=" N LYS C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL C 52 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 67 Processing helix chain 'C' and resid 87 through 91 removed outlier: 4.266A pdb=" N ASN C 90 " --> pdb=" O ASP C 87 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N TYR C 91 " --> pdb=" O ALA C 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 87 through 91' Processing helix chain 'C' and resid 92 through 97 removed outlier: 3.719A pdb=" N ALA C 96 " --> pdb=" O ASP C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 112 removed outlier: 4.338A pdb=" N ASP C 111 " --> pdb=" O ALA C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 234 Processing helix chain 'C' and resid 244 through 250 removed outlier: 4.313A pdb=" N LEU C 248 " --> pdb=" O GLY C 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 17 Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 27 through 34 Processing helix chain 'D' and resid 37 through 62 removed outlier: 3.871A pdb=" N ILE D 62 " --> pdb=" O PHE D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 93 Processing helix chain 'D' and resid 94 through 102 removed outlier: 3.865A pdb=" N GLN D 100 " --> pdb=" O ASP D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 110 removed outlier: 3.828A pdb=" N ILE D 108 " --> pdb=" O PHE D 104 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE D 109 " --> pdb=" O VAL D 105 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR D 110 " --> pdb=" O GLY D 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 104 through 110' Processing helix chain 'D' and resid 111 through 121 removed outlier: 4.047A pdb=" N MET D 115 " --> pdb=" O ASN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 125 removed outlier: 3.876A pdb=" N SER D 125 " --> pdb=" O ALA D 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 122 through 125' Processing helix chain 'D' and resid 126 through 158 removed outlier: 3.628A pdb=" N VAL D 144 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE D 151 " --> pdb=" O THR D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 202 removed outlier: 3.900A pdb=" N ALA D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 206 Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 24 through 31 Processing helix chain 'E' and resid 34 through 63 removed outlier: 3.708A pdb=" N GLY E 40 " --> pdb=" O LYS E 36 " (cutoff:3.500A) Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 78 through 102 removed outlier: 3.696A pdb=" N ARG E 100 " --> pdb=" O MET E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 107 Processing helix chain 'E' and resid 109 through 117 Proline residue: E 114 - end of helix Processing helix chain 'E' and resid 119 through 133 removed outlier: 3.771A pdb=" N PHE E 123 " --> pdb=" O ASN E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 164 Processing helix chain 'E' and resid 165 through 167 No H-bonds generated for 'chain 'E' and resid 165 through 167' Processing helix chain 'E' and resid 175 through 191 Processing helix chain 'E' and resid 192 through 194 No H-bonds generated for 'chain 'E' and resid 192 through 194' Processing helix chain 'F' and resid 2 through 30 removed outlier: 3.629A pdb=" N LYS F 28 " --> pdb=" O PHE F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 63 removed outlier: 3.569A pdb=" N ALA F 58 " --> pdb=" O LYS F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 96 removed outlier: 3.775A pdb=" N ASP F 96 " --> pdb=" O PRO F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 104 Processing helix chain 'F' and resid 126 through 130 removed outlier: 3.951A pdb=" N GLY F 129 " --> pdb=" O GLU F 126 " (cutoff:3.500A) 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 196 removed outlier: 6.104A pdb=" N ASP F 191 " --> pdb=" O LYS F 187 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N TRP F 192 " --> pdb=" O TYR F 188 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LYS F 194 " --> pdb=" O GLY F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 199 No H-bonds generated for 'chain 'F' and resid 197 through 199' Processing helix chain 'F' and resid 243 through 250 Processing helix chain 'F' and resid 284 through 297 removed outlier: 3.943A pdb=" N MET F 288 " --> pdb=" O GLY F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 317 Processing helix chain 'F' and resid 319 through 330 Processing helix chain 'F' and resid 354 through 363 Processing helix chain 'F' and resid 369 through 373 removed outlier: 4.002A pdb=" N CYS F 373 " --> pdb=" O PRO F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 393 Processing helix chain 'F' and resid 397 through 399 No H-bonds generated for 'chain 'F' and resid 397 through 399' Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 6.365A pdb=" N ILE A 2 " --> pdb=" O ASP A 212 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 22 removed outlier: 3.831A pdb=" N LEU A 274 " --> pdb=" O SER A 17 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL A 19 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ARG A 276 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N SER A 21 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 9.830A pdb=" N VAL A 278 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N VAL A 323 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N SER A 263 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N VAL A 325 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA A 265 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N ARG A 327 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N GLN A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 31 removed outlier: 6.575A pdb=" N ASN A 80 " --> pdb=" O GLN A 88 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL A 90 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLU A 78 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE A 92 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL A 76 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL A 94 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLY A 74 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY A 74 " --> pdb=" O VAL A 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 43 removed outlier: 7.072A 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 83 through 85 removed outlier: 4.101A pdb=" N GLU C 85 " --> pdb=" O LEU C 75 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 138 through 142 removed outlier: 3.754A pdb=" N LEU C 138 " --> pdb=" O ALA C 151 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA C 151 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AA9, first strand: chain 'F' and resid 47 through 49 removed outlier: 3.656A pdb=" N ILE F 35 " --> pdb=" O THR F 49 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N THR F 36 " --> pdb=" O MET F 119 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LEU F 121 " --> pdb=" O THR F 36 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N SER F 38 " --> pdb=" O LEU F 121 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS F 82 " --> pdb=" O GLU F 122 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 208 through 213 removed outlier: 3.517A pdb=" N ILE F 208 " --> pdb=" O ALA F 172 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N THR F 259 " --> pdb=" O GLU F 171 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LYS F 151 " --> pdb=" O ILE F 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 175 through 178 Processing sheet with id=AB3, first strand: chain 'F' and resid 351 through 352 removed outlier: 4.245A pdb=" N TYR F 351 " --> pdb=" O CYS F 337 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N HIS F 336 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR F 307 " --> pdb=" O HIS F 336 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ALA F 338 " --> pdb=" O TYR F 307 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR F 309 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR F 375 " --> pdb=" O LEU F 402 " (cutoff:3.500A) 698 hydrogen bonds defined for protein. 1965 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: 2.73 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.40: 6128 1.40 - 1.60: 9154 1.60 - 1.80: 119 1.80 - 2.00: 46 2.00 - 2.20: 8 Bond restraints: 15455 Sorted by residual: bond pdb=" C12 IQT B 506 " pdb=" C13 IQT B 506 " ideal model delta sigma weight residual 1.454 1.278 0.176 2.00e-02 2.50e+03 7.77e+01 bond pdb=" C1 IQT B 506 " pdb=" C7 IQT B 506 " ideal model delta sigma weight residual 1.479 1.376 0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" C4 FMN B 501 " pdb=" C4A FMN B 501 " ideal model delta sigma weight residual 1.485 1.386 0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" C4 FMN C 301 " pdb=" C4A FMN C 301 " ideal model delta sigma weight residual 1.485 1.386 0.099 2.00e-02 2.50e+03 2.43e+01 bond pdb=" C4A FMN B 501 " pdb=" N5 FMN B 501 " ideal model delta sigma weight residual 1.300 1.377 -0.077 2.00e-02 2.50e+03 1.48e+01 ... (remaining 15450 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 20643 2.37 - 4.75: 268 4.75 - 7.12: 29 7.12 - 9.49: 4 9.49 - 11.87: 1 Bond angle restraints: 20945 Sorted by residual: angle pdb=" C PRO F 31 " pdb=" N THR F 32 " pdb=" CA THR F 32 " ideal model delta sigma weight residual 121.54 129.98 -8.44 1.91e+00 2.74e-01 1.95e+01 angle pdb=" N VAL C 84 " pdb=" CA VAL C 84 " pdb=" C VAL C 84 " ideal model delta sigma weight residual 113.53 109.29 4.24 9.80e-01 1.04e+00 1.87e+01 angle pdb=" CB MET F 10 " pdb=" CG MET F 10 " pdb=" SD MET F 10 " ideal model delta sigma weight residual 112.70 124.57 -11.87 3.00e+00 1.11e-01 1.56e+01 angle pdb=" CA MET C 242 " pdb=" CB MET C 242 " pdb=" CG MET C 242 " ideal model delta sigma weight residual 114.10 120.71 -6.61 2.00e+00 2.50e-01 1.09e+01 angle pdb=" C SER C 103 " pdb=" N ILE C 104 " pdb=" CA ILE C 104 " ideal model delta sigma weight residual 121.97 127.88 -5.91 1.80e+00 3.09e-01 1.08e+01 ... (remaining 20940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.66: 8875 34.66 - 69.31: 323 69.31 - 103.97: 22 103.97 - 138.63: 0 138.63 - 173.28: 3 Dihedral angle restraints: 9223 sinusoidal: 3781 harmonic: 5442 Sorted by residual: dihedral pdb=" C14 IQT B 506 " pdb=" C15 IQT B 506 " pdb=" C16 IQT B 506 " pdb=" C17 IQT B 506 " ideal model delta sinusoidal sigma weight residual 87.07 -99.65 -173.28 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C14 IQT B 506 " pdb=" C15 IQT B 506 " pdb=" C16 IQT B 506 " pdb=" O4 IQT B 506 " ideal model delta sinusoidal sigma weight residual 157.21 -29.57 -173.22 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C13 IQT B 506 " pdb=" C14 IQT B 506 " pdb=" C15 IQT B 506 " pdb=" C16 IQT B 506 " ideal model delta sinusoidal sigma weight residual 108.58 -52.21 160.79 1 3.00e+01 1.11e-03 2.07e+01 ... (remaining 9220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1438 0.032 - 0.064: 585 0.064 - 0.095: 222 0.095 - 0.127: 100 0.127 - 0.159: 11 Chirality restraints: 2356 Sorted by residual: chirality pdb=" CA TRP B 103 " pdb=" N TRP B 103 " pdb=" C TRP B 103 " pdb=" CB TRP B 103 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.31e-01 chirality pdb=" CA LEU C 248 " pdb=" N LEU C 248 " pdb=" C LEU C 248 " pdb=" CB LEU C 248 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CA PRO F 218 " pdb=" N PRO F 218 " pdb=" C PRO F 218 " pdb=" CB PRO F 218 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.04e-01 ... (remaining 2353 not shown) Planarity restraints: 2621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 IQT B 506 " 0.205 2.00e-02 2.50e+03 1.88e-01 3.52e+02 pdb=" C13 IQT B 506 " -0.210 2.00e-02 2.50e+03 pdb=" C14 IQT B 506 " -0.163 2.00e-02 2.50e+03 pdb=" C15 IQT B 506 " 0.168 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 IQT B 506 " -0.084 2.00e-02 2.50e+03 1.84e-01 3.39e+02 pdb=" C11 IQT B 506 " 0.234 2.00e-02 2.50e+03 pdb=" C12 IQT B 506 " -0.252 2.00e-02 2.50e+03 pdb=" C13 IQT B 506 " 0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7 IQT B 506 " 0.086 2.00e-02 2.50e+03 6.95e-02 6.04e+01 pdb=" C8 IQT B 506 " -0.040 2.00e-02 2.50e+03 pdb=" C9 IQT B 506 " 0.064 2.00e-02 2.50e+03 pdb=" N1 IQT B 506 " -0.105 2.00e-02 2.50e+03 pdb=" O5 IQT B 506 " -0.006 2.00e-02 2.50e+03 ... (remaining 2618 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 337 2.70 - 3.25: 14687 3.25 - 3.80: 23379 3.80 - 4.35: 31754 4.35 - 4.90: 53428 Nonbonded interactions: 123585 Sorted by model distance: nonbonded pdb=" OD2 ASP A 396 " pdb=" OG SER A 404 " model vdw 2.146 3.040 nonbonded pdb=" O PHE A 345 " pdb=" OG SER B 50 " model vdw 2.160 3.040 nonbonded pdb=" O ASN B 375 " pdb=" O HOH B 601 " model vdw 2.199 3.040 nonbonded pdb=" OG SER D 30 " pdb=" OH TYR D 141 " model vdw 2.208 3.040 nonbonded pdb=" N GLU E 71 " pdb=" OE1 GLU E 71 " model vdw 2.226 3.120 ... (remaining 123580 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: 2.320 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: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.210 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 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 0.176 15462 Z= 0.211 Angle : 0.684 21.537 20959 Z= 0.352 Chirality : 0.043 0.159 2356 Planarity : 0.007 0.188 2621 Dihedral : 17.072 173.282 5751 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.71 % Favored : 95.13 % Rotamer: Outliers : 1.98 % Allowed : 20.42 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.19), residues: 1910 helix: 0.90 (0.18), residues: 844 sheet: -0.72 (0.42), residues: 157 loop : -1.39 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 63 TYR 0.026 0.002 TYR C 150 PHE 0.021 0.001 PHE F 11 TRP 0.023 0.002 TRP B 103 HIS 0.004 0.001 HIS C 199 Details of bonding type rmsd covalent geometry : bond 0.00440 (15455) covalent geometry : angle 0.65637 (20945) hydrogen bonds : bond 0.13757 ( 698) hydrogen bonds : angle 5.61447 ( 1965) metal coordination : bond 0.00824 ( 7) metal coordination : angle 7.41202 ( 14) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 0.609 Fit side-chains REVERT: A 162 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.6865 (tm-30) REVERT: A 200 ARG cc_start: 0.8797 (mtm110) cc_final: 0.8594 (mtp180) REVERT: A 284 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7397 (pp20) REVERT: B 57 MET cc_start: 0.8313 (mmt) cc_final: 0.8052 (mmt) REVERT: B 152 LYS cc_start: 0.8121 (mtpt) cc_final: 0.7388 (mptp) REVERT: B 406 LYS cc_start: 0.7743 (mtpp) cc_final: 0.7107 (mmpt) REVERT: C 31 VAL cc_start: 0.7296 (p) cc_final: 0.7036 (t) REVERT: C 137 ILE cc_start: 0.2615 (OUTLIER) cc_final: 0.2096 (mm) REVERT: C 148 MET cc_start: 0.0550 (pmt) cc_final: -0.0373 (mpt) REVERT: C 242 MET cc_start: 0.2295 (tmm) cc_final: 0.1086 (mmp) REVERT: C 248 LEU cc_start: 0.3869 (pt) cc_final: 0.3438 (pt) REVERT: D 44 MET cc_start: 0.8273 (tpt) cc_final: 0.7890 (tpp) REVERT: D 50 PHE cc_start: 0.6923 (t80) cc_final: 0.5895 (m-10) REVERT: D 71 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.7426 (ptt-90) REVERT: E 36 LYS cc_start: 0.7847 (tptt) cc_final: 0.7303 (mmtt) REVERT: E 61 ASN cc_start: 0.8495 (m-40) cc_final: 0.8198 (m-40) REVERT: E 168 ASP cc_start: 0.8790 (t0) cc_final: 0.8371 (t0) REVERT: F 118 ASP cc_start: 0.5724 (p0) cc_final: 0.4693 (m-30) REVERT: F 122 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.7011 (mp0) REVERT: F 214 MET cc_start: 0.6584 (ptt) cc_final: 0.5914 (ptp) REVERT: F 402 LEU cc_start: 0.7779 (mp) cc_final: 0.7469 (mm) outliers start: 31 outliers final: 17 residues processed: 178 average time/residue: 0.6338 time to fit residues: 124.7823 Evaluate side-chains 164 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 258 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 100 GLN F 176 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.173332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.112636 restraints weight = 16648.737| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.87 r_work: 0.3004 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.0595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15462 Z= 0.152 Angle : 0.609 20.017 20959 Z= 0.303 Chirality : 0.043 0.166 2356 Planarity : 0.005 0.056 2621 Dihedral : 10.380 110.380 2415 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.50 % Favored : 95.34 % Rotamer: Outliers : 3.83 % Allowed : 18.32 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.19), residues: 1910 helix: 0.96 (0.18), residues: 864 sheet: -0.59 (0.42), residues: 154 loop : -1.43 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 63 TYR 0.015 0.002 TYR F 217 PHE 0.013 0.001 PHE F 318 TRP 0.024 0.002 TRP B 103 HIS 0.004 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00361 (15455) covalent geometry : angle 0.58114 (20945) hydrogen bonds : bond 0.04943 ( 698) hydrogen bonds : angle 4.74683 ( 1965) metal coordination : bond 0.00873 ( 7) metal coordination : angle 7.02034 ( 14) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 162 time to evaluate : 0.632 Fit side-chains REVERT: A 39 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.7630 (ttt) REVERT: A 109 GLN cc_start: 0.7299 (mt0) cc_final: 0.7012 (mt0) REVERT: A 162 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.6833 (tm-30) REVERT: A 212 ASP cc_start: 0.8564 (m-30) cc_final: 0.8195 (m-30) REVERT: A 284 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7405 (pp20) REVERT: B 57 MET cc_start: 0.8394 (mmt) cc_final: 0.8025 (mmt) REVERT: B 152 LYS cc_start: 0.8315 (mtpt) cc_final: 0.7605 (mptp) REVERT: B 406 LYS cc_start: 0.7759 (mtpp) cc_final: 0.7126 (mmpt) REVERT: C 137 ILE cc_start: 0.2534 (OUTLIER) cc_final: 0.2028 (mm) REVERT: C 148 MET cc_start: 0.0747 (pmt) cc_final: -0.0370 (mpp) REVERT: C 242 MET cc_start: 0.2151 (tmm) cc_final: 0.0842 (mmp) REVERT: D 44 MET cc_start: 0.8278 (tpt) cc_final: 0.7913 (tpp) REVERT: D 50 PHE cc_start: 0.6955 (t80) cc_final: 0.5957 (m-10) REVERT: D 71 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7523 (ptt-90) REVERT: D 204 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7842 (pm20) REVERT: E 36 LYS cc_start: 0.7919 (tptt) cc_final: 0.7585 (mtpp) REVERT: E 61 ASN cc_start: 0.8563 (m-40) cc_final: 0.8274 (m-40) REVERT: E 122 ILE cc_start: 0.7848 (OUTLIER) cc_final: 0.7359 (mm) REVERT: E 168 ASP cc_start: 0.8919 (t0) cc_final: 0.8507 (t0) REVERT: F 118 ASP cc_start: 0.5840 (p0) cc_final: 0.4777 (m-30) REVERT: F 214 MET cc_start: 0.6619 (ptt) cc_final: 0.5875 (ptp) REVERT: F 402 LEU cc_start: 0.7907 (mp) cc_final: 0.7593 (mm) outliers start: 60 outliers final: 17 residues processed: 207 average time/residue: 0.6121 time to fit residues: 140.4531 Evaluate side-chains 176 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain F residue 258 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 128 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 chunk 116 optimal weight: 0.6980 chunk 145 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.174445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.114714 restraints weight = 16719.420| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.96 r_work: 0.2971 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15462 Z= 0.122 Angle : 0.556 18.401 20959 Z= 0.279 Chirality : 0.042 0.168 2356 Planarity : 0.004 0.057 2621 Dihedral : 9.744 104.234 2398 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.08 % Favored : 95.76 % Rotamer: Outliers : 3.77 % Allowed : 19.08 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.19), residues: 1910 helix: 1.21 (0.18), residues: 859 sheet: -0.33 (0.44), residues: 142 loop : -1.36 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 63 TYR 0.016 0.001 TYR D 141 PHE 0.011 0.001 PHE D 188 TRP 0.023 0.001 TRP B 103 HIS 0.003 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00281 (15455) covalent geometry : angle 0.52826 (20945) hydrogen bonds : bond 0.04376 ( 698) hydrogen bonds : angle 4.54374 ( 1965) metal coordination : bond 0.00939 ( 7) metal coordination : angle 6.69975 ( 14) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 169 time to evaluate : 0.600 Fit side-chains REVERT: A 39 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.7583 (ttt) REVERT: A 109 GLN cc_start: 0.7235 (mt0) cc_final: 0.6948 (mt0) REVERT: A 162 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.6935 (tm-30) REVERT: A 284 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7389 (pp20) REVERT: B 152 LYS cc_start: 0.8322 (mtpt) cc_final: 0.7511 (mmtt) REVERT: B 406 LYS cc_start: 0.7751 (mtpp) cc_final: 0.7124 (mmpt) REVERT: C 87 ASP cc_start: 0.3134 (p0) cc_final: 0.1633 (m-30) REVERT: C 137 ILE cc_start: 0.2765 (OUTLIER) cc_final: 0.2250 (mm) REVERT: C 148 MET cc_start: 0.0765 (pmt) cc_final: -0.0298 (mpp) REVERT: C 242 MET cc_start: 0.1982 (tmm) cc_final: 0.0694 (mmp) REVERT: D 44 MET cc_start: 0.8275 (tpt) cc_final: 0.7946 (tpp) REVERT: D 50 PHE cc_start: 0.6934 (t80) cc_final: 0.5952 (m-10) REVERT: D 71 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7500 (ptt-90) REVERT: D 99 LYS cc_start: 0.6252 (OUTLIER) cc_final: 0.5197 (pptt) REVERT: D 204 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7878 (pm20) REVERT: E 1 MET cc_start: 0.6402 (OUTLIER) cc_final: 0.6164 (tpt) REVERT: E 36 LYS cc_start: 0.7816 (tptt) cc_final: 0.7522 (mtpp) REVERT: E 122 ILE cc_start: 0.7667 (OUTLIER) cc_final: 0.7139 (mm) REVERT: E 165 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.7892 (ptmt) REVERT: E 168 ASP cc_start: 0.8878 (t0) cc_final: 0.8510 (t0) REVERT: F 10 MET cc_start: 0.5944 (mmt) cc_final: 0.5567 (mmm) REVERT: F 118 ASP cc_start: 0.5996 (p0) cc_final: 0.4869 (m-30) REVERT: F 214 MET cc_start: 0.6573 (ptt) cc_final: 0.5749 (ptp) REVERT: F 225 MET cc_start: 0.5678 (mtp) cc_final: 0.5352 (mtt) REVERT: F 264 PHE cc_start: 0.6672 (m-80) cc_final: 0.6399 (m-80) REVERT: F 300 LYS cc_start: 0.7142 (OUTLIER) cc_final: 0.6481 (mmmm) REVERT: F 402 LEU cc_start: 0.7898 (mp) cc_final: 0.7585 (mm) outliers start: 59 outliers final: 16 residues processed: 211 average time/residue: 0.6126 time to fit residues: 143.3380 Evaluate side-chains 184 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 300 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 108 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 137 optimal weight: 8.9990 chunk 185 optimal weight: 3.9990 chunk 146 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 123 optimal weight: 6.9990 chunk 163 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 overall best weight: 3.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.169493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.108506 restraints weight = 16832.090| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.09 r_work: 0.2921 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 15462 Z= 0.307 Angle : 0.719 23.666 20959 Z= 0.358 Chirality : 0.049 0.173 2356 Planarity : 0.005 0.055 2621 Dihedral : 10.447 100.601 2397 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.55 % Favored : 94.35 % Rotamer: Outliers : 4.53 % Allowed : 18.83 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.18), residues: 1910 helix: 0.61 (0.18), residues: 872 sheet: -0.55 (0.42), residues: 152 loop : -1.49 (0.19), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 63 TYR 0.022 0.002 TYR D 141 PHE 0.019 0.002 PHE F 406 TRP 0.024 0.002 TRP B 103 HIS 0.006 0.002 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00771 (15455) covalent geometry : angle 0.69121 (20945) hydrogen bonds : bond 0.06674 ( 698) hydrogen bonds : angle 4.87987 ( 1965) metal coordination : bond 0.01610 ( 7) metal coordination : angle 7.67233 ( 14) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 161 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.7528 (ttt) REVERT: A 162 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.6893 (tm-30) REVERT: B 57 MET cc_start: 0.8486 (mmt) cc_final: 0.8024 (mmt) REVERT: B 152 LYS cc_start: 0.8353 (mtpt) cc_final: 0.7593 (mptp) REVERT: B 406 LYS cc_start: 0.7870 (mtpp) cc_final: 0.7225 (mmpt) REVERT: C 38 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7972 (mmpt) REVERT: C 137 ILE cc_start: 0.2677 (OUTLIER) cc_final: 0.2108 (mm) REVERT: C 148 MET cc_start: 0.1145 (pmt) cc_final: 0.0017 (mpp) REVERT: C 176 LEU cc_start: 0.2500 (OUTLIER) cc_final: 0.2095 (tp) REVERT: C 221 LEU cc_start: 0.0484 (OUTLIER) cc_final: 0.0188 (tt) REVERT: C 242 MET cc_start: 0.1969 (tmm) cc_final: 0.0652 (mmp) REVERT: C 248 LEU cc_start: 0.3667 (OUTLIER) cc_final: 0.3396 (pt) REVERT: D 44 MET cc_start: 0.8236 (tpt) cc_final: 0.7883 (tpp) REVERT: D 50 PHE cc_start: 0.7069 (t80) cc_final: 0.6017 (m-10) REVERT: D 71 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7494 (ptt-90) REVERT: D 99 LYS cc_start: 0.6387 (OUTLIER) cc_final: 0.5315 (pptt) REVERT: E 36 LYS cc_start: 0.7935 (tptt) cc_final: 0.7590 (mtpp) REVERT: E 61 ASN cc_start: 0.8660 (m-40) cc_final: 0.8336 (m-40) REVERT: E 122 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7392 (mm) REVERT: E 165 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.7971 (ptmt) REVERT: F 10 MET cc_start: 0.5943 (mmt) cc_final: 0.5566 (mmm) REVERT: F 118 ASP cc_start: 0.5841 (p0) cc_final: 0.4863 (m-30) REVERT: F 214 MET cc_start: 0.7034 (ptt) cc_final: 0.6241 (ptp) REVERT: F 225 MET cc_start: 0.5762 (mtp) cc_final: 0.5378 (mtt) REVERT: F 300 LYS cc_start: 0.7196 (OUTLIER) cc_final: 0.6532 (mmmm) REVERT: F 402 LEU cc_start: 0.7975 (mp) cc_final: 0.7637 (mm) outliers start: 71 outliers final: 30 residues processed: 217 average time/residue: 0.6147 time to fit residues: 148.3508 Evaluate side-chains 196 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 300 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 101 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 chunk 176 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 145 optimal weight: 0.6980 chunk 112 optimal weight: 0.1980 chunk 146 optimal weight: 0.6980 chunk 173 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.174480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.114686 restraints weight = 16733.108| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.13 r_work: 0.3003 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 15462 Z= 0.111 Angle : 0.545 19.190 20959 Z= 0.274 Chirality : 0.042 0.159 2356 Planarity : 0.004 0.059 2621 Dihedral : 9.495 90.562 2396 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.98 % Favored : 95.92 % Rotamer: Outliers : 3.13 % Allowed : 20.49 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.19), residues: 1910 helix: 1.16 (0.18), residues: 859 sheet: -0.31 (0.44), residues: 142 loop : -1.36 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 63 TYR 0.016 0.001 TYR D 141 PHE 0.010 0.001 PHE D 188 TRP 0.023 0.001 TRP B 103 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00249 (15455) covalent geometry : angle 0.51590 (20945) hydrogen bonds : bond 0.04070 ( 698) hydrogen bonds : angle 4.46260 ( 1965) metal coordination : bond 0.00788 ( 7) metal coordination : angle 6.83249 ( 14) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 157 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 162 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.6908 (tm-30) REVERT: A 212 ASP cc_start: 0.8483 (m-30) cc_final: 0.8210 (m-30) REVERT: B 152 LYS cc_start: 0.8391 (mtpt) cc_final: 0.7614 (mmtt) REVERT: B 406 LYS cc_start: 0.7730 (mtpp) cc_final: 0.7120 (mmpt) REVERT: C 38 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7951 (mmpt) REVERT: C 87 ASP cc_start: 0.3078 (p0) cc_final: 0.1651 (m-30) REVERT: C 148 MET cc_start: 0.1009 (pmt) cc_final: -0.0099 (mpp) REVERT: C 221 LEU cc_start: 0.0503 (OUTLIER) cc_final: 0.0216 (tt) REVERT: C 242 MET cc_start: 0.1957 (tmm) cc_final: 0.0621 (mmp) REVERT: C 249 THR cc_start: 0.4286 (OUTLIER) cc_final: 0.3973 (m) REVERT: D 44 MET cc_start: 0.8224 (tpt) cc_final: 0.7876 (tpp) REVERT: D 50 PHE cc_start: 0.6964 (t80) cc_final: 0.5964 (m-10) REVERT: E 36 LYS cc_start: 0.7843 (tptt) cc_final: 0.7534 (mtpp) REVERT: E 61 ASN cc_start: 0.8621 (m-40) cc_final: 0.8284 (m-40) REVERT: E 122 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7238 (mm) REVERT: E 165 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.7795 (ptmt) REVERT: E 168 ASP cc_start: 0.8790 (t0) cc_final: 0.8472 (t70) REVERT: F 10 MET cc_start: 0.5966 (mmt) cc_final: 0.5635 (mmm) REVERT: F 105 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: F 118 ASP cc_start: 0.6117 (p0) cc_final: 0.4987 (m-30) REVERT: F 214 MET cc_start: 0.6797 (ptp) cc_final: 0.6005 (ptp) REVERT: F 264 PHE cc_start: 0.6505 (m-80) cc_final: 0.6238 (m-80) REVERT: F 300 LYS cc_start: 0.7092 (OUTLIER) cc_final: 0.6432 (mmmm) REVERT: F 402 LEU cc_start: 0.7978 (mp) cc_final: 0.7639 (mm) outliers start: 49 outliers final: 18 residues processed: 194 average time/residue: 0.5016 time to fit residues: 108.1807 Evaluate side-chains 177 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 300 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 51 optimal weight: 5.9990 chunk 110 optimal weight: 0.5980 chunk 128 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 97 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 chunk 186 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.173932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.114660 restraints weight = 16623.158| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.10 r_work: 0.2970 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15462 Z= 0.151 Angle : 0.576 19.753 20959 Z= 0.288 Chirality : 0.043 0.161 2356 Planarity : 0.004 0.058 2621 Dihedral : 9.393 89.955 2390 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.66 % Favored : 95.24 % Rotamer: Outliers : 3.64 % Allowed : 20.23 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.19), residues: 1910 helix: 1.11 (0.18), residues: 864 sheet: -0.04 (0.45), residues: 132 loop : -1.37 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 63 TYR 0.019 0.001 TYR D 141 PHE 0.013 0.001 PHE E 28 TRP 0.024 0.002 TRP F 250 HIS 0.007 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00367 (15455) covalent geometry : angle 0.54786 (20945) hydrogen bonds : bond 0.04710 ( 698) hydrogen bonds : angle 4.50347 ( 1965) metal coordination : bond 0.00979 ( 7) metal coordination : angle 6.87274 ( 14) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 155 time to evaluate : 0.404 Fit side-chains REVERT: A 39 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.7584 (ttt) REVERT: A 162 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.6867 (tm-30) REVERT: A 212 ASP cc_start: 0.8471 (m-30) cc_final: 0.8184 (m-30) REVERT: B 152 LYS cc_start: 0.8261 (mtpt) cc_final: 0.7472 (mmtt) REVERT: B 256 GLN cc_start: 0.7419 (mm-40) cc_final: 0.7202 (mm-40) REVERT: B 406 LYS cc_start: 0.7627 (mtpp) cc_final: 0.6987 (mmpt) REVERT: C 38 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7964 (mmpt) REVERT: C 87 ASP cc_start: 0.2958 (p0) cc_final: 0.1513 (m-30) REVERT: C 148 MET cc_start: 0.1268 (pmt) cc_final: 0.0141 (mpp) REVERT: C 221 LEU cc_start: 0.0375 (OUTLIER) cc_final: 0.0094 (tt) REVERT: C 242 MET cc_start: 0.2079 (tmm) cc_final: 0.0751 (mmp) REVERT: C 249 THR cc_start: 0.4187 (OUTLIER) cc_final: 0.3853 (m) REVERT: D 44 MET cc_start: 0.8140 (tpt) cc_final: 0.7771 (tpp) REVERT: D 50 PHE cc_start: 0.6876 (t80) cc_final: 0.5866 (m-10) REVERT: D 99 LYS cc_start: 0.6198 (OUTLIER) cc_final: 0.5277 (pptt) REVERT: E 36 LYS cc_start: 0.7805 (tptt) cc_final: 0.7479 (mtpp) REVERT: E 61 ASN cc_start: 0.8580 (m-40) cc_final: 0.8245 (m-40) REVERT: E 122 ILE cc_start: 0.7650 (OUTLIER) cc_final: 0.7160 (mm) REVERT: E 165 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.7705 (ptmt) REVERT: F 10 MET cc_start: 0.5916 (mmt) cc_final: 0.5571 (mmm) REVERT: F 105 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7141 (mp0) REVERT: F 118 ASP cc_start: 0.6060 (p0) cc_final: 0.4947 (m-30) REVERT: F 214 MET cc_start: 0.6833 (ptp) cc_final: 0.6002 (ptp) REVERT: F 264 PHE cc_start: 0.6504 (m-80) cc_final: 0.6209 (m-80) REVERT: F 300 LYS cc_start: 0.7020 (OUTLIER) cc_final: 0.6370 (mmmm) REVERT: F 402 LEU cc_start: 0.7911 (mp) cc_final: 0.7567 (mm) outliers start: 57 outliers final: 26 residues processed: 196 average time/residue: 0.4653 time to fit residues: 101.9973 Evaluate side-chains 190 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 300 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 36 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 154 optimal weight: 10.0000 chunk 152 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.172850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.112591 restraints weight = 16606.047| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.96 r_work: 0.2979 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15462 Z= 0.189 Angle : 0.607 21.055 20959 Z= 0.303 Chirality : 0.044 0.165 2356 Planarity : 0.005 0.057 2621 Dihedral : 9.504 91.151 2390 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.61 % Favored : 95.29 % Rotamer: Outliers : 3.83 % Allowed : 19.97 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.19), residues: 1910 helix: 0.98 (0.18), residues: 868 sheet: -0.18 (0.44), residues: 140 loop : -1.43 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 63 TYR 0.021 0.002 TYR D 141 PHE 0.020 0.002 PHE C 152 TRP 0.024 0.002 TRP B 103 HIS 0.008 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00468 (15455) covalent geometry : angle 0.57852 (20945) hydrogen bonds : bond 0.05185 ( 698) hydrogen bonds : angle 4.58723 ( 1965) metal coordination : bond 0.01101 ( 7) metal coordination : angle 7.13239 ( 14) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 155 time to evaluate : 0.459 Fit side-chains REVERT: A 39 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.7583 (ttt) REVERT: A 162 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.6905 (tm-30) REVERT: A 212 ASP cc_start: 0.8573 (m-30) cc_final: 0.8364 (m-30) REVERT: B 152 LYS cc_start: 0.8348 (mtpt) cc_final: 0.7545 (mmtt) REVERT: B 256 GLN cc_start: 0.7570 (mm-40) cc_final: 0.7358 (mm-40) REVERT: B 406 LYS cc_start: 0.7829 (mtpp) cc_final: 0.7179 (mmpt) REVERT: C 20 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7875 (mt) REVERT: C 38 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7948 (mmpt) REVERT: C 148 MET cc_start: 0.1257 (pmt) cc_final: 0.0196 (mpp) REVERT: C 176 LEU cc_start: 0.2650 (OUTLIER) cc_final: 0.2434 (tp) REVERT: C 221 LEU cc_start: 0.0485 (OUTLIER) cc_final: 0.0217 (tt) REVERT: C 242 MET cc_start: 0.2112 (tmm) cc_final: 0.0736 (mmp) REVERT: C 249 THR cc_start: 0.4230 (OUTLIER) cc_final: 0.4016 (m) REVERT: D 44 MET cc_start: 0.8280 (tpt) cc_final: 0.7924 (tpp) REVERT: D 50 PHE cc_start: 0.7023 (t80) cc_final: 0.6000 (m-10) REVERT: D 99 LYS cc_start: 0.6247 (OUTLIER) cc_final: 0.5275 (pptt) REVERT: E 1 MET cc_start: 0.6485 (OUTLIER) cc_final: 0.6261 (tpt) REVERT: E 36 LYS cc_start: 0.7898 (tptt) cc_final: 0.7567 (mtpp) REVERT: E 61 ASN cc_start: 0.8671 (m-40) cc_final: 0.8338 (m-40) REVERT: E 122 ILE cc_start: 0.7806 (OUTLIER) cc_final: 0.7277 (mm) REVERT: E 165 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.7800 (ptmt) REVERT: F 10 MET cc_start: 0.5992 (mmt) cc_final: 0.5630 (mmm) REVERT: F 105 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7213 (mp0) REVERT: F 118 ASP cc_start: 0.6128 (p0) cc_final: 0.5038 (m-30) REVERT: F 140 ASN cc_start: 0.5935 (OUTLIER) cc_final: 0.5058 (t0) REVERT: F 214 MET cc_start: 0.6965 (ptp) cc_final: 0.6129 (ptp) REVERT: F 264 PHE cc_start: 0.6567 (m-80) cc_final: 0.6288 (m-80) REVERT: F 300 LYS cc_start: 0.7050 (OUTLIER) cc_final: 0.6407 (mmmm) REVERT: F 402 LEU cc_start: 0.8053 (mp) cc_final: 0.7698 (mm) outliers start: 60 outliers final: 28 residues processed: 197 average time/residue: 0.4631 time to fit residues: 101.8709 Evaluate side-chains 192 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 140 ASN Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 300 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 79 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 174 optimal weight: 20.0000 chunk 111 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 205 GLN E 197 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 = 0.172603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.110698 restraints weight = 16658.976| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.03 r_work: 0.2967 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15462 Z= 0.153 Angle : 0.587 20.501 20959 Z= 0.292 Chirality : 0.044 0.238 2356 Planarity : 0.004 0.057 2621 Dihedral : 9.343 89.361 2390 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.40 % Favored : 95.50 % Rotamer: Outliers : 3.64 % Allowed : 20.80 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.19), residues: 1910 helix: 1.06 (0.18), residues: 864 sheet: 0.12 (0.46), residues: 126 loop : -1.39 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 63 TYR 0.019 0.001 TYR D 141 PHE 0.019 0.001 PHE C 152 TRP 0.023 0.002 TRP B 103 HIS 0.003 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00371 (15455) covalent geometry : angle 0.55833 (20945) hydrogen bonds : bond 0.04717 ( 698) hydrogen bonds : angle 4.51204 ( 1965) metal coordination : bond 0.00925 ( 7) metal coordination : angle 7.02408 ( 14) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 152 time to evaluate : 0.583 Fit side-chains REVERT: A 39 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.7582 (ttt) REVERT: A 162 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.6871 (tm-30) REVERT: A 212 ASP cc_start: 0.8585 (m-30) cc_final: 0.8363 (m-30) REVERT: B 152 LYS cc_start: 0.8310 (mtpt) cc_final: 0.7512 (mmtt) REVERT: B 406 LYS cc_start: 0.7715 (mtpp) cc_final: 0.7070 (mmpt) REVERT: C 38 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7928 (mmpt) REVERT: C 148 MET cc_start: 0.1533 (pmt) cc_final: 0.0585 (mpp) REVERT: C 219 ASP cc_start: 0.1156 (OUTLIER) cc_final: 0.0489 (m-30) REVERT: C 221 LEU cc_start: 0.0429 (OUTLIER) cc_final: 0.0076 (tt) REVERT: C 242 MET cc_start: 0.2218 (tmm) cc_final: 0.0764 (mmp) REVERT: C 249 THR cc_start: 0.4291 (OUTLIER) cc_final: 0.3985 (m) REVERT: D 44 MET cc_start: 0.8258 (tpt) cc_final: 0.7897 (tpp) REVERT: D 50 PHE cc_start: 0.6987 (t80) cc_final: 0.5972 (m-10) REVERT: D 99 LYS cc_start: 0.6240 (OUTLIER) cc_final: 0.5295 (pptt) REVERT: E 1 MET cc_start: 0.6383 (OUTLIER) cc_final: 0.6154 (tpt) REVERT: E 61 ASN cc_start: 0.8627 (m-40) cc_final: 0.8291 (m-40) REVERT: E 122 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7183 (mm) REVERT: E 165 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.7766 (ptmt) REVERT: F 10 MET cc_start: 0.5907 (mmt) cc_final: 0.5553 (mmm) REVERT: F 105 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: F 118 ASP cc_start: 0.6076 (p0) cc_final: 0.5000 (m-30) REVERT: F 140 ASN cc_start: 0.5780 (OUTLIER) cc_final: 0.5058 (t0) REVERT: F 158 GLU cc_start: 0.4628 (OUTLIER) cc_final: 0.4348 (tt0) REVERT: F 214 MET cc_start: 0.6943 (ptp) cc_final: 0.6082 (ptp) REVERT: F 264 PHE cc_start: 0.6497 (m-80) cc_final: 0.6202 (m-80) REVERT: F 300 LYS cc_start: 0.7021 (OUTLIER) cc_final: 0.6378 (mmmm) REVERT: F 402 LEU cc_start: 0.8007 (mp) cc_final: 0.7649 (mm) outliers start: 57 outliers final: 29 residues processed: 195 average time/residue: 0.5461 time to fit residues: 119.0918 Evaluate side-chains 195 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 152 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 140 ASN Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 300 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 130 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 101 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 145 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.170958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.111472 restraints weight = 16622.356| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.96 r_work: 0.2942 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 15462 Z= 0.294 Angle : 0.712 24.722 20959 Z= 0.352 Chirality : 0.049 0.229 2356 Planarity : 0.005 0.053 2621 Dihedral : 9.928 94.299 2390 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.50 % Favored : 94.40 % Rotamer: Outliers : 3.45 % Allowed : 21.00 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.18), residues: 1910 helix: 0.63 (0.18), residues: 870 sheet: -0.25 (0.43), residues: 138 loop : -1.55 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 55 TYR 0.021 0.002 TYR D 141 PHE 0.019 0.002 PHE F 406 TRP 0.024 0.002 TRP B 103 HIS 0.012 0.002 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00743 (15455) covalent geometry : angle 0.68261 (20945) hydrogen bonds : bond 0.06376 ( 698) hydrogen bonds : angle 4.80162 ( 1965) metal coordination : bond 0.01563 ( 7) metal coordination : angle 7.91407 ( 14) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 153 time to evaluate : 0.504 Fit side-chains REVERT: A 39 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.7610 (ttt) REVERT: A 162 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.6891 (tm-30) REVERT: A 212 ASP cc_start: 0.8670 (m-30) cc_final: 0.8463 (m-30) REVERT: B 152 LYS cc_start: 0.8377 (mtpt) cc_final: 0.7642 (mptp) REVERT: B 406 LYS cc_start: 0.7895 (mtpp) cc_final: 0.7238 (mmpt) REVERT: C 38 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7900 (mmpt) REVERT: C 148 MET cc_start: 0.1529 (pmt) cc_final: 0.0566 (mpp) REVERT: C 156 GLU cc_start: 0.0485 (tt0) cc_final: 0.0150 (tt0) REVERT: C 219 ASP cc_start: 0.1276 (OUTLIER) cc_final: 0.0525 (m-30) REVERT: C 221 LEU cc_start: 0.0629 (OUTLIER) cc_final: 0.0305 (tt) REVERT: C 242 MET cc_start: 0.2073 (tmm) cc_final: 0.0496 (mpp) REVERT: C 249 THR cc_start: 0.4374 (OUTLIER) cc_final: 0.4075 (m) REVERT: D 24 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.7183 (mt0) REVERT: D 44 MET cc_start: 0.8263 (tpt) cc_final: 0.7909 (tpp) REVERT: D 50 PHE cc_start: 0.7071 (t80) cc_final: 0.6042 (m-10) REVERT: D 99 LYS cc_start: 0.6292 (OUTLIER) cc_final: 0.5318 (pptt) REVERT: E 1 MET cc_start: 0.6607 (OUTLIER) cc_final: 0.6357 (tpt) REVERT: E 61 ASN cc_start: 0.8699 (m-40) cc_final: 0.8374 (m-40) REVERT: E 122 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7403 (mm) REVERT: E 165 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.7978 (ptmt) REVERT: F 10 MET cc_start: 0.6134 (mmt) cc_final: 0.5704 (mmm) REVERT: F 105 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7317 (mp0) REVERT: F 118 ASP cc_start: 0.5825 (p0) cc_final: 0.4892 (m-30) REVERT: F 158 GLU cc_start: 0.4473 (OUTLIER) cc_final: 0.4169 (tt0) REVERT: F 214 MET cc_start: 0.7237 (ptp) cc_final: 0.6345 (ptp) REVERT: F 300 LYS cc_start: 0.7160 (OUTLIER) cc_final: 0.6518 (mmmm) outliers start: 54 outliers final: 28 residues processed: 195 average time/residue: 0.5422 time to fit residues: 117.7244 Evaluate side-chains 194 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 300 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 121 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 181 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 162 optimal weight: 20.0000 chunk 144 optimal weight: 0.9980 chunk 157 optimal weight: 0.0870 chunk 20 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 HIS D 171 ASN E 197 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 = 0.173393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.112079 restraints weight = 16646.102| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.00 r_work: 0.2990 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15462 Z= 0.123 Angle : 0.571 20.648 20959 Z= 0.284 Chirality : 0.043 0.193 2356 Planarity : 0.004 0.060 2621 Dihedral : 9.291 90.446 2390 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.29 % Favored : 95.60 % Rotamer: Outliers : 2.36 % Allowed : 21.76 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.19), residues: 1910 helix: 1.06 (0.18), residues: 866 sheet: 0.02 (0.45), residues: 128 loop : -1.44 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 63 TYR 0.020 0.001 TYR F 248 PHE 0.015 0.001 PHE C 152 TRP 0.022 0.002 TRP B 103 HIS 0.006 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00287 (15455) covalent geometry : angle 0.54074 (20945) hydrogen bonds : bond 0.04284 ( 698) hydrogen bonds : angle 4.49464 ( 1965) metal coordination : bond 0.00773 ( 7) metal coordination : angle 7.09573 ( 14) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 150 time to evaluate : 0.565 Fit side-chains REVERT: A 162 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.6890 (tm-30) REVERT: A 212 ASP cc_start: 0.8480 (m-30) cc_final: 0.8204 (m-30) REVERT: B 152 LYS cc_start: 0.8269 (mtpt) cc_final: 0.7499 (mmtt) REVERT: B 406 LYS cc_start: 0.7720 (mtpp) cc_final: 0.7088 (mmpt) REVERT: C 38 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7902 (mmpt) REVERT: C 148 MET cc_start: 0.1432 (pmt) cc_final: 0.0561 (mpp) REVERT: C 221 LEU cc_start: 0.0809 (OUTLIER) cc_final: 0.0603 (tt) REVERT: C 242 MET cc_start: 0.1850 (tmm) cc_final: 0.0251 (mpp) REVERT: C 249 THR cc_start: 0.4267 (OUTLIER) cc_final: 0.3974 (m) REVERT: D 44 MET cc_start: 0.8201 (tpt) cc_final: 0.7853 (tpp) REVERT: D 50 PHE cc_start: 0.6992 (t80) cc_final: 0.5989 (m-10) REVERT: D 99 LYS cc_start: 0.6236 (OUTLIER) cc_final: 0.5330 (pptt) REVERT: E 1 MET cc_start: 0.6363 (OUTLIER) cc_final: 0.6159 (tpt) REVERT: E 61 ASN cc_start: 0.8638 (m-40) cc_final: 0.8281 (m-40) REVERT: E 122 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7265 (mm) REVERT: E 165 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.7778 (ptmt) REVERT: E 168 ASP cc_start: 0.8850 (t0) cc_final: 0.8520 (t70) REVERT: F 10 MET cc_start: 0.6046 (mmt) cc_final: 0.5713 (mmm) REVERT: F 105 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7273 (mp0) REVERT: F 118 ASP cc_start: 0.5974 (p0) cc_final: 0.4930 (m-30) REVERT: F 158 GLU cc_start: 0.4436 (OUTLIER) cc_final: 0.4178 (tt0) REVERT: F 214 MET cc_start: 0.7046 (ptp) cc_final: 0.6159 (ptp) REVERT: F 264 PHE cc_start: 0.6462 (m-80) cc_final: 0.6172 (m-80) REVERT: F 300 LYS cc_start: 0.7016 (OUTLIER) cc_final: 0.6365 (mmmm) outliers start: 37 outliers final: 20 residues processed: 180 average time/residue: 0.5949 time to fit residues: 118.6742 Evaluate side-chains 177 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 300 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 72 optimal weight: 0.5980 chunk 70 optimal weight: 0.0020 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 174 optimal weight: 9.9990 chunk 4 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 160 optimal weight: 0.0870 overall best weight: 0.6968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.174817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.115882 restraints weight = 16668.564| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.16 r_work: 0.3001 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15462 Z= 0.111 Angle : 0.553 18.222 20959 Z= 0.275 Chirality : 0.042 0.176 2356 Planarity : 0.004 0.062 2621 Dihedral : 8.871 90.370 2390 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.50 % Favored : 95.39 % Rotamer: Outliers : 2.23 % Allowed : 22.21 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.19), residues: 1910 helix: 1.32 (0.18), residues: 860 sheet: 0.25 (0.47), residues: 123 loop : -1.30 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 63 TYR 0.015 0.001 TYR D 141 PHE 0.013 0.001 PHE C 152 TRP 0.023 0.001 TRP B 103 HIS 0.003 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00255 (15455) covalent geometry : angle 0.52582 (20945) hydrogen bonds : bond 0.03862 ( 698) hydrogen bonds : angle 4.39137 ( 1965) metal coordination : bond 0.00737 ( 7) metal coordination : angle 6.59100 ( 14) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5449.18 seconds wall clock time: 93 minutes 33.23 seconds (5613.23 seconds total)