Starting phenix.real_space_refine on Fri Jul 3 16:47:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9udf_64068/07_2026/9udf_64068.cif Found real_map, /net/cci-nas-00/data/ceres_data/9udf_64068/07_2026/9udf_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 { model { file = "/net/cci-nas-00/data/ceres_data/9udf_64068/07_2026/9udf_64068.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9udf_64068/07_2026/9udf_64068.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9udf_64068/07_2026/9udf_64068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9udf_64068/07_2026/9udf_64068.map" } 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-dev-6108/lib/python3.11/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, 30 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Chain breaks: 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: 3.02, per 1000 atoms: 0.20 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: 1.01 Conformation dependent library (CDL) restraints added in 612.7 milliseconds 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: 0.54 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: 2.48 Time building geometry restraints manager: 1.29 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: 2.620 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.850 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 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 are 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/Z covalent geometry : bond 0.00440 / 0.21 (15455) covalent geometry : angle 0.65637 / 0.35 (20945) hydrogen bonds : bond 0.13757 / 9.10 ( 698) hydrogen bonds : angle 5.61447 / 3.93 ( 1965) metal coordination : bond 0.00824 / 0.41 ( 7) metal coordination : angle 7.41202 / 4.56 ( 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 : 0.548 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: 0.5622 time to fit residues: 111.0922 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 : 0.359 ------------------------------------------------------------------------------- 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... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.174431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.115292 restraints weight = 16622.149| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.86 r_work: 0.2991 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.0531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15462 Z= 0.151 Angle : 0.605 20.184 20959 Z= 0.302 Chirality : 0.043 0.163 2356 Planarity : 0.005 0.056 2621 Dihedral : 10.448 114.962 2415 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.50 % Favored : 95.34 % Rotamer: Outliers : 3.57 % Allowed : 18.44 % Favored : 77.98 % 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 are not related in a simple way. whole: -0.41 (0.19), residues: 1910 helix: 0.94 (0.18), residues: 864 sheet: -0.67 (0.41), residues: 166 loop : -1.44 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 63 TYR 0.016 0.001 TYR C 150 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/Z covalent geometry : bond 0.00356 / 0.15 (15455) covalent geometry : angle 0.57658 / 0.30 (20945) hydrogen bonds : bond 0.05238 / 3.49 ( 698) hydrogen bonds : angle 4.79799 / 3.33 ( 1965) metal coordination : bond 0.00885 / 0.45 ( 7) metal coordination : angle 7.05366 / 4.39 ( 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 214 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 158 time to evaluate : 0.562 Fit side-chains REVERT: A 39 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.7595 (ttt) REVERT: A 162 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.6776 (tm-30) REVERT: A 212 ASP cc_start: 0.8501 (m-30) cc_final: 0.8098 (m-30) REVERT: A 284 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7351 (pp20) REVERT: A 366 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8271 (p) REVERT: B 57 MET cc_start: 0.8281 (mmt) cc_final: 0.7967 (mmt) REVERT: B 152 LYS cc_start: 0.8239 (mtpt) cc_final: 0.7509 (mptp) REVERT: B 406 LYS cc_start: 0.7663 (mtpp) cc_final: 0.7022 (mmpt) REVERT: C 137 ILE cc_start: 0.2549 (OUTLIER) cc_final: 0.2050 (mm) REVERT: C 148 MET cc_start: 0.0635 (pmt) cc_final: -0.0515 (mpt) REVERT: C 242 MET cc_start: 0.2161 (tmm) cc_final: 0.0853 (mmp) REVERT: D 44 MET cc_start: 0.8164 (tpt) cc_final: 0.7801 (tpp) REVERT: D 50 PHE cc_start: 0.6852 (t80) cc_final: 0.5835 (m-10) REVERT: D 71 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7398 (ptt-90) REVERT: D 204 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7756 (pm20) REVERT: E 36 LYS cc_start: 0.7863 (tptt) cc_final: 0.7525 (mtpp) REVERT: E 61 ASN cc_start: 0.8505 (m-40) cc_final: 0.8212 (m-40) REVERT: E 122 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7238 (mm) REVERT: E 168 ASP cc_start: 0.8835 (t0) cc_final: 0.8426 (t0) REVERT: F 118 ASP cc_start: 0.5789 (p0) cc_final: 0.4716 (m-30) REVERT: F 214 MET cc_start: 0.6569 (ptt) cc_final: 0.5823 (ptp) REVERT: F 402 LEU cc_start: 0.7816 (mp) cc_final: 0.7503 (mm) outliers start: 56 outliers final: 17 residues processed: 200 average time/residue: 0.5052 time to fit residues: 112.7779 Evaluate side-chains 175 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 366 THR Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain C residue 9 LYS 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: 9.9990 chunk 116 optimal weight: 0.6980 chunk 145 optimal weight: 4.9990 chunk 81 optimal weight: 0.0070 chunk 113 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 147 optimal weight: 0.0770 chunk 105 optimal weight: 9.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 100 GLN F 78 GLN F 176 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.176396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.116969 restraints weight = 16743.299| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.00 r_work: 0.3038 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15462 Z= 0.101 Angle : 0.534 16.610 20959 Z= 0.268 Chirality : 0.041 0.158 2356 Planarity : 0.004 0.057 2621 Dihedral : 9.510 101.342 2398 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.82 % Favored : 96.02 % Rotamer: Outliers : 3.51 % Allowed : 19.02 % Favored : 77.47 % 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 are not related in a simple way. whole: -0.01 (0.19), residues: 1910 helix: 1.34 (0.18), residues: 858 sheet: -0.23 (0.45), residues: 142 loop : -1.32 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 63 TYR 0.016 0.001 TYR F 188 PHE 0.012 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/Z covalent geometry : bond 0.00221 / 0.10 (15455) covalent geometry : angle 0.50723 / 0.27 (20945) hydrogen bonds : bond 0.03790 / 2.52 ( 698) hydrogen bonds : angle 4.43540 / 3.08 ( 1965) metal coordination : bond 0.00815 / 0.39 ( 7) metal coordination : angle 6.43826 / 4.03 ( 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 225 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 170 time to evaluate : 0.559 Fit side-chains REVERT: A 162 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7984 (tp30) REVERT: A 212 ASP cc_start: 0.8566 (m-30) cc_final: 0.8178 (m-30) REVERT: B 152 LYS cc_start: 0.8326 (mtpt) cc_final: 0.7542 (mmtt) REVERT: B 406 LYS cc_start: 0.7742 (mtpp) cc_final: 0.7111 (mmpt) REVERT: C 31 VAL cc_start: 0.7372 (OUTLIER) cc_final: 0.7154 (t) REVERT: C 137 ILE cc_start: 0.2703 (OUTLIER) cc_final: 0.2233 (mm) REVERT: C 148 MET cc_start: 0.0868 (pmt) cc_final: -0.0256 (mpp) REVERT: C 242 MET cc_start: 0.2027 (tmm) cc_final: 0.0620 (mmp) REVERT: D 44 MET cc_start: 0.8296 (tpt) cc_final: 0.7993 (tpp) REVERT: D 50 PHE cc_start: 0.6923 (t80) cc_final: 0.5956 (m-10) REVERT: D 204 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7856 (pm20) REVERT: E 36 LYS cc_start: 0.7779 (tptt) cc_final: 0.7488 (mtpp) REVERT: E 122 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.7092 (mm) REVERT: E 165 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.7756 (ptmt) REVERT: E 168 ASP cc_start: 0.8808 (t0) cc_final: 0.8460 (t70) REVERT: F 118 ASP cc_start: 0.6072 (p0) cc_final: 0.4931 (m-30) REVERT: F 214 MET cc_start: 0.6479 (ptt) cc_final: 0.5718 (ptp) REVERT: F 225 MET cc_start: 0.5629 (mtp) cc_final: 0.5329 (mtt) REVERT: F 264 PHE cc_start: 0.6843 (m-80) cc_final: 0.6560 (m-80) REVERT: F 300 LYS cc_start: 0.7124 (OUTLIER) cc_final: 0.6468 (mmmm) REVERT: F 402 LEU cc_start: 0.7889 (mp) cc_final: 0.7578 (mm) outliers start: 55 outliers final: 14 residues processed: 210 average time/residue: 0.5278 time to fit residues: 123.3626 Evaluate side-chains 173 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 GLU 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 31 VAL 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 110 THR Chi-restraints excluded: chain D residue 128 ILE 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 165 LYS Chi-restraints excluded: chain E residue 190 PHE Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain F residue 204 VAL 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: 7.9990 chunk 119 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 chunk 185 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 123 optimal weight: 7.9990 chunk 163 optimal weight: 8.9990 chunk 171 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.171184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.110425 restraints weight = 16830.168| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.02 r_work: 0.2908 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 15462 Z= 0.293 Angle : 0.707 22.584 20959 Z= 0.351 Chirality : 0.049 0.172 2356 Planarity : 0.005 0.054 2621 Dihedral : 10.085 100.645 2389 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.45 % Favored : 94.40 % Rotamer: Outliers : 4.15 % Allowed : 19.27 % Favored : 76.58 % 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 are not related in a simple way. whole: -0.51 (0.19), residues: 1910 helix: 0.77 (0.18), residues: 863 sheet: -0.47 (0.42), residues: 152 loop : -1.43 (0.19), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 63 TYR 0.022 0.002 TYR D 141 PHE 0.019 0.002 PHE E 28 TRP 0.025 0.002 TRP B 103 HIS 0.007 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00738 / 0.29 (15455) covalent geometry : angle 0.68084 / 0.35 (20945) hydrogen bonds : bond 0.06476 / 4.32 ( 698) hydrogen bonds : angle 4.83577 / 3.35 ( 1965) metal coordination : bond 0.01533 / 0.80 ( 7) metal coordination : angle 7.45159 / 4.55 ( 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 226 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 161 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.7510 (ttt) REVERT: A 162 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.6795 (tm-30) REVERT: A 284 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7454 (pp20) REVERT: B 152 LYS cc_start: 0.8322 (mtpt) cc_final: 0.7574 (mptp) REVERT: B 406 LYS cc_start: 0.7738 (mtpp) cc_final: 0.7082 (mmpt) REVERT: C 38 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7961 (mmpt) REVERT: C 148 MET cc_start: 0.1008 (pmt) cc_final: -0.0059 (mpp) REVERT: C 176 LEU cc_start: 0.2565 (OUTLIER) cc_final: 0.2062 (tp) REVERT: C 221 LEU cc_start: 0.0412 (OUTLIER) cc_final: 0.0146 (tt) REVERT: C 242 MET cc_start: 0.1990 (tmm) cc_final: 0.0635 (mmp) REVERT: C 249 THR cc_start: 0.4340 (OUTLIER) cc_final: 0.4042 (m) REVERT: D 44 MET cc_start: 0.8181 (tpt) cc_final: 0.7834 (tpp) REVERT: D 50 PHE cc_start: 0.6929 (t80) cc_final: 0.5878 (m-10) REVERT: D 99 LYS cc_start: 0.6361 (OUTLIER) cc_final: 0.5307 (pptt) REVERT: E 36 LYS cc_start: 0.7872 (tptt) cc_final: 0.7525 (mtpp) REVERT: E 61 ASN cc_start: 0.8509 (m-40) cc_final: 0.8242 (m-40) REVERT: E 122 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7210 (mm) REVERT: E 165 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.7879 (ptmt) REVERT: F 10 MET cc_start: 0.5846 (mmt) cc_final: 0.5425 (mmm) REVERT: F 118 ASP cc_start: 0.5794 (p0) cc_final: 0.4808 (m-30) REVERT: F 214 MET cc_start: 0.6861 (ptt) cc_final: 0.6031 (ptp) REVERT: F 300 LYS cc_start: 0.7104 (OUTLIER) cc_final: 0.6444 (mmmm) REVERT: F 402 LEU cc_start: 0.7897 (mp) cc_final: 0.7570 (mm) outliers start: 65 outliers final: 25 residues processed: 210 average time/residue: 0.5377 time to fit residues: 126.2327 Evaluate side-chains 188 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 127 VAL 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 249 THR 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 145 LEU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain E residue 94 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 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: 8.9990 chunk 6 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 176 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 146 optimal weight: 0.5980 chunk 173 optimal weight: 10.0000 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.173552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.113007 restraints weight = 16772.122| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.08 r_work: 0.2997 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15462 Z= 0.125 Angle : 0.557 19.463 20959 Z= 0.280 Chirality : 0.042 0.160 2356 Planarity : 0.004 0.058 2621 Dihedral : 9.425 92.746 2387 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.14 % Favored : 95.76 % Rotamer: Outliers : 3.57 % Allowed : 20.04 % 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 are not related in a simple way. whole: -0.20 (0.19), residues: 1910 helix: 1.12 (0.18), residues: 859 sheet: -0.31 (0.44), residues: 144 loop : -1.35 (0.19), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 186 TYR 0.017 0.001 TYR D 141 PHE 0.010 0.001 PHE F 11 TRP 0.023 0.001 TRP B 103 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (15455) covalent geometry : angle 0.52788 / 0.28 (20945) hydrogen bonds : bond 0.04411 / 2.92 ( 698) hydrogen bonds : angle 4.52657 / 3.14 ( 1965) metal coordination : bond 0.00844 / 0.42 ( 7) metal coordination : angle 6.86091 / 4.24 ( 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 215 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 159 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.7654 (ttt) REVERT: A 162 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.6869 (tm-30) REVERT: A 212 ASP cc_start: 0.8541 (m-30) cc_final: 0.8133 (m-30) REVERT: A 284 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7367 (pp20) REVERT: B 57 MET cc_start: 0.8374 (mmt) cc_final: 0.8093 (mmt) REVERT: B 152 LYS cc_start: 0.8388 (mtpt) cc_final: 0.7607 (mmtt) REVERT: B 406 LYS cc_start: 0.7720 (mtpp) cc_final: 0.7098 (mmpt) REVERT: C 31 VAL cc_start: 0.7481 (OUTLIER) cc_final: 0.7217 (t) REVERT: C 38 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7957 (mmpt) REVERT: C 87 ASP cc_start: 0.3136 (p0) cc_final: 0.1724 (m-30) REVERT: C 148 MET cc_start: 0.1062 (pmt) cc_final: -0.0055 (mpp) REVERT: C 221 LEU cc_start: 0.0595 (OUTLIER) cc_final: 0.0314 (tt) REVERT: C 242 MET cc_start: 0.1915 (tmm) cc_final: 0.0594 (mmp) REVERT: C 249 THR cc_start: 0.4321 (OUTLIER) cc_final: 0.4015 (m) REVERT: D 44 MET cc_start: 0.8217 (tpt) cc_final: 0.7875 (tpp) REVERT: D 50 PHE cc_start: 0.6942 (t80) cc_final: 0.5948 (m-10) REVERT: D 99 LYS cc_start: 0.6215 (OUTLIER) cc_final: 0.5245 (pptt) REVERT: D 115 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7600 (ttt) REVERT: E 36 LYS cc_start: 0.7856 (tptt) cc_final: 0.7537 (mtpp) REVERT: E 61 ASN cc_start: 0.8494 (m-40) cc_final: 0.8223 (m-40) REVERT: E 122 ILE cc_start: 0.7680 (OUTLIER) cc_final: 0.7177 (mm) REVERT: E 165 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.7760 (ptmt) REVERT: E 168 ASP cc_start: 0.8824 (t0) cc_final: 0.8478 (t70) REVERT: F 10 MET cc_start: 0.5941 (mmt) cc_final: 0.5583 (mmm) REVERT: F 105 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7118 (mp0) REVERT: F 118 ASP cc_start: 0.6109 (p0) cc_final: 0.4993 (m-30) REVERT: F 214 MET cc_start: 0.6781 (ptt) cc_final: 0.5975 (ptp) REVERT: F 225 MET cc_start: 0.5612 (mtp) cc_final: 0.5188 (mtt) REVERT: F 264 PHE cc_start: 0.6564 (m-80) cc_final: 0.6259 (m-80) REVERT: F 300 LYS cc_start: 0.7056 (OUTLIER) cc_final: 0.6412 (mmmm) REVERT: F 402 LEU cc_start: 0.7944 (mp) cc_final: 0.7618 (mm) outliers start: 56 outliers final: 22 residues processed: 199 average time/residue: 0.5532 time to fit residues: 122.5936 Evaluate side-chains 187 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 366 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain C residue 31 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 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 115 MET 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 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 105 GLU Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 250 TRP 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: 0.6980 chunk 128 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 118 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 97 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.173522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.112819 restraints weight = 16675.272| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.15 r_work: 0.2958 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15462 Z= 0.132 Angle : 0.557 18.883 20959 Z= 0.279 Chirality : 0.042 0.159 2356 Planarity : 0.004 0.058 2621 Dihedral : 9.179 88.499 2387 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.66 % Favored : 95.24 % Rotamer: Outliers : 3.64 % Allowed : 19.85 % Favored : 76.52 % 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 are not related in a simple way. whole: -0.10 (0.19), residues: 1910 helix: 1.18 (0.18), residues: 863 sheet: 0.03 (0.46), residues: 128 loop : -1.33 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 63 TYR 0.021 0.001 TYR F 248 PHE 0.011 0.001 PHE E 28 TRP 0.023 0.001 TRP B 103 HIS 0.006 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (15455) covalent geometry : angle 0.52990 / 0.28 (20945) hydrogen bonds : bond 0.04420 / 2.94 ( 698) hydrogen bonds : angle 4.46400 / 3.10 ( 1965) metal coordination : bond 0.00839 / 0.42 ( 7) metal coordination : angle 6.72337 / 4.12 ( 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 214 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 157 time to evaluate : 0.531 Fit side-chains REVERT: A 39 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.7540 (ttt) REVERT: A 162 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.6899 (tm-30) REVERT: A 284 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7368 (pp20) REVERT: B 57 MET cc_start: 0.8313 (mmt) cc_final: 0.7914 (mmt) REVERT: B 152 LYS cc_start: 0.8259 (mtpt) cc_final: 0.7483 (mmtt) REVERT: B 406 LYS cc_start: 0.7658 (mtpp) cc_final: 0.7030 (mmpt) REVERT: C 38 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7957 (mmpt) REVERT: C 87 ASP cc_start: 0.2936 (p0) cc_final: 0.1686 (m-30) REVERT: C 148 MET cc_start: 0.1105 (pmt) cc_final: 0.0144 (mpp) REVERT: C 221 LEU cc_start: 0.0549 (OUTLIER) cc_final: 0.0301 (tt) REVERT: C 242 MET cc_start: 0.2124 (tmm) cc_final: 0.0667 (mmp) REVERT: D 44 MET cc_start: 0.8204 (tpt) cc_final: 0.7845 (tpp) REVERT: D 50 PHE cc_start: 0.6905 (t80) cc_final: 0.5914 (m-10) REVERT: D 99 LYS cc_start: 0.6202 (OUTLIER) cc_final: 0.5270 (pptt) REVERT: E 36 LYS cc_start: 0.7713 (tptt) cc_final: 0.7401 (mtpp) REVERT: E 122 ILE cc_start: 0.7605 (OUTLIER) cc_final: 0.7078 (mm) REVERT: E 165 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.7751 (ptmt) REVERT: E 168 ASP cc_start: 0.8857 (t0) cc_final: 0.8480 (t0) REVERT: F 10 MET cc_start: 0.5881 (mmt) cc_final: 0.5533 (mmm) REVERT: F 105 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7106 (mp0) REVERT: F 118 ASP cc_start: 0.6018 (p0) cc_final: 0.4910 (m-30) REVERT: F 214 MET cc_start: 0.6725 (ptp) cc_final: 0.5886 (ptp) REVERT: F 220 GLU cc_start: 0.5144 (mt-10) cc_final: 0.4932 (mt-10) REVERT: F 264 PHE cc_start: 0.6501 (m-80) cc_final: 0.6204 (m-80) REVERT: F 300 LYS cc_start: 0.6963 (OUTLIER) cc_final: 0.6320 (mmmm) REVERT: F 402 LEU cc_start: 0.7912 (mp) cc_final: 0.7564 (mm) outliers start: 57 outliers final: 27 residues processed: 198 average time/residue: 0.5113 time to fit residues: 113.2348 Evaluate side-chains 192 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 366 THR 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 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 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 D residue 165 VAL 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 240 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: 0.0980 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: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 197 GLN F 142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.173072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.112689 restraints weight = 16653.254| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.01 r_work: 0.2971 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15462 Z= 0.180 Angle : 0.602 20.497 20959 Z= 0.300 Chirality : 0.044 0.164 2356 Planarity : 0.005 0.057 2621 Dihedral : 9.342 90.943 2387 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.71 % Favored : 95.18 % Rotamer: Outliers : 3.83 % Allowed : 20.17 % Favored : 76.01 % 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 are not related in a simple way. whole: -0.26 (0.19), residues: 1910 helix: 1.02 (0.18), residues: 867 sheet: -0.18 (0.44), residues: 138 loop : -1.38 (0.19), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 63 TYR 0.020 0.002 TYR D 141 PHE 0.021 0.002 PHE C 152 TRP 0.029 0.002 TRP F 250 HIS 0.008 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.18 (15455) covalent geometry : angle 0.57398 / 0.30 (20945) hydrogen bonds : bond 0.05093 / 3.39 ( 698) hydrogen bonds : angle 4.56237 / 3.17 ( 1965) metal coordination : bond 0.01044 / 0.53 ( 7) metal coordination : angle 7.01317 / 4.27 ( 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 216 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 156 time to evaluate : 0.402 Fit side-chains REVERT: A 39 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.7531 (ttt) REVERT: A 162 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.6868 (tm-30) REVERT: A 212 ASP cc_start: 0.8505 (m-30) cc_final: 0.8196 (m-30) REVERT: A 284 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7347 (pp20) REVERT: B 152 LYS cc_start: 0.8268 (mtpt) cc_final: 0.7474 (mmtt) REVERT: B 256 GLN cc_start: 0.7447 (mm-40) cc_final: 0.7225 (mm-40) REVERT: B 406 LYS cc_start: 0.7687 (mtpp) cc_final: 0.7027 (mmpt) REVERT: C 38 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7943 (mmpt) REVERT: C 87 ASP cc_start: 0.2620 (p0) cc_final: 0.1401 (m-30) REVERT: C 137 ILE cc_start: 0.2285 (OUTLIER) cc_final: 0.1771 (mm) REVERT: C 148 MET cc_start: 0.1376 (pmt) cc_final: 0.0470 (mpp) REVERT: C 156 GLU cc_start: 0.0222 (tt0) cc_final: -0.0074 (tt0) REVERT: C 176 LEU cc_start: 0.2646 (OUTLIER) cc_final: 0.2299 (tp) REVERT: C 221 LEU cc_start: 0.0508 (OUTLIER) cc_final: 0.0287 (tt) REVERT: C 242 MET cc_start: 0.2082 (tmm) cc_final: 0.0656 (mmp) REVERT: C 249 THR cc_start: 0.4171 (OUTLIER) cc_final: 0.3971 (m) REVERT: D 44 MET cc_start: 0.8177 (tpt) cc_final: 0.7824 (tpp) REVERT: D 50 PHE cc_start: 0.6904 (t80) cc_final: 0.5883 (m-10) REVERT: D 99 LYS cc_start: 0.6253 (OUTLIER) cc_final: 0.5291 (pptt) REVERT: E 61 ASN cc_start: 0.8562 (m-40) cc_final: 0.8237 (m-40) REVERT: E 122 ILE cc_start: 0.7661 (OUTLIER) cc_final: 0.7126 (mm) REVERT: E 165 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.7708 (ptmt) REVERT: F 10 MET cc_start: 0.5803 (mmt) cc_final: 0.5409 (mmm) REVERT: F 105 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7151 (mp0) REVERT: F 118 ASP cc_start: 0.6065 (p0) cc_final: 0.4970 (m-30) REVERT: F 140 ASN cc_start: 0.6081 (OUTLIER) cc_final: 0.5831 (t0) REVERT: F 158 GLU cc_start: 0.4675 (OUTLIER) cc_final: 0.4467 (tt0) REVERT: F 214 MET cc_start: 0.6886 (ptp) cc_final: 0.6035 (ptp) REVERT: F 264 PHE cc_start: 0.6489 (m-80) cc_final: 0.6153 (m-80) REVERT: F 300 LYS cc_start: 0.6999 (OUTLIER) cc_final: 0.6364 (mmmm) REVERT: F 402 LEU cc_start: 0.7928 (mp) cc_final: 0.7574 (mm) outliers start: 60 outliers final: 26 residues processed: 201 average time/residue: 0.5298 time to fit residues: 118.8755 Evaluate side-chains 195 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 154 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 366 THR 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 38 LYS Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 137 ILE 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 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 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 158 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 79 optimal weight: 2.9990 chunk 183 optimal weight: 0.0970 chunk 145 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 98 optimal weight: 0.0270 chunk 174 optimal weight: 20.0000 chunk 111 optimal weight: 0.7980 chunk 55 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 15 optimal weight: 0.6980 overall best weight: 0.9238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 205 GLN E 197 GLN F 142 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.174162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.113169 restraints weight = 16686.323| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.95 r_work: 0.3009 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15462 Z= 0.117 Angle : 0.555 18.386 20959 Z= 0.277 Chirality : 0.042 0.249 2356 Planarity : 0.004 0.058 2621 Dihedral : 9.020 87.854 2387 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.19 % Favored : 95.71 % Rotamer: Outliers : 3.06 % Allowed : 20.74 % 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 are not related in a simple way. whole: 0.03 (0.19), residues: 1910 helix: 1.35 (0.18), residues: 852 sheet: 0.09 (0.46), residues: 128 loop : -1.30 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 63 TYR 0.021 0.001 TYR F 248 PHE 0.018 0.001 PHE C 152 TRP 0.023 0.001 TRP B 103 HIS 0.006 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (15455) covalent geometry : angle 0.52796 / 0.28 (20945) hydrogen bonds : bond 0.04145 / 2.75 ( 698) hydrogen bonds : angle 4.40667 / 3.07 ( 1965) metal coordination : bond 0.00772 / 0.37 ( 7) metal coordination : angle 6.63925 / 4.08 ( 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 203 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 155 time to evaluate : 0.616 Fit side-chains REVERT: A 39 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.7587 (ttt) REVERT: A 162 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7997 (tp30) REVERT: A 212 ASP cc_start: 0.8544 (m-30) cc_final: 0.8245 (m-30) REVERT: A 284 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7336 (pp20) REVERT: B 152 LYS cc_start: 0.8297 (mtpt) cc_final: 0.7529 (mmtt) REVERT: B 256 GLN cc_start: 0.7469 (mm-40) cc_final: 0.7258 (mm-40) REVERT: B 406 LYS cc_start: 0.7709 (mtpp) cc_final: 0.7090 (mmpt) REVERT: C 38 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7960 (mmpt) REVERT: C 87 ASP cc_start: 0.2977 (p0) cc_final: 0.1750 (m-30) REVERT: C 148 MET cc_start: 0.1485 (pmt) cc_final: 0.0559 (mpp) REVERT: C 176 LEU cc_start: 0.2624 (OUTLIER) cc_final: 0.2264 (tp) REVERT: C 221 LEU cc_start: 0.0724 (OUTLIER) cc_final: 0.0515 (tt) REVERT: C 242 MET cc_start: 0.2235 (tmm) cc_final: 0.0673 (mmp) REVERT: C 249 THR cc_start: 0.4261 (OUTLIER) cc_final: 0.3948 (m) REVERT: D 44 MET cc_start: 0.8217 (tpt) cc_final: 0.7866 (tpp) REVERT: D 50 PHE cc_start: 0.6902 (t80) cc_final: 0.5937 (m-10) REVERT: D 99 LYS cc_start: 0.6246 (OUTLIER) cc_final: 0.5351 (pptt) REVERT: E 61 ASN cc_start: 0.8614 (m-40) cc_final: 0.8284 (m-40) REVERT: E 122 ILE cc_start: 0.7637 (OUTLIER) cc_final: 0.7151 (mm) REVERT: E 165 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.7781 (ptmt) REVERT: E 168 ASP cc_start: 0.8858 (t0) cc_final: 0.8515 (t70) REVERT: F 10 MET cc_start: 0.5855 (mmt) cc_final: 0.5515 (mmm) REVERT: F 105 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: F 118 ASP cc_start: 0.6013 (p0) cc_final: 0.4952 (m-30) REVERT: F 214 MET cc_start: 0.6797 (ptp) cc_final: 0.5916 (ptp) REVERT: F 264 PHE cc_start: 0.6471 (m-80) cc_final: 0.6130 (m-80) REVERT: F 300 LYS cc_start: 0.6981 (OUTLIER) cc_final: 0.6345 (mmmm) REVERT: F 402 LEU cc_start: 0.7958 (mp) cc_final: 0.7608 (mm) outliers start: 48 outliers final: 25 residues processed: 191 average time/residue: 0.5227 time to fit residues: 111.7370 Evaluate side-chains 184 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 366 THR 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 38 LYS Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 52 VAL 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 225 THR 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 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 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: 5.9990 chunk 101 optimal weight: 10.0000 chunk 55 optimal weight: 0.0770 chunk 145 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 165 optimal weight: 8.9990 chunk 161 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 197 GLN F 142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.171686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.111861 restraints weight = 16640.640| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.09 r_work: 0.2957 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1468 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= 0.198 Angle : 0.629 20.622 20959 Z= 0.313 Chirality : 0.045 0.193 2356 Planarity : 0.005 0.056 2621 Dihedral : 9.277 89.974 2386 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.08 % Favored : 94.82 % Rotamer: Outliers : 3.06 % Allowed : 21.44 % Favored : 75.49 % 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 are not related in a simple way. whole: -0.23 (0.19), residues: 1910 helix: 1.02 (0.18), residues: 864 sheet: 0.06 (0.45), residues: 128 loop : -1.36 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 63 TYR 0.021 0.002 TYR D 141 PHE 0.044 0.002 PHE C 244 TRP 0.023 0.002 TRP B 103 HIS 0.005 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.20 (15455) covalent geometry : angle 0.60194 / 0.31 (20945) hydrogen bonds : bond 0.05253 / 3.50 ( 698) hydrogen bonds : angle 4.57131 / 3.18 ( 1965) metal coordination : bond 0.01092 / 0.55 ( 7) metal coordination : angle 7.02412 / 4.26 ( 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 199 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 151 time to evaluate : 0.608 Fit side-chains REVERT: A 39 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.7563 (ttt) REVERT: A 162 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.6896 (tm-30) REVERT: A 212 ASP cc_start: 0.8617 (m-30) cc_final: 0.8360 (m-30) REVERT: A 284 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7415 (pp20) REVERT: B 152 LYS cc_start: 0.8322 (mtpt) cc_final: 0.7526 (mmtt) REVERT: B 256 GLN cc_start: 0.7519 (mm-40) cc_final: 0.7311 (mm-40) REVERT: B 406 LYS cc_start: 0.7823 (mtpp) cc_final: 0.7173 (mmpt) REVERT: C 38 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7903 (mmpt) REVERT: C 87 ASP cc_start: 0.2695 (p0) cc_final: 0.1479 (m-30) REVERT: C 148 MET cc_start: 0.1575 (pmt) cc_final: 0.0632 (mpp) REVERT: C 156 GLU cc_start: 0.0382 (tt0) cc_final: 0.0041 (tt0) REVERT: C 176 LEU cc_start: 0.2642 (OUTLIER) cc_final: 0.2388 (tp) REVERT: C 221 LEU cc_start: 0.0641 (OUTLIER) cc_final: 0.0439 (tt) REVERT: C 242 MET cc_start: 0.1891 (tmm) cc_final: 0.0356 (mpp) REVERT: C 249 THR cc_start: 0.4252 (OUTLIER) cc_final: 0.3920 (m) REVERT: D 44 MET cc_start: 0.8279 (tpt) cc_final: 0.7922 (tpp) REVERT: D 50 PHE cc_start: 0.7034 (t80) cc_final: 0.6022 (m-10) REVERT: D 99 LYS cc_start: 0.6283 (OUTLIER) cc_final: 0.5324 (pptt) REVERT: E 61 ASN cc_start: 0.8636 (m-40) cc_final: 0.8311 (m-40) REVERT: E 122 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7273 (mm) REVERT: E 165 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.7795 (ptmt) REVERT: F 10 MET cc_start: 0.5878 (mmt) cc_final: 0.5506 (mmm) REVERT: F 105 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: F 118 ASP cc_start: 0.6043 (p0) cc_final: 0.4979 (m-30) REVERT: F 140 ASN cc_start: 0.5998 (OUTLIER) cc_final: 0.5739 (t0) REVERT: F 158 GLU cc_start: 0.4452 (OUTLIER) cc_final: 0.4235 (tt0) REVERT: F 214 MET cc_start: 0.7021 (ptp) cc_final: 0.6162 (ptp) REVERT: F 264 PHE cc_start: 0.6525 (m-80) cc_final: 0.6219 (m-80) REVERT: F 300 LYS cc_start: 0.7004 (OUTLIER) cc_final: 0.6368 (mmmm) REVERT: F 402 LEU cc_start: 0.8018 (mp) cc_final: 0.7657 (mm) outliers start: 48 outliers final: 28 residues processed: 188 average time/residue: 0.5445 time to fit residues: 113.6526 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 : 0.478 ------------------------------------------------------------------------------- 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 366 THR 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 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 225 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 25 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 121 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 162 optimal weight: 20.0000 chunk 144 optimal weight: 0.7980 chunk 157 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 116 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 = 0.3929 r_free = 0.3929 target = 0.173305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.111778 restraints weight = 16695.359| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.01 r_work: 0.2976 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 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 0.044 15462 Z= 0.140 Angle : 0.577 19.085 20959 Z= 0.288 Chirality : 0.043 0.189 2356 Planarity : 0.004 0.058 2621 Dihedral : 9.058 89.373 2386 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.29 % Favored : 95.60 % Rotamer: Outliers : 2.81 % Allowed : 21.63 % 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 are not related in a simple way. whole: -0.09 (0.19), residues: 1910 helix: 1.20 (0.18), residues: 858 sheet: 0.10 (0.45), residues: 128 loop : -1.33 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 63 TYR 0.018 0.001 TYR F 248 PHE 0.029 0.001 PHE C 244 TRP 0.023 0.002 TRP B 103 HIS 0.003 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (15455) covalent geometry : angle 0.55059 / 0.29 (20945) hydrogen bonds : bond 0.04455 / 2.95 ( 698) hydrogen bonds : angle 4.46192 / 3.11 ( 1965) metal coordination : bond 0.00870 / 0.43 ( 7) metal coordination : angle 6.76101 / 4.14 ( 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 193 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 149 time to evaluate : 0.527 Fit side-chains REVERT: A 39 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.7546 (ttt) REVERT: A 162 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7975 (tp30) REVERT: A 212 ASP cc_start: 0.8566 (m-30) cc_final: 0.8255 (m-30) REVERT: A 284 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7353 (pp20) REVERT: B 152 LYS cc_start: 0.8301 (mtpt) cc_final: 0.7514 (mmtt) REVERT: B 256 GLN cc_start: 0.7472 (mm-40) cc_final: 0.7262 (mm-40) REVERT: B 406 LYS cc_start: 0.7710 (mtpp) cc_final: 0.7078 (mmpt) REVERT: C 38 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7914 (mmpt) REVERT: C 87 ASP cc_start: 0.2742 (p0) cc_final: 0.1563 (m-30) REVERT: C 148 MET cc_start: 0.1571 (pmt) cc_final: 0.0683 (mpp) REVERT: C 176 LEU cc_start: 0.2610 (OUTLIER) cc_final: 0.2401 (tp) REVERT: C 242 MET cc_start: 0.1953 (tmm) cc_final: 0.0213 (mpp) REVERT: C 249 THR cc_start: 0.4212 (OUTLIER) cc_final: 0.3895 (m) REVERT: D 44 MET cc_start: 0.8257 (tpt) cc_final: 0.7882 (tpp) REVERT: D 50 PHE cc_start: 0.6965 (t80) cc_final: 0.5993 (m-10) REVERT: D 99 LYS cc_start: 0.6275 (OUTLIER) cc_final: 0.5373 (pptt) REVERT: E 61 ASN cc_start: 0.8613 (m-40) cc_final: 0.8251 (m-40) REVERT: E 122 ILE cc_start: 0.7666 (OUTLIER) cc_final: 0.7152 (mm) REVERT: E 165 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.7770 (ptmt) REVERT: F 10 MET cc_start: 0.5950 (mmt) cc_final: 0.5599 (mmm) REVERT: F 105 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7211 (mp0) REVERT: F 118 ASP cc_start: 0.5950 (p0) cc_final: 0.4918 (m-30) REVERT: F 140 ASN cc_start: 0.5961 (OUTLIER) cc_final: 0.5711 (t0) REVERT: F 214 MET cc_start: 0.6952 (ptp) cc_final: 0.6074 (ptp) REVERT: F 264 PHE cc_start: 0.6467 (m-80) cc_final: 0.6133 (m-80) REVERT: F 300 LYS cc_start: 0.6956 (OUTLIER) cc_final: 0.6326 (mmmm) REVERT: F 402 LEU cc_start: 0.8031 (mp) cc_final: 0.7682 (mm) outliers start: 44 outliers final: 25 residues processed: 185 average time/residue: 0.5221 time to fit residues: 107.3766 Evaluate side-chains 185 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 148 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 366 THR 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 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 225 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 25 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 49 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 72 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 174 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.172287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.111270 restraints weight = 16719.810| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.93 r_work: 0.2989 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15462 Z= 0.167 Angle : 0.606 20.102 20959 Z= 0.301 Chirality : 0.044 0.190 2356 Planarity : 0.005 0.057 2621 Dihedral : 9.158 90.144 2386 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.87 % Favored : 95.03 % Rotamer: Outliers : 2.81 % Allowed : 21.63 % 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 are not related in a simple way. whole: -0.20 (0.19), residues: 1910 helix: 1.04 (0.18), residues: 869 sheet: -0.03 (0.44), residues: 136 loop : -1.35 (0.19), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 63 TYR 0.020 0.001 TYR D 141 PHE 0.027 0.002 PHE C 244 TRP 0.023 0.002 TRP B 103 HIS 0.004 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (15455) covalent geometry : angle 0.57931 / 0.30 (20945) hydrogen bonds : bond 0.04898 / 3.26 ( 698) hydrogen bonds : angle 4.52472 / 3.15 ( 1965) metal coordination : bond 0.00998 / 0.50 ( 7) metal coordination : angle 6.93318 / 4.21 ( 14) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5213.44 seconds wall clock time: 89 minutes 30.87 seconds (5370.87 seconds total)